VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 10 2003 - 15:42:33 CDT

Hi,
  Surf is actually a standalone program that you can run
separately from VMD. The "Surf" representation in VMD just
handles writing input files and reading the output from Surf
and then generates geometry from the Surf output.

You can run Surf by hand from the command line if you want,
that would give you 100% control over what it does. When VMD
is installed correctly, the Surf binary can be run from its
installation directory, i.e.: /usr/local/lib/vmd/surf_SOLARIS2_64

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Sep 10, 2003 at 01:24:15PM -0500, suzie.k.hight.1 wrote:
> Hello,
> I am relatively new to VMD and have a (hopefully) simple question:
> Is there any way to see and print out numerical output from the SURF
> calculation that generates the SURF representation?
> I would like to have a list of the solvent accessible surface area for
> each residue in my protein, and be able to correlate this with the visual
> representation.
> Thanks!
> Suzie 

-- 
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              
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