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RELEASE-NOTES
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Release 1.1.11
o FEATURE: One can now dynamically edit SMILES in layla
o FEATURE: Anisotropic atom representation
[thanks to Global Phasing]
o FEATURE: Better linking across sequence gaps in RNA and DNA
o FEATURE: Electrostatic representation [Stuart McNicholas]
o FEATURE: Acedrg atom types are now parsed from dictionaries
o FEATURE: Function partition_map_by_chain() added
o OTHER: Various non-user-visible changes for Flatpak compatibility
-----
Release 1.1.10
o FEATURE: Noughties-physics - add a refinement/atom manipulation mode
so that Coot behaves like it used to up to (and including)
version 0.8.x:
coot.set_refine_use_noughties_physics()
o FEATURE: Layla now displays QED Scores for molecules
o FEATURE: read_coordinates() added to the Coot API
o FEATURE: Cryo-EM servalcat use added to the Coot API
o CHANGE: Network download files now follow the XDG Base Directory Protocol
o CHANGE: HUD Ramachandran Plot is now pickable
o CHANGE: Ligands with no dictionary are drawn with bonds in "Colour by Chain"
mode
o CHANGE: Python requests is no longer a dependency
o BUG-FIX: Scroll wheel indicator in the Display Manager now correctly updates
on use of a key-binding to change the scrollable map
o BUG-FIX: Ugly least-squares fit dialog has been modernized.
o BUG-FIX: Fix the callback actions for the "Display Hydrogen Atoms" in
the Bonds control dialog.
o BUG-FIX: rework the calculation of pkg_data_dir() - particularly in the
case of relocatable binaries
-----
Release 1.1.09
o FEATURE: Coot is now a (mostly) XDG Base Directory-compliant application
[guano-be-gone]
o FEATURE: tomo_section_view() function added to the api
o FEATURE: to_generic_object_add_points() added to the api (so that many point
can now be added quickly)
o FEATURE: generic_object_mesh_calculate_normals() function added to the API.
This averages winding-based normals for shared vertices.
o CHANGE: In "configure" relocatable bianries are no longer enabled by default.
Use --enable-relocatable-binaries to turn them on if needed.
o CHANGE: rework logic of the glyco chiral test for BETA1-6 and ALPHA1-6 links
[Markus Meier]
o CHANGE: "Replace Residue" now works as an overlay
o CHANGE: Allow bonding of HET-groups in polymer bonds
o CHANGE: mmrrcc renamed to coot-mmrrcc
o CHANGE: The ligand/solvent molecule is now closed after being added with
jiggle-fit
o CHANGE: Add a key-binding for "Residue Info" (Ctrl-I)
o CHANGE: Executable name changed from "coot-bin" to MacCoot on macOS
o BUG-FIX: Fix Change Chain ID GUI (thanks Simon Vecchioni)
o BUG-FIX: "Add Terminal Residue" now works for RNA and DNA
o BUG-FIX: Fix all-atom refinement mode
----
Release 1.1.08
o FEATURE: Scene Presets added to the Draw menu
o CHANGE: "Mutate" is now a button so that it can now be
used to mutate RNA and DNA.
o BUG-FIX: mutate_by_overlap() fixed [thanks Simon Vecchioni]
o BUG-FIX: The "Generic Display Objects" dialog now dynamically
updates (no need to close it an open it again to see new
generic display objects).
o BUG-FIX: Undisplaying a model while the Display Manager dialog
is not displayed now correctly sets the state of the Display
checkbutton.
