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RELEASE-NOTES
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RELEASE-NOTES
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-----
Pre-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 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 BUG-FIX: set the suggested file name in the classic dialog on saving
coordinates [Andy Purkiss, Arnaud Basle]
o BUG-FIX: Typsetting improvements for Oxygen atoms in lidia
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: 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.
o FEATURE: keyboard-based Go To Residue for quicker navigation.
o CHANGE: NCS ghost work using LSQ to get the matrix, not SSM.
o CHANGE: Display manager toggle buttons replaced with check
buttons.
o CHANGE: make-dynamically-transformed-ncs-maps takes an extra
argument specifying if new maps should overwrite previous maps of
the same name.
o CHANGE: Extensions menu re-worked.
o CHANGE: Keyboard zooming is now smoothed.
o BUG-FIX: the chi angle bond highlighting works again.
o BUG-FIX: The Cancel button in Save Restraints now works.
o BUG-FIX: Check/Delete waters in Check mode no longer causes a
crash when the "Close" button is clicked.
o BUG-FIX: Atom elements are inferred from the atom name.
o BUG-FIX: writing of cifs from the Restraints editor has been
improved [JED].
o BUG-FIX: chiral restraints specified as "BOTH" can now be edited.
o BUG-FIX: "Flip peptide" now flips the peptide H atom too [Joel Bard].
o BUG-FIX: Ligands can now have their torsions manipulated in
CA+Ligands mode [Ingo Korndoerfer].
o BUG-FIX: NCS residue range edits now apply to more than the first
peer.
o BUG-FIX: Coot now can read PART cards with a site occupancy
factor from a SHELXL .res file [Mirek Gilski].
o BUG-FIX: Fixed crash on using multiple geometry (Distance and
Angles) dialogs.
o BUG-FIX: The Reset View button has been reworked.
o BUG-FIX: Ball & Stick additional representations has been
reworked and now move as the molecule gets updated.
o BUG-FIX: Ramachandran improvement function has been improved.
o BUG-FIX: Rotamers and simple refinement now work with residues
with insertion codes.
o BUG-FIX: The rotamer graph no longer rescales on updating a
molecule.
-----
Release 0.5 Ueno
o FEATURE: Coot now has a Preferences dialog.
o FEATURE: Coot now is PDB version 3.0 compliant.
o FEATURE: Additional Representations added [Tadeusz Skarzynski].
o FEATURE: "Fixed Atoms" for refinement have been introduced.
o FEATURE: Monomer restraints can be edited in a GUI and are
exported to the scripting layer.
o FEATURE: Coot can now make difference maps.
o FEATURE: The state file now remembers the refinement map number
[Herb Klei].
o FEATURE: Add dialog position preferences to Extensions.
o FEATURE: The state file now remembers the scroll-wheel (contour
changing) map [Kevin Madauss].
o FEATURE: Add a variable reduce-molecule-updates-current, that
when set by the user causes an update of the probed molecule, not
the generation of a new one [Bob Nolte].
o FEATURE: Add Terminal Residue now assigns the correct residue
type (if a PIR sequence has been given for side-chain docking)
[Bob Nolte].
o FEATURE: "Pukka Puckers?" validation tool for RNA. Based on
Davis et al. (2007) Molprobity: all atom contacts and structure
validation for proteins and nucleic acids, Nucleic Acids
Research 35, W375-W383.
o FEATURE: "Active site" hilighting. Cheap and cheerful solid
modelling of ligand and neighbouring residues [Herb Klei].
o FEATURE: Double-clicking on an atom labels it (CCP4mg
compatibility).
o FEATURE: "Eigen-flip" function added. Use to quickly flip around
ligands.
o FEATURE: it is now possible to add a setting so that atoms with
zero occupancy are not moved when refining:
set-refinement-move-atoms-with-zero-occupancy [Rajiv Chopra]
o FEATURE: Refmac can be run from Coot without the user having to
explicitly set the column labels.
o FEATURE: NCS Copy Chain is now available as a GUI extension.
o FEATURE: The ability to turn on chi angles that move hydrogens is
now available from the Chi Angles dialog.
o FEATURE: The "About" dialog contains references.
o CHANGE: Key bindings mechanism has changed. Now we are able to
display key binding in a GUI widget.
o CHANGE: Molprobity Tools (probe and reduce) will only now work
with those binaries that are hybrid_36 enabled.
o CHANGE: Picking has been changed to somewhat favour those atoms
at the front of the slab.
o CHANGE: When deleting a residue while displaying validation
graphs, the graphs get updated immediately [JED]
o CHANGE: In CA display mode, only CAs can now be picked.
o CHANGE: Nudge centre axes are now relative to the screen rather
than in world coordinates.
o CHANGE: NCS skipping changed. Hopefully faster now [Steven
Sheriff]. Also works in the case of hetero dimers with NCS [Phil
Evans].
o CHANGE: default bond width changed to 5.
o CHANGE: Traffic lights verticalized.
o CHANGE: Symmetry colour info added to state file [Doug Kuntz].
