VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 13 2005 - 09:52:30 CDT

Matthew,
  In order to get the SASA for individual unit, in the context of the
rest of the structure, you'll need to use the "-restrict" option.
Here's an example that calculates the per-residue SASA for the top
molecule and colors the molecule by the resulting per-residue values,
using "-restrict" to limit the area calculation to just the residue
I'm measuring:

##
## 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 Fri, May 13, 2005 at 02:33:36PM +0000, Matthew Wilce wrote:
> Dear VMDers,
> I am using measure sasa to calculate buried surface area. To do this I am calculating the SA of two chains separately and together and the calculating the difference
> set saA [measure sasa 1.4 $chainA]
> set saB [measure sasa 1.4 $chainB]
> set asAB [measure sasa 1.4 $chainAB]
> set BuriedSurfaceArea [expr $saA + $saB - $saAB]
>
> Does this look right?
>
> When I do this I get some buried surface area even for chains that are not with 4 angstroms of each other???
>
> I have used -samples 100
>
> I have a large number of these measurement I wound rather not go through each one and draw points to check what is happening and then judiciously use -restrict $sel
>
> Is there a better way of doing this? I am using sasa inappropriately?
>
> Any help appreciated.
>
> thanks
>
> Matt 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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