Chapter 17.1 Macromolecular model building and validation using Coot

Crystallography of biological macromolecules

Second Online Edition (2012)

Part 17. Model building and computer graphics

  1. P. Emsley1,
  2. B. Lohkamp2,
  3. K. Cowtan3

Published Online: 14 APR 2012

DOI: 10.1107/97809553602060000853

International Tables for Crystallography

International Tables for Crystallography

How to Cite

Emsley, P., Lohkamp, B. and Cowtan, K. 2012. Macromolecular model building and validation using Coot. International Tables for Crystallography. F:17:17.1:443–447.

Author Information

  1. 1

    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK

  2. 2

    Department of Medical Biochemistry and Biophysics, Karolinska Institute, SE-171 77 Stockholm, Sweden

  3. 3

    Department of Chemistry, University of York, Heslington, York YO10 5DD, UK

Publication History

  1. Published Online: 14 APR 2012


The Coot software package is a tool for interactive macromolecular model building and validation. The software is designed to be easy to learn for novice users by ensuring that tools for common tasks are ‘discoverable’ without consulting the documentation, while also providing enhanced usability for experts through customizable key bindings and extensive scripting interfaces. These considerations have resulted in substantial use throughout the crystallographic community. 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. Several of the most important tools are described together with the underlying methods employed.


  • Coot;
  • model building;
  • validation