[phenixbb] problem converting PDB file to mmcif for deposition

Francois Berenger berenger at riken.jp
Thu Jan 19 17:39:50 PST 2012


On 01/20/2012 03:45 AM, Salameh, Mohd A., Ph.D. wrote:
> Hi Everybody,
>
> I encountered a problem recently in converting my PDB file to mmcif
>
> using the pdb_extract tool in rcsb.

Can you give this a try (from the openbabel package on Ubuntu or Debian 
Linux):
babel [INPUT].pdb [OUTPUT].mmcif

Regards,
Francois.

 > It simply writes out an empty
>
> file!! I wonder if any of you have faced such a problem before and
>
> know the solution!! I carefully examined the PDB file header and I
>
> couldn’t really find a reason why this PDB failed to be converted. I
>
> only use PHENIX for molecular replacement and refinement. I used the
>
> default TLS refinement so I assume the whole structure will be refinedas
> a group. I hope somebody is familiar withthis can help me out.
>
> Thank you very much, Mohd
>
>
>
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