VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 17 2014 - 10:40:21 CST

Boris,
  Generating a more informative error message in this particular case
is trickier than you might guess. The code that is generating the error
doesn't know what the exact cause of the mismatching atom count is.
It cannot tell the difference between a file format that includes both
structure and trajectory, or the case where there is an existing structure
loaded, and you're merely trying to add trajectory frames to it (your case,
although it seems this was not your actual intent). I will make the error
message more verbose so as to suggest the most likely causes more clearly
in the future.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Feb 11, 2014 at 05:15:13PM -0500, Boris Steipe wrote:
> Sure. There is nothing in the entire error that refers to the previously loaded molecule. Since I thought to be loading a new molecule, while VMD was still working on the old molecule, the following tweak to the error message would have made the source of the problem clear:
>
> ERROR) Error reading optional structure information for 0:3zoo from coordinate file 1oxy
> ^^^^^^^^^^
>
>
>
>
>
> On 2014-02-11, at 12:03 PM, Bennion, Brian wrote:
>
> > Hello,
> >
> > Will you suggest an alternative error message that is not misleading or is more informative for this case?
> > The fact that the number of atoms is not the same always suggests that a previous file is loaded and its data (number of atoms) is not compatible with the file being loaded.
>
> It wouldn't have suggested that for me - having never had a need to load "optional structural information" from a PDB file into another molecule in the last eight years or so of using VMD, I wasn't even aware that that's possible.
>
>
> > VMD didn't "know" that you wanted to load a new molecule.
>
> And I didn't know that there is a use-case for loading coordinates into an existing molecule :-)
>
> Cheers,
> Boris
>
>
>
> >
> > Brian
> >
> > ________________________________________
> > From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of Boris Steipe [boris.steipe_at_utoronto.ca]
> > Sent: Tuesday, February 11, 2014 7:51 AM
> > To: vmd-l list
> > Subject: Re: vmd-l: VMD can't read 1OXY
> >
> > Ah. I see. The problem isn't in the file. Now I understand: I had loaded 3zoo prior to 1oxy and had overlooked to set the "Load files for:" selection in the File Browser to "New Molecule". When any file is then loaded "for" 0:3zoo the error occurs reproducibly. It's just that the error message pointed me into a completely different direction ...
> >
> > Bottom line: user error and misleading error message.
> > Thanks,
> > Boris
> >
> >
> > On 2014-02-10, at 11:20 PM, Axel Kohlmeyer wrote:
> >
> >> On Mon, Feb 10, 2014 at 10:16 PM, Boris Steipe <boris.steipe_at_utoronto.ca> wrote:
> >>> VMD can't read 1OXY from PDB Web download, local file or even after I edit it to contain only the ATOM records.
> >>>
> >>> Error message:
> >>>
> >>> ERROR) Error reading optional structure information from coordinate file 1oxy
> >>> ERROR) Will ignore structure information in this file.
> >>> Info) Using plugin webpdb for coordinates from file 1oxy
> >>> ERROR) Incorrect number of atoms (5006) in
> >>> ERROR) coordinate file 1oxy
> >>> Info) Finished with coordinate file 1oxy.
> >>>
> >>> This contains no information that I could use to troubleshoot :-(
> >>>
> >>> Chimera works fine for the file, this mail is just FYI.
> >>> Kind regards,
> >>> B.
> >>>
> >>
> >>
> >> hmmm... works for me:
> >> vmd > The PDB is supported by RCSB, the NSF, US PHS, NIH, NCRP, NIGMS, NLM,
> >> and US DoE, who are not liable for the data. PDB files shall not be
> >> sold. See ftp://ftp.rcsb.org/advisory.doc for full details.
> >> Info) Using plugin webpdb for structure file 1OXY
> >> Info) Using plugin webpdb for coordinates from file 1OXY
> >> Info) Determining bond structure from distance search ...
> >> Info) Analyzing structure ...
> >> Info) Atoms: 5006
> >> Info) Bonds: 4811
> >> Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
> >> Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> >> Info) Residues: 909
> >> Info) Waters: 333
> >> Info) Segments: 1
> >> Info) Fragments: 341 Protein: 6 Nucleic: 0
> >> Info) Finished with coordinate file 1OXY.
> >> Info) VMD for LINUXAMD64, version 1.9.2a35 (October 24, 2013)
> >> Info) Exiting normally.
> >>
> >>
> >>
> >>>
> >>
> >>
> >>
> >> --
> >> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> >> College of Science & Technology, Temple University, Philadelphia PA, USA
> >> International Centre for Theoretical Physics, Trieste. Italy.
> >
> >
> >
> 

-- 
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