----
Release 1.1.07
No user-visible changes
----
Release 1.1.06
No user-visible changes
----
Release 1.1.05
No user-visible changes
----
Release 1.1.04
o FEATURE: Particle effects for done difference map peaks
o CHANGE: Refinement cannot now proceed if there are no bond restraints for any
of the refining residues
o BUG-FIX: Add coot namespace to state save file
o BUG-FIX: Fix symmetry of difference map peaks
----
Release 1.1.03
o FEATURE: outline active residue on leftquote
o FEATURE: Shortcuts dialog
o FEATURE: Goodsell NCS colouring mode
o FEATURE: Improved Gaussian surfaces
o FEATURE: Generic objects are now part of SSAO and shadow framebuffers
o FEATURE: "Coot Points" added to updating difference maps
o FEATURE: Animate the removal of NBC outliers
o FEATURE: Semi-dark background mode
o CHANGE: Layla updates
o BUG-FIX: command line arguments are now recognised
o BUG-FIX: Limit the radius of water atoms
o BUG-FIX: Fixup for rigid-body fit toolbar buttons
o BUG-FIX: Trackpad-mode no only for Mac
o BUG-FIX: Add handler for trans-peptide and planar peptide refinement checkbuttons
----
Release 1.1.02
o BUG-FIX: Configuration of guile
----
Release 1.1.01
o BUG-FIX: Added an operator<() function for density_correlation_stats_info_t
to fix compilation issue.
[Yoshitaka Moriwaki]
----
Release 1.1
18 months after the release of Coot 1 it's time for Coot 1.1
Coot 1.1 is a major change beyond Coot 1. It has required a lot of
writing and rewriting and has been the focus of my work since last year.
Technically (but briefly) we have rewritten the GUI again so that it is
now is based on GTK4 (Coot 1 used GTK3). This has meant a lot of rewiring
under the hood so that things behave similar to before [1].
Many things, that is. Not all things. There are a few important
differences - they are for the better (although you may not initially
think so).
o View rotation is on right-mouse (except on Mac).
o Functions are activate in "Select First" mode (that means bringing
the atom/residue/chain of interest to the centre of the screen)
and then choosing the function. This is more consistent with the
use of hot-key/key-bindings.
o Widget "focus" is different in GTK4 - I don't yet fully understand it
at the moment, so, in case Coot "forgets" to revert focus back to the
main graphics widget, there is a "Grab Focus" button in the horizontal
toolbar.
o Many of the menu items have been moved around. Now they are far more
likely to be where they will finally end up.
o "Modelling" (as we like to label it in the UK) has its own top-level.
o "Modules" is now also on the top-level instead of being in the
"Calculate" menu.
Not everything made it:
o "Symmetry by Molecule" has been removed (for the moment).
o RCrane and the glycan builder have yet to be brought back to working
order.
o FLEV, QED breakouts and Chemical Feature Clusters are still missing.
o The PISA interface is missing.
I am grateful for the contributions from Jakub Smulski for help with
this over the last year and to Global Phasing for the funding. Martin
Noble has written the ribbon and surface representation code.
At the moment, the terminal output is a bit verbose with debugging output.
That will be reduced or removed in due course.
Although I've not tried it, I hope/expect that this Coot will run very
sweetly on a M2 Pro MacBook Pro... "M2 good, M3 better" - I suppose?
Binaries:
Binaries have always been issue with Coot. The problem is that a
project of the scale of Coot needs (at least) 3 people [2],
o one for the scientific developments/new algorithms and publications
o one for the development of the GUI (and graphics in the case of Coot)
o one for the deployment of binaries - it takes time to produce binaries
for numerous versions of numerous operating systems and the many
changing/improving dependencies (to me this feels like a constantly
changing, never complete jigsaw puzzle)
And, although I recognise its importance, I just keep dropping the ball
for the third one (is has little intrinsic pleasure for me and is
completely invisible career-wise).
Coot on "Linux":
There is a build-script, build-coot-3-3 that works for me, soup to
nuts on a modern Ubuntu system. Not so much on Fedora though. I will
try to help if you try this method and things go wrong. Python and
its add-ons are exquisitely tricky to build and is not well documented,
however [3].
https://raw.githubusercontent.com/pemsley/coot/main/build-it-3-3
Coot on macOS:
Some Mac users might like to consider using Homebrew. At some stage
I hope that
$ brew install coot
will (just) work. But that will involve input from by Yoshitaka
Moriwaki who is looking after Coot in Homebrew (that might take a
month or two). Right now, Mac-using homebrew-using Coot
enthusiasts can follow issue 33 on github:
https://github.com/pemsley/coot/issues/33
Coot on "Windows":
Bernhard Lohkamp is the font of all wisdom when it comes to
WinCoot. He will let us know his schedule. (Within a month though,
that is my understanding.)
via CCP4:
In the coming weeks CCP4 will review Coot 1.1 and decide if it is
acceptable to be added to the suite. If approved, that is the path
of least effort for me and many users.
