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RELEASE-NOTES
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-----
Release 0.8.9.2
o FEATURE: LINK info added to header browser
o FEATURE: External angle restraints are now available (corresponding to REFMAC type
0 restraints) - mini-rsr included [Robbie Joosten]
o FEATURE: raster3d output now includes labels [Vito Calderone]
o FEATURE: API for user-defined unimodal torsion restraints (for pyranoses) [Juan Hermoso]
o FEATURE: "Variable" bond widths i.e. as you zoom out, the bond lines get thinner
[Erec Stebbins]
(set-use-variable-bond-thickness 1)
o CHANGE: Iron-Sulfur clusters are now bonded using the dictionary (and so appear "cubic")
[Hannah Bridges]
o CHANGE: Edit -> Copy Fragment now has a "Move it Here" check-button
o CHANGE: Old interface to PRODRG removed [Elinor Breiner]
o CHANGE: Jiggle-fit speed up by using backbone mode if possible
o CHANGE: Forwards-fitting a terminal residue now correctly positions the O atom
of the current residue that corresponds to the new residue
o CHANGE: Planar peptide restraints now apply to PTRANS restraints as well as TRANS
restraints
o CHANGE: "Linear" refine no longer exists, the refinement button now uses the same
interface as sphere refine. Residues now have environments but "finding peptide
links by residue number, no matter how far the residues are away from each
other" has been removed
o CHANGE: Squares to cirlces in the Ramachandran Plot
o CHANGE: Default is now not to generate a monomer on reading a dictionary cif file
o CHANGE: More functions added to the coot_extended python module
o CHANGE: RCrane restored
o CHANGE: Add link-by-torsion-to-NAG-core-NAG-SER.tab so that add_linked_residue()
can link a NAG to a SER
o CHANGE: CA Zone -> Mainchain builds in both directions
o CHANGE: Alignment gap penalty changed to -3.0
o CHANGE: Merging a ligand molecule now adds the ligand to the closest chain - unless
a merging molecule ligand has been specified
o BUG-FIX: the H atom in a peptide is now moved along with the other peptide atoms
on a cis->trans conversion (and vice versa)
o BUG-FIX: align-and-mutate occasional reversing of residues fixed [Rob Kirchdoerfer]
O BUG-FIX: Using PDB-REDO now loads an anomalous map also (if possible) [Robbie Joosten]
o BUG-FIX: Fix typo in template-keybindings-to-preferences that causes initial
installation of key-bindings to fail sometimes [Colin Palmer].
o BUG-FIX: The slow update on deleting deviant extra distance restraints has been
been replaced with a faster version [JED]
o BUG-FIX: db_mainchain() fragment/chain indexing bug fixed [Oliver Clarke]
o BUG-FIX: db_mainchain() no longer crashes when using negative residue numbers
[Oliver Clarke]
o BUG-FIX: Delete All Carbohydrate now works with carbohydrate with insertion codes
-----
Release 0.8.9.1
o FEATURE: Auto-NCS Jumping menu item added to the NCS submenu
o FEATURE: Tool-tips for residues in Sequence View
o FEATURE: Added a function to limit the display radius for models
o FEATURE: New button to display only the the last model molecule
o FEATURE: Acedrg Link generation GUI (in the CCP4 Module)
o FEATURE: "Jiggle-fit Ligand" menu item added to the Ligand menu
o FEATURE: GUI to use Refmac to generate structure factors from an EM map
(in the Cryo-EM module)
o FEATURE: Interactive "Nudge Residue" dialog added to Cryo-EM module
o CHANGE: The refinement map is now set before refinement of solutions
in ligand fitting [Keith Wilson]
o CHANGE: The Mutate Residue Range can now mutate RNA and has a
check for numbering consistency [Donna Matzov]
o CHANGE: Map density histogram is cached for speedier display
of Map Properties dialog for Cryo-EM maps
o CHANGE: RCrane removed from the interface (for now)
o CHANGE: Carbohydrate fitting weighting scheme improved (should work
better for cryo-EM maps)
o BUG-FIX: cif-reading in Classic dialogs no longer causes a crash
o BUG-FIX: Phosphorus atoms are now orange in Colour by Chain mode
