Features and development of Coot

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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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Most cited references 25

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Structure validation by Calpha geometry: phi,psi and Cbeta deviation.

Simon C. Lovell, Ian W. Davis, W Bryan Arendall … (2003)

Geometrical validation around the Calpha is described, with a new Cbeta measure and updated Ramachandran plot. Deviation of the observed Cbeta atom from ideal position provides a single measure encapsulating the major structure-validation information contained in bond angle distortions. Cbeta deviation is sensitive to incompatibilities between sidechain and backbone caused by misfit conformations or inappropriate refinement restraints. A new phi,psi plot using density-dependent smoothing for 81,234 non-Gly, non-Pro, and non-prePro residues with B < 30 from 500 high-resolution proteins shows sharp boundaries at critical edges and clear delineation between large empty areas and regions that are allowed but disfavored. One such region is the gamma-turn conformation near +75 degrees,-60 degrees, counted as forbidden by common structure-validation programs; however, it occurs in well-ordered parts of good structures, it is overrepresented near functional sites, and strain is partly compensated by the gamma-turn H-bond. Favored and allowed phi,psi regions are also defined for Pro, pre-Pro, and Gly (important because Gly phi,psi angles are more permissive but less accurately determined). Details of these accurate empirical distributions are poorly predicted by previous theoretical calculations, including a region left of alpha-helix, which rates as favorable in energy yet rarely occurs. A proposed factor explaining this discrepancy is that crowding of the two-peptide NHs permits donating only a single H-bond. New calculations by Hu et al. [Proteins 2002 (this issue)] for Ala and Gly dipeptides, using mixed quantum mechanics and molecular mechanics, fit our nonrepetitive data in excellent detail. To run our geometrical evaluations on a user-uploaded file, see MOLPROBITY (http://kinemage.biochem.duke.edu) or RAMPAGE (http://www-cryst.bioc.cam.ac.uk/rampage). Copyright 2003 Wiley-Liss, Inc.

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REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use.

Alexei A. Vagin, Roberto A Steiner, Andrey Lebedev … (2004)

One of the most important aspects of macromolecular structure refinement is the use of prior chemical knowledge. Bond lengths, bond angles and other chemical properties are used in restrained refinement as subsidiary conditions. This contribution describes the organization and some aspects of the use of the flexible and human/machine-readable dictionary of prior chemical knowledge used by the maximum-likelihood macromolecular-refinement program REFMAC5. The dictionary stores information about monomers which represent the constitutive building blocks of biological macromolecules (amino acids, nucleic acids and saccharides) and about numerous organic/inorganic compounds commonly found in macromolecular crystallography. It also describes the modifications the building blocks undergo as a result of chemical reactions and the links required for polymer formation. More than 2000 monomer entries, 100 modification entries and 200 link entries are currently available. Algorithms and tools for updating and adding new entries to the dictionary have also been developed and are presented here. In many cases, the REFMAC5 dictionary allows entirely automatic generation of restraints within REFMAC5 refinement runs.

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Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT.

E Blanc, P Roversi, C Vonrhein … (2004)

BUSTER-TNT is a maximum-likelihood macromolecular refinement package. BUSTER assembles the structural model, scales observed and calculated structure-factor amplitudes and computes the model likelihood, whilst TNT handles the stereochemistry and NCS restraints/constraints and shifts the atomic coordinates, B factors and occupancies. In real space, in addition to the traditional atomic and bulk-solvent models, BUSTER models the parts of the structure for which an atomic model is not yet available ('missing structure') as low-resolution probability distributions for the random positions of the missing atoms. In reciprocal space, the BUSTER structure-factor distribution in the complex plane is a two-dimensional Gaussian centred around the structure factor calculated from the atomic, bulk-solvent and missing-structure models. The errors associated with these three structural components are added to compute the overall spread of the Gaussian. When the atomic model is very incomplete, modelling of the missing structure and the consistency of the BUSTER statistical model help structure building and completion because (i) the accuracy of the overall scale factors is increased, (ii) the bias affecting atomic model refinement is reduced by accounting for some of the scattering from the missing structure, (iii) the addition of a spatial definition to the source of incompleteness improves on traditional Luzzati and sigmaA-based error models and (iv) the program can perform selective density modification in the regions of unbuilt structure alone.

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Author and article information

Conference

Journal ID (nlm-ta): Acta Crystallogr D Biol Crystallogr

Journal ID (publisher-id): Acta Cryst. D

Title: Acta Crystallographica Section D: Biological Crystallography

Publisher: International Union of Crystallography

ISSN (Print): 0907-4449

ISSN (Electronic): 1399-0047

Publication date (Print): 01 April 2010

Publication date (Electronic): 24 March 2010

Publication date PMC-release: 24 March 2010

Volume: 66

Issue: Pt 4 ( publisher-idID: d100400 )

Pages: 486-501

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

Article

Publisher ID: ba5144 Coden ID: ABCRE6 Publisher Item ID: S0907444910007493

DOI: 10.1107/S0907444910007493

PMC ID: 2852313

PubMed ID: 20383002

SO-VID: 351595a8-69b1-4957-8c2b-f9b779c3a675

License:

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.

Conference name: Experimental phasing and radiation damage

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History

Date received : 09 June 2009

Date accepted : 26 February 2010

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Most cited references 25

Structure validation by Calpha geometry: phi,psi and Cbeta deviation.

REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use.

Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT.

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Cited by 11,183