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Title: Programming new geometry restraints: Parallelity of atomic groups

Journal Article · · Journal of Applied Crystallography (Online)
 [1];  [1];  [2];  [3]
  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.
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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.

Research Organization:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1213056
Journal Information:
Journal of Applied Crystallography (Online), Vol. 48, Issue 4; ISSN 1600-5767
Publisher:
International Union of CrystallographyCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 11 works
Citation information provided by
Web of Science

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Cited By (2)

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

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Related Subjects

75 CONDENSED MATTER PHYSICS
SUPERCONDUCTIVITY AND SUPERFLUIDITY
59 BASIC BIOLOGICAL SCIENCES
restraints
atomic model refinement
parallel planes
cctbx
PHENIX
gradient calculation