o BUG-FIX: Molecule information extraction from wikipedia made more robust
o BUG-FIX: N-terminal Hydrogen atoms now refined correctly
o BUG-FIX: Fix crash on Replace Residue with a nucleotide [Elinor Breiner]
o BUG-FIX: Fix crash on invalid SMILES input for LIDIA
o BUG-FIX: Fix crash on wrong molecule index for some cif data function [JED]
----
Release 0.8.9
o FEATURE: Improved Ramachandran Plot, now with residue selection
o FEATURE: Use of threads and accumulation in map contouring
o FEATURE: secondary structure interface added to the the API
o FEATURE: delete-chain and delete-sidechains-for-chain added to the API
o FEATURE: Added a user-defined modelling toolbar button to refine tandem residues
o FEATURE: experimental peptide orientation optimisation function added (also in mini-rsr)
o CHANGE: Refinement speed-up
o CHANGE: Add-terminal-residue speed-up
o CHANGE: Glyo module improved with distance restraints and better GUI
o CHANGE: Better density fit graph scaling
o CHANGE: Use ETKDG for embedding in pyrogen
o CHANGE: Use less precision on writing the aniso ADPs for SHELX ins
o CHANGE: Optional Fourier Transform-based Ramachandran Plot target function added
o CHANGE: Bond-thicknesses improved in colour-by-chain.
o CHANGE: Robust MOL-file parsing added to lidia
o CHANGE: A density value histogram has been added to the map properties dialog
o CHANGE: Pepflip residue indexing improved
o CHANGE: Updated Ligand fitting in the tutorial
o BUG-FIX: Hydrogen atoms are no longer used in rotamer clash score
o BUG-FIX: Geman-McClure distance restraints activation bug fix
o BUG-FIX: delete-atom no longer crashes when given an invalid model molecule number
o BUG-FIX: Adding a terminal OXT no longer causes a crash
o BUG-FIX: Ramachandran plot is updated on "Undo"
o BUG-FIX: Chiral centre distortion representation fixed
------
Release 0.8.8
o FEATURE: C++11 compilers will multi-thread multiple map contouring
o FEATURE: SMILES -> simple 3D menu item added
o CHANGE: Delete residue range speeded up [Oliver Clarke]
o CHANGE: PG4 added to other solvent ligands
o CHANGE: Solid model lighting adjusted
o CHANGE: The Flexible? conformer-generation checkbutton repositioned [JED]
o CHANGE: Find Ligands added to the Ligands menu
o CHANGE: Move molecule here checkbutton position reordered
o CHANGE: Renumber residue range dialog improved by addition of terminii
checkbuttons
o BUG-FIX: Chains with non-overlapping residue numbers can now be merged
without specifying the residue range
o BUG-FIX: Colour by B-factor and Occupancy modes restored [Hans Raaijmakers]
o BUG-FIX: Network interface to Drugbank follows server changes
o BUG-FIX: Correct the PNG image output image size from Lidia
o BUG-FIX: Refmac monomer library is restored (after server crash)
o BUG-FIX: Use XYP not XYL for carbohydrate tree additions
o BUG-FIX: Peptide Omega validation graph tool-tip label corrected [Nigel Moriarty]
o BUG-FIX: Restore missing waters in FLEV
o BUG-FIX: Fix crash on conformer search with no dictionary [JED]
o BUG-FIX: Fix pyrogen dictionary double-quoted primed atom names [JED]
------
Release 0.8.7
o FEATURE: Lidia now has canvas scaling
o FEATURE: Lidia now has CH3 superatoms, atom name and index display modes
o FEATURE: Atom renaming to reference comp_id now has a place on the
Ligand menu
o FEATURE: Sequence View dynamically updates after a residue zone deletion
o FEATURE: NCS local update now has a place on the NCS menu
o CHANGE: File -> SMILES has been removed
o CHANGE: Additional parameters available in the ligand-fitting dialog
o CHANGE: Non-bonded contact restraints calculation speed up
o BUG-FIX: Fix side-chain plane restraints for sphere-refined residues with
alt confs
o BUG-FIX: MSE atoms are HETATMs after mutation [Sivasankar Putta]
o BUG-FIX: CD bump exception in HYP NBC across link [Jens Kaiser]
o BUG-FIX: Bond-dragging in Lidia now cleaned up
o BUG-FIX: Correct bonds to W in WO4.
