VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jul 03 2003 - 14:37:27 CDT

Dear VMD-L,
  I wanted to summarize the final result on this. It should have
been obvious, but its easy to forget these things sometimes:
  VMD and MSMS have to "guess" atom radii when they are given
PDB files, since PDB files don't contain this type of information.
Sanjeev noticed that he was getting slightly different surfaces from
VMD than he got from MSMS when he ran it manually. It turns out that
VMD and MSMS make slightly different guesses for atom radii when they
are not provided this information explicitly. This is why he got different
results from the surface calculations when using MSMS from within VMD
versus running it manually. If your atom radii are important to you,
make sure you use PSF files or another structure file format which
provides VMD with the actual atom radii so it doesn't have to guess
based on the string names of the atoms.

Thanks,
  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
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