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About Coot
Coot is a powerful macromolecular model-building tool for analysing X-ray data and models (i.e.
proteins, ligands, RNA and DNA). There are many tools for model manipulation and building, such
as minimization, molecular superposition, fragment rotation/translations, rotamer-fitting, de novo
building and refinement.
Coot is used by scientists using X-ray crystallography or cryo-EM for analysis of proteins,
electron density maps, protein interactions and drug design.
License: GPL-2.0+ and GPL-3.0+ and LGPL-3.0+
proteins, ligands, RNA and DNA). There are many tools for model manipulation and building, such
as minimization, molecular superposition, fragment rotation/translations, rotamer-fitting, de novo
building and refinement.
Coot is used by scientists using X-ray crystallography or cryo-EM for analysis of proteins,
electron density maps, protein interactions and drug design.
License: GPL-2.0+ and GPL-3.0+ and LGPL-3.0+
| Release info | Update on Oct 20, 2026 |
|---|---|
| Release notes | o FEATURE: Protein-ligand interactions: detection and reporting of pi-stacking halogen bonds, and hydrogen bonds. o FEATURE: Read SHELX-style small-molecule cif files (from COD say) and make maps from the embedded reflection data. o FEATURE: Read Gaussian/ORCA cube files. o FEATURE: AutoDock Vina: receptor and ligand preparation and execution scripts, with flexible-receptor support. o FEATURE: Bendix-style helices and tube representations o FEATURE: Servalcat: X-ray refinement with user keywords and ligand dictionaries, with refinement tracking graphs o FEATURE: pyrogen: AceDRG bond and angle values from (optional) SQLite AceDRG tables, with idealization of the ligand coordinates against the generated dictionary o FEATURE: Superpose Ligands from range/pair atom picks o FEATURE: Layla: QED desirability curves; AceDRG input "via mmCIF" (CCD-style export) o 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. o FEATURE: New and updated icons, and icons-only / labels-only styles for the vertical toolbar; Shift-L shortcut o FEATURE: File -> Open Recent menu. MTZ entries remember their column choices, so the map reopens without the column dialog o 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) o FEATURE: --cod command-line option to fetch a COD entry o FEATURE: set_worm_tube_radius(imol, radius) o CHANGE: Coordinate mmCIF files are now written using GEMMI o CHANGE: Faster map contouring (marching-cubes vertex de-duplication replaced by a flat array) o CHANGE: Default model specularity strength changed to 0.25 o CHANGE: "Untyped"… |
| Listing data | Flathub |
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