------
Release 0.8.6.1
o BUG-FIX: Fix typo in findligand shell script
Release 0.8.6
o FEATURE: Added man pages
o CHANGE: bfactan renamed coot-bfactan
o CHANGE: no backups for each residue in fill_partial residues() function.
o CHANGE: User control over max and min distance to the protein in findwaters
o CHANGE: Go-To-Ligand function now has better animation
o CHANGE: Included a speed-up for the non-bonded contact restraints generation
-----
Release 0.8.5
o BUG-FIX: Fix conformer-related crash when showing ligand view of some metals
[Oliver Clarke]
o BUG-FIX: coot-mini-rsr no longer crashes when given a non-existent file-name
for a map
-----
Release 0.8.4
o FEATURE: Generic display objects can now be attached to a molecule number:
attach_generic_object_to_molecule(obj_no, imol)
o FEATURE: Patterson from intensities: make_and_draw_patterson_using_intensities()
o FEATURE: Added function closest_atom_simple_py() which returns the closest atom
to the centre of the screen (without CA subsitution)
o FEATURE: chemical feature clustering (import cfc_ligand_sites)
o FEATURE: Ramachandran plot now has a "Outliers Only" mode
o CHANGE: fill-partial-residue now works with ROTAMERSEARCHLOWRES rather than
ROTAMERSEARCHHIGHRES.
o CHANGE: Many functions now dynamically update the sequence dialog
o CHANGE: Improved lighting when displaying solid objects
o CHANGE: Typesetting improvements in lidia
o BUG-FIX: Set the suggested file name in the classic dialog on saving
coordinates [Andy Purkiss, Arnaud Basle]
o BUG-FIX: Setting the formal charge in lidia now works properly
o BUG-FIX: Correct wrapper for findligand and findwaters [Kuan-Fu Gabriel Lin]
o BUG-FIX: FLEV "problematic ligand" reduced in frequency
o BUG-FIX: OXT-related refinement improved
o BUG-FIX: Remove long bond between CB and OXT in HETATM CYS [Dale Tronrud]
o BUG-FIX: mini-rsr now optionally uses trans peptide restrints
o BUG-FIX: 4-char Hydrogen atom names from PBDx are now correctly read (folding in an
mmdb2 fix)
-----
Release 0.8.3
o FEATURE: Add ligand percentile scoring to the API and GUI
o FEATURE: Residue correlations and distortion scores added to
cooot-mini-rsr output
o FEATURE: cis-peptides and twisted trans-peptide are marked up
o FEATURE: Optionally add "balls" to standard stick mode
o CHANGE: mini-rsr is now called coot-mini-rsr
o CHANGE: Hydrogen atoms are not longer fit to density
o CHANGE: Toolbars are now resizable
o CHANGE: coot-download directory is no longer created on starting coot [Marcin W.]
o CHANGE: Middle-mouse pan added [Martín X]
o CHANGE: N-terminal addition of peptides has been improved
o CHANGE: If the dictionary file from PDBe is empty, now over-write it
o BUG-FIX: fix atom index check in add_atom_label() [Gabriele Balducci]
o BUG-FIX: Chiral volume restraints correctly output from
coot.make-shelx-restraints
o BUG-FIX: Save Symmetry coordinates with a .cif filename now saves coordinates
as mmCIF [Wolfram Tempel]
o BUG-FIX: Fix typo in python gui transform_map_using_lsq_matrix() [Gyorgy Snell]
o BUG-FIX: Highlight Interesting Site no longer has over-sized primitives
-----
Release 0.8.2
o FEATURE: Add dictionary-based atom name matching in pyrogen [EJD]
o FEATURE: Add ligand fragment flipping [JED]
o FEATURE: SMILES drag and drop added to LBG
o FEATURE: Use pyrogen by default if mogul available [JED]
o FEATURE: Surface points are now exported from HOLE.
