VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Feb 28 2006 - 17:35:00 CST

Hi,
  Just to clarify, are you asking for a script that gives you a list
of atoms which have a non-zero solvent accessible surface area?
In general, if you have an atom selection for which you want to retrieve
the atom names and coordinates, you can do this:
  set sel [atomselect top "protein"]
  set namesandcoords [$sel get { name x y z }]

If rather than just using "protein" as your selection critera, you wanted
to select by solvent accessible surface area, you'd need to build a list of
per-atom SASA values, then select those that have values greater than zero
(or some other cutoff), and then use that list in a subsequent selection.
That's a more sophisticated script, and you'll want to read the User's Guide
about the "measure sasa" command.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Feb 28, 2006 at 11:22:13PM +0000, kovzany_at_go.com wrote:
> Dear All,
>
> Is there an easy way in VMD to get a set of atoms (with their names
> and coordinates) representing VdW or solvent accessible surface of a
> given molecule?
>
> thanks,
>
> PK 

-- 
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