VMD-L Mailing List

From: Yongcheng Zhou (zhouyon1_at_math.msu.edu)
Date: Fri Aug 18 2006 - 15:54:13 CDT

Hi, there,

We know that there is a MSMS plugin in VMD with which one can directly
illustrate the molecular surface. However, there are still some
good reasons for users to generate MSMS surface and then show this
surface with MSMS:

1) The SURF and MSMS function in VMD read the default radii of atoms.
   These radii might be different from those used by users in their
   specific applications.

2) One can only gradually adjust the density of triangulation of MSMS in
   VMD. This will significantly increase the computational time in
   generating the surface of large molecules at large triangulation
   density.

However, when I was trying to load .face file generated with MSMS into
VMD by checking 'load data into molecule' and choose 'MSMS Surface Mesh',
it said

    Reading raw graphics failed

This is understandable because the .face file generated by MSMS does not
contain all the information of the surface. It must be used together
with .vert file. Therefore, my question is:

What is the format of 'MSMS Surface Mesh' file in VMD? and
How can we generate this file?

Many thanks,

Yongcheng