VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 28 2005 - 12:12:13 CST

Justin,
  Yeah, the last one I sent uses "residue" rather than "resid" as I
tested on a different structure that had duplicated resid values just
as you mention. If you have any other suggestions for improving it,
let me know.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Feb 28, 2005 at 09:41:47AM -0800, Justin Gullingsrud wrote:
> Nice script! I'd recommend, though, that you select by residue rather
> than resid, in case there are multiple chains with identical resids
> (as is common in pdb files).
>
> Justin
>
>
> On Mon, 28 Feb 2005 10:13:25 -0600, John Stone <johns_at_ks.uiuc.edu> wrote:
> > 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
> >
>
>
> --
> The spirit of Plato dies hard. We have been unable to escape the
> philosophical tradition that what we can see and measure in the world
> is merely the superficial and imperfect representation of an
> underlying reality.
> -- S.J. Gould, "The Mismeasure of Man" 

-- 
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