o FEATURE: Clicking on a Het-group now reports the name in the status bar
[Dave Brown]
o FEATURE: Added function map-statistics to return map statistics
[Alejandro Virrueta]
o CHANGE: EDS Resolution addeded to PDB Validation dialog [Frank von Delft]
o CHANGE: The Residue numbers are reported in the refinement dialog
when creating a cis-peptide [Dave Brown]
o CHANGE: Ligands in Rainbow mode are no longer blue
o CHANGE: Colour-by-chain now shows disulphide bonds
o CHANGE: Refinement drag elasticity increased
[Everyone who tried to use it in 0.8.1 :-(]
o CHANGE: Global translations towards the molecule centre removed on
model morphing
o BUG-FIX: Improvement in PDB->SHELXL ins output [Andrea Thorn]
o BUG-FIX: Fix problem of deleting all atoms in Baton Build atoms
molecule
o BUG-FIX: The NCS master chain in Copy NCS Residue Range now works
[Airlie McCoy]
o BUG-FIX: "Clear Latest Distance" crashes coot. Fixed [Emily Arturo]
o BUG-FIX: Fix output format of external restraints [Richard Bunker]
o BUG-FIX: Torsion-based ligand fitting improvements [Rob Nicholls]
o BUG-FIX: A model with hydrogens displayed in CA+Ligands mode used
to show the hydrogens even if hydrogens were off - Fixed now.
[Alex Wlodawer]
o BUG-FIX: Fix occassional graph data range anomaly [Rob Nicholls]
o BUG-FIX: Add missing plane distortions in print_residue_distortions()
o BUG-FIX: PISA interface works with newer version of pisa
[Maria Jose Sanchez Barrena]
o BUG-FIX: Only check once for probe when showing the Validation menu.
o BUG-FIX: Resetting of Own font colour on opening the preferences
dialog fixed.
-----
Release 0.8.1
o CHANGE: Generic Dislay Objects dialog improved.
o CHANGE: Water validation dialogs are now transient
o CHANGE: Ctrl-R for Rock View
o CHANGE: Least Squares Fit dialog now remembers its values
o BUG-FIX: stippling for line and text geometry and environment
distances updated
o BUG-FIX: Jiggle fit moves atoms with zero occupancies.
o BUG-FIX: Problem with CA-Zone -> Mainchain fixed.
o BUG-FIX: The amount that the other atoms ove with moving the
picked atom has been reduced (but is configurable)
o BUG-FIX: Sort chains and residues has been fixed.
o BUG-FIX: Add Template Keybindings for Python now works
-----
Release 0.8
o FEATURE: Added a interface for Cootilus
o FEATURE: Pubchem support for drag and drop
o FEATURE: Added glyo and ProSMART modules
o FEATURE: Auto-open MTZ files with x.F_phi.F & x.F_phi.phi for any
value of x.
o FEATURE: When input map seems to be from EM, ignore modal density
values for statistics calculation
o FEATURE: labels and on-screen text can now be rendered with stroke
characters instead of bitmaps
(set-use-stroke-characters 1)
set_use_stroke_characters(1)
o FEATURE: Enable the running of python commands from the command line
o FEATURE: Install appdata for GNOME Software Center [Richard Hughes]
o FEATURE: New program compare-dictionaries added
o FEATURE: New program make-shelx-restraints added
o FEATURE: pdb validation data parser and gui attached to Fetch
accession code.
