VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Jun 07 2007 - 08:29:33 CDT

On Thu, 7 Jun 2007, Lambert van Eijck wrote:

LvE> Hi,

hi lambert!

LvE> I installed VMD 1.8.6 (linux) and I don't see my molecule when reading a
LvE> trajectory. The XYZ arrow shows up and when I do the same for a pdb file
LvE> it *does* show up. Even the example dcd file from the 'proteins' directory
LvE> is not shown.
LvE>
LvE> I get no error messages and the n.o. atoms and frames is correctly
LvE> displayed.

can you please tell us exactly the sequence of commands that
you were executing, so that we can try to reproduce this.
from your desription so far, one can only guess...

please note, that for VMD to show something reasonable, it needs
to know the 'structure' of your molecule (which atoms types, residues
etc). many trajectory file formats do not contain this information,
but only the coordinate data, one usually first loads a matching
.psf or equivalent file (.pdb and .xyz do also work, if you delete
the frames afterwards) and _then_ the .dcd/.trr/.xtc/.trj file.

LvE> I've installed VMD (compiled version) on an intel and amd machine, but
LvE> both show this problem.

LvE> Because the XYZ axes show up, I doubt whether this is a opelgl
LvE> problem.

agreed.

LvE>
LvE> Can anyone help me on this?

we can try.

cheers,
   axel.

LvE>
LvE> best regards,
LvE>
LvE> Lambert
LvE>
LvE> 

-- 
=======================================================================
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
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If you make something idiot-proof, the universe creates a better idiot.