VMD-L Mailing List

From: Luis Gracia (lug2002_at_med.cornell.edu)
Date: Mon May 15 2006 - 17:53:28 CDT

Hi,

This might work. Load an additional structure (like a pdb file with just
one frame) and apply the result from measure avpos to that structure.

For example, if mol 0 contains 30 frames, get is't avpos. Then change
the coordinates to mol 1 (has only one frame), and write the pdb file:

set ave [measure avpos [atomselect 0 "all"]]
set sel [atomselect 1 "all"]
$sel set {x y z} $ave
$sel writepdb "average.pdb"

Best,

Luis

Luis Gracia, PhD
Department of Physiology & Biophysics
Weill Medical College of Cornell University
1300 York Avenue, Box 75
New York, NY 10021

Tel: (212) 746-6375
Fax: (212) 746-8690
lug2002_at_med.cornell.edu

ziemys_at_ecr6.ohio-state.edu said the following on 05/15/06 15:43:
> Hi,
>
> Is a way to use 'measure avpos' to use for average structure creation ?
>
> I tried to the product of 'measure avpos' to write to PDB file without success - it seems that it prodices just the list of averaged {x y z} for particles.
>
>
> Arturas
>
>
>