VMD-L Mailing List

From: J. Nathan Scott (scottjn_at_chemistry.montana.edu)
Date: Thu Jan 26 2012 - 13:07:28 CST

Hi John,

To be honest I don't suppose it matters all that much to me if the plot is
in the VMD display window or in another window, as long as both are visible
at the same time on the desktop screen. The key feature that I'm looking
for, that I've seen in presentations by others, is some sort of time marker
(vertical line, arrow, etc.) that keeps time with the trajectory. I'd like
to be able to drag the VMD time slider back and forth and have the plot
window marker track those movements.

All of the data I'm imagining visualizing this way are just reals, one per
frame, that I've generated by processing the individual trajectory frames
in some fashion. I was thinking a static graph window would be fine, most
of the trajectories I'm working with are fairly short (~5ns) with 5001 1 ps
frames so showing the entire time trajectory of the plotted variable would
not be too crowded I think. I suppose axis limit controls could be useful
(i.e. show only frames 2000 to 3000 in the graph window).

Like I said though, it's the moving marker that keeps time with the
trajectory that I think would be incredibly useful for the analysis I'm
currently doing. As it is now when I see a dynamic event in the trajectory
and want to examine concurrent changes in some calculated quantity
(excitation energy of a chromophore, for instance, or oscillator strength
of a transition), I have to stop, identify the frame number, find that
value on the x-axis of some plot, and then look at what is happening in y.

I hope I'm making sense here, and I'd be extremely grateful for any further
advice you (or anyone else out there) could offer.

Best Wishes,
-Nathan

On Thu, Jan 26, 2012 at 11:19 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> 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
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
> 

-- 
----------
J. Nathan Scott, Ph.D.
Postdoctoral Fellow
Department of Chemistry and Biochemistry
Montana State University