o CHANGE: the argument order for "mutate" scripting function
have been canonicalised.
o CHANGE: set-symmetry-colour-merge now takes only a fraction
argument.
o CHANGE: Mutate no longer changes the atom order in the pdb file.
o CHANGE: Next Residue/Previous residue reworked so that it now
jumps over gaps and goes to the right residue when encountering
insertion codes.
o CHANGE: Don't allow translation drag of intermediate atoms during
rotamer selection.
o CHANGE: Reference structures now have strand markup in the
header, so they can now be used as the reference structures for
"Build Strand".
o CHANGE: Bond parameters changes (bond width and hydrogens state)
now work immediately, no need to press the "Apply" button [FvD].
o CHANGE: Colour by Chain style also now displays zero occupancy
markers [PRE].
o CHANGE: Modelling toolbar can now be removed or docked in
different positions.
o BUG-FIX: chiral volumes are now correctly handled for multiple
monomer bespoke ligand dictionaries.
o BUG-FIX: Hydrogens names are better handled after an undo
operation - no longer do they fly off when refining [Joel Bard]
o BUG-FIX: Non-flexible ligands can be added to ligand search when
the "flexible?" option is selected. Previously the ligand search
was aborted.
o BUG-FIX: Flexible ligand fitting when the torsion period is 0 and
for ligands that have bonding defined from a cif file (no atom left
behind).
o BUG-FIX: side-by-side stereo mode improved [Randy Read].
o BUG-FIX: Now coot does not crash on when displaying NPD atoms
in anisotropic representation [Mitch Miller].
o BUG-FIX: Now coot does not crash when opening "Cell & Symmetry"
with no molecules loaded.
o BUG-FIX: Coot no longer crashes when deleting a residue with an
Alt Conf [JED].
o BUG-FIX: Coot can now do rotamers on a MSE residue [Mark Saper]
o BUG-FIX: Can now read SHELXL .ins files with lowercase symops.
o BUG-FIX: On additions to a SHELXL molecule: better handling of
UNIT and SFAC cards [GMS].
o BUG-FIX: EQUIV cards from SHELXL handled better.
o BUG-FIX: Adding waters to a SHELXL molecule now adds them with
default occupancy 11.0 [Tobias Beck]
o BUG-FIX: Go To Atom dialog is properly updated on merging
molecules.
o BUG-FIX: Coot no longer crashes when opening the Bond Parameters
dialog before a pdb file has been read.
o BUG-FIX: NCS Loop function now properly mutates residues in the
peer chains [PRE].
o BUG-FIX: Add Terminal Residue deletes the TER record (if it
existed) of previous C-terminus [PRE].
o BUG-FIX: Povray output improved.
o BUG-FIX: The representation is no longer changed after editing
atoms in CA+ligs representation.
-----
Release 0.4.1 "Kendall^2"
o BUG-FIX: Fix problem of key press with no map causing crash.
Release 0.4 "Kendall"
o FEATURE: Kevin Cowtan has given us "Cootaneer" [slim-line
side-chain-assigning Buccaneer for Coot]
o FEATURE: Richardson Rotamers (instead of Dunbrack's) are used by
default. Rotamers are named int the dialog (the probability
limits are no longer meaninful) [Dirk Kostrewa]
o FEATURE: New environment variable COOT_SCHEME_EXTRA_DIR
introduced. If the directory pointed to by COOT_SCHEME_EXTRA_DIR
exists, then Coot will read all the .scm files in that directory
:::: CORRECTION ::::
That should be COOT_SCHEME_EXTRAS_DIR (note the extra "S").
o FEATURE: Cis-peptide GUI added to extensions
o FEATURE: Chiral volumes are added to the geometry target
function. Check for chiral volume and cis-peptide errors introduced
on refinement. Add Chi-squared values to Accept/Reject dialog
(along with traffic lights in the Gtk2 version)
o FEATURE: Old backup-files cleaner-upper added
o FEATURE: CCP4i aliases are also added to the Project Dir options
in the file selector [Ingo Korndoerfer]
o FEATURE: Multiple model ligand overlaying [Bob Nolte]
o FEATURE: NCS matching (Kleywegt Plots) work using SHELXL molecules
o FEATURE: Add "Laplacian" transform (the magnitude of the curvature)
function for maps
o FEATURE: Select residues (for new molecule) by sphere [Joel Bard]
o FEATURE: Cell expansion/contraction function for EM users
o FEATURE: skeletons now appear in Raster3D output and are properly
coloured using the colour wheel.
o FEATURE: a new command has been introduce, so that one can
highlight the command equivalent of gui operations using colour.
e.g.: (set-console-display-commands-hilights 1 1 4).
o FEATURE: binary builds now are scriptable in Python and scheme.
o FEATURE: GTK2 version has toolbar modelling buttons.
o FEATURE: a mapman bones reader has been introduced.
o FEATURE: Key presses . and , now work when navigating the checked
waters "baddies" dialog.
o FEATURE: label-all-CAs function added.
o FEATURE: Dynamic Distances (distances to intermediate atoms)
added [Found in the Distances and Angles dialog].