VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Dec 20 2012 - 09:56:01 CST

Hi,
  Using callbacks is definitely the best way for you to trigger
your own code to perform an analysis evaluation and/or display
representation changes as you described. In regards to the best
way to actually do the analytical steps you describe, that's a much
broader question that is hard to answer without knowing precisely
what you want to do. There are many plugins that compute distances
of one kind or another, so I think that finding one that does something
similar to what you have in mind might indeed be a good starting point.
Perhaps look at how the contact map tool works for starters?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Dec 19, 2012 at 12:36:22PM -0500, Chris Ing wrote:
> I'm trying to make a more responsive game out of an Interactive MD
> simulation.
> The game might simply be a protein and ligand in a box and the objective
> of the game is to dock the ligand such that it satisfies some positional
> or energetic criteria. I believe that numerous people, including me, have
> done this simulation using interactive MD.
> The catch is that I'd really like to find a way to tell the gamer that
> they have succeeded. Ideally, the VMD representation (color) of the
> complex would gradually change the closer they got to the correct
> solution, however, I'm not sure that's possible.
> I've briefly looked at the "imdmenu1.0" plugin and in particular the
> callback whenever a new frame is received. This seems like a good starting
> point. From here I could initiate a naive distance check between the known
> final position of the ligand in the binding site and the position of the
> ligand at the current frame. Then I could update the VMD representation
> accordingly.
> Is this the best approach for real-time processing of the interactive MD
> data? Is there an similar TCL script (perhaps an existing plugin) that
> computes distances between regions of a protein that I could borrow from?
> Thanks for your time,
> -Chris Ing
> University of Toronto 

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