o FEATURE: Added match-residue-and-dictionary() function for atom
name matching of similar monomers
o FEATURE: Added function to move a reference chain to a
symmetry-related position
o FEATURE: Add parallel nucleotide plane restraints
o CHANGE: Bond colours against a white background have been improved
o CHANGE: Main gui icons are now pngs
o CHANGE: Pyrogen bundled in enhanced-ligand version
o CHANGE: Deuteriums are pink
o CHANGE: Extra restraints added to Raster3D input
o CHANGE: Geman-McClure M-estimator used for extra distance restraints
o BUG-FIX: CA-mode now works for MSEs
o BUG-FIX: Mo bonding improved
o BUG-FIX: Unbonded CA now have stars in CA mode
o BUG-FIX: Better output of ligand fitting solutions [Andre White]
o BUG-FIX: Adjust hydrogens also on nomenclature correction
o BUG-FIX: Multi-solution ligand fitting fixed
o BUG-FIX: Wedge bonds can now be converted to single bonds in LBG
o BUG-FIX: Mol2 file atoms names are now preserved [Markus Rudolf]
o BUG-FIX: B-factor colouring now fixed [Oliver Smart]
o BUG-FIX: HOLE implementation handles large radii better
o BUG-FIX: Improved SHELX .ins parsing [Dale Tronrud]
o BUG-FIX: mmCIF output atom name quoting fix
o BUG-FIX: atom quad type check test fix [David Binderman]
------
Release 0.7.2
o BUG-FIX: Iodines are written to the correct column (Steven Sheriff)
------
Release 0.7.1
o FEATURE: Navigation via residue triple.
o FEATURE: csv mogul output parser.
o CHANGE: Updated interface to JLigand
o CHANGE: Sequence View improved.
o CHANGE: Bond orders for Het-groups in CA+ligands mode.
o CHANGE: Optional use of build-info at compile time.
o BUG-FIX: Ligand fitting improved/fixed.
o BUG-FIX: Drag and drop improved.
o BUG-FIX: Fix up for reading of molprobity files.
o BUG-FIX: Use Extended HM symbols when converting from clipper
symmetry to mmdb symmetry.
o BUG-FIX: Get Drug feature improved.
o BUG-FIX: Better use of extant ring info when drawing rings in LIDIA.
o BUG-FIX: Scale factor for sharpening fixed [Chang Liu]
------
Release 0.7
o FEATURE: Het-groups are now represented with bond orders.
o FEATURE: Ligand Builder - working in conjunction with cprodrg.
o FEATURE: RCrane [RNA builder]
o FEATURE: Cootaneer [RNA builder]
o FEATURE: PDBe Recent structure browser.
o FEATURE: JLigand interface.
o CHANGE: symmetry operator number are no longer zero indexed. Add
trans component to symmetry file names. [Steven Sheriff].
o CHANGE: Dotted surfaces now are coloured by atom type and are at
atomic radii rather than 1A.
o CHANGE: map transformation no longer has symmetry overwrite
problems [JED].
o BUG-FIX: Fix missing C7 on DA -> DT mutation [Sabine Schneider].
o BUG-FIX: TER records on base mutation [James Parker].
o BUG-FIX: DNA in sequence view [Miguel Ortiz Lombardia].
o BUG-FIX: Update Go To Atom dialog after water merging [Bob Nolte].
o BUG-FIX: fix memory leak in fit-protein function [Ed Pozharski].
o BUG-FIX: Improved "Place Helix Here".
------
Release 0.6.2
o FEATURE: PISA Interfaces can now be represented in Coot (requires
pisa version 1.06 or later).
o FEATURE: Regularize sphere function introduced.
o FEATURE: --update-self to update pre-release binary from server.
o FEATURE: SBase molecules can be imported (under Search Monomer
Library).
o FEATURE: prodrg-ify ligand function added (generates restraints
for the specified residue).
o FEATURE: higly-coordinated waters metal substitution search added.
o FEATURE: Rudimentary support for reading 3D MDL mol2 files.
o FEATURE: New map representation styles, solid/transparent and
"cut-glass".
o CHANGE: Align & Mutate now provides a simple dialog with the
alignment.
o CHANGE: Environment distances are separated into bumps and bonds
[Bob Nolte].
