VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Nov 06 2006 - 09:30:58 CST

On Mon, 6 Nov 2006, Javaria Ahmed wrote:

JA> Is it possible to delete selected atoms from a molecule in VMD. Like, I can
JA> label an individual atom, can i delete it as well?

vmd in its current implementation assumes that the number of atoms
in a molecule does not change (please keep in mind, that vmd was
conceived as a molecule _viewer_).

JA> And able to save the modified pdb or psf file as well.

you can create a selection containing only the subset of atoms that
you are interested in and save that. however, if you try to save
a .psf file this way, it _will_ be incomplete, as the .psf writer
only writes the new bond-lists and keeps the rest empty.
deleting atoms will require at least a new computation of the
exclusion lists, but most likely also a retyping of atoms, which
needs you to run psfgen (e.g. via autopsf).

cheers,
   axel.

JA>
JA> Regards,
JA>
JA> Javaria
JA> 

-- 
=======================================================================
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.