What about 0.9.x?
I will maintain the back-end/libraries until April 2024, then I will
reassess. It's just too much trouble to change the GUI though.
Future:
With such a massive change set [4], there are bound to be bugs, so I imagine
a flurry of patch releases in the forthcoming weeks.
With this bad boy [5] out the door and with Lucrezia Catapano coming
back on-line I can spend more time on Moorhen [6] and the Blender
interface - hooray!
If you've got this far and can get this Coot to run, I have added an Easter
Egg for today (I'll tell you what it is: coot.halloween()).
[1] To give you an idea of the scope of this work (and the speed at which the
interface for Coot was implemented) look how long it takes to rewrite a
GUI:
https://fosspost.org/gtk-4-0-released/
[2] According to a Basic COCOMO model I found, a project of this size is the
output that can be expected from a team of 300 working for 56 months (make
of that what you will)
[3] https://www.bassi.io/articles/2022/12/02/on-pygobject
[4] The patch to go from 0.9.8.92 to 1.1 is 850k lines
[5] meanings 3 and 4 in the wiktionary
[6] moorhen.org
----
Release 0.9.8.94
o CHANGE: Add a more informative message on failure to generate rtop in
transform-map-using-lsq-matrix [Martin Maly]
o CHANGE: The pyranose link restraints logic has changed - hopefully more
accurate now [Andrey Lebedev]
o BUG-FIX: the logic of the glyco-tree glyco chiral test for ALPHA1-6 and
BETA1-6 has been reversed (i.e. corrected) [Markus Meier]
---
Release 0.9.8.93
o CHANGE: Electrostatic surface removed from the UI
o CHANGE: Clean-up for the residue selection in peptide omega analysis (don't draw
cis-peptides for residues that are not peptides)
o BUG-FIX: Fix erroneous mutation of DNA bases to RNA bases in mutate-residue-range
[Keitaro Yamashita]
o BUG-FIX: Add back the negative map contour levels into the input file for Raster3d
o BUG-FIX: Atom-name fix-up for "HH" in TYR - now TYR with hydrogen atoms can be refined.
----
Release 0.9.8.92
o FEATURE: Added copy_from_ncs_master_to_specific_other_chains_py(). Now one can update
(only) specific peer chains (instead of all of them as was previously the case)
[Oli Clarke]
o BUG-FIX: Change the linking code once more - fixes erroneous DNA+protein links
[Keitaro Yamashita].
----
Release 0.9.8.91
o BUG-FIX: Restore missing peptide omega plot [Steven Sheriff]
o BUG-FIX: Check/Delete waters no longer considers hydrogen atoms in close-contact analysis
o BUG-FIX: Replace Residue works for residues in the B chain [Paul Bond]
----
Release 0.9.8.9
o FEATURE: Use add_hydrogen_atoms_to_residue() in mutate_internal() if the residue
has hydrogen atoms [Clemens Vonrhein].
o FEATURE: Add add_hydrogen_atoms_to_residue() to the API.
o CHANGE: Allow the addition of hydrogen atoms to nitrogen atoms with energy
type NR5.
o CHANGE: Remove flaky Biscu-it QED interface.
o BUG-FIX: Change the link-finding algorithm to handle the AA-RNA link in
the new monomer library [Keitaro Yamashita].
