VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jan 26 2012 - 12:19:32 CST

Hi,
  Yes, this can be done in VMD with various scripting.
It's not clear from your email what type of data you're trying to
plot, nor whether you want it plotted within the VMD graphics window
or in an independent window? Both are possible, but the approaches
are quite different. If you want to draw things into the VMD graphics
window (e.g. superimposed over the molecule) then you would use the VMD
"draw" or "graphics" commands to do this. If you want to plot things to
a graph in a seperate window, you could either use the existing multiplot
plugin (for static graph data) or write a small script to do something
customized for dynamically changing data in a separate Tcl/Tk window that
is synced with the active trajectory frame in VMD. If you can tell us
more specifically what you're trying to plot and where you want the plot
to show up, we can provide more tips.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jan 26, 2012 at 10:40:08AM -0700, J. Nathan Scott wrote:
> Hello all,
>
> I've tried some Googling and looking through the plugins and manual, but
> I'm guessing the visualization feature I'm looking for has a name that I
> simply don't know. What I would like to do is superimpose over a
> trajectory a white box where some externally sourced data is plotted, with
> a marker of some sort that keeps time with the dynamics of the trajectory.
>
> I've seen this done in talks before (though I *don't* recall if it was VMD
> being used) and finally have a good reason to try this sort of
> visualization with some of my own data. For instance, we calculate
> excitation energies for biological chromophores, and it would be quite
> helpful to watch the dynamics and see exactly what is happening to the
> excitation energy as the local environment and/or chromophore structure
> changes.
>
> Can anyone tell me if such a feature is available in VMD, either natively
> or through a plugin, or if not perhaps another visualization package that
> has this ability?
>
> My sincere thanks for any help you can provide!
>
> --
> ----------
> J. Nathan Scott, Ph.D.
> Postdoctoral Fellow
> Department of Chemistry and Biochemistry
> Montana State University 

-- 
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