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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.

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 a communications medium takes up about half the time, and the method used to draw the triangles has not been optimized.

There are two environment variables which can affect the Surf display option:

It would be nice to have a faster though perhaps more imprecise surface rendering method. If you can suggest one, we can look into incorporating it.



Andrew Dalke
Tue May 14 16:49:45 CDT 1996