VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 24 2002 - 10:11:10 CDT

Dear Luca,
  At present we don't have an easy way to accomplish this in VMD,
there are numerous scripting mechanisms that can be used to provide
a dynamically changing bonds representation, but we haven't made this
a built-in feature yet. We have looked at generally implementing
dynamically changing bond visualization, and there are a few gotchas
we have to work around. One idea I think might make sense would be
for us to implement a special representation just for this purpose, which
would avoid problems with having to update all of the molecule data
structures every animated timestep. This would give most of what people
want without us having to rewrite the rest of the code. Long-term, we
want to pursue a better solution, but this might be a good initial
mechanism. We'll see what we can come up with for a VMD 1.8 pre-release,
and announce when it is available... In the mean time, if you're interested
in the script-based mechanisms for accomplishing this, let us know.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Apr 24, 2002 at 03:07:32PM +0200, Luca UvA wrote:
> How can I force the drawing of a bond when two (identical) atoms are closer than a distance that I can give?
> I have a PDB input file and I would like that every frame VMD checked the distance between my atoms and drawed a bond with the above criterion: is that possible? 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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