VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 28 2005 - 10:17:54 CST

You're right that the "buried" keyword is a shortcut that's hardwired
to match various residues, and it doesn't take into account the actual
structure you've got loaded. Another method that likely has more merit,
would be to calculate the solvent accessible surface area, and use that
as your measure of "buried" or "surface" etc. You could run a script setting
the user field for each residue with its SASA, and then use a selection like
"user > 1.0" or something like that as a heuristic to determine which residues
are exposed and which are not. One could even do this for all of the atoms
invidually, but it would take a while to calculate. Try using the
"user > 1.0" with a script like this one and let me know if that helps.

##
## 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 to color by SASA
##
mol modcolor 0 [molinfo top] User
mol colupdate 0 [molinfo top] 1
mol scaleminmax [molinfo top] 0 auto

  

On Mon, Feb 28, 2005 at 02:42:52PM +0100, Mgr. Lubos Vrbka wrote:
> hi all,
>
> i guess this must have been asked before, but i couldn't find any
> solution to my problem. i want to get list of all residues defining a
> surface of my protein. i know i can do "surface" or "protein and not
> buried" selection, but this doesn't seem to work ok. from what i've seen
> in the documentation, "buried" is defined as
> residues named ALA LEU VAL ILE PHE CYS MET TRP
> so if any of the other residues is "buried" inside the protein, it
> doesn't work correctly. does this mean, that some kind of assumption
> "hydrophobic = buried" is made?
>
> is there any way how to get the desired information? will i'll have to
> somehow parse surf/msms outputs?
>
> thank you for help. best regards,
> lubos
>
> --
> .....................................................
> Mgr. Lubos Vrbka
>
> Center for Biomolecules and Complex Molecular Systems
> Institute of Organic Chemistry and Biochemistry
> Academy of Sciences of the Czech Republic
> Prague, Czech Republic
> ..................................................... 

-- 
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