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Features and development of Coot

a , * , b , c , d

Acta Crystallographica Section D: Biological Crystallography

International Union of Crystallography

Experimental phasing and radiation damage

Coot, model building

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      Abstract

      Coot is a molecular-graphics program designed to assist in the building of protein and other macromolecular models. The current state of development and available features are presented.

      Abstract

      Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program 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. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics. The software is designed to be easy to learn for novice users, which is 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 focused on providing tools for expert users, with customisable key bindings, extensions and an extensive scripting interface. The software is under rapid development, but has already achieved very widespread use within the crystallographic community. The current state of the software is presented, with a description of the facilities available and of some of the underlying methods employed.

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      Affiliations
      [a ]Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England
      [b ]Department of Medical Biochemistry and Biophysics, Karolinska Institute, SE-171 77 Stockholm, Sweden
      [c ]Department of Chemistry, University of California, 1156 High Street, Santa Cruz, CA 95064, USA
      [d ]Department of Chemistry, University of York, Heslington, York YO10 5DD, England
      Author notes
      Correspondence e-mail: paul.emsley@ 123456bioch.ox.ac.uk
      Conference
      Acta Crystallogr D Biol Crystallogr
      Acta Cryst. D
      Acta Crystallographica Section D: Biological Crystallography
      International Union of Crystallography
      0907-4449
      1399-0047
      01 April 2010
      24 March 2010
      24 March 2010
      : 66
      : Pt 4 ( publisher-idID: d100400 )
      : 486-501
      2852313
      20383002
      ba5144
      10.1107/S0907444910007493
      ABCRE6 S0907444910007493
      © Emsley et al. 2010

      This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

      Experimental phasing and radiation damage
      Categories
      Research Papers

      Microscopy & Imaging

      model building, coot

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