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