Surf

This option uses the molecular surface solver written by Amitabh Varshney when he was at the University of North Carolina. When this option is used, the radii and coordinates are written to a temporary file and the 'surf' executable is run with the probe radius as a parameter. When finished, the output is written to another temporary file which is then read by VMD and colored and displayed. The value of the probe radius is controlled by the sphere radius, and this is identical to the probe size in Å.

• Probe - Probe radius used to construct the molecular surface
• Wireframe - The surface can optionally be drawn using lines rather than solid triangles

This surface is rather slow in both generation and display for systems over several hundred atoms. The SURF calculation is quite exact and will show complete detail even when it isn't needed. The use of disk space as an interprocess communications medium takes up about half of the run time.

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

• SURF_BIN - location of the SURF binary (defaults to SURF_$ARCH as defined in the vmd startup script)

A helpful trick when constructing surfaces is to use the ``Apply Changes Automatically'' toggle button on the graphics form wisely. That is, since surfaces often take a long time to build, changing viewing parameters such as the probe radius can cause long delays. By default, each time you hit the probe radius button, VMD rebuilds the surface. If you want to reduce or enlarge the probe radius by several increments, then you would end up rebuilding the surface multiple times. By toggling the afore-mentioned button, you can force VMD to update on your command only. This trick is sometimes helpful with other representations as well.

For a much faster but possibly less precise surface rendering method, see the description of MSMS later in this document.