VMD-L Mailing List

From: Adrian Kaats (akaats_at_yahoo.ca)
Date: Tue Mar 25 2008 - 07:41:38 CDT

Hi John,
 
 Yup, I think I may have brought this up in the past as well.

Anyway, that's exactly what I'm doing: writing a script to split a PDB file by MODEL, cobble each separate model back together with the primary and secondary structure, and connect info, and load 'em up separately (I'm finally getting acquainted with regexp - wish I'd done it before :).

I'll send the script in when/if its working nicely.

Best Regards,

Adrian

John Stone <johns_at_ks.uiuc.edu> wrote:
Hi,
  VMD can't presently allow structures with differing atom counts to
be loaded into the same molecule, and unfortunately, our current PDB
reader plugin always attempts to load multi-model structures into the
same molecule as a form of trajectory. It's been on the todo list for
a while to change this behavior, but it isn't done yet. Thanks for
you comments. For now you could use a script to split the file into
separate pieces and load them into separate molecules in VMD.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Mar 21, 2008 at 10:19:35AM -0400, Adrian Kaats wrote:
> Hi,
>
> Is it possible to get VMD to load a PDB file with different numbers of atoms in its models (records between MODEL and ENDMDL). If I understand correctly, that this isn't done automatically is due to a restriction in the PDB Plugin.
>
> Is there a nice way around this? That is, can I get a PDB consisting of several models with different atom numbers (e.g. the biological unit of OmpF - PDB Id 2omf) to be loaded with all of the models in separate frames?
>
> If not, in a future version, would it be possible to have this implemented as an option when loading a PDB file?
>
> Thanks,
>
> Adrian Kaats
> Ph.D. Candidate
> Department of Biomedical Engineering
> McGill University
>
>
>
>
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078
       
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