is a software package used in macromolecular crystallography for model building, validation, and analysis. It is an open-source graphical user interface (GUI) to the Crystallographic Object-Oriented Toolkit (COOT) library, which is a library of C++ objects and functions for macromolecular crystallography. The use of Coot
is to interactively build and refine protein and nucleic acid models, using the electron density maps from X-ray crystallography and non-crystallographic symmetry (NCS) data. Coot can also be used to visualize maps, density, and models.
Coot provides an easy to use interface for studying 3D structures of macromolecules and analyzing their properties.
1. Model Building: Coot provides tools for building and refining protein and nucleic acid models. It can also use NCS data to extend and refine existing models.
2. Model Validation: Coot has a comprehensive set of model validation tools, including Ramachandran plots, rotamer analysis, and clash analysis.
3. Map Visualization: Coot provides an interactive graphics interface to view electron density maps, including 2D and 3D visualizations.
4. Model Visualization: Coot can visualize models in both 2D and 3D, with the ability to rotate, zoom, and pan the model.
5. Map/Model Comparison: Coot can compare maps to models, and display the differences between them.
6. Scripting: Coot has an embedded scripting language that can be used to automate the model building and refinement process.
7. Refinement: Coot has tools for refining models and maps, including real-space refinement and simulated annealing.
8. Molecular Dynamics: Coot has a built-in molecular dynamics engine that can be used to simulate the movement of molecular structures.
9. Analysis: Coot has a suite of analysis tools, such as residue analysis, solvent accessibility analysis, and bond analysis.
10. Database Search: Coot has a built-in search engine that can be used to search databases such as PDB and RCSB for similar structures.
11. Export: Coot can export models and maps in a variety of formats, including CIF, PDB, and Mol2.
Overall, Coot is a powerful and comprehensive software package for macromolecular crystallography. It is an open-source, user-friendly GUI that can be used for model building, validation, visualization, and analysis. It also has a number of advanced features, such as scripting, map/model comparison, and database search.