Research Article: An editor for the generation and customization of geometry restraints

Date Published: February 01, 2017

Publisher: International Union of Crystallography

Author(s): Nigel W. Moriarty, Eli J. Draizen, Paul D. Adams.


Obtaining a restraint dictionary for novel ligands or improving restraints for known ligands can require their manual modification. This can be tedious and error-prone. REEL is a restraints editor that provides quick, easy and accurate development, allowing global changes and fine-tuning of individual restraints.

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Restraint dictionaries are used in macromolecular structure refinement to help compensate for the typically low data-to-parameter ratio. Chemical restraints, which form a subclass of all restraints and are the most fundamental, are based on the internal coordinates of a molecular entity and generally include bonds, angles, dihedrals, chirals and planes. Each of the restraints is assigned an ideal value and an estimated standard deviation to define the center and curvature of the parabolic function for calculating the residual and gradient of the restraint (for more details, see Evans, 2007 ▸). A summation of the restraint residuals and the gradients is used as the functional to minimize the geometry term in the structure-refinement process. One limitation of the restraints paradigm is the need for the Cartesian coordinates of the molecule geometry to be consistent with the restraints. A simple example is a poorly modeled chiral center. The gradients from the chiral restraint and the angle restraints involved do not provide a pathway to the global minima of the moiety, but rather minimize to a chemical unreasonable configuration similar to an umbrella that is a local minima in the restraint paradigm but is not so in chemical reality. This is a shortcoming that can surface in poor models that provide chemically inaccurate geometries outside the radius of convergence of the restraints framework.

Editors allow the operator to change a computer file. One of the most basic is a text editor that allows the entry and deletion of ASCII characters in a simple text file. The same concept holds for a restraints editor, however here the atomicity of edits is geometry restraints that are being added and deleted. The smallest item that can be added or deleted in a text file is a single character; however, in a restraints editor the smallest item is a single restraint. However, a single restraint can have its internal values changed.




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