VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jun 06 2006 - 12:59:57 CDT

Sam,
  MSMS and Surf don't determine which atoms are on the surface, rather,
they determine the polygonal mesh that defines the solvent surface for a
group of atoms. This is done without explicitly calculating the sort of
information you're looking for. The best suggestion I have for this is
to write a script and use the "measure sasa" command to calculate the
per-atom solvent accessible surface area values, assign the resulting
value to the "user" or "beta" fields, and then use the solvent accessible
surface area to select the atoms you're interested in. Beware that this
method can also catch atoms that line internal cavities however.
I believe I posted some scripts for this purpose on VMD-L previously.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jun 06, 2006 at 01:13:16PM +0200, Sam Ansari wrote:
> Dear All,
>
> searching in the archive didn't give me a satisfying solution to my
> problem.
> I am trying to retrieve amino acids that lay on the surface of
> proteins. There is the atom selection keyword 'surface' which seems
> to only mark/unmark certain types of amino acids that most-likely
> appear on the surface/core of proteins. Here, I am rather interested
> in a method as it is used in the representation styles 'MSMS' or 'Surf'.
> I wonder if there is a way to access the temporally saved lists of
> atoms that were found by MSMS or Surf.
>
> Any input is appreciated.
>
>
>
> Sam 

-- 
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