VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Mar 19 2007 - 11:29:09 CDT

Adrian,
  I tested this out and I see what the problem is. The current version
of the PDB plugin for VMD will not read the other models in the 2OMF file
as trajectory frames because they have a differing number of atoms.
You could simply split this file into three files at the "MODEL" keywords
within the file, and then load the individual pieces into VMD. Support
for files of this type is already on the TODO list for the PDB reader plugin,
but I haven't had time to start on it yet. The same issue applies to one
or two other file formats which can embed multiple strutures which cannot
be treated as independent trajectory frames. I need to make some small
changes to the VMD plugin API to better support these formats.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Mar 15, 2007 at 07:58:17PM -0400, Adrian Kaats wrote:
> Hi all,
>
> I am once again having trouble with viewing the 'assumed' biological unit of OmpF (pdb 2OMF). I have attached the biological unit downloaded from RCSB. When I load the molecule, only one subunit is recognized (frames = 1). I can't figure out (from inspecting the PDB file) why this is the case.
>
> Any ideas?
>
> Thanks,
>
> Adrian
>
> ------
> Graduate Student
> Biomedical Engineering
> McGill University
>
>
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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