An editor for the generation and customization of geometry restraints

Moriarty, Nigel W.; Draizen, Eli J.; Adams, Paul D.

doi:10.1107/S2059798316016570

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

Journal Article · Wed Feb 01 00:00:00 EST 2017 · Acta Crystallographica. Section D. Structural Biology

DOI:https://doi.org/10.1107/S2059798316016570· OSTI ID:1379703

Moriarty, Nigel W. ^[1];

^[1]; Adams, Paul D. ^[2]

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE; National Inst. of Health (NIH) (United States)

Grant/Contract Number:: AC02-05CH11231; 1P01 GM063210

OSTI ID:: 1379703

Journal Information:: Acta Crystallographica. Section D. Structural Biology, Vol. 73, Issue 2; ISSN 2059-7983

Publisher:: IUCrCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 27 works

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Why is interoperability between the two fields of chemical crystallography and protein crystallography so difficult? Brink, Alice; Helliwell, John R. IUCrJ, Vol. 6, Issue 5 https://doi.org/10.1107/s2052252519010972	journal	August 2019
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Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner, Dorothee; Afonine, Pavel V.; Baker, Matthew L. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.43042	text	January 2019
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