skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: From deep TLS validation to ensembles of atomic models built from elemental motions. Addenda and corrigendum

Abstract

Researcher feedback has indicated that in Urzhumtsevet al.[(2015)Acta Cryst.D71, 1668–1683] clarification of key parts of the algorithm for interpretation of TLS matrices in terms of elemental atomic motions and corresponding ensembles of atomic models is required. Also, it has been brought to the attention of the authors that the incorrect PDB code was reported for one of test models. Lastly, these issues are addressed in this article.

Authors:
 [1];  [2];  [3];  [3];  [4]
  1. Inst. of Genetics and Molecular and Cellular Biology (IGBMC), Illkirch (France). Centre for Integrative Biology; Univ. de Lorraine, Vandoeuvre-les-Nancy (France)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging Division
  3. Univ. of California, San Francisco, CA (United States). Dept. of Bioengineering and Therapeutic Sciences
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging Division; Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE; National Institutes of Health (NIH)
OSTI Identifier:
1377458
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Acta Crystallographica. Section D. Structural Biology
Additional Journal Information:
Journal Volume: 72; Journal Issue: 9; Journal ID: ISSN 2059-7983
Publisher:
IUCr
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 59 BASIC BIOLOGICAL SCIENCES; TLS model; TLS matrices; ensemble of atomic models; atomic displacement matrices; model validation; addenda and corrigendum

Citation Formats

Urzhumtsev, Alexandre, Afonine, Pavel V., Van Benschoten, Andrew H., Fraser, James S., and Adams, Paul D. From deep TLS validation to ensembles of atomic models built from elemental motions. Addenda and corrigendum. United States: N. p., 2016. Web. doi:10.1107/S2059798316013048.
Urzhumtsev, Alexandre, Afonine, Pavel V., Van Benschoten, Andrew H., Fraser, James S., & Adams, Paul D. From deep TLS validation to ensembles of atomic models built from elemental motions. Addenda and corrigendum. United States. doi:10.1107/S2059798316013048.
Urzhumtsev, Alexandre, Afonine, Pavel V., Van Benschoten, Andrew H., Fraser, James S., and Adams, Paul D. Wed . "From deep TLS validation to ensembles of atomic models built from elemental motions. Addenda and corrigendum". United States. doi:10.1107/S2059798316013048. https://www.osti.gov/servlets/purl/1377458.
@article{osti_1377458,
title = {From deep TLS validation to ensembles of atomic models built from elemental motions. Addenda and corrigendum},
author = {Urzhumtsev, Alexandre and Afonine, Pavel V. and Van Benschoten, Andrew H. and Fraser, James S. and Adams, Paul D.},
abstractNote = {Researcher feedback has indicated that in Urzhumtsevet al.[(2015)Acta Cryst.D71, 1668–1683] clarification of key parts of the algorithm for interpretation of TLS matrices in terms of elemental atomic motions and corresponding ensembles of atomic models is required. Also, it has been brought to the attention of the authors that the incorrect PDB code was reported for one of test models. Lastly, these issues are addressed in this article.},
doi = {10.1107/S2059798316013048},
journal = {Acta Crystallographica. Section D. Structural Biology},
number = 9,
volume = 72,
place = {United States},
year = {2016},
month = {8}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 1 work
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

The Computational Crystallography Toolbox : crystallographic algorithms in a reusable software framework
journal, January 2002

  • Grosse-Kunstleve, Ralf W.; Sauter, Nicholas K.; Moriarty, Nigel W.
  • Journal of Applied Crystallography, Vol. 35, Issue 1
  • DOI: 10.1107/S0021889801017824

Overview of the CCP 4 suite and current developments
journal, March 2011

  • Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444910045749

TLS from fundamentals to practice
journal, October 2013


From deep TLS validation to ensembles of atomic models built from elemental motions
journal, July 2015

  • Urzhumtsev, Alexandre; Afonine, Pavel V.; Van Benschoten, Andrew H.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 71, Issue 8
  • DOI: 10.1107/S1399004715011426

PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
  • DOI: 10.1107/S0907444909052925

    Works referencing / citing this record:

    From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation
    journal, June 2018

    • Afonine, Pavel V.; Adams, Paul D.; Urzhumtsev, Alexandre
    • Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 7
    • DOI: 10.1107/s2059798318005764

    Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
    journal, October 2019

    • Liebschner, Dorothee; Afonine, Pavel V.; Baker, Matthew L.
    • Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 10
    • DOI: 10.1107/s2059798319011471