MSMS

Another molecular surface renderer is `MSMS', a program written by Michael Sanner of Olsen's lab at Scripps. This program is much faster than Surf, and can be a better choice depending on how it is used. See the web page http://www.scripps.edu/pub/olson-web/people/sanner/html/msms_home.html for more details. Available options include

• Which Atoms - should the surface be of the selection (0) or of the contribution of this selection to the surface of all the atoms? (1)
• Sample Density - triangle density on the surface (typical values are 1.0 for molecules with more than one thousand atoms and 3.0 for smaller molecules)
• Probe Radius - Probe radius used to construct the molecular surface
• Representation Method - The surface can optionally be drawn using lines rather than solid triangles

There is an environment variable which can affect the MSMS display option:

• MSMSSERVER - location of the MSMS binary (defaults to msms which is assumed to be in the user's path) On Windows machines, sets this as a systemwide environment variable in the environment variables window found in the system properties control panel.