Coot 1.3.4 was released on 20th October 2026.

Release Notes for 1.3.4

  • FEATURE: Protein-ligand interactions: detection and reporting of pi-stacking, halogen bonds and hydrogen bonds

  • FEATURE: Read SHELX-style small-molecule cif files (from COD say) and make maps from the embedded reflection data

  • FEATURE: Read Gaussian/ORCA cube files

  • FEATURE: AutoDock Vina: receptor and ligand preparation and execution scripts, with flexible-receptor support

  • FEATURE: Bendix-style helices and tube representations

  • FEATURE: Servalcat: X-ray refinement with user keywords and ligand dictionaries, with refinement tracking graphs

  • FEATURE: pyrogen: AceDRG bond and angle values from (optional) SQLite AceDRG tables, with idealization of the ligand coordinates against the generated dictionary

  • FEATURE: Superpose Ligands from range/pair atom picks

  • FEATURE: Layla: QED desirability curves; AceDRG input “via mmCIF” (CCD-style export)

  • FEATURE: Chapi/API additions: get_ligand_interactions_as_json(), get_atom_differences(), add_named_glyco_tree(), refine_regularize_with_range_picked_atoms(), set_default_model_material_*(), set_colour_map_for_map_colored_by_other_map(), get_non_standard_residues_in_molecule(), chemical_feature_clustering(), clear_fixed_atoms_during_refinement(); residue_spec_t is now hashable and comparable

  • FEATURE: New and updated icons, and icons-only / labels-only styles for the vertical toolbar; Shift-L shortcut

  • FEATURE: File → Open Recent menu. MTZ entries remember their column choices, so the map reopens without the column dialog

  • FEATURE: If there is a state script, Coot now asks at startup whether it should be run (--no-state-script or --script turn this off)

  • FEATURE: --cod command-line option to fetch a COD entry

  • FEATURE: set_worm_tube_radius(imol, radius)

  • CHANGE: Coordinate mmCIF files are now written using GEMMI

  • CHANGE: Faster map contouring (marching-cubes vertex de-duplication replaced by a flat array)

  • CHANGE: Default model specularity strength changed to 0.25

  • CHANGE: “Untyped” ligand interactions are now drawn grey

  • CHANGE: “Fetch Ligand Restraints” no longer creates a new ligand molecule

  • CHANGE: Gaussian surfaces, generic surfaces and tubes use the model material - so set the material before the surface is calculated

  • CHANGE: Dictionary torsion restraints with an esd of more than 200 degrees are no longer used in refinement

  • CHANGE: The EMDB map code is now also read from downloaded mmCIF files (previously only from PDB files)

  • CHANGE: pyrogen: pH-7 protonation states as AceDRG does - carboxylates as C=O/C-O(-) and protonated secondary and tertiary amines (not sulfonamides). Formal charges are written to _chem_comp_atom.charge. This applies to the Chapi pyrogen functions too

  • CHANGE: “All Waters” moved down in the Delete menu

  • BUG-FIX: AceDRG link interface: fix custom link matching for DNA/RNA groups and set the charge correctly

  • BUG-FIX: Fix the bonding to hydrogen atoms when no dictionary is present

  • BUG-FIX: Fix a Chapi/GUI inconsistency where donor-acceptor pairs without hydrogens were treated as a clash

  • BUG-FIX: Fix specular highlights on surfaces and instanced objects (the eye position given to the shaders was wrong)

  • BUG-FIX: Fix the outline of selected atoms when the atoms are wider than the bonds

  • BUG-FIX: Closing the main window from the window manager now saves the state and asks about unsaved changes, as File → Exit does

  • BUG-FIX: Fix the Cancel button in the Run Script dialog; Return in the Go To Atom entries now works

  • BUG-FIX: align_to_closest_chain() now chooses the closest chain

  • BUG-FIX: b_factor_from_map() now returns the fitted B-factor

  • BUG-FIX: Chapi: fix_atom_selection_during_refinement() now works

  • BUG-FIX: The ligand view no longer tries to draw haem groups

  • BUG-FIX: pyrogen: X-H bonds now have the correct nuclear distances (value_dist_nucleus) in the dictionary

  • BUG-FIX: Fix the plane restraint gradients for planes whose atoms have different esds - refinement could stop early with no progress (e.g. for ligands with fused aromatic rings)