VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Sep 20 2004 - 16:02:12 CDT
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Hi,
I've taken a look at this and there does seem to be a bug preventing
the PDB reader plugin from handling this file correctly. The correct behavior
for VMD would be to abort loading the file because:
1) VMD doesn't presently allow multi-structure files to be loaded into
separate molecules
2) VMD requires trajectories to consist of exactly the same number of atoms
for each frame.
Neither one of these is good for your structure, so VMD should have aborted
loading it. I suspect the bug is in the PDB plugin itself, but we'll see.
Longer term, I intend to teach VMD to optionally read files like this into
separate molecules which would make more sense, but this hasn't happened
yet, so in the short term it will not allow you to read this
variant of multi-structure PDB file. I hope to address this soon however.
John Stone
vmd_at_ks.uiuc.edu
On Mon, Sep 20, 2004 at 03:39:29PM -0500, John Stone wrote:
>
> Hi,
> Can you send me an example PDB that exhibits the behavior you're
> describing? We have many such files that work fine, so it may be
> that you've got some samples that break the existing code.
>
> Thanks,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Sep 20, 2004 at 04:34:41PM -0400, Nicholson, James D Mr ARO wrote:
> > It looks like VMD 1.8.2 & 1.8.1 are not obeying the MODEL/ENDMDL cards
> > in a PDB file like they should. The first structure shows up fine, but,
> > the second structure has a crazy connectivity. PyMol & Insight handle
> > it fine.
> >
> >
> >
>
> --
> 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
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
-- 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 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
- Next message: Margaret Shun Cheung: "Re: how to make a snapshot that..."
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- In reply to: John Stone: "Re: BUG with MODEL card in PDB file"
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