UCSF Chimera—A visualization system for exploratory research and analysis

  1. Eric F. Pettersen,
  2. Thomas D. Goddard,
  3. Conrad C. Huang,
  4. Gregory S. Couch,
  5. Daniel M. Greenblatt,
  6. Elaine C. Meng,
  7. Thomas E. Ferrin*

Article first published online: 1 JUL 2004

DOI: 10.1002/jcc.20084

Issue

Journal of Computational Chemistry

Journal of Computational Chemistry

Volume 25, Issue 13, pages 1605–1612, October 2004

Additional Information

How to Cite

Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C. and Ferrin, T. E. (2004), UCSF Chimera—A visualization system for exploratory research and analysis. J. Comput. Chem., 25: 1605–1612. doi: 10.1002/jcc.20084

Author Information

  1. Computer Graphics Laboratory, Department of Pharmaceutical Chemistry, University of California, 600 16th Street, San Francisco, California 94143-2240

*Computer Graphics Laboratory, Department of Pharmaceutical Chemistry, University of California, 600 16th Street, San Francisco, California 94143-2240

Publication History

  1. Issue published online: 1 JUL 2004
  2. Article first published online: 1 JUL 2004
  3. Manuscript Accepted: 6 MAY 2004
  4. Manuscript Received: 24 FEB 2004

Funded by

  • NIH. Grant Number: P41-RR01081

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Keywords:

  • molecular graphics;
  • extensibility;
  • visualization;
  • multiscale modeling;
  • sequence alignment

Abstract

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

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