VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jun 17 2003 - 12:22:39 CDT

Sanjeev,
  We don't alter the vertices themselves, we take exactly what
MSMS returns and use them in VMD. As you say, ACTC doesn't actually
modify the vertices, it only re-orders the triangles and vertices to
facilitate rendering them in fans and strips. How are you comparing
the vertices in VMD with the ones you get when you run MSMS manually?
Most likely you are getting the transformed coordinates from VMD if
you are using one of the "Render" interfaces to export geometry.
Also, VMD doesn't run MSMS via the file-based interface, we communicate
with MSMS via sockets, so MSMS's behavior may be slightly different
since the features are different between the file-based interface
and the socket interfaces in MSMS. If you tell me how you are attempting
to compare the vertices I can presumably help you get what you want.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jun 17, 2003 at 10:54:00PM +0530, Sanjeev B.S. wrote:
> > Assuming you're using one of the versions of VMD that has ACTC
> built-in, then yes, VMD does post-processing of the triangulated geometry
> returned by MSMS so that instead of a random list of triangles, we get
> what is called a "triangle strip".
>
> +++ Hi! Thanks for the response. Yes, I am indeed using VMD 1.8b6. But
> what I saw was that the points that MSMS generated were not the points on
> the surface. From what I understood of ACTC, it facilitates with
> triangulating for a given set of points. But my problem is that I see the
> points themselves being shifted, and MSMS(VMD) points seem to be of lower
> probe radius! Does this happen or something went wrong this end?
>
> With good day wishes,
> -Sanjeev 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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