Coot 1.3.2 was released on 10th August 2026.

Release Notes for 1.3.2

  • FEATURE: Add AI button: for people who want to use an LLM to communicate with Coot

  • 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

  • FEATURE: Command terminal with command completion and a natural-language command interface [Jordan Dialpuri]

  • FEATURE: Read and write PDBQT files (AutoDock/Vina docking)

  • FEATURE: Multi-pick delete waters

  • FEATURE: Cavity detection (KVFinder-style) with subpocket segmentation

  • FEATURE: Carbohydrate: N-linked glycan building (“N-linked Glycan LMA”) reworked in C++; fixes for glyco link bugs

  • FEATURE: Layla: “Search for Similar” - find monomers in the monomer library using acedrg atom types

  • FEATURE: Layla: “Show Alerts” structural-alert highlighting

  • FEATURE: Layla: CCP4i2 mode, multi-format save dialog and SMILES I/O [Jakub Smulski]

  • FEATURE: Hydrogen-bond information now included in the atom overlap dots analysis

  • 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()

  • FEATURE: Chapi: Cremer-Pople puckering sphere visualization for carbohydrate ring analysis [Jordan Dialpuri]

  • FEATURE: Chapi: Altona-Sundaralingam ribose pucker calculation [Jordan Dialpuri]

  • CHANGE: First startup dialog now saves preferences immediately rather than on exit

  • CHANGE: Ligand-fitting code made more robust

  • CHANGE: Fluorine atoms are now drawn slightly blue

  • CHANGE: EM maps now use a coarser contour-level step (0.3 sigma)

  • CHANGE: Rework the code that gives ions big radii

  • CHANGE: Non-drawn bonds now also apply to the B-factor and occupancy representations

  • CHANGE: NCS ghost generation is skipped for molecules with more than 100 chains

  • CHANGE: ALA and GLY no longer get rotamer validation information

  • CHANGE: -h command line option now works like --help

  • CHANGE: Python docstrings are now generated for many more of the scripting API functions

  • CHANGE: Icons updated to their symbolic counterparts for recent Adwaita [Jakub Smulski]

  • BUG-FIX: Fix NVIDIA driver crash on GL context re-realize (HUD instanced draw)

  • BUG-FIX: Fix abort in instanced-mesh setup when there are zero instances

  • BUG-FIX: Fix map memory not being released on closing a map molecule

  • BUG-FIX: Fix memory leak in the CA-CA distance spots

  • BUG-FIX: Fix missing heteroatom labels in Layla (all atoms were shown as carbon; also on older Pango)

  • BUG-FIX: Layla: fix generator dialog progress bar stuck after the job exits

  • BUG-FIX: Fix the placement of the SVG widget in the FLE View dialog [Oli Clarke]

  • BUG-FIX: Fix the placement of buttons and overall spacing of the Superpose Ligands dialog

  • BUG-FIX: Same ligand-name fixes for match_torsions()

  • BUG-FIX: Fix the vertical scrolling of the sequence view

  • BUG-FIX: Ligand-fitting: Conformer option now insensitive without conformer generation

  • BUG-FIX: Copy Fragment molecule selector now has a default

  • BUG-FIX: Now we use the user-defined colour for symmetry-related atoms

  • BUG-FIX: Fix crash when using Flatpak binary on contact dots for a molecule without contacts [Jiang Haizhu]