Coot specifications


Unique identifier OMICS_06370
Name Coot
Alternative name Crystallographic Object-Oriented Toolkit
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Paul Emsley <>

Coot articles


Handling ligands with Coot.

2012 Acta Crystallogr D Biol Crystallogr
PMID: 22505262
DOI: 10.1107/S0907444912000200

Coot citations

PMCID: 5863366

[…] model was the chitinase from clonostachys rosea (pdb code 3g6l). preliminary rigid-body refinement was carried out using refmac [49]. subsequently, several rounds of extensive model building with coot [50] combined with automatic restrain refinement with flat bulk solvent correction and using maximum likelihood target features, led to a model covering residues ala35-asn423. at the latter […]

PMCID: 5834254

[…] available to researchers upon request to the corresponding authors., initial model of the chimeric reporter was built using the i-tasser server [63]. manual modeling operations were performed in coot [64] and molecular graphics were generated in pymol [65] [available at:]., the primers were synthesized and page purified by idt dna. fugene 6 transfection reagent […]

PMCID: 5726637

[…] was performed using refmac5[21] alternated with manual model building in coot 0.7[22]. sugar residues and other compounds present were placed manually using coot. water molecules were added by coot and checked manually. the addition of alternative conformations where necessary resulted in a final structure that was validated by the wwpdb validation server ( and deposited […]

PMCID: 5758874

[…] (28) and aimless in ccp4i suite (29). phases were obtained by molecular replacement using balbes and protein structure was finally obtained with cycles of tracing and refinement using the program coot (30) and refmac5 (31), respectively. the ramachandran plot for refined rcsbcrossed structure showed 95.1% of residues in favored region, 4.8% in allowed region and 0.1% in generously allowed […]

PMCID: 5517649

[…] asymmetric unit. data statistics are given in table 1. an initial model was created using molecular replacement, starting with pdb 3wmv as a search model. manual modifications were carried out with coot51. refinement was carried out with refmac52 and the ccp4 suite53. tls group refinement was not used. the ramachandran plot of the native model shows no residues in unusual positions. isotropic […]

Coot institution(s)
Structure and Biophysics, DS, AstraZeneca, Alderley Park, Macclesfield, UK; Department of Biochemistry, University of Oxford, Oxford, UK
Coot funding source(s)
This project was funded by the Collaborative Computational Project Number 4.

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