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Title: Polder maps: Improving OMIT maps by excluding bulk solvent

Abstract

The crystallographic maps that are routinely used during the structure-solution workflow are almost always model-biased because model information is used for their calculation. As these maps are also used to validate the atomic models that result from model building and refinement, this constitutes an immediate problem: anything added to the model will manifest itself in the map and thus hinder the validation. OMIT maps are a common tool to verify the presence of atoms in the model. The simplest way to compute an OMIT map is to exclude the atoms in question from the structure, update the corresponding structure factors and compute a residual map. It is then expected that if these atoms are present in the crystal structure, the electron density for the omitted atoms will be seen as positive features in this map. This, however, is complicated by the flat bulk-solvent model which is almost universally used in modern crystallographic refinement programs. This model postulates constant electron density at any voxel of the unit-cell volume that is not occupied by the atomic model. Consequently, if the density arising from the omitted atoms is weak then the bulk-solvent model may obscure it further. A possible solution to this problemmore » is to prevent bulk solvent from entering the selected OMIT regions, which may improve the interpretative power of residual maps. This approach is called a polder (OMIT) map. Polder OMIT maps can be particularly useful for displaying weak densities of ligands, solvent molecules, side chains, alternative conformations and residues both in terminal regions and in loops. As a result, the tools described in this manuscript have been implemented and are available in PHENIX.« less

Authors:
 [1];  [1];  [1];  [1];  [1]; ORCiD logo [2];  [3]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  2. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
National Institutes of Health (NIH); USDOE
OSTI Identifier:
1344357
Alternate Identifier(s):
OSTI ID: 1379713
Report Number(s):
LA-UR-16-24457
Journal ID: ISSN 2059-7983; ACSDAD; TRN: US1700899
Grant/Contract Number:  
AC52-06NA25396; AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Acta Crystallographica. Section D. Structural Biology
Additional Journal Information:
Journal Volume: 73; Journal Issue: 2; Journal ID: ISSN 2059-7983
Publisher:
IUCr
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Biological Science

Citation Formats

Liebschner, Dorothee, Afonine, Pavel V., Moriarty, Nigel W., Poon, Billy K., Sobolev, Oleg V., Terwilliger, Thomas Charles, and Adams, Paul D. Polder maps: Improving OMIT maps by excluding bulk solvent. United States: N. p., 2017. Web. doi:10.1107/S2059798316018210.
Liebschner, Dorothee, Afonine, Pavel V., Moriarty, Nigel W., Poon, Billy K., Sobolev, Oleg V., Terwilliger, Thomas Charles, & Adams, Paul D. Polder maps: Improving OMIT maps by excluding bulk solvent. United States. doi:10.1107/S2059798316018210.
Liebschner, Dorothee, Afonine, Pavel V., Moriarty, Nigel W., Poon, Billy K., Sobolev, Oleg V., Terwilliger, Thomas Charles, and Adams, Paul D. Wed . "Polder maps: Improving OMIT maps by excluding bulk solvent". United States. doi:10.1107/S2059798316018210. https://www.osti.gov/servlets/purl/1344357.
@article{osti_1344357,
title = {Polder maps: Improving OMIT maps by excluding bulk solvent},
author = {Liebschner, Dorothee and Afonine, Pavel V. and Moriarty, Nigel W. and Poon, Billy K. and Sobolev, Oleg V. and Terwilliger, Thomas Charles and Adams, Paul D.},
abstractNote = {The crystallographic maps that are routinely used during the structure-solution workflow are almost always model-biased because model information is used for their calculation. As these maps are also used to validate the atomic models that result from model building and refinement, this constitutes an immediate problem: anything added to the model will manifest itself in the map and thus hinder the validation. OMIT maps are a common tool to verify the presence of atoms in the model. The simplest way to compute an OMIT map is to exclude the atoms in question from the structure, update the corresponding structure factors and compute a residual map. It is then expected that if these atoms are present in the crystal structure, the electron density for the omitted atoms will be seen as positive features in this map. This, however, is complicated by the flat bulk-solvent model which is almost universally used in modern crystallographic refinement programs. This model postulates constant electron density at any voxel of the unit-cell volume that is not occupied by the atomic model. Consequently, if the density arising from the omitted atoms is weak then the bulk-solvent model may obscure it further. A possible solution to this problem is to prevent bulk solvent from entering the selected OMIT regions, which may improve the interpretative power of residual maps. This approach is called a polder (OMIT) map. Polder OMIT maps can be particularly useful for displaying weak densities of ligands, solvent molecules, side chains, alternative conformations and residues both in terminal regions and in loops. As a result, the tools described in this manuscript have been implemented and are available in PHENIX.},
doi = {10.1107/S2059798316018210},
journal = {Acta Crystallographica. Section D. Structural Biology},
number = 2,
volume = 73,
place = {United States},
year = {Wed Feb 01 00:00:00 EST 2017},
month = {Wed Feb 01 00:00:00 EST 2017}
}

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