VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 22 2009 - 14:14:01 CDT

Hi,
  You might find this script interesting to look at:

##
## 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

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Apr 19, 2009 at 07:01:49AM -0700, zizi moradi wrote:
> Dear All,
>  
> I like to know,is there any script  to calculate the Solvent Accessible Surface areas for non polar and polar part of a protein or Nucleic Acid in VMD?
>  
> Thanks,
>  
> Zizi
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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