VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Sep 06 2006 - 11:46:23 CDT

On 9/6/06, pinisetty dinesh <pinisettydinesh_at_yahoo.com> wrote:
> Hi,
> I was wondering if its possible in VMD, to slice
> up a snapshot after loading .gro file. I want to store
> all the atom co-ordinates after slicing it up. Can

what do you mean by 'slicing up'?
picking a subset of atoms and then save only those?
this can be done with atomselection from the vmd console.

say you want to save all atoms with an x-value larger than 1.0:

set sel [atomselect top {x > 1.0}]
$sel writepdb slice1.pdb

of course this works for any kind of subset of atoms that
can be described by the atom selection language.

cheers,
  axel.

> anyone help me out how to do it, if its possible with
> VMD.
> Any suggestions would be greatly appreciated.
> Sincerely,
> Dinesh.
>
>
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-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.