Coot is a molecular graphics program developed for structural biologists, providing tools for X-ray structure solution, structure comparison, analysis, and publication-quality graphics. It is a stand-alone package distributed as 'Coot' and is part of the CCP4mg initiative. The program is designed to be user-friendly and extendable, offering functionalities for model-building, map-fitting, and integration with other CCP4 programs. Coot is built around two major libraries: mmdb for handling macromolecular coordinates and Clipper for crystallographic objects and computation. It is event-driven, with functions executed in response to user actions such as mouse movements or clicks. Key features include symmetry handling, electron density mapping, and integration with REFMAC for refinement. Coot also supports rigid-body refinement, rotamer selection, and ligand finding, using advanced algorithms to improve model accuracy. The program includes a robust system for regularizing and refining molecular models, using analytical gradients derived from the mmCIF dictionaries of REFMAC. It also provides tools for finding ligands and water molecules, using density clustering and eigenvalue analysis. Additionally, Coot supports the addition of terminal residues and skeletonization of molecular structures, enabling the identification of folds and non-crystallographic symmetry. Coot's functionality is similar to other molecular graphics programs such as O, Xtalview, and QUANTA, but it is designed to be more transparent, user-friendly, and extendable. The program is capable of generating electron-density maps from structure factor files and allows for interactive refinement and model building. It also includes a system for determining potential Cα positions based on pseudo-torsion angles and opening angles, using likelihood assignments from high-resolution structures in the PDB. The program is supported by a range of references and is developed by a team of researchers, including Paul Emsley and Kevin Cowtan. It is funded by various grants and is widely used in the field of structural biology for its comprehensive set of tools and its ability to integrate with other CCP4 programs.Coot is a molecular graphics program developed for structural biologists, providing tools for X-ray structure solution, structure comparison, analysis, and publication-quality graphics. It is a stand-alone package distributed as 'Coot' and is part of the CCP4mg initiative. The program is designed to be user-friendly and extendable, offering functionalities for model-building, map-fitting, and integration with other CCP4 programs. Coot is built around two major libraries: mmdb for handling macromolecular coordinates and Clipper for crystallographic objects and computation. It is event-driven, with functions executed in response to user actions such as mouse movements or clicks. Key features include symmetry handling, electron density mapping, and integration with REFMAC for refinement. Coot also supports rigid-body refinement, rotamer selection, and ligand finding, using advanced algorithms to improve model accuracy. The program includes a robust system for regularizing and refining molecular models, using analytical gradients derived from the mmCIF dictionaries of REFMAC. It also provides tools for finding ligands and water molecules, using density clustering and eigenvalue analysis. Additionally, Coot supports the addition of terminal residues and skeletonization of molecular structures, enabling the identification of folds and non-crystallographic symmetry. Coot's functionality is similar to other molecular graphics programs such as O, Xtalview, and QUANTA, but it is designed to be more transparent, user-friendly, and extendable. The program is capable of generating electron-density maps from structure factor files and allows for interactive refinement and model building. It also includes a system for determining potential Cα positions based on pseudo-torsion angles and opening angles, using likelihood assignments from high-resolution structures in the PDB. The program is supported by a range of references and is developed by a team of researchers, including Paul Emsley and Kevin Cowtan. It is funded by various grants and is widely used in the field of structural biology for its comprehensive set of tools and its ability to integrate with other CCP4 programs.