VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jul 27 2005 - 10:30:31 CDT

Hi,
  I've attached a simple script that calculates the per-residue
SASA for the selected molecule. You should be able to adapt this
to calculate only the SASA for the residue of interest, and to
the atomselect frame command to select the timestep of interest,
and write out the SASA value for the residue(s) of interest to your
ASCII file. See the script below:

  John Stone
  vmd_at_ks.uiuc.edu

##
## Example script that sets the "User" data field with SASA values
##

##
## Get list of residues (use 'residue' and not 'resid' so we don't get
## duplicate residues from unusual PDB files..)
##
set allsel [atomselect top all]
set residlist [lsort -unique [$allsel get residue]]

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

##
## change the "color by" and "trajectory" tab settings to color by SASA
##
mol modcolor 0 [molinfo top] User
mol colupdate 0 [molinfo top] 1
mol scaleminmax [molinfo top] 0 auto

On Wed, Jul 27, 2005 at 02:58:45PM +0200, Andrea Carotti wrote:
> Hi all,
> I need to have the value of the SASA of a single residue in a protein
> trajectory file stored in an ascii file.
> Is it possible to make with vmd?
> Someone could suggest me the simplest and fastest way to solve my problem?
> Thanks a lot in advance
> Andrea
>
> ------------
> Andrea Carotti
> Dip. Farmaco-chimico (Università di Bari)
> via E. Orabona, 4 ## CAP 70124 ## BARI (Italy)
> web: http://www.farmchim.uniba.it/samba/modeling.htm
> phone: (+39) 080 5442551 ## fax: (+39) 080 5442230 

-- 
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