The article introduces Coot, a molecular graphics tool developed by the CCP4 group at the University of York. Coot is designed to support structural biologists in the process of determining protein structures using X-ray crystallographic data. It provides tools for model building, map fitting, and publication-quality graphics. Key features of Coot include symmetry coordinates, electron-density map contouring, and the ability to move coordinates in various ways. The tool is event-driven, meaning functions are executed in response to user actions such as mouse clicks or movements. Coot integrates with other CCP4 programs, such as *REFMAC* for refinement, and uses libraries like mmdb and Clipper for handling macromolecular coordinates and crystallographic objects. The article also details specific functionalities, such as rigid-body refinement, rotamer placement, ligand and water molecule detection, and the addition of terminal residues. The appendices provide mathematical derivations for the regularization and refinement derivatives used in Coot.The article introduces Coot, a molecular graphics tool developed by the CCP4 group at the University of York. Coot is designed to support structural biologists in the process of determining protein structures using X-ray crystallographic data. It provides tools for model building, map fitting, and publication-quality graphics. Key features of Coot include symmetry coordinates, electron-density map contouring, and the ability to move coordinates in various ways. The tool is event-driven, meaning functions are executed in response to user actions such as mouse clicks or movements. Coot integrates with other CCP4 programs, such as *REFMAC* for refinement, and uses libraries like mmdb and Clipper for handling macromolecular coordinates and crystallographic objects. The article also details specific functionalities, such as rigid-body refinement, rotamer placement, ligand and water molecule detection, and the addition of terminal residues. The appendices provide mathematical derivations for the regularization and refinement derivatives used in Coot.