VMD-L Mailing List
From: Boris Steipe (boris.steipe_at_utoronto.ca)
Date: Tue Feb 11 2014 - 09:51:10 CST
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.