[phenixbb] cif_as_mtz assertion error

Eric Williams ericwilliams at pobox.com
Wed Jun 13 07:36:35 PDT 2012


I'm trying to run phenix.cif_as_mtz on a large number of PDB entries, and
several entries give me an assertion error. The example below is from 8icz,
but the error always seems to be the same.

Traceback (most recent call last):
  File
"/media/funky/phenix-1.8-1069/build/intel-linux-2.6/../../cctbx_project/mmtbx/command_line/cif_as_mtz.py",
line 544, in <module>
    run(sys.argv[1:])
  File
"/media/funky/phenix-1.8-1069/build/intel-linux-2.6/../../cctbx_project/mmtbx/command_line/cif_as_mtz.py",
line 135, in run

incompatible_flags_to_work_set=command_line.options.incompatible_flags_to_work_set)
  File
"/media/funky/phenix-1.8-1069/build/intel-linux-2.6/../../cctbx_project/mmtbx/command_line/cif_as_mtz.py",
line 197, in process_files
    r_free_flags   = r_free_flags).mtz_object()
  File "/media/funky/phenix-1.8-1069/cctbx_project/mmtbx/utils.py", line
2001, in __init__
    skip_twin_detection = True)
  File "/media/funky/phenix-1.8-1069/cctbx_project/mmtbx/utils.py", line
2113, in get_r_factor
    twin_laws                = twin_laws)
  File "/media/funky/phenix-1.8-1069/cctbx_project/mmtbx/utils.py", line
1556, in fmodel_simple
    assert f_obs.sys_absent_flags().data().count(True)==0

Any ideas? Thanks. :)

Eric Williams
PhD candidate
Intelligent Systems Program
University of Pittsburgh
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