o CHANGE: Move molecule here only moves small molecules by default
now. There is an check button to allow big molecules [Kevin
Madauss].
o CHANGE: In MTZ reading Expert Mode, if the low resolution limit is
not set, then presume that it was 999.9A [Randy Read].
o CHANGE: Faster, multiprocessor electrostatic surfaces [Martin
Noble].
o CHANGE: pointer distances are updated on go-to-blob [JED].
o CHANGE: COOT_SCHEME_EXTRA_DIR and COOT_PYTHON_EXTRAS_DIR are now
":"-separated lists [Thomas Womack].
o CHANGE: Real-space refinement is now interruptible [JED].
o CHANGE: NCS skipping now works in the reverse chain order too
(Shift-O) [JED].
o CHANGE: Residues are checked atom by atom against the dictionary
and refinement is not started if there is not complete agreement
(for non-Hydrogen atoms) [JED].
o CHANGE: Merged molecules are undisplayed after merging.
o CHANGE: "Replace residue" will use a dictionary and model for a
particular 3-letter code if they have been already read in (rather
than run libcheck blindly) [Ian Tickle].
o CHANGE: SSM overlayed molecule now takes symmetry, cell and origin
of reference molecule.
o CHANGE: Waters are now represented with "~" in the sequence view -
so that there is a distinction between waters and interesting
hetatoms.
o CHANGE: Using the scroll wheel with Ctrl and Shift will change the
represention of the molecule that has the active residue.
o CHANGE: difference_map_peaks() function now takes an addition
argument specifying the minimum distance between peak (filtering
out close smaller peaks).
o CHANGE: Waters are no longer considered when calculating the clash
score during rotamer fit.
o BUG-FIX:: Hydrogens on waters are no longer checked against the
difference map in the water validation test.
o BUG-FIX: Water search now avoids close contacts to waters
generated in the same round.
o BUG-FIX: Water check in gtk1 version no longer tries to
dereference the difference map active checkbutton - fixes crash
[Subhangi Ghosh].
o BUG-FIX: Fix crash on rigid-body refine by atom selection with
residue gaps [Joel Bard].
o BUG-FIX: Fix crash on Ramachandran restraints with planar peptide
restraints with alt confs [Peter Simone, Andrew Purkiss].
o BUG-FIX: rename residue works on only the specified chain.
o BUG-FIX: anomalous maps are now properly recovered from the state
file [Phil Evans].
o BUG-FIX: Symmetry is updated on accepting a Rotate/Translate
modification [Ezra Peisach].
o BUG-FIX: Rotate/Translate on a residue with an insertion code now
picks and moves the correct atoms.
o BUG-FIX: NCS differences were broken by gaps of different lengths
[Ingo Korndoerfer].
o BUG-FIX: Unconventionally formatted atom tree records in
restraints cif now no longer cause a crash when using Chi Angles
[JED].
o BUG-FIX: Fix the crash when sphere refine was used at the same
time that the geometry graph was displayed [JED].
o BUG-FIX: Fix crash when update peptide omega distortion graph
[Horacio Botti].
o BUG-FIX: rotate/translate large fragments now works better.
o BUG-FIX: transform-map function fixed for 5 arguments.
o BUG-FIX: Sort-chains no longer loses header information [Bob
Nolte].
o BUG-FIX: Environment distances are no longer drawn between atoms
with differing non-blank alt-confs.
o BUG-FIX: mmCIF file writing fixed.
o BUG-FIX: Zero occupancy marker on hydrogens are not undisplayed
properly [JED].
o BUG-FIX: refining with structures from .res files sometimes crash
when writing backup file on Mac [Derek Logan].
o BUG-FIX: Rotating/translating ligands in CA+Ligands mode now works
[Jim Thorpe].
o BUG-FIX: Platinum can now have sensible bonds to N and O [John
Helliwell].
o BUG-FIX: Ramachandran plots work at the end of chains chains with
missing residues [JED].
o BUG-FIX: Environment distances display toggling anomolies cleaned
up [Ed Pozharski].
o BUG-FIX: Sequence view failed with SHELX molecules with high
residue numbers [Stefan Becker].
o BUG-FIX: SSM superposition now superposes the correct molecules
when the option menus are not adjusted [Sam Stampfter].
o BUG-FIX: colour-by-chain with C-only mode long non-C bonds fixed
[Petra Loenze].