----
Release 0.9.8.8
o FEATURE: Better atom colours in colour-by-chain-and-dictionary mode.
o CHANGE: Monomer search now uses the new dictionary
o CHANGE: Molecules read in as mmCIF (.cif) are now by default saved as .cif
o CHANGE: Atoms with element "Cl" are now drawn as CL.
o BUG-FIX: the zoom state is now correctly set in the saved state file
o BUG-FIX: additional symmetry check for peaks from flood filling (Paul Bond)
o BUG-FIX: Link-generation improvements.
----
Release 0.9.8.7
o FEATURE: res_tracer() added to the API
o FEATURE: read_mtz() added to the API [ChatGPT guessed at this function name, and there is
no reason for it not to be there]
o BUG-FIX: PDBe URLs fixed for downloading dictionaries with pyrogen
o BUG-FIX: Carbohydrate Linking fixed again [Keitaro Yamashita and others]
o BUG-FIX: RNA linking fixed [Keitaro Yamashita and Andrey Lebadev]
o NOTE: Coot is now tested against the new monomer library.
----
Release 0.9.8.6
o CHANGE: More auto-read column pairs added [Clemens Vonrhein]
o BUG-FIX: Adding a K to a molecule put the atom name in the correct column
[John Smith, Steven Sheriff]
o BUG-FIX: Carbohydrate Linking fixed [Keitaro Yamashita and others]
o BUG-FIX: delete_hydrogen_atoms() deletes deuterium atoms also [Lucrezia Catapano]
----
Release 1.0.06
o FEATURE: Add user-define colours to molecular ribbons representation.
o FEATURE: AlphaFold pLDDT colour scheme.
o FEATURE: Added load_gltf_mode() to the API.
----
Release 0.9.8.4
Release 0.9.8.5
o FEATURE: AlphaFold pLDDT colour scheme.
o CHANGE: Don't load files from ~/.coot if it is a directory.
o CHANGE: Don't consider carbonyl oxygens in merge fragments.
o CHANGE: Waters have a larger radius.
o CHANGE: Added bad NBC interaction annotation.
o BUG-FIX: Atom picking is no longer allowed in "Edit Chi Angles."
Thanks Juno Krahn.
o BUG-FIX: configure improvement for checking Python.
Thanks Juno Krahn.
o BUG-FIX: mutate_residue_range() now in the coot namesspace in auto_assign_sequence_from_map()
o CHANGE: Inter-chain links can now be refined. [Keitaro Yamashita]
o BUG-FIX: Reenable the picking of hydrogen atoms in rotation/translation
Thank you Taro Yamada.
o BUG-FIX: Fix up interesting_residues_gui(). Fixes problem in "Residues with Missing Atoms"
Reported by EJD.
o BUG-FIX: The GL Ramachandran plot is only displayed during refinement.
----
Release 1.0.05
o FEATURE: Contour level is now added to the status bar
o FEATURE: spin speed is now user-settable
o FEATURE: "mask by chain" added to Cryo-EM module
o FEATURE: Difference Map Peaks now has an "Update" button (should your difference
map change) [Sam Horrell]
o FEATURE: ability to change map colour by hexcolour
o FEATURE: triple-refine auto-accept key-binding added (H)
o FEATURE: "Outline" mode added to shader
o FEATURE: Window resize buttons added to the interface for Mac OS - don't pull on
the window, use these instead
o CHANGE: Rotamer markup during RSR now on by default
o CHANGE: Remove map colour change menu items
o CHANGE: Residue Info dialog now reports the chain-id and residue number
o CHANGE: Shaders are initialized after framebuffer - should now validate correctly
on Mac OS
o CHANGE: clipping plane adjustment step size decreased in perspective mode
o CHANGE: dialogs now filter files by default and save/restore previous directory
o BUG-FIX: Renumber residue range dialog fixed
o BUG-FIX: Ribbon representation checkbuttons no longer can grab focus
o BUG-FIX: right-mouse during refinement no longer picks atoms
o BUG-FIX: anchored atoms now displayed correctly
o BUG-FIX: Unmodelled blobs dialog fixed
----
Release 1.0.04
o configure of backward improved
----
Release 1.0.03
o FEATURE: backward can be configured to use libdw if available
-DBACKWARD_HAS_DW=1 added to CXXFLAGS
o BUG-FIX: "Validation Outliers" dialog now works
o BUG-FIX: "Ramachandran Outliers" dialog now works
o BUG-FIX: GL Ramachandran Plot now clickable after window resize
o BUG-FIX: coot python module improved
o BUG-FIX: Views Panel improved
o BUG-FIX: Display Manager window no longer blank on re-opening
o BUG-FIX: Dynarama glade file now installed correctly - Ramachandran plots now
work [Charles Ballard]
----
Release 1.0.02
o BUG-FIX: sort out the coot_wrap*.cc files
----
Release 1.0.01
o FEATURE: Space during RSR clicks the OK button
o FEATURE: NCS Ghosts now work again
o BUG-FIX: Add missing header files [Hew Jenkins]
o BUG-FIX: Don't rotate the view during RSR atom pull on Mac OS.
