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Title: Programming new geometry restraints: Parallelity of atomic groups

Abstract

Improvements in structural biology methods, in particular crystallography and cryo-electron microscopy, have created an increased demand for the refinement of atomic models against low-resolution experimental data. One way to compensate for the lack of high-resolution experimental data is to use a priori information about model geometry that can be utilized in refinement in the form of stereochemical restraints or constraints. Here, the definition and calculation of the restraints that can be imposed on planar atomic groups, in particular the angle between such groups, are described. Detailed derivations of the restraint targets and their gradients are provided so that they can be readily implemented in other contexts. Practical implementations of the restraints, and of associated data structures, in the Computational Crystallography Toolbox(cctbx) are presented.

Authors:
 [1];  [1];  [2];  [3]
+ Show Author Affiliations
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California Berkeley, Berkeley, CA (United States). Dept. of Bioengineering.
  3. Centre for Integrative Biology, IGBMC, Illkirch (France); Universite de Lorraine, Nancy (France). Dept. de Physique.
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1213056
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Applied Crystallography (Online)
Additional Journal Information:
Journal Name: Journal of Applied Crystallography (Online); Journal Volume: 48; Journal Issue: 4; Journal ID: ISSN 1600-5767
Publisher:
International Union of Crystallography
Country of Publication:
United States
Language:
English
Subject:
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; 59 BASIC BIOLOGICAL SCIENCES; restraints; atomic model refinement; parallel planes; cctbx; PHENIX; gradient calculation

Citation Formats

Sobolev, Oleg V., Afonine, Pavel V., Adams, Paul D., and Urzhumtsev, Alexandre. Programming new geometry restraints: Parallelity of atomic groups. United States: N. p., 2015. Web. doi:10.1107/S1600576715010432.
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Sobolev, Oleg V., Afonine, Pavel V., Adams, Paul D., & Urzhumtsev, Alexandre. Programming new geometry restraints: Parallelity of atomic groups. United States. https://doi.org/10.1107/S1600576715010432
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Sobolev, Oleg V., Afonine, Pavel V., Adams, Paul D., and Urzhumtsev, Alexandre. Sat . "Programming new geometry restraints: Parallelity of atomic groups". United States. https://doi.org/10.1107/S1600576715010432. https://www.osti.gov/servlets/purl/1213056.
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@article{osti_1213056,
title = {Programming new geometry restraints: Parallelity of atomic groups},
author = {Sobolev, Oleg V. and Afonine, Pavel V. and Adams, Paul D. and Urzhumtsev, Alexandre},
abstractNote = {Improvements in structural biology methods, in particular crystallography and cryo-electron microscopy, have created an increased demand for the refinement of atomic models against low-resolution experimental data. One way to compensate for the lack of high-resolution experimental data is to use a priori information about model geometry that can be utilized in refinement in the form of stereochemical restraints or constraints. Here, the definition and calculation of the restraints that can be imposed on planar atomic groups, in particular the angle between such groups, are described. Detailed derivations of the restraint targets and their gradients are provided so that they can be readily implemented in other contexts. Practical implementations of the restraints, and of associated data structures, in the Computational Crystallography Toolbox(cctbx) are presented.},
doi = {10.1107/S1600576715010432},
journal = {Journal of Applied Crystallography (Online)},
number = 4,
volume = 48,
place = {United States},
year = {Sat Aug 01 00:00:00 EDT 2015},
month = {Sat Aug 01 00:00:00 EDT 2015}
}
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Journal Article:
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Publisher's Version of Record
https://doi.org/10.1107/S1600576715010432
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    Works referencing / citing this record:

    Introduction to crystallographic refinement of macromolecular atomic models
    journal, July 2019

    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
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