VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Nov 29 2007 - 04:08:08 CST

On Nov 29, 2007 4:30 AM, Vincent Wolowski <vwolowski_at_gmail.com> wrote:
> Dear John,
>
> thank you very much for your answer!
> Xavier Cavin suggested to me that I could possibly use the Intersurf
> TCL script to get the information about the interface residues.
> Is there any documentation/example that could show me the way for this?

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

axel.

>
> Best regards,
> Vincent
>
>
>
> On Nov 27, 2007 8:53 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> > Vincent,
> > To my knowledge there isn't any convenient interface into the logic
> > of Intersurf that would provide the means for this. You could probably
> > also use the Delaunay triangulation that Intersurf calculates in order to
> > compute both of these pieces of information however. The surface returned
> > by Intersurf could presumably be used to calculate an area, but this may
> > or may not be what you're looking for. I'd suggest starting with the Delaunay
> > triangulation calculations and go from there, unless someone knows of an
> > existing code that already does all of this.
> >
> > Cheers,
> > John Stone
> > johns_at_ks.uiuc.edu
> >
> >
> > On Tue, Nov 27, 2007 at 08:34:40PM +0100, Vincent Wolowski wrote:
> > > Hello,
> > >
> > > is it possible to use Intersurf to determine the interface residues
> > > (for example as with PDBSum)?
> > > Can Intersurf give the boundary size of the interface?
> > > I would be very thankful for a comment.
> > >
> > > Best regards,
> > > Vincent
> >
> > --
> > 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
> >
>
> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.