VMD-L Mailing List

From: Chris Ing (ing.chris_at_gmail.com)
Date: Thu Jan 03 2013 - 18:14:29 CST

Thank you John Stone,
 I took your advice and used a modified version of the calcDataDist
function in the contact map tool for my ligand docking IMD game.
Essentially it amounts to a few distance calculations from the residues in
the binding pocket to the ligand for each IMD time step, nothing too
high-tech.

 Next question, is it possible to change the color of a molecular
representation based on one of the VMD defined color scales? I would love
to have my ligand change color along a gradient based on the value of this
calcDataDist metric that I have defined (a number between 100-1000). The
best I have come up with this setting a molecule color to a user-defined
one like this "mol modcolor 1 0 ColorID 18" and then redefining it with a
new RGB value like: "color change rgb 18 0.9599999785423279
0.7200000286102295 0.0". The trouble is that I don't have a nicely defined
slice through RGB space off hand in order to color my ligand. Is there a
better way of doing this?

-Chris Ing
University of Toronto

On Thu, Dec 20, 2012 at 10:56 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> 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
>
> --
> NIH Center 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
>