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MAP_CHANNELS : a computation tool to aid in the visualization and characterization of solvent channels in macromolecular crystals
Author(s) -
Juers Douglas H.,
Ruffin Jon
Publication year - 2014
Publication title -
journal of applied crystallography
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.429
H-Index - 162
ISSN - 1600-5767
DOI - 10.1107/s160057671402281x
Subject(s) - computation , visualization , bottleneck , macromolecule , anisotropy , materials science , solvent , tortuosity , scalar (mathematics) , computer science , field (mathematics) , computational science , topology (electrical circuits) , crystallography , chemical physics , chemistry , algorithm , geometry , porosity , physics , data mining , mathematics , optics , combinatorics , organic chemistry , composite material , embedded system , pure mathematics , biochemistry
A computation tool is described that facilitates visualization and characterization of solvent channels or pores within macromolecular crystals. A scalar field mapping the shortest distance to protein surfaces is calculated on a grid covering the unit cell and is written as a map file. The map provides a multiscale representation of the solvent channels, which when viewed in standard macromolecular crystallographic software packages gives an intuitive sense of the solvent channel architecture. The map is analysed to yield descriptors of the topology and the morphology of the solvent channels, including bottleneck radii, tortuosity, width variation and anisotropy.