VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 08 2003 - 10:44:23 CDT

Dear Georgios,
  Can you send me a copy of one of the PDB files that gives you problems?
When you load the PDB files, do you see these atoms listed in the
Graphics->Representations window, "selections" tab, with the "name"
keyword highlighted? (i.e. click on the "name" keyword in the selections
tab, and you should be able to scroll through a list of all of the atom
names that VMD has loaded in the current molecule..)

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jul 08, 2003 at 10:39:38AM +0200, Georgios Scheiner-Bobis wrote:
> I have been using VMD for some time now and think this is a very
> good program. I am, however, facing a problem and hope by sending
> out this message for some help.
> Some of the pdb files I have been using recently have, next to the
> protein information, also the coordinates for PO4, MG2+ or water. This
> I can see by using a different structure analysis program.
> Nevertheless, when I open the same files in VMD, I do not find the
> above mentioned atoms or molecules any longer. My question is: does
> anybody know how to solve this problem?
>
> Thanks a lot,
>
>
> Georgios 

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