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Title: An editor for the generation and customization of geometry restraints

Abstract

Chemical restraints for use in macromolecular structure refinement are produced by a variety of methods, including a number of programs that use chemical information to generate the required bond, angle, dihedral, chiral and planar restraints. These programs help to automate the process and therefore minimize the errors that could otherwise occur if it were performed manually. Furthermore, restraint-dictionary generation programs can incorporate chemical and other prior knowledge to provide reasonable choices of types and values. However, the use of restraints to define the geometry of a molecule is an approximation introduced with efficiency in mind. The representation of a bond as a parabolic function is a convenience and does not reflect the true variability in even the simplest of molecules. Another complicating factor is the interplay of the molecule with other parts of the macromolecular model. Finally, difficult situations arise from molecules with rare or unusual moieties that may not have their conformational space fully explored. These factors give rise to the need for an interactive editor for WYSIWYG interactions with the restraints and molecule. Restraints Editor, Especially Ligands (REEL) is a graphical user interface for simple and error-free editing along with additional features to provide greater control of themore » restraint dictionaries in macromolecular refinement.« less

Authors:
 [1]; ORCiD logo [1];  [2]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE; National Inst. of Health (NIH) (United States)
OSTI Identifier:
1379703
Grant/Contract Number:  
AC02-05CH11231; 1P01 GM063210
Resource Type:
Accepted Manuscript
Journal Name:
Acta Crystallographica. Section D. Structural Biology
Additional Journal Information:
Journal Volume: 73; Journal Issue: 2; Journal ID: ISSN 2059-7983
Publisher:
IUCr
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; crystallographic refinement; geometric restraints; ideal geometry; graphical user interfaces; PHENIX

Citation Formats

Moriarty, Nigel W., Draizen, Eli J., and Adams, Paul D. An editor for the generation and customization of geometry restraints. United States: N. p., 2017. Web. https://doi.org/10.1107/S2059798316016570.
Moriarty, Nigel W., Draizen, Eli J., & Adams, Paul D. An editor for the generation and customization of geometry restraints. United States. https://doi.org/10.1107/S2059798316016570
Moriarty, Nigel W., Draizen, Eli J., and Adams, Paul D. Wed . "An editor for the generation and customization of geometry restraints". United States. https://doi.org/10.1107/S2059798316016570. https://www.osti.gov/servlets/purl/1379703.
@article{osti_1379703,
title = {An editor for the generation and customization of geometry restraints},
author = {Moriarty, Nigel W. and Draizen, Eli J. and Adams, Paul D.},
abstractNote = {Chemical restraints for use in macromolecular structure refinement are produced by a variety of methods, including a number of programs that use chemical information to generate the required bond, angle, dihedral, chiral and planar restraints. These programs help to automate the process and therefore minimize the errors that could otherwise occur if it were performed manually. Furthermore, restraint-dictionary generation programs can incorporate chemical and other prior knowledge to provide reasonable choices of types and values. However, the use of restraints to define the geometry of a molecule is an approximation introduced with efficiency in mind. The representation of a bond as a parabolic function is a convenience and does not reflect the true variability in even the simplest of molecules. Another complicating factor is the interplay of the molecule with other parts of the macromolecular model. Finally, difficult situations arise from molecules with rare or unusual moieties that may not have their conformational space fully explored. These factors give rise to the need for an interactive editor for WYSIWYG interactions with the restraints and molecule. Restraints Editor, Especially Ligands (REEL) is a graphical user interface for simple and error-free editing along with additional features to provide greater control of the restraint dictionaries in macromolecular refinement.},
doi = {10.1107/S2059798316016570},
journal = {Acta Crystallographica. Section D. Structural Biology},
number = 2,
volume = 73,
place = {United States},
year = {2017},
month = {2}
}

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