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| Coot (software) | |
|---|---|
| Name | Coot |
| Caption | Model-building, validation and visualization software for macromolecular crystallography and cryo-EM |
| Developer | Collaborative Computational Project Number 4; University of York; University of Cambridge |
| Released | 2004 |
| Programming language | C, C++, Fortran, Python |
| Operating system | Linux, macOS, Windows |
| Platform | x86, x86-64 |
| Genre | Structural biology, model building, molecular graphics |
| License | GPL |
Coot (software) is an interactive molecular-graphics application designed for model building, validation and visualization of macromolecular structures derived from X-ray crystallography and cryo-electron microscopy. It integrates model manipulation, density interpretation and validation tools to support investigators working with proteins, nucleic acids and complexes determined at atomic or near-atomic resolution. The project has origins in collaborative efforts among academic groups and is widely used alongside major structural biology resources.
Coot was initiated within collaborations among groups affiliated with University of York, University of Cambridge, the Collaborative Computational Project Number 4 and contributors from laboratories associated with MRC Laboratory of Molecular Biology, European Molecular Biology Laboratory and various synchrotron facilities. The application addresses needs arising from structural projects deposited in the Protein Data Bank and complements pipelines maintained by institutions such as EMBL-EBI, RCSB PDB and national centers like Brookhaven National Laboratory. Coot interacts with computational methods developed in communities around packages such as Phenix, CCP4, REFMAC, BUSTER and SHELX.
Coot provides real-time model building, map interpretation, ligand fitting, validation metrics and automated refinement helpers. Standard features include map display for electron density maps (2mFo-DFc, mFo-DFc), rotamer analysis tied to libraries from sources like Richardson Lab, backbone Ramachandran analysis inspired by work at Duke University and clash detection used in depositions to Protein Data Bank. Additional tools include real-space refinement, morphing between conformations, jiggle fit, automated ligand placement comparable to methods in AutoDock workflows, and density modification interfaces used in pipelines from Diamond Light Source and National Synchrotron Light Source.
The codebase combines components written in C, C++, Fortran and Python and relies on graphical and numerical libraries developed by academic software ecosystems. Build and integration have been coordinated with projects such as GTK, OpenGL, Mesa (computer graphics), and numeric libraries used in packages maintained at Lawrence Berkeley National Laboratory and university computational groups. Development follows open-source practices familiar from initiatives led by Free Software Foundation-aligned projects and uses version control and issue tracking conventions common in collaborative science software. Contributors have included researchers with affiliations to University of California, San Francisco, Yale University, Max Planck Society and various national research laboratories.
Coot’s graphical user interface provides interactive windows for 3D visualization, map slicing, sequence display and validation panes; it supports scripting via an embedded Python interpreter similar to scripting interfaces in PyMOL and integrates inspection workflows paralleling tools from UCSF Chimera and ChimeraX. Command-driven and menu-driven interactions facilitate tasks common to structural biologists working at facilities such as Advanced Photon Source, SOLEIL and SPring-8. Coot is used in laboratory courses at institutions like University of Oxford and Massachusetts Institute of Technology and in structure-determination tutorials associated with meetings organized by Cold Spring Harbor Laboratory and Gordon Research Conferences.
Coot reads and writes coordinate and map formats standard in structural biology, including files exchanged with Protein Data Bank deposition systems, map formats produced by packages like CCP4 and MRC (file format), and model formats compatible with refinement tools such as REFMAC, Phenix.refine and BUSTER. It also interoperates with ligand dictionaries and restraint formats produced by tools like eLBOW and Grade (Global Phasing) and can export images and scripts used by visualization projects maintained at European Bioinformatics Institute and educational portals run by Wellcome Trust.
An extensible plugin architecture and Python bindings enable community-contributed extensions that mirror efforts in plugin ecosystems of PyMOL, UCSF Chimera and ChimeraX. Common plugins provide automated ligand placement, map segmentation, real-space correlation analysis, and links to validation services run by wwPDB partners and validation servers at PDBe. Researchers from laboratories at Stanford University, Harvard University and ETH Zurich have contributed scripts and modules for tasks such as ensemble refinement, glycan building and specialized visualization for cryo-EM maps.
Coot is integral to workflows for macromolecular model building and validation used in structural projects ranging from single-protein X-ray crystallography studies deposited in the Protein Data Bank to large macromolecular assemblies characterized at cryo-EM centers like EMBL and national facilities. It is routinely cited in publications from research groups at Johns Hopkins University, Cold Spring Harbor Laboratory, Imperial College London and industrial research groups in pharmaceutical companies involved in structure-based drug design, fragment screening campaigns connected to initiatives such as those sponsored by Wellcome Trust and collaborative consortia funded by agencies including the National Institutes of Health and European Research Council.
Category:Crystallography software Category:Molecular graphics software Category:Structural bioinformatics