VMD-L Mailing List

From: Vincent Wolowski (vwolowski_at_gmail.com)
Date: Thu Nov 29 2007 - 03:30:37 CST

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?

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
>