o BUG-FIX: Fix Pyrogen Oxygen atom types
o BUG-FIX: geometry_graphs_builder.glade installed correctly [Charles Ballard]
o BUG-FIX: Calculate -> Run Script dialog now works
o BUG-FIX: Draw -> Screenshot -> Simple now works (uses the "Plain" framebuffer)
o BUG-FIX: Removed some debugging
----
Coot 1
18 years after the release of Coot 0 it's time that I actually released Coot 1.
Coot 1 is a major change beyond Coot 0. It has required a lot of writing and rewriting [1]
and has been the preponderance of my work since 2017. I have had to learn how to program
graphics from scratch using the new style. Much of the GUI internals has been
rewritten [2].
My experience with 0.9 was that I sat on it, bug-fixing for a long time, releasing it
too late. I don't want to repeat that mistake. So here we are, there's a lot of good new
stuff in Coot 1, but it's not as slick as it might be (or will become).
o Update graphics to use OpenGL 3.3
o Update Python to use version 3.9
o Update GTK+ to use version 3
While many of the features that were available in 0.9.x have been reworked or
reimplemented, there are some gaps. Dropped features include Cross-hairs, Stereo, Pisa
interface, built-in key-bindings, NCS Ghosts, Edit Phi/Psi, antialiasing, Kleywegt
plots, the clipping dialog, Chemical Feature Clustering, Dynamically-Transformed/NCS
Maps, LSQ plane distances, dynamic distances, CABLAM-markup, the test suite,
user-defined colour schemes, anisotropic atoms, CURLEW, Scheme GUI scripting,
Skeletonization and Baton-Building.
"So, is there anything that _does_ work?" - you might ask...
The GUI has been updated, I have tried to cut down on the number of dialogs, the Real
Space Refinement in particular has seen quite a lot of work. The GUI now uses dark mode
if the theme is installed [3]. Several menu items have been relocated. More menus are now
alphabetically ordered [4].
The graphics is, by default, now based on triangles instead of lines which affords a
more pleasing representation (density maps can be represented using both modes) and one
can have a more expeditious if not pleasant experience with a fast graphics card and a
big screen. The various graphics effects and filters can be tailored to some extent by
changing the configuration using the GUI or by editing/replacing the shaders.
Full-screen mode is now an option [5].
Overall, the GUI has only had light testing. At the moment, it's probably best to
avoid closing dialogs using the window manager. The "OK" button now appears after the
"Cancel" button in dialogs.
Python scripting now has uses a history from previous sessions and the functions need
to be used with namespaces/modules (e.g. "coot", or "coot_utils"). Coot (or coot) is
now a module that can be imported into python.
This build compiles with the RDKit and optionally MoleculestoTriangles from Martin Noble.
The map and the model can now be exported to glTF files (for use in Blender and other
3D modelling software).
The build script for Coot 1, called build-it-3-3 can be found in the "Build from Scratch"
menu on the web page (you will need to have already installed cmake and Gtk+). The catch
though is that (at least in my hands) Python and friends are frustratingly difficult to
install, so it's possible/likely that the build script won't work. Likewise,
the script doesn't work for Mac OS either. But it is currently the best method to get
binaries so I will support it if you try it [6]. (Homebrew might be another method.)
