Document Detail


Software extensions to UCSF chimera for interactive visualization of large molecular assemblies.
MedLine Citation:
PMID:  15766548     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Many structures of large molecular assemblies such as virus capsids and ribosomes have been experimentally determined to atomic resolution. We consider four software problems that arise in interactive visualization and analysis of large assemblies: how to represent multimers efficiently, how to make cartoon representations, how to calculate contacts efficiently, and how to select subassemblies. We describe techniques and algorithms we have developed and give examples of their use. Existing molecular visualization programs work well for single protein and nucleic acid molecules and for small complexes. The methods presented here are proposed as features to add to existing programs or include in next-generation visualization software to allow easy exploration of assemblies containing tens to thousands of macromolecules. Our approach is pragmatic, emphasizing simplicity of code, reliability, and speed. The methods described have been distributed as the Multiscale extension of the UCSF Chimera (www.cgl.ucsf.edu/chimera) molecular graphics program.
Authors:
Thomas D Goddard; Conrad C Huang; Thomas E Ferrin
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, P.H.S.    
Journal Detail:
Title:  Structure (London, England : 1993)     Volume:  13     ISSN:  0969-2126     ISO Abbreviation:  Structure     Publication Date:  2005 Mar 
Date Detail:
Created Date:  2005-03-15     Completed Date:  2005-08-23     Revised Date:  2007-11-14    
Medline Journal Info:
Nlm Unique ID:  101087697     Medline TA:  Structure     Country:  United States    
Other Details:
Languages:  eng     Pagination:  473-82     Citation Subset:  IM    
Affiliation:
Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA.
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MeSH Terms
Descriptor/Qualifier:
Algorithms*
Imaging, Three-Dimensional / methods*
Models, Molecular*
Molecular Structure
Multiprotein Complexes / chemistry*
Software*
Grant Support
ID/Acronym/Agency:
P41 RR-01081/RR/NCRR NIH HHS
Chemical
Reg. No./Substance:
0/Multiprotein Complexes

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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