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Coot (software)
The program Coot (Crystallographic Object-Oriented Toolkit)〔P. Emsley, B. Lohkamp, W.G. Scott and K. Cowtan (2010) ''Features and Development of Coot''. Acta Crystallographica D66, 486-501 ()〕〔P. Emsley and K. Cowtan (2004) ''Coot: model-building tools for molecular graphics''. Acta Crystallographica D60, 2126-2132 ()〕 is used to display and manipulate atomic models of macromolecules, typically of proteins or nucleic acids, using 3D computer graphics. It is primary focussed on the building and validation of atomic models into 3-dimensional electron density maps obtained by X-ray crystallography methods, although it has also been applied to data from electron microscopy.
== Overview ==
Coot displays electron density maps and atomic models and allows model manipulations such as idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, and Ramachandran idealization. The software is designed to be easy-to-learn for novice users, achieved by ensuring that tools for common tasks are 'discoverable' through familiar user interface elements (menus and toolbars), or by intuitive behaviour (mouse controls). Recent developments have enhanced the usability of the software for expert users, with customisable key bindings, extensions, and an extensive scripting interface.
Coot is free software, distributed under the GNU GPL. It is available from the Coot web site〔(The Coot website )〕 originally at the University of York, and now at the MRC Laboratory of Molecular Biology. Pre-compiled binaries are also available for Linux and Windows from the web page and CCP4, and for Mac OS X through Fink and CCP4. Additional support is available through the Coot wiki and an active COOT mailing list.〔(The Coot wiki )〕〔(Coot Mailing List )〕
The primary author is Paul Emsley (MRC-LMB at Cambridge). Other contributors include Kevin Cowtan, Bernhard Lohkamp and Stuart McNicholas (University of York), William Scott (University of California at Santa Cruz), and Eugene Krissinel (Daresbury Laboratory).
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