Journal
STRUCTURE
Volume 13, Issue 3, Pages 473-482Publisher
CELL PRESS
DOI: 10.1016/j.str.2005.01.006
Keywords
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Funding
- NCRR NIH HHS [P41 RR001081, P41 RR-01081] Funding Source: Medline
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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.
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