VMD-L Mailing List
From: Boris Steipe (boris.steipe_at_utoronto.ca)
Date: Tue Feb 11 2014 - 16:15:13 CST
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:
> 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 :-)
> 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.
> 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,
>> 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.