VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jun 16 2003 - 18:48:56 CDT

Sanjeev,
  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". This gives VMD up to 3x speed improvement over just
rendering the triangles as-is. Basically ACTC finds neighboring triangles
and orders the vertices in a special way so that we can render them with
OpenGL with a 66% reduction in the number of vertex transformations
required. If you're curious, visit the ACTC web site here:
  http://www.plunk.org/~grantham/public/actc/index.html

Enjoy,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Jun 15, 2003 at 01:02:38AM +0530, Sanjeev B.S. wrote:
> Hello,
> I am using MSMS for computation of several parameters and VMD as
> front-end for visualization. I observed that for the same criteria of
> probe radius and density, the veritices (in 1st 3 colums in .vert file)
> are not identical to those nodes seen in mesh! I am surprised there is a
> clear. Does for triangulation VMD uses some optimization so either of
> MSMS/VMD is more accurate, or is it problem with my apporach itself?
>
> Thanks for any comments/feedback.
>
> With good day wishes,
> -Sanjeev
> 

-- 
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