VMD-L Mailing List

From: Mgr. Lubos Vrbka (lubos.vrbka_at_uochb.cas.cz)
Date: Wed Mar 01 2006 - 00:44:11 CST

hi,
> Just to clarify, are you asking for a script that gives you a list
> of atoms which have a non-zero solvent accessible surface area?
> In general, if you have an atom selection for which you want to retrieve
> the atom names and coordinates, you can do this:
> set sel [atomselect top "protein"]
> set namesandcoords [$sel get { name x y z }]
>
> If rather than just using "protein" as your selection critera, you wanted
> to select by solvent accessible surface area, you'd need to build a list of
> per-atom SASA values, then select those that have values greater than zero
> (or some other cutoff), and then use that list in a subsequent selection.
> That's a more sophisticated script, and you'll want to read the User's Guide
> about the "measure sasa" command.
>
maybe this script might be of some use to you... it's maybe a little too
complicated for your needs, but it could give you a good start...

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
http://www.molecular.cz/~vrbka
.....................................................

SASA All Residue Calculator 1.1
-------------------------------

REQUIREMENTS: VMD Version 1.8.3 or greater

CHANGELOG:
        1.1 fixed some wrong variable names
                
DESCRIPTION:
        Script for detailed SASA analysis. Calculates SASA for every residue
        of a given selection (e.g. protein) ad prints it out. It can be used
        to identify residues more/less exposed to the solvent. Works also
        for whole trajectories, were it calculates average SASA value.

HOW IT WORKS:
        Takes one frame after another. Splits given selection to single residues
        and calculates SASA for each of them by using
        measure sasa _radius_ _whole_sel_ -restrict _residue_
        construct.
        This procedure can be very time consuming (360 residue protein, 2000 frames
        trajectory = 7 hours on 3GHz Athlon).
        See the script itself for more information.

PROCEDURES:
        getAllResSASA - main procedure

EXAMPLE USAGE AND OUTPUT:
        usage:
        getAllResSASA "selection" probe_radius <startframe <endframe>>
        Optional startframe/endframe parameters define range of frames from
        the trajectory, that should be analyzed. If omitted, whole trajectory
        is parsed.
        
        example:
        source _sasa_res.tcl
        getAllResSASA "protein" 1.5 1 100
        This performs the analysis on frames 1 to 100 of the trajectory and
        prints average SASA values for every residue of the protein to file
        res_sasa.dat using following format
            residue resname SASA
        i.e.,
            0 GLU 195.54
            1 THR 140.93
            2 THR 66.38
            3 ALA 7.58
            4 LEU 0.51
            5 VAL 0.59
            ...
        
DOWNLOAD FILE:
        _sasa_res.tcl

AUTHOR:
        Lubos Vrbka (shnek (at) tiscali (dot) cz)