HOLLOW: generating accurate representations of channel and interior surfaces in molecular structures

An accurate rendering of interior surfaces can facilitate the analysis of mechanisms at atomic-level detail, such as the transport of substrates in the ammonia channel. In molecular viewers, one must remove the exterior surface that obscures the channel surface by clipping the viewing plane or manua...

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Bibliographic Details
Published in:BMC structural biology 2008-11, Vol.8 (1), p.49-49
Main Authors: Ho, Bosco K, Gruswitz, Franz
Format: Article
Language:English
Subjects:
Atoms
Biological research
Biology, Experimental
Computer Graphics
Models, Molecular
Molecular Structure
Protein Conformation
Proteins
Software
Surface Properties
Technology application
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Summary:An accurate rendering of interior surfaces can facilitate the analysis of mechanisms at atomic-level detail, such as the transport of substrates in the ammonia channel. In molecular viewers, one must remove the exterior surface that obscures the channel surface by clipping the viewing plane or manually selecting the channel residues in order to display a partial surface. Neither method is entirely satisfactory, as unwanted additional pieces of surfaces are always generated. To cleanly visualize a channel surface, we present HOLLOW, a program that generates a "casting" of the interior volume of the protein as dummy atoms. We show that the molecular surface of the dummy atoms closely approximates the channel surface, where this complementary surface of the protein channel can be displayed without superfluous surfaces. The use of HOLLOW significantly simplifies the generation of channel surfaces, and other interior surfaces of protein structures. HOLLOW is written in PYTHON and is available at http://hollow.sourceforge.net.
ISSN:1472-6807
1472-6807
DOI:10.1186/1472-6807-8-49