VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Feb 05 2007 - 12:09:15 CST

On Sun, 4 Feb 2007 wolfinbm_at_uci.edu wrote:

MW> Hello
MW> I am trying to save the positions of different PET molecules as I load
MW> them up and drag them around. If I attempt to save a structure something
MW> like this:
MW>
MW> (PET=Polyethylene Terephthalate molecule)
MW>
MW> PET PET PET PET
MW> PET PET PET PET
MW>
MW> as *.vmd

matt,

please keep in mind that a 'saved state' .vmd file only contains
the description of the visualization and _not_ the coordinates.
so if you do any manipulation you have to also save the coordinates
(e.g. as described by cesar) and then combine the individual files
into one large file and operate on that file.

MW>
MW> I end up with garbage when I reload, i.e. 8 molecules with all their atoms
MW> in the same positions:
MW>
MW> PET <x8 in exact same position>
MW>
MW> I also can't find any other save function that doesn't involve saving just
MW> the information about a single molecule (it seems kind of ridiculous to
MW> have a coordinate file for what could be thousands of PET molecules in the
MW> membrane).

especially for large array the scripted translation/rotation of
an atom selection has a lot of appeal.

cheers,
   axel.

MW>
MW> Thanks for any help
MW> Matt Wolfinbarger
MW> 

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