VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Nov 05 2002 - 10:27:26 CST

Tom,
  At present VMD does not interface to the other features of
MSMS. You could certainly write a Tcl script which could
drive MSMS from within VMD using VMD's atom selections much
like one does for the surface calculation use of MSMS.
If you can do the proposed calculation running MSMS by hand,
then my suggestion would be to drive MSMS with Tcl scripts
from within VMD.

If you save the cavity surfaces MSMS calculates, you could
render them all, and though they wouldn't be a proper union or
intersection it might still be useful to be able to see them.
The major problem with doing constructive solid geometry with
this sort of data is that you can't have any cracks in the
surface mesh. Once you get the cavity surfaces into VMD, you
could export a POV-Ray scene, and it might be possible for
you to get POV-Ray to do CSG unions and intersections. If
you have any cracks in the surface however, you'd get an
incorrect looking image at the places where the cracks are.

For now, I'd recommend controlling MSMS with a Tcl script, and
reading the triangulated geometry back in and using draw commands on it.
We could probably write an "MSMS" file reader plugin that could read
the triangulated geometry much more efficiently, which would make it
a lot easier to do this sort of thing over a trajectory etc.

Once some useful Tcl scripts have been built up, it may be worth
building their functionality more tightly into VMD, or turning them
into a VMD extension.

  John Stone
  vmd_at_ks.uiuc.edu

> Dear VMD,
>
> Is there a way to run MSMS from within vmd with different command line
> options?
>
> In particular I want to run a trajectory thru vmd and calculate
> volumes/areas of the trajectory for each snapshot
> looking for cavities within the system as I animate it.
>
> Part 1) I'm not worried about displaying the surfaces, just finding
> cavity volumes.
> Part 2) If I save all of the cavity surfaces, is there someway to form a
> "union" and/or "interesection" of the surfaces
> in order to see what the average cavity size is?
> NOTE: This can be applied to a single water molecule during the
> course of a trajectory to find it's "diffusion volume".
> This might be a nice trick for showing the water channels that
> ya'll
> found in the membrane pores.
>
> What's the best way to do this?
>
> Thanks,
> TOm
>
>
>
> --
> -----------------------------------------
> Thomas C. Bishop, Ph.D.
> Joint Faculty Appointments Program Professor
> Center for Bioenvironmental Research
> -----------------------------------------
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> -----------------------------------------
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> bishop_at_tulane.edu
> -----------------------------------------
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> -----------------------------------------
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> tbishop_at_xula.edu
> ----------------------------------------- 

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