Coot

Coot performs model building and validation of biological macromolecular structures (Crystallographic Object-Oriented Toolkit) by displaying and interpreting electron-density maps for macromolecular crystallography.

Key Features:

• Electron-density map visualization: Displays electron-density maps alongside atomic models for map interpretation and model fitting.
• Model building and manipulation: Supports manual rotation and translation, mutations, and atomic model adjustments.
• Idealization: Provides idealization processes and Ramachandran idealization for backbone and geometry refinement.
• Real-space refinement: Performs real-space refinement to optimize atomic positions against electron-density maps.
• Rigid-body fitting: Enables rigid-body fitting of model fragments into density.
• Ligand search and fitting: Includes ligand search functionality and tools for ligand placement and fitting.
• Solvation and water placement: Supports solvation procedures and placement of solvent molecules.
• Rotamer adjustments: Facilitates rotamer selection and adjustment for side-chain conformations.
• Integration with external programs: Interfaces to external programs for further refinement, validation, and graphics generation.
• Publication-quality graphics: Generates graphics suitable for publication and structural analysis.
• Support for X-ray structure solution workflows: Provides functions useful for X-ray structure solution, comparison, and analysis.

Scientific Applications:

• Macromolecular X-ray crystallography: Model building and refinement of proteins, nucleic acids, and complexes using experimental electron-density maps.
• Structure validation: Validation of geometry, rotamers, and conformational quality including Ramachandran analysis.
• Ligand modeling: Identification, placement, and refinement of ligands within electron density.
• Solvent modeling: Placement and refinement of solvent molecules during model completion.
• Comparative structural analysis: Comparison and analysis of models for structural interpretation and hypothesis generation.
• Graphics for publication: Preparation of publication-quality representations of macromolecular structures and maps.

Methodology:

Displays electron-density maps with atomic models and performs idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamer adjustments, Ramachandran idealization, and interfaces to external refinement/validation/graphics programs.