-----
Release 0.6.1
o FEATURE: Quick-save - bound to Ctrl-S.
o FEATURE: Binary updates (pre-releases) now available.
o FEATURE: tutorial data can be loaded from a Extensions menu item
o FEATURE: A means to set the refinement weight so that the
resulting chi squareds are 1.0 (or close) [Katya Heldwein]
o CHANGE: "Save dialog positions" now also saves the Edit Chi Angles
dialog position [Markus Rudolph].
o CHANGE: Coot can now go through proxies (http_proxy environment
variable) to get News and Updates.
o CHANGE: Baton manipulation is now possible when the skeleton runs
out.
o CHANGE: Hydrogen representation now thin and grey monotone.
o CHANGE: Interface to sidechain docking improved [Phil Evans].
o CHANGE: Updates to sync with new EDS (Electron Density Server).
o CHANGE: Filenames of mtzs and pdb in the current directory are now
stored as relative in the state file [Andre White].
o CHANGE: Default image type for screenshot is now PNG [Joel Bard].
o CHANGE: --python --no-graphics results in a python prompt at the
command line [Gabor Bunkoczi].
o BUG-FIX: Check waters by difference map now works again [Misty X].
o BUG-FIX: SSM alignment crash fixed [Ed Pozharski].
o BUG-FIX: Splitting a sidechain with zero occupancy no longer
leaves atoms with negative occupancy [Takaaki Fukami].
o BUG-FIX: Shift-spacing through waters, deleting active water now
goes to previous atom [Ingo Korndoerfer].
o BUG-FIX: No torsion restraints added when the esd of the torsion
is 0 (Phenix compatibility) [Joel Bard].
o BUG-FIX: Rotamers and Edit Chi now works for MSEs [Clemens Vonrhein].
o BUG-FIX: Hydrogen environment distances now are synchronised with
the display of hydrogens [JED].
o BUG-FIX: Phosphate-backbone mode enabled for symmetry [Miguel
Ortiz Lombardia].
o BUG-FIX: Carbon-Iodine bond length limit lengthened.
o BUG-FIX: Go To Atom dialog is updated after simple mutation of a
base [Miguel Ortiz Lombardia]
o BUG-FIX: Coot no longer things that a SHELXL BLOC card is an atom
[Zbigniew Dauter].
o BUG-FIX: LINKs between symmetry related molecules are no longer
drawn as long vectors to the same molecule [Alejandro Buschazzio]
o BUG-FIX: sugar chains now find the linkage type better (rather
than forcing seemingly-random chain breaks) [JED].
o BUG-FIX: Go to Atom keyboarding chain-id superfluous functions
removed [JED].
o BUG-FIX: Don't crash when calculating NCS on reading bogus chains
from a PDB mmCIF file [Christian Engel].
-----
Release 0.6
o FEATURE: User-defined clicks [Joel Bard].
o FEATURE: SHELXL interfaces allows the user to modify the input before
running the SHELXL executable [Tobias Beck].
o FEATURE: Now compatible with Zalman M220W.
o FEATURE: Post-manipulation function hook added [JED].
o FEATURE: "Sphere" (residue selection) refinement.
o FEATURE: function to (re-)calculate probe dots around a give point
[Joel Bard].
o FEATURE: monomer and residue selection dipoles.
o FEATURE: Interactive map sharpening [Randy Read, Alex Brunger].
o FEATURE: LINK bonds are are now represented.
o FEATURE: "Backrub rotamers" at low (2.7 or worse) resolution.
o FEATURE: Baton build parameters (e.g. "backwards") now have a GUI
[Phil Evans].