Bernhard Lohkamp has been working on the WinCoot version - I will defer WinCoot
questions to him.
Mac Coot is now native (no X11/XQuartz needed). I would be interested to see how a
natively-compiled [7] version works on a M1 Max processor [8,9].
Judging from previous experience, a few rapid iterations of bug-fix releases will be
needed. After this, the version numbers will become sane - it's my plan to release a new
major version every year or so.
[1] new as in OpenGL 3.3 or later - using shaders - I don't mean Vulkan (that's for the
future)
[2] the patch from the 0.9.x version is 285k lines
[3] I recommend it
[4] rather than chronologically
[5] double-tap Esc key (the first time) to revert to standard display
[6] I have be working with CCP4 collaborators to use their system to build Coot binaries.
Hopefully the binaries will be available stand-alone, as well as integrated into
the CCP4 Suite via that method
[7] so that's a different meaning of "native"
[8] the little testing I have done on a recent intel MacBook Pro shows unimpressive
performance (Iris graphics, retina display)
[9] Thanks to my Mac-using colleagues for their feedback.
----
Release 0.9.8.4 [Fumbled release]
----
Release 0.9.8.3 [Fumbled release]
----
Release 0.9.8.2
o CHANGE: Don't try to read ~/.coot on startup if it is a directory
o BUG-FIX: Regenerate the bonds after a cis-trans conversion
o BUG-FIX: Fix crash on picking intermediate atoms in Real Space Refinement
[Nikos Pinotsis]
o BUG-FIX: Hydrogen atoms are now pickable again in Rotation/Translation
[Taro Yamada]
----
Release 0.9.8.1
o BUG-FIX: Python test for averaged maps fixed
o BUG-FIX: Pythonic and scheme get_drug() function fixed
o BUG-FIX: downloaded curlew files are now copied, not renamed.
----
Release 0.9.8
o BUG-FIX: Fix python extension scripts
o BUG-FIX: Fix active item in Bond Parameters bond-width combobox
o BUG-FIX: Now can parse cif files with long molecule names (Eugene Krissinel)
o BUG-FIX: Fix bond orders in RNA and DNA
o BUG-FIX: Fix crash when parsing data_lib in mmcif files
o BUG-FIX: Fix Wikipedia redirect of molecule name
o BUG-FIX: rename() is no longer used when installing curlew files
o BUG-FIX: Fix crash on using the Generic Objects dialog Close button
----
Release 0.9.7
o FEATURE: Add angles in coot-ligand-validation
o FEATURE: "Updating Maps" added to the API and GUI
o FEATURE: Stereo style can now be switched back to how it used to be in 2010 [Dirk Kostrewa]
o CHANGE: Better B-factors for added waters
o CHANGE: Windows build script updates
o CHANGE: RSR GM restraints now filtered by distance difference
o BUG-FIX: Python GUI and updates to match scheme version - now pyrogen work on Windows
o BUG-FIX: Fix gui simple mutation crash [John Bollinger].
