VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 12 2010 - 16:33:23 CDT

What happens if you click "fit all" or "every residue"? I'm wondering
if your scaling value of 0.04 is creating a problem with that plugin.
I'm forwarding your note to the Barry Isralewitz, as he's the author
of the contact map plugin and may have other comments.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Aug 12, 2010 at 05:17:12PM -0400, Ian Stokes-Rees wrote:
> The data I'm using is coming from a Maestro CMS file. I am comparing the
> distances between two the residues of two domains. What is going wrong
> with the contact map rendering in this image?
>
> http://dl.dropbox.com/u/1561496/shared/VMD-ContactMap.png
>
> The vertical axis labels don't correspond to the data, and when I click on
> the dark spots, the residues that are highlighted in VMD don't make sense
> as contact spots.
>
> TIA,
>
> Ian
>
> --
> Ian Stokes-Rees, PhD W: http://hkl.hms.harvard.edu
> ijstokes_at_hkl.hms.harvard.edu T: +1 617 432-5608 x75
> NEBioGrid, Harvard Medical School C: +1 617 331-5993 

-- 
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