Chimera

Netropsin bound to double-stranded DNA. The special representations were created with the Nucleotides extension.
Image from Chimera Image Gallery
© 2004 The Regents of the University of California; all rights reserved.

UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated.

To use in the Core on a Linux or SGI workstation, simply type:

setup chimera

then type:

See the PDF-format quick reference for a basic guide to command-line commands.

The up-to-date full documentation is available online from the Chimera website.

There is also now an expanded tutorial for beginners.

How does one cite Chimera?

Publications with images or results from Chimera should include an acknowledgement similar to the following:

Molecular graphics images were produced using the UCSF Chimera package from the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIH P41 RR-01081).

and should cite one or more of the Chimera references, such as:

Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., and Ferrin, T.E. "UCSF Chimera - A Visualization System for Exploratory Research and Analysis." J. Comput. Chem. 25(13):1605-1612 (2004).

Solvent-excluded molecular surfaces are created with the help of the package:

Sanner, M.F., Olson, A.J., and Spehner, J.C. "Reduced surface: an efficient way to compute molecular surfaces." Biopolymers 38(3):305-320 (1996).

Raytraced images are produced with POV-Ray:

Persistence of Vision Pty. Ltd. (2004).
Persistence of Vision (TM) Raytracer.
Persistence of Vision Pty. Ltd., Williamstown, Victoria, Australia.
http://www.povray.org/