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Nucleic Acids Research 2006 34(4):e29; doi:10.1093/nar/gnj031
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Published online 14 February 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

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Nucleic acid visualization with UCSF Chimera

Gregory S. Couch, Donna K. Hendrix1 and Thomas E. Ferrin*

Computer Graphics Laboratory, Department of Pharmaceutical Chemistry, University of California 600 16th Street, San Francisco, CA 94143-2240, USA 1Department of Plant and Microbial Biology 111 Koshland Hall # 3102 University of California Berkeley, CA 94720-3102, USA

*To whom correspondence should be addressed. Tel: +1 415 476 2299; Fax: +1 415 502 1755; Email: tef{at}cgl.ucsf.edu

Received December 14, 2005. Revised January 31, 2006. Accepted January 31, 2006.

With the increase in the number of large, 3D, high-resolution nucleic acid structures, particularly of the 30S and 50S ribosomal subunits and the intact bacterial ribosome, advancements in the visualization of nucleic acid structural features are essential. Large molecular structures are complicated and detailed, and one goal of visualization software is to allow the user to simplify the display of some features and accent others. We describe an extension to the UCSF Chimera molecular visualization system for the purpose of displaying and highlighting nucleic acid characteristics, including a new representation of sugar pucker, several options for abstraction of base geometries that emphasize stacking and base pairing, and an adaptation of the ribbon backbone to accommodate the nucleic acid backbone. Molecules are displayed and manipulated interactively, allowing the user to change the representations as desired for small molecules, proteins and nucleic acids. This software is available as part of the UCSF Chimera molecular visualization system and thus is integrated with a suite of existing tools for molecular graphics.


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[Abstract] [Full Text] [PDF]


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