VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Tue Feb 11 2014 - 09:42:22 CST

Hi Boris,
Is it only this pdb, or does it also not work with other pdb codes? My
version of VMD loads 1OXY fine too.
-Josh Vermaas

On 02/10/2014 10:20 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.
>
>
>
>
>