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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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  • 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 factorsmore » 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. The tools described in this manuscript have been implemented and are available inPHENIX.« less
  • Aerosol properties above clouds have been retrieved over the South East Atlantic Ocean during the fire season 2006 using satellite observations from POLDER (Polarization and Directionality of Earth Reflectances). From June to October, POLDER has observed a mean Above-Cloud Aerosol Optical Thickness (ACAOT) of 0.28 and a mean Above-Clouds Single Scattering Albedo (ACSSA) of 0.87 at 550nm. These results have been used to evaluate the simulation of aerosols above clouds in 5 AeroCom (Aerosol Comparisons between Observations and Models) models (GOCART, HadGEM3, ECHAM5-HAM2, OsloCTM2 and SPRINTARS). Most models do not reproduce the observed large aerosol load episodes. The comparison highlightsmore » the importance of the injection height and the vertical transport parameterizations to simulate the large ACAOT observed by POLDER. Furthermore, some models overestimate the ACSSA. In accordance with recent recommendations of the black carbon refractive index, a higher prescription of the imaginary part allows a better comparison with POLDER’s ACSSA.« less
  • Scientific computations and collaborations increasingly rely on the network to provide high-speed data transfer, dissemination of results, access to instruments, support for computational steering, etc. The Energy Sciences Network is establishing a science data network to provide user driven bandwidth allocation. In a shared network environment, some reservations may not be granted due to the lack of available bandwidth on any single path. In many cases, the available bandwidth across multiple paths would be sufficient to grant the reservation. In this paper we investigate how to utilize the available bandwidth across multiple paths in the case of bulk data transfer.
  • Magneto-optical images of flux patterns in a ring of epitaxial YBa{sub 2}Cu{sub 3}O{sub 7-{delta}} film with an artificial 10{sup o} grain boundary are used to determine the ratio of the grain-boundary critical current to the bulk critical current. This ratio which first increases slowly with temperature is found to make a sharp upturn above 77 K showing that the grain-boundary critical current quickly converges to the bulk value at higher temperatures. From the measured ratio and the grain-boundary critical current obtained from magnetization, the temperature dependence of the bulk critical current is recovered.