VMD is used mainly for displaying molecular structures. Think of it as a fancy version of Rasmol.
Molecules may be drawn as lines, bonds, CPK, licorice, VDW spheres, ribbons, tubes, surface, secondary structure, cartoons, etc. and colored by atom, residue, segment, or molecule as well as by mass, charge, occupancy, position, etc. By using VMD's powerful atom selection language, multiple molecular representations may be applied to arbitrary groups of atoms simultaneously.
Image Output Format
Additional display objects allow VMD to write input files for the popular rendering packages Raster3D, Rayshade, POV-Ray and Radiance to produce photorealistic images suitable for film recorders, etc. VMD can also read and display Raster3D input scripts, postscript, and VRML.
How do I run it?
VMD runs on the SGI computers, loop, turn, coil.
You can access VMD by logging in and typing
vmd
For more information on VMD, visit the VMD Home Page.