From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Dec 16 2004 - 13:55:00 CST

Vani,
  Still catching up on email after being out of town last week...
The 'measure sasa' command uses the atom radii VMD gets from either
it's built-in radii assignment heuristic (which only really covers 5
atom names) when no other radii are provided, or from the original
structure files. You can override the atom radii by assigning them with
the appropriate '$sel set radius' atomselect subcommands. Let us know
if you need help assigning your own radii.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Dec 09, 2004 at 08:20:37AM -0800, Vani Krishna wrote:
>
> John:
> Thanks for the info. I have downloaded the new
> version. Just a quick question, what definition is
> used for van der Waal's radii to 'measure sasa'.? I
> was looking at some information and there were couple
> of options: radii by Lee & richards; Radii by Chothia.
>
> Thanks
> VAni
>
> --- John Stone <johns_at_ks.uiuc.edu> wrote:
>
> >
> > You can try the new "measure sasa" command found in
> > the test
> > version of VMD 1.8.3 available here:
> > http://www.ks.uiuc.edu/Research/vmd/alpha
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >
> > On Wed, Dec 08, 2004 at 04:07:55PM -0800, Vani
> > Krishna wrote:
> > >
> > > Hello:
> > >
> > > Is there a script/method to calculate the solvent
> > > accessable surface area in VMD? Any helpful
> > > suggestions would be appreciated
> > >
> > > Thanks
> > > Vani
> > >
> > >
> > >
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>
>
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-- 
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