UCSF Chimera-A visualization system for exploratory research and analysis

The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension...

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Bibliographic Details
Published inJournal of computational chemistry Vol. 25; no. 13; pp. 1605 - 1612
Main Authors Pettersen, Eric F., Goddard, Thomas D., Huang, Conrad C., Couch, Gregory S., Greenblatt, Daniel M., Meng, Elaine C., Ferrin, Thomas E.
Format Journal Article
LanguageEnglish
Published New York John Wiley & Sons, Inc 01.10.2004
Wiley Subscription Services, Inc
Subjects
Amino Acid Sequence
Analysis
Computer Graphics
extensibility
Models, Molecular
Molecular Conformation
molecular graphics
Molecular Sequence Data
multiscale modeling
Sequence Alignment
Software
Thermodynamics
Visualization
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Summary:The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large‐scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real‐world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1605–1612, 2004
Bibliography:ark:/67375/WNG-CPNGNQ2F-M
NIH - No. P41-RR01081
ArticleID:JCC20084
istex:7F5E235169445BEA0F69F7B51E9520DB4ED272F3
ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ISSN:0192-8651
1096-987X
DOI:10.1002/jcc.20084