Release Notes for 1.3.2
https://github.com/pemsley/coot/releases/tag/Release-1.3.2
o FEATURE: Add AI button: for people who want to use an LLM to
communicate with Coot
o FEATURE: Rotate/Translate Zone: the fragment can now be moved by
click-dragging on the atoms and rotated about its centre
using ctrl-shift-drag
o FEATURE: Command terminal with command completion and a
natural-language command interface [Jordan Dialpuri]
o FEATURE: Read and write PDBQT files (AutoDock/Vina docking)
o FEATURE: Multi-pick delete waters
o FEATURE: Cavity detection (KVFinder-style) with subpocket
segmentation
o FEATURE: Carbohydrate: N-linked glycan building ("N-linked
Glycan LMA") reworked in C++; fixes for glyco link bugs
o FEATURE: Layla: "Search for Similar" - find monomers in the
monomer library using acedrg atom types
o FEATURE: Layla: "Show Alerts" structural-alert highlighting
o FEATURE: Layla: CCP4i2 mode, multi-format save dialog and
SMILES I/O [Jakub Smulski]
o FEATURE: Hydrogen-bond information now included in the atom
overlap dots analysis
o FEATURE: Chapi Scripting API additions: get_cremer_pople(),
get_monomer_name(), get_InChI(), get_hetgroups(),
delete_all_waters(), delete_all_hetgroups(),
get_monomer_restraints_as_json(),
read_interesting_places_json(),
servalcat_refine_xray_with_keywords(),
get_sequence_view(),
split_multi_model_molecule_and_merge()
o FEATURE: Chapi: Cremer-Pople puckering sphere visualization for
carbohydrate ring analysis [Jordan Dialpuri]
o FEATURE: Chapi: Altona-Sundaralingam ribose pucker calculation
[Jordan Dialpuri]
o CHANGE: First startup dialog now saves preferences immediately
rather than on exit
o CHANGE: Ligand-fitting code made more robust
o CHANGE: Fluorine atoms are now drawn slightly blue
o CHANGE: EM maps now use a coarser contour-level step
(0.3 sigma)
o CHANGE: Rework the code that gives ions big radii
o CHANGE: Non-drawn bonds now also apply to the B-factor and
occupancy representations
o CHANGE: NCS ghost generation is skipped for molecules with
more than 100 chains
o CHANGE: ALA and GLY no longer get rotamer validation
information
o CHANGE: -h command line option now works like --help
o CHANGE: Python docstrings are now generated for many more of
the scripting API functions
o CHANGE: Icons updated to their symbolic counterparts for
recent Adwaita [Jakub Smulski]
o BUG-FIX: Fix NVIDIA driver crash on GL context re-realize (HUD
instanced draw)
o BUG-FIX: Fix abort in instanced-mesh setup when there are zero
instances
o BUG-FIX: Fix map memory not being released on closing a map
molecule
o BUG-FIX: Fix memory leak in the CA-CA distance spots
o BUG-FIX: Fix missing heteroatom labels in Layla (all atoms were
shown as carbon; also on older Pango)
o BUG-FIX: Layla: fix generator dialog progress bar stuck after
the job exits
o BUG-FIX: Fix the placement of the SVG widget in the FLE View
dialog
o BUG-FIX: Fix the placement of buttons and overall spacing of
the Superpose Ligands dialog
o BUG-FIX: Fixes for match_torsions()
o BUG-FIX: Fix the vertical scrolling of the sequence view
o BUG-FIX: Ligand-fitting: Conformer option now insensitive without
conformer generation
o BUG-FIX: Copy Fragment molecule selector now has a default
o BUG-FIX: Now we use the user-defined colour for symmetry-related
atoms
o BUG-FIX: Fix crash when using Flatpak binary on contact dots for a
molecule without contacts [Jiang Haizhu]
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