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Title: Metrics for comparison of crystallographic maps

Journal Article · · Acta Crystallographica. Section D: Biological Crystallography (Online)
 [1];  [2];  [3];  [4];  [5]
  1. Univ. de Strasbourg, Illkirch (France). Centre for Integrative Biology; Univ. de Lorraine, Nancy (France). Faculte des Sciences et Technologies.
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  3. Russian Academy of Sciences (RAS), Pushchino (Russian Federation). Inst. of Matematical Problems of Biology.
  4. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  5. Lawrence Berkeley National Lab., CA (United States); Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering.
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We use numerical comparison of crystallographic contour maps extensively in structure solution and model refinement, analysis and validation. However, traditional metrics such as the map correlation coefficient (map CC, real-space CC or RSCC) sometimes contradict the results of visual assessment of the corresponding maps. This article explains such apparent contradictions and suggests new metrics and tools to compare crystallographic contour maps. The key to the new methods is rank scaling of the Fourier syntheses. Also, the new metrics are complementary to the usual map CC and can be more helpful in map comparison, in particular when only some of their aspects, such as regions of high density, are of interest.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
Sponsoring Organization:
USDOE
Grant/Contract Number:
AC02-05CH11231; AC52-06NA25396
OSTI ID:
1213565
Alternate ID(s):
OSTI ID: 1321738
Report Number(s):
LA-UR-14-21189; ABCRE6; PII: S1399004714016289
Journal Information:
Acta Crystallographica. Section D: Biological Crystallography (Online), Vol. 70, Issue 10; ISSN 1399-0047
Publisher:
International Union of CrystallographyCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 24 works
Citation information provided by
Web of Science

Cited By (7)

Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding journal February 2017
RIDL : a tool to investigate radiation-induced density loss journal May 2018
Mask-based approach to phasing of single-particle diffraction data journal January 2016
Mask-based approach to phasing of single-particle diffraction data. II. Likelihood-based selection criteria journal January 2019
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. text January 2019
Improvement of cryo-EM maps by density modification. journalarticle January 2020
Improvement of cryo-EM maps by density modification journal August 2020

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Related Subjects

36 MATERIALS SCIENCE
Fourier syntheses
crystallographic contour maps
map comparison
sigma scale
rank scaling
correlation coefficients
59 BASIC BIOLOGICAL SCIENCES
97 MATHEMATICS AND COMPUTING