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/.
Copyright 2004 Wiley Periodicals, Inc.