From: Bennion, Brian (
Date: Tue Feb 11 2014 - 12:17:16 CST

Obvious or not is in the eye of the beholder. A simple search of the email archives would have saved more time than beating a poor pdb file to death. Reading the literature in the library to solve my problem is what I remember from grad school. I guess that's been replaced by (insert your favorite search engine). Do I still make silly mistakes, sure...

Thanks for the queue to reminiscence on some fun(?!) days.
From: Ivan Gregoretti []
Sent: Tuesday, February 11, 2014 10:01 AM
To: Bennion, Brian
Cc: vmd-l list
Subject: Re: vmd-l: VMD can't read 1OXY

Perhaps the error message could say, for example, that the user has
not cleaned up the variables in memory prior to loading the current

Sometimes, the utterly obvious is not so obvious for everyone.
Remember when you were a graduate student?

Thank you,


Ivan Gregoretti, PhD

On Tue, Feb 11, 2014 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. VMD didn't "know" that you wanted to load a new molecule.
> Brian
> ________________________________________
> From: [] on behalf of Boris Steipe []
> 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 <> 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 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
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.