o FEATURE: Move waters to surround protein [Garib Murshudov]
o FEATURE: rotate/translate zone by residue ranges
o FEATURE: Rigid-body fit by residue ranges.
o FEATURE: Multi-select on reading coordinates is enabled.
o FEATURE: Immediate access to coordinates from CIF dictionaries
that contain coordinates (no need for LIBCHECK in such cases).
o FEATURE: Nudge-residue (bound to Ctrl-arrow keys).
o FEATURE: A dialog has been added from map averaging [Bob Nolte].
o FEATURE: Rename residue [Alexander Schiffer].
o CHANGE: partial charges added to electrostatic surface calculation.
o CHANGE: shift-click and ctrl-click in the file selectors now work
for reading in several coordinates files [Roberto Steiner].
o CHANGE: SEGIDs are more intelligently inherited [Steven Sheriff,
Bob Nolte].
o CHANGE: Transformed make take the cell and symmetry of the
reference coordinates.
o CHANGE: Transformed maps take on the cell and spacegroup of the
reference coordinates.
o CHANGE: Coordinates Molecules transformed by LSQ take on the cell
and spacegroup of the reference coordinates.
o CHANGE: Pukka-puckers? fixed and re-enabled.
o CHANGE: Ramachandran Plots now have molecule name labels [Wendy Offen].
o CHANGE: The save coordinates dialogs active item is the first
molecule with unsaved changes (rather than simply the first
molecule) [Herb Klei]
o CHANGE: "Go To Blob" now goes to the front blob, no matter what
the density level of blobs/density behind it is [JED].
o CHANGE: Don't display the geometry distance if the molecule
corresponding to the start or end point is not displayed [JED].
o CHANGE: Using the internal alignment, the weights of the affine
gap penalty have been changed to favour mutations and larger gaps
rather than several small gaps.
o CHANGE: the restraints editor now uses strings
(positive/negative/both) rather than number to represent the sign
for chiral volumes [Andrew Leslie]
o CHANGE: the restraints editor now adds a new entry to the
dictionary when the comp-id is changed.
o CHANGE: Additional representations now have an "All off" button.
o CHANGE: Chi angles rotation now include a "reverse fragment" option.
o CHANGE: "Add strand here" moved next to "Add Helix Here".
o CHANGE: Convert PDB format 3.x prime atom names to star names (to
correspond to current Refmac dictionary).
o BUG-FIX: TER records are removed on addition of waters [Herb Klei].
o BUG-FIX: Align vs PIR file improved [Bob Nolte]
o BUG-FIX: Single HETATMs now are refined by rigid body (as waters
are) when using Refine Zone.
o BUG-FIX: new atoms (and waters) are added as HETATMs if
appropriate [David Mathog].
o BUG-FIX: TER records for water chains are no longer tested in
water validation tests [Herb Klei].
o BUG-FIX: NCS chain jumping now works on heterodimers [Jianghai Zhu].
o BUG-FIX: The Chain Reordering function in Extensions has been fixed.
o BUG-FIX: Torsion angle refinement convergence improved [JED].
o BUG-FIX: Ramachandran Green spot no longer disappears on refinement.
o BUG-FIX: Limit the sequence view canvas X parameters, so that we
don't get X11 errors and crash [Felix Frolow].
o BUG-FIX: Additional representations appear in both "eyes" in
side-by-side mode.
o BUG-FIX: Delete-atom spewing binary fixed [JED].
-----
Release 0.5.2 Uneno
o BUG-FIX: Fix annoying shift-key-labels-atoms bug
Release 0.5.1 Uneno
o FEATURE: A "Delete Molecule" button is now available in the
Display Manager [TJS].
o FEATURE: show-rotamer-dialog is now available from the scripting
layer (hence `quick rotamer' keybinding) [FvD].
o FEATURE: Manual definition of NCS ghost matrices - GUI added.
o FEATURE: overlay-my-ligands function introduced.
o FEATURE: A simple interface to electrostatic surfaces has been
introduced (Extensions -> Representations).
o FEATURE: rotate-chi feature introduced. For use with a PowerMate.