From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 28 2005 - 10:13:25 CST

Francis,
  Here's a script that colors all of the residues in a molecule
by their solvent accessible surface area. Let me know if this
is helpful.

##
## Example script that sets the "User" data field with SASA values
##
mol delete all
mol addfile 1ap9

##
## Get list of residues
##
set allsel [atomselect top all]
set residlist [lsort -unique [$allsel get resid]]

##
## Make an atom selection, set the User field with the SASA value for
## the selected atom
##
foreach r $residlist {
  set sel [atomselect top "resid $r"]
  set rsasa [measure sasa 1.4 $allsel -restrict $sel]
  $sel set user $rsasa
  $sel delete
  puts "resdidue $r, sasa: $rsasa"
}

##
## change the "color by" and "trajectory" tab settings so that
## the new color values, and start it animating...
##
mol modcolor 0 [molinfo top] User
mol colupdate 0 [molinfo top] 1
mol scaleminmax [molinfo top] 0 auto

On Thu, Feb 17, 2005 at 04:42:44PM -0600, John Stone wrote:
>
> Hi,
> I'm sure you could code up some Tcl script that used the
> "measure sasa" command with the 'restrict' flag to query the
> SASA for each residue, one by one. Any that are non-zero are
> then contributors, so that should be pretty easy to crunch.
> Give that a try and let us know if that works well enough for
> your purposes. I don't know how fast it'll run, but it's a good
> first step to try anyway.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Feb 17, 2005 at 05:33:15PM -0500, Francis Reyes wrote:
> > I'm looking for leads to determine the residues which constitute the
> > solvent accessible surface area . Any ideas would be appreciated.
> >
> >
> > ------------------------------------------------------------------
> > Francis E. Reyes
> > Department of Chemistry, Pennsylvania State University
> > 104 Chemistry Research Building
> > Box 215
> > University Park, PA 16802
> >
> > ruckerz(at)psu.edu
> > ------------------------------------------------------------------
>
> --
> 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

-- 
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