VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Feb 10 2014 - 22:20:25 CST

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.