VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Aug 18 2006 - 16:24:55 CDT

Hi,
  I have a few suggestions which will solve your problems below.

On Fri, Aug 18, 2006 at 04:54:13PM -0400, Yongcheng Zhou wrote:
> 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.

If you need to set the radii differently, this is trivial to do using
the VMD atom selection commands, and you can set the radii to anything
you want, including ridiculous values:
  set sel [atomselect top "name CA"]
  $sel set radius 4.0
  $sel delete
or
  set sel [atomselect top "chain A"]
  $sel set radius 4.0
  $sel delete
or
  set sel [atomselect top "element Si"]
  $sel set radius 4.0
  $sel delete

If you view your structure in "VDW", you'll see the radii change as soon
as your command completes. Once this is ready, you can make your MSMS
surface as you wish.

If you want to save your custom radii, you may find it useful to save
the resulting structure into a PQR file so that you don't have to re-make
the custom radii the next time you want to view the structure in VMD.
(PQR files have radii information, whereas PDB and many other formats do not..)
You can do this with:
  $sel writepqr myfile.pqr

> 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.

This is not correct. The "apply changes automatically" button can
be de-selected, and then you can alter the triangulation density,
setting it to anything you want. You can then click "Apply" manually
when you're satisfied with your settings, and re-enable the "apply changes
automatically" button when you're done.

> 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:

You must provide BOTH the .face and .vert files, and they must be named
the same, and be contained in the same directory, .e.g.:
   foo.face and foo.vert
or
   /my/favorite/dir/foo.face and /my/favorite/dir/foo.vert

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

They are created by MSMS when you run it manually at the
command line. The format of the files is described in the
MSMS documentation as I recall.

  John Stone
  vmd_at_ks.uiuc.edu 

-- 
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: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078