o BUG-FIX: add a null function (no-coot-tips) for those that have this in their startup scripts
o BUG-FIX: Fix crash when coot tries to exit while the refinement is still refining [James Holton]
----
Release 0.9.6
o FEATURE: Middle-mouse and double-clicking on moving atoms is now enabled
(for recentre and label)
o FEATURE: -P mode added to pyrogen (no coordinates optimization)
o FEATURE: model_correlation_stats_per_residue_range() added to the API
o FEATURE: Molecular (i.e. not crystallographic) symmetry added
o FEATURE: coot-find-ligand has a mode to merely generate conformers
o FEATURE: added function to the API to flip the side-chain of the active atom
of the moving atoms: side-chain-flip-180-intermediate-atoms
[Oliver Clarke]
o FEATURE: New program coot-identify-protein, identifies a protein from a poly-ALA
fragment and a set of sequences
o CHANGE: Adjust the NBC model once more for 1-4 atoms involving Hydrogen atoms
o CHANGE: Water-water contacts are now considered by default in atom overlap analysis
o CHANGE: Adjust the initial RSR step size (no more wild water refinement)
o CHANGE: Increase the initial step size for refinement for large fragments
o CHANGE: Post-refinement restraints analysis added
o CHANGE: Trans-peptide restraints added/removed as needed for cis-trans conversion
of intermediate atoms
o CHANGE: API accept_moving_atoms() can now return the refinement results
o CHANGE: Remove libcheck as a restraints generator option
o CHANGE: Turn off EM-mode for PANDDA maps (Frank von Delft)
o CHANGE: "Residues with missing atoms" function no longer considers OP3. Additionally,
missing atom names are written to the terminal (Lothar Essar)
o CHANGE: MMFF94 target geometry now used in minimization in pyrogen by default
o CHANGE: Atom Overlaps optional toolbutton added
o BUG-FIX: Linking (shell) to the Coot executable now works (Marcin Wodjyr)
o BUG-FIX: --ccp4 mode fixed/improved
o BUG-FIX: Clean up bit-rotten chemical feature clustering
o BUG-FIX: rotamer-fit now runs the post-manipulation hook
o BUG-FIX: No longer fail to load scheme scripts if the user-name is not in the passwd file
o BUG-FIX: Better crash-catcher diagnostics (thanks Kevin Cowtan)
o BUG-FIX: Chiral restraints improved in pyrogen (Rob Nicholls)
o BUG-FIX: add-hydrogen-atoms no longer adds a hydrogen atom to an CYS SG if it is linked
----
Release 0.9.5
o FEATURE: Search monomer library has images
o FEATURE: New comamnd-line program coot-ligand-validation
o FEATURE: Add "Label Atoms in Residue" menu item
o FEATURE: Add command line argument --run-state-script
o FEATURE: Add function set_torsion_restraints_weight() to the API
o FEATURE: Real space refinement now has dynamic weights (under More Control)
o CHANGE: Fall-back to monomer atoms for the chemical diagram when there are missing
atoms in the model for hetgroups
o CHANGE: Scheme interface to refmac is now non-blocking
o CHANGE: set_map_is_difference_map() function now takes an argument (so that you can now
say that a map is not a difference map)
o CHANGE: Map density histogram is now improved
o CHANGE: 1-4 Non-bonded contacts adjusted
o CHANGE: Chiral volume sigma reduced to 0.1 A^3
o CHANGE: Change the configuration of RDKit in configure
Now use --with-enhanced-ligand-tools and --with-rdkit-prefix=prfx
o BUG-FIX: fix up the use of residue-exists? in mutate-it
o BUG-FIX: installation of side-chain data [thanks John Bollinger]
o BUG-FIX: refine_zone() on a single residue works again
----
Release 0.9.4.1
o BUG-FIX: Fix crash on reading some CCP4/MRC maps
o BUG-FIX: Colour-by-chain fixed again: now respects the draw-missing-residues-loops
setting
o BUG-FIX: Fix the installation of side-chain-data
----
Release 0.9.4
o FEATURE: Add function for Backrub Rotamer for chain
o FEATURE: Faster reading of maps for cryo-EM reconstructions
o FEATURE: Add "no-recontour on panning" mode
o FEATURE: function add_hydrogens_atoms() added to the API
o FEATURE: function assign_sequence_to_active_fragment() added to the API
o FEATURE: Add "Atom Overlaps" to the Validation menu
o FEATURE: Add an entry for weight change in the active map selection dialog
o CHANGE: Remove Prodrg-ify from the interface
o CHANGE: Better application of Ramachandran restraints
o CHANGE: Link with latest and greatest version of Python 2
o CHANGE: Fill partial residues now faster as residues are now refined at the same time
o CHANGE: API function change argument order for add_OXT_to_residue()
o CHANGE N-linked glycosylation feature: weight change. Now more robust and useful
in cryo-EM
o CHANGE: Represent formal charge in the restraints editor. Remove partial charge.
