VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 22 2005 - 11:05:33 CDT

Paul,
  In addition to the Intersurf plugin that someone else mentioned, you
can use the "within" atom selection in combination with "Surf" or "MSMS"
(requires MSMS be downloaded and installed of course) to display only the
portion of the surface near the ligand of interest. The use of the atom
selection language is described in detail in the VMD User's Guide.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Aug 18, 2005 at 08:54:31AM -0400, 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
> ================================= 

-- 
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