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Bioinformatics Advance Access published online on April 27, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl152
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received February 1, 2006
Revised March 21, 2006
Accepted April 16, 2006

Applications note

map2mod - a server for evaluation of crystallographic models and their agreement with electron density maps

Olga Kirillova 1 * and Wladek Minor 1

1 Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA

* To whom correspondence should be addressed.
Olga Kirillova, E-mail: olga{at}iwonka.med.virginia.edu


  Abstract

Summary: Here we report on recent developments of the map2mod server. It has been designed for validation of protein models created by X-ray data interpretation. It can also be used during the refinement process since it is able to indicate problem regions in the model. Apart from evaluation of model quality, it has an option to remove atoms of side chains, which are not consistent with the maps as well as improperly placed water molecules. There are two additional options: checking the B-factors of atoms in the provided model and comparison of R and Rfree values obtained as the result of refinement with the averages characteristic for the data resolution shell.

Availability: The map2mod server is freely available for all user community (http://jurand.med.virginia.edu/m2m/map2model.html).

Associate Editor: Anna Tramontano
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