From: Hui-Hsu Tsai (tsaih_at_ncifcrf.gov)
Date: Thu Dec 16 2004 - 15:44:26 CST

  John,
 
  Does the built-in ASA program include the periodic boundary
  condition in its calculation?

  Thanks.

  Gavin
  

On Thu, 16 Dec 2004, John Stone wrote:

>
> 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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