From: John Stone (
Date: Wed Aug 16 2006 - 23:26:54 CDT

  If you've run MSMS manually from the command line, you cannot do much
with the resulting surface .vert and .face files by themselves.
The best way to use VMD to view MSMS surfaces is to load the PDB file
into VMD itself, and have VMD invoke MSMS for you, which retains all of
the atom attributes at each vertex, which allows VMD to color the resulting
MSMS surface by the various properties you asked about. All you need to
do is select the "MSMS" representation in VMD, and you should be in

  John Stone

On Tue, Aug 15, 2006 at 09:19:18PM +0000, Arturas Ziemys wrote:
> Hi,
> I generated MSMS surface, which is done with some modifications in 'atmtypenumbers'(required for 'pdb_to_xyzr'). I load it into VMD, but I can do nothing with it. I'm using Linux (Suse10.1).
> How can I color it according some property in atoms (e.g. beta, occupation, user, etc.) ?
> BTW, I could use VMD warpped MSMS/pdb_to_xyzr/atmtypenumbers code, if I would know how to modify some stuff inside ...
> Best
> Arturas

NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email:                 Phone: 217-244-3349
  WWW:      Fax: 217-244-6078