VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu May 22 2008 - 05:23:24 CDT

On Thu, 22 May 2008, INPE (Ingrid Viveka Pettersson) wrote:

ingrid,

IP> I have a crystal structure which includes crystal water. Some of
IP> these crystal waters are bridging interactions between different
IP> amino acids in the protein and I would like to keep them. However,
IP> when I read the structure (a PDB file) into VMD, the water molecues
IP> are not read in, only the protein. I have look in the manulas but

the _are_ read in. you may not see them, as there only are the oxyens
and thus they are only small points instead of lines. the molecule
file readers in VMD have _no_ clue of the chemistry, and thus do
not discriminate between atoms.

IP> have not found any information about this. Is there anyone of you
IP> who has experince about this and know how to solve the problem?

create a selection for those waters and show them with a
different representation (cpk, vdw) and you should see them.

cheers,
    axel.

IP> Regards,
IP>
IP> Ingrid Pettersson
IP>
IP>
IP> ___________________________________
IP>
IP> Ingrid Pettersson
IP> Research Scientist
IP> Structure & Biophysical Chemistry
IP>
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IP> Novo Nordisk Park
IP> DK-2760 Måløv
IP> Denmark
IP> +45 4443 4506 (direct)
IP> +45 30754506 (mobile)
IP> inpe_at_novonordisk.com
IP>
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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.