[phenixbb] pdb conversion to 3.2 format

Jeff Headd jjheadd at lbl.gov
Mon Aug 22 09:34:08 PDT 2011

Hi Luca,

Thanks for pointing out this bug, an error crept into the code for
loading the remediation dictionary. I've fixed the bug and checked in
the changes, so the next nightly installer will have the fix.

You are correct that pdb_remediatior is not available in the last
release (1.7.1-743), as it was added more recently. It is present in
recent nightly Phenix builds.

If you have any further problems, please let me know.


On Mon, Aug 22, 2011 at 9:14 AM, Luca Pellegrini <lp212 at cam.ac.uk> wrote:
> Hi,
> I am trying to use iotbx.pdb_remediator to convert PDB atom names to 3.2 format (as suggested by Nat Echols in a recent post to Coot mail-list). Unfortunately I get the following error message:
> lp212-mp2281 58% iotbx.pdb_remediator file_name=refine.pdb output_file=refine_3.2.pdb_file
> Traceback (most recent call last):
>  File "/usr/local/cctbx/cctbx_sources/iotbx/command_line/pdb_remediator.py", line 54, in <module>
>    run(sys.argv[1:])
>  File "/usr/local/cctbx/cctbx_sources/iotbx/command_line/pdb_remediator.py", line 51, in run
>    remediator.remediator(params)
>  File "/usr/local/cctbx/cctbx_sources/iotbx/pdb/remediation/remediator.py", line 257, in remediator
>    user_dict)
>  File "/usr/local/cctbx/cctbx_sources/iotbx/pdb/remediation/remediator.py", line 95, in build_hash
>    test=os.path.isfile), "rb")
> TypeError: coercing to Unicode: need string or buffer, NoneType found
> It looks like a python problem, but I am afraid my insight ends here. Can anyone tell me how to fix this, please? I am not sure if it matters, but iotbx_pdb_remediator was not in my phenix installation (PHENIX-1.7.1-743 on MacOSX 10.6.8), so I installed cctbx separately.
> Thanks!
> Luca
> Luca Pellegrini
> Department of Biochemistry
> University of Cambridge
> 80 Tennis Court Road
> Cambridge CB2 1GA - UK
> Email: lp212 at cam.ac.uk
> Tel: 0044-1223-760469
> Fax: 0044-1223-766002
> Sanger building, room 3.59
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