[phenixbb] pdb conversion to 3.2 format

Luca Pellegrini lp212 at cam.ac.uk
Mon Aug 22 09:14:56 PDT 2011


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>
  File "/usr/local/cctbx/cctbx_sources/iotbx/command_line/pdb_remediator.py", line 51, in run
  File "/usr/local/cctbx/cctbx_sources/iotbx/pdb/remediation/remediator.py", line 257, in remediator
  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.


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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