Map2mod - A server for evaluation of crystallographic models and their agreement with electron density maps

Olga Kirillova; Wladek Minor

doi:10.1093/bioinformatics/btl152

Map2mod - A server for evaluation of crystallographic models and their agreement with electron density maps

Olga Kirillova, Wladek Minor

Research output: Contribution to journal › Article › peer-review

4 Scopus citations

Abstract

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 R_free values obtained as the result of refinement with the averages characteristic for the data resolution shell.

Original language	English
Pages (from-to)	1660-1661
Number of pages	2
Journal	Bioinformatics
Volume	22
Issue number	13
DOIs	https://doi.org/10.1093/bioinformatics/btl152
State	Published - 1 Jul 2006
Externally published	Yes

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10.1093/bioinformatics/btl152

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abstract = "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.",

author = "Olga Kirillova and Wladek Minor",

note = "Funding Information: The authors would like to thank M. Zimmerman for useful comments on Perl scripting, M. Chruszcz for notes and advices during the testing of the server and anonymous referees for critical reading of the manuscript. The research has been supported by NIGMS grant P-50-GM62414.",

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AU - Minor, Wladek

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N2 - 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.

AB - 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.

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Map2mod - A server for evaluation of crystallographic models and their agreement with electron density maps

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