o BUG-FIX: globularize() now works for nucleic acid chains
o BUG-FIX: Fix up the "Dock Sequence" dialog - now is called "Assign Sequence"
o BUG-FIX: Colour-by-chain colours fixed again
o BUG-FIX: Conditionally delete OP3 when extending nucleotide chains
o BUG-FIX: Fix up hardware stereo
----
Release 0.9.3
o BUG-FIX: Colour-by-chain colours no longer run out [Huw Jenkins]
o BUG-FIX: undo-redo no longer creates duplicate atoms when
using cif files
----
Release 0.9.2
o BUG-FIX: Fix crash in raster3d output [Vito Calderone]
o BUG-FIX: Colour-by-B-factor modes fixed and improved
o BUG-FIX: Fix atom colours in Colour-by-Chain mode
----
Release 0.9.1
o FEATURE: fat atoms for some metals and halides
o FEATURE: add a "Rescale" entry and button for the density fit validation graph
o FEATURE: add label_closest_atoms_in_neighbour_residues to the API and added to the Draw menu
o FEATURE: missing-residue loops can now be undisplayed: set_draw_missing_residues_loops()
o FEATURE: find pep-flips using based on difference map
o FEATURE: Add "Proportional editing" for atom-pull neighbour displacement
[c.f. Tristan's ISOLDE]. Use Ctrl-scroll to change the radius
o FEATURE: carbon atoms in Colour-by-Chain mode have their own colour index
o FEATURE: add a menu items for the addition of hydrogen atoms
o FEATURE: backup file names can now be decolonized
o FEATURE: flip_hand() function added - for reversing the hand of Cryo-EM maps
o FEATURE: add "backward" for better core dump reporting
o FEATURE: "Delete Residue" added - bound to Ctrl-D
o FEATURE: add_nucleotide() added to the API [Gianluca Cascarano]
o FEATURE: Distances added to raster3d output [Vito Calderone]
o CHANGE: Waters can no longer be placed directly on top of another atom
o CHANGE: Sequence view is docked by default - now with current-residue highlighting
o CHANGE: Bond orders used for colour-by-chain mode
o CHANGE: Increase weight on atom-pull restraint
o CHANGE: More sane rotation Ctrl-base rotation in Rotation/Translation mode [Mattias Barone]
o CHANGE: contact dots now use Fibonacci spheres - goodbye UV pole crowding
o CHANGE: improvements to dictionary reading and reporting of mismatches
o CHANGE: single-letter entry added to residue type selector for mutations
o CHANGE: rework the linking algorithm so that residues with a residue number gap but close
N and C atoms can now be linked.
o CHANGE: Fourier filtered Jiggle-Fit now followed by rigid-body refinement at full
resolution
o CHANGE: assign_sequence_from_file() rewritten and generalize for all-chain search [Bob Nolte]
o BUG-FIX: fix the generation of link metal oxygens restraints when the atoms are reversed.
o BUG-FIX: fix crash in lbg network molecule retrival
o BUG-FIX: Merging a ligand in merge-molecules no longer steps the residue number by 100 when
adding the same ligand type [Keith Wilson]
o BUG-FIX: Curlew's "Install" and "Uninstall" buttons work better
o BUG-FIX: mutate_by_overlap now works for nucleotides
o BUG-FIX: backup file name generation cleaned up
o BUG-FIX: tidied up the GLY representation in CA+sidechains mode
o BUG-FIX: Apply the dynamic transformation to NCS ghost maps [Randy Read]
o BUG-FIX: remove neighbour-generation memory leak
o BUG-FIX: getopt usage reworked - the command line should behave better on some systems
-----
Release 0.9
This release has been a long-term effort (4 years according to my notes). It is powerful but not as
clean and stable as I would have liked, but I don't want to delay any longer. Many of the additions
and updates have been focused on the problems posed by cryo-EM reconstructions.