VMD

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting created by the Theoretical and Computational Biophysics Group (TCBG) at the Univesity of Illinois at Urbana-Champaign, an NIH Resource for Macromolecular Modeling and Bioinformatics.

Citation information

If you publish results obtained using VMD, please cite:

"Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38."

Additional information about citing VMD may be found at http://www.ks.uiuc.edu/Research/vmd/allversions/cite.html

Basic Usage Information

CAVE (console)
Currently no support for visualization in the VisCube though VMD is installed for use as a client. You should open your data file, make appropriate modifications (e.g. representations), and use the File/Render command to export the molecule as VRML-2. It is then best to use the vmd-vrml2-optimzer to optimize the VRML-2 encoding for greater efficiency. You can then view the molecule in the CAVE using InstantPlayer-cave.

Stereo Wall (yakko)
From the command line, run

vmd-wall