VMD-L Mailing List

From: Ian Stokes-Rees (ijstokes_at_hkl.hms.harvard.edu)
Date: Fri Aug 13 2010 - 16:11:29 CDT

On 8/12/10 5:33 PM, John Stone wrote:
> 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.

I had what I think is a beginner error -- I didn't include "protein and
..." in the selections, so I was pulling in water molecules as well
(AFAICT). Having added "protein and ..." to the selections, the default
zoom ranges were weired, but once I adjusted the zoom, I got a
reasonably nice contact map.

My next problem was that highlighting a region, which I assumed would
act as a residue selection mechanism, highlighted structures on one axis
in the contact map but not the other, and in the VMD window only the
*un-highlighted* axis residues were identified along the contact map
surface.

It would still be brilliant to get an animation of the contact map over
the course of an MD simulation.

Ian