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Title: FEM: Feature-enhanced map

Abstract

A method is presented that modifies a 2mFobs - DFmodel σA-weighted map such that the resulting map can strengthen a weak signal, if present, and can reduce model bias and noise. The method consists of first randomizing the starting map and filling in missing reflections using multiple methods. This is followed by restricting the map to regions with convincing density and the application of sharpening. The final map is then created by combining a series of histogram-equalized intermediate maps. In the test cases shown, the maps produced in this way are found to have increased interpretability and decreased model bias compared with the starting 2mFobs - DFmodel σA-weighted map.

Authors:
 [1];  [1];  [2];  [1];  [3];  [4];  [5];  [6]
+ Show Author Affiliations
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  3. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  4. Jozef Stefan Inst. (IJS), Ljubljana (Slovenia)
  5. Centre for Integrative Biology, Illkirch (France); Universite de Lorraine, Vandoeuvre les Nancy (France)
  6. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California Berkeley, Berkeley, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE; National Institutes of Health (NIH)
OSTI Identifier:
1213460
Alternate Identifier(s):
OSTI ID: 1321743
Report Number(s):
LA-UR-14-24675
Journal ID: ISSN 1399-0047; ABCRE6; PII: S1399004714028132
Grant/Contract Number:  
AC02-05CH11231; AC52-06NA25396
Resource Type:
Accepted Manuscript
Journal Name:
Acta Crystallographica. Section D: Biological Crystallography (Online)
Additional Journal Information:
Journal Name: Acta Crystallographica. Section D: Biological Crystallography (Online); Journal Volume: 71; Journal Issue: 3; Journal ID: ISSN 1399-0047
Publisher:
International Union of Crystallography
Country of Publication:
United States
Language:
English
Subject:
36 MATERIALS SCIENCE; Fourier map; map sharpening; map kurtosis; model bias; map improvement; density modification; PHENIX; cctbx; FEM; featureenhanced map; OMIT; 59 BASIC BIOLOGICAL SCIENCES; feature-enhanced map

Citation Formats

Afonine, Pavel V., Moriarty, Nigel W., Mustyakimov, Marat, Sobolev, Oleg V., Terwilliger, Thomas C., Turk, Dusan, Urzhumtsev, Alexandre, and Adams, Paul D. FEM: Feature-enhanced map. United States: N. p., 2015. Web. doi:10.1107/S1399004714028132.
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Afonine, Pavel V., Moriarty, Nigel W., Mustyakimov, Marat, Sobolev, Oleg V., Terwilliger, Thomas C., Turk, Dusan, Urzhumtsev, Alexandre, & Adams, Paul D. FEM: Feature-enhanced map. United States. https://doi.org/10.1107/S1399004714028132
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Afonine, Pavel V., Moriarty, Nigel W., Mustyakimov, Marat, Sobolev, Oleg V., Terwilliger, Thomas C., Turk, Dusan, Urzhumtsev, Alexandre, and Adams, Paul D. Thu . "FEM: Feature-enhanced map". United States. https://doi.org/10.1107/S1399004714028132. https://www.osti.gov/servlets/purl/1213460.
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@article{osti_1213460,
title = {FEM: Feature-enhanced map},
author = {Afonine, Pavel V. and Moriarty, Nigel W. and Mustyakimov, Marat and Sobolev, Oleg V. and Terwilliger, Thomas C. and Turk, Dusan and Urzhumtsev, Alexandre and Adams, Paul D.},
abstractNote = {A method is presented that modifies a 2mFobs - DFmodel σA-weighted map such that the resulting map can strengthen a weak signal, if present, and can reduce model bias and noise. The method consists of first randomizing the starting map and filling in missing reflections using multiple methods. This is followed by restricting the map to regions with convincing density and the application of sharpening. The final map is then created by combining a series of histogram-equalized intermediate maps. In the test cases shown, the maps produced in this way are found to have increased interpretability and decreased model bias compared with the starting 2mFobs - DFmodel σA-weighted map.},
doi = {10.1107/S1399004714028132},
journal = {Acta Crystallographica. Section D: Biological Crystallography (Online)},
number = 3,
volume = 71,
place = {United States},
year = {Thu Feb 26 00:00:00 EST 2015},
month = {Thu Feb 26 00:00:00 EST 2015}
}
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https://doi.org/10.1107/S1399004714028132
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    • Paulsen, Peter Aasted; Custódio, Tânia F.; Pedersen, Bjørn Panyella
    • Deutsches Elektronen-Synchrotron, DESY, Hamburg
    • DOI: 10.3204/pubdb-2020-04649
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