VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 12 2010 - 16:43:46 CDT

If you just wanted to display atom-atom distances, this is a
built-in feature. If you want to display time-varying
residue-residue distances, you'll have to write a short bit of
script. It's really not that hard, and it's worth your time to
learn how to do basic scripts like this. Effectively, the script
would contain a single routine that deletes any existing label,
then draws a new one by computing the center of mass or some other
weighting for each of the two residues, and then draws a line connecting
the two COMs, and a text label with the value. To compute the COMs,
you would create an atom selection for the two residues, then use
a variant of the command "measure center weight mass" ... to compute
the cartesian coordinates for each residue. From there, you'd draw
the line and the text. I think you'll find several of the example
scripts in Axel's CPMD/VMD tutorial useful to learn from:
  http://sites.google.com/site/akohlmey/redirect

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Aug 12, 2010 at 04:56:18PM -0400, Ian Stokes-Rees wrote:
> I have a 2000 frame animation. I'd like to add a representation which
> is a distance line between two residues -- the standard sort of thing
> you get on any engineering drawing:
>
> | 5.5 A |
> res_y ---------------------------- res_y
> | |
>
> This seems like a standard sort of thing to do, but I can't see a way to
> easily do this without learning a lot of VMD scripting details to add
> this on a frame by frame basis (I'm sure if I knew Tcl and VMD, this
> would be almost trivially easy, but acquiring that knowledge will likely
> take me many hours to days of trial and error).
>
> Also, I would love to have an animated contact map of two domains in an
> MD simulation. Is such a thing possible?
>
> Thanks,
>
> 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