Coot is an interactive molecular graphics application for macromolecular model building, refinement and validation.
The software is designed for structural biology workflows where atomic models need to be inspected and adjusted against experimental density. It displays molecular models and map data in a graphical environment and provides interactive tools for building and correcting structures rather than acting only as a passive molecular viewer.
Coot uses GTK for its interface together with OpenGL for graphics. Its code also makes use of established crystallographic libraries including MMDB and Clipper. The program can be used to refine model geometry, inspect structural problems and manipulate macromolecular models while keeping the relevant experimental data visible.
A major strength of Coot is the breadth of its model-building workflow. The application provides tools for selecting and editing regions of a structure, fitting models to density, working with ligands and checking the quality of a model. These facilities are useful during the iterative process of examining a structure, making corrections and validating the result.
Coot is used for macromolecular crystallography and also supports workflows involving cryo-EM density maps. The software is available as a standalone application and is also used alongside wider crystallographic software environments. Its focus remains hands-on model building, refinement and validation of biological macromolecules.
This is free and open source software.
Key Features
- Provides interactive macromolecular model building.
- Displays atomic models together with experimental density maps.
- Offers interactive refinement and model-validation tools.
- Supports workflows for macromolecular crystallography and cryo-EM.
- Provides tools for manipulating and correcting structural models.
- Supports ligand-related model-building workflows.
- Offers scripting facilities for automating structural biology workflows.
- Uses GTK, OpenGL, MMDB and Clipper.
Website: github.com/pemsley/coot
Support:
Developer: Paul Emsley
License: GNU General Public License v3.0
Coot is written primarily in C++. Learn C++ with our recommended free books and free tutorials.
Related Software
| Chemistry: Molecular Editors and Visualisation | |
|---|---|
| PyMOL | Molecular graphics system for visualizing structures and producing images |
| Avogadro | Advanced molecular editor and visualization application |
| Gabedit | Graphical interface for computational chemistry packages and modelling |
| Jmol | 3D molecular viewer for chemicals, crystals, materials and biomolecules |
| Patinae | Programmable molecular visualization toolkit with desktop and Python support |
| Coot | Interactive macromolecular model building, refinement and validation toolkit |
| IQmol3 | Molecular builder and visualization package for computational chemistry |
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