Metrics for comparison of crystallographic maps

Urzhumtsev, Alexandre; Afonine, Pavel V.; Lunin, Vladimir Y.; Terwilliger, Thomas C.; Adams, Paul D.

doi:10.1107/S1399004714016289

Title: Metrics for comparison of crystallographic maps

Abstract

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.

Authors:

Urzhumtsev, Alexandre ^[1]; Afonine, Pavel V. ^[2]; Lunin, Vladimir Y. ^[3]; Terwilliger, Thomas C. ^[4]; Adams, Paul D. ^[5]

Univ. de Strasbourg, Illkirch (France). Centre for Integrative Biology; Univ. de Lorraine, Nancy (France). Faculte des Sciences et Technologies.
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Russian Academy of Sciences (RAS), Pushchino (Russian Federation). Inst. of Matematical Problems of Biology.
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Lawrence Berkeley National Lab., CA (United States); Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering.

Publication Date:: Wed Oct 01 00:00:00 EDT 2014

Research Org.:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 1213565

Alternate Identifier(s):: OSTI ID: 1321738

Report Number(s):: LA-UR-14-21189
Journal ID: ISSN 1399-0047; ABCRE6; PII: S1399004714016289

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: 70; Journal Issue: 10; Journal ID: ISSN 1399-0047

Publisher:: International Union of Crystallography

Country of Publication:: United States

Language:: English

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

Citation Formats


                    Urzhumtsev, Alexandre, Afonine, Pavel V., Lunin, Vladimir Y., Terwilliger, Thomas C., and Adams, Paul D. Metrics for comparison of crystallographic maps.  United States: N. p., 2014. 
Web.  doi:10.1107/S1399004714016289.

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                    Urzhumtsev, Alexandre, Afonine, Pavel V., Lunin, Vladimir Y., Terwilliger, Thomas C., & Adams, Paul D. Metrics for comparison of crystallographic maps.  United States.  https://doi.org/10.1107/S1399004714016289

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                    Urzhumtsev, Alexandre, Afonine, Pavel V., Lunin, Vladimir Y., Terwilliger, Thomas C., and Adams, Paul D. Wed .  
"Metrics for comparison of crystallographic maps".  United States.  https://doi.org/10.1107/S1399004714016289.  https://www.osti.gov/servlets/purl/1213565.

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@article{osti_1213565,

  title        = {Metrics for comparison of crystallographic maps},

  author       = {Urzhumtsev, Alexandre and Afonine, Pavel V. and Lunin, Vladimir Y. and Terwilliger, Thomas C. and Adams, Paul D.},

  abstractNote = {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.},

  doi          = {10.1107/S1399004714016289},

  journal      = {Acta Crystallographica. Section D: Biological Crystallography (Online)},

  number       = 10,

  volume       = 70,

  place        = {United States},

  year         = {Wed Oct 01 00:00:00 EDT 2014},

  month        = {Wed Oct 01 00:00:00 EDT 2014}

}

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Works referencing / citing this record:

Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding
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DOI: 10.1002/jmr.2618

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Journal of Applied Crystallography, Vol. 51, Issue 3
DOI: 10.1107/s1600576718005241

Mask-based approach to phasing of single-particle diffraction data
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Lunin, Vladimir Y.; Lunina, Natalia L.; Petrova, Tatiana E.
Acta Crystallographica Section D Structural Biology, Vol. 72, Issue 1
DOI: 10.1107/s2059798315022652

Mask-based approach to phasing of single-particle diffraction data. II. Likelihood-based selection criteria
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Lunin, Vladimir Y.; Lunina, Natalia L.; Petrova, Tatiana E.
Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 1
DOI: 10.1107/s2059798318016959

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
text, January 2019

Liebschner, Dorothee; Afonine, Pavel V.; Baker, Matthew L.
Apollo - University of Cambridge Repository
DOI: 10.17863/cam.43042

Improvement of cryo-EM maps by density modification.
journalarticle, January 2020

Terwilliger, Thomas C.; Ludtke, Steven J.; Read, Randy J.
Springer Science and Business Media LLC
DOI: 10.17863/cam.55997

Improvement of cryo-EM maps by density modification
journal, August 2020

Terwilliger, Thomas C.; Ludtke, Steven J.; Read, Randy J.
Nature Methods, Vol. 17, Issue 9
DOI: 10.1038/s41592-020-0914-9

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Title: Metrics for comparison of crystallographic maps

Abstract

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