VMD-L Mailing List

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Thu Aug 18 2005 - 14:24:07 CDT

You will probably get a few responses to this question. but a plugin does
exist that might help you out.

http://www.ks.uiuc.edu/Research/vmd/plugins/intersurf/

Brian

On Thu, 18 Aug 2005, paul d jones wrote:

> Hi!
>
> I am currently using cache workstation pro (by fujitsu) to look at an
> enzyme ligand complex. This particular package has a nice feature where
> it will show the surface of the active site near the ligand, without
> showing the complete enzyme surface. This is nice because it allows me
> to see if I need to place a methyl group (for instance) somewhere on the
> ligand to increase it hydrophobic interactions (as an example). The
> problem is that there is no way to export this surface to an external
> renderer for generation of publication quality images (< 300 DPI).
>
> My question is, can VMD be used to construct a similar surface from a
> PDB file? If so, could someone give me a link to a tutorial or provide a
> basic outline of how I could do this?
>
> If VMD cannot do this, could I make a feature request? :-)
>
> Thanks a bunch.
>
> Paul
> --
> =================================
> Paul D. Jones, Ph.D.
> NIH Postdoctoral Fellow
> Dept. of Entomology
> University of California, Davis
> (530) 754.8884
> =================================
>

************************************************
  Brian Bennion, Ph.D.
  Bioscience Directorate
  Lawrence Livermore National Laboratory
  P.O. Box 808, L-448 bennion1_at_llnl.gov
  7000 East Avenue phone: (925) 422-5722
  Livermore, CA 94550 fax: (925) 424-6605
************************************************