Hi, I'm having difficulty running phenix.real_space_correlation. I get the following error when comparing a pdb to a ccp4 map: phenix.real_space_correlation ../17may31a_cryoSPARC_C1.pdb ../17may31a_cryoSPARC_C1.ccp4 ------------------------------------------------------------------------------- Input PDB file name: ../17may31a_cryoSPARC_C1.pdb ************************************************* Number of scatterers: 95640 At special positions: 0 Unit cell: (592.359, 589.659, 590.506, 90, 90, 90) Space group: P 1 (No. 1) ------------------------------------------------------------------------------- Input map file name: ../17may31a_cryoSPARC_C1.ccp4 ************************************************** Map type: CCP4-format Traceback (most recent call last): File "/opt/X-tal_suite/phenix-1.12-2829/build/../modules/cctbx_project/mmtbx/command_line/real_space_correlation.py", line 10, in <module> command_name = "phenix.real_space_correlation") File "/opt/X-tal_suite/phenix-1.12-2829/modules/cctbx_project/mmtbx/real_space_correlation.py", line 335, in cmd_run (fobs_handle.file_name, map_handle.file_name)) NameError: global name 'fobs_handle' is not defined I get the following error when comparing a pdb to the reflection files. phenix.real_space_correlation ../17may31a_cryoSPARC_C1.pdb ../17may31a_cryoSPARC_C1.mtz ------------------------------------------------------------------------------- Input PDB file name: ../17may31a_cryoSPARC_C1.pdb ************************************************* Number of scatterers: 95640 At special positions: 0 Unit cell: (592.359, 589.659, 590.506, 90, 90, 90) Space group: P 1 (No. 1) ------------------------------------------------------------------------------- Input reflection file name: ../17may31a_cryoSPARC_C1.mtz ******************************************************** Miller array info: ../17may31a_cryoSPARC_C1.mtz:F-obs,SIGF-obs Observation type: xray.amplitude Type of data: double, size=762857 Type of sigmas: double, size=762857 Number of Miller indices: 762857 Anomalous flag: False Unit cell: (278.528, 278.528, 278.528, 90, 90, 90) Space group: P 1 (No. 1) Systematic absences: 0 Centric reflections: 0 Resolution range: 278.528 3.90017 Completeness in resolution range: 1 Completeness with d_max=infinity: 1 Wavelength: 1.0000 Traceback (most recent call last): File "/opt/X-tal_suite/phenix-1.12-2829/build/../modules/cctbx_project/mmtbx/command_line/real_space_correlation.py", line 10, in <module> command_name = "phenix.real_space_correlation") File "/opt/X-tal_suite/phenix-1.12-2829/modules/cctbx_project/mmtbx/real_space_correlation.py", line 354, in cmd_run r_free_flags = r_free_flags) File "/opt/X-tal_suite/phenix-1.12-2829/modules/cctbx_project/mmtbx/utils/__init__.py", line 1572, in fmodel_simple ro = outliers_rejection,om=optimize_mask) File "/opt/X-tal_suite/phenix-1.12-2829/modules/cctbx_project/mmtbx/utils/__init__.py", line 1559, in get_fmodel twin_law = tl) File "/opt/X-tal_suite/phenix-1.12-2829/modules/cctbx_project/mmtbx/utils/__init__.py", line 1507, in fmodel_manager n_resolution_bins_output = n_resolution_bins_output) File "/opt/X-tal_suite/phenix-1.12-2829/modules/cctbx_project/mmtbx/f_model/f_model.py", line 439, in __init__ if(f_calc is None): f_calc = self.compute_f_calc(miller_array=f_obs) File "/opt/X-tal_suite/phenix-1.12-2829/modules/cctbx_project/mmtbx/f_model/f_model.py", line 526, in compute_f_calc exp_table_one_over_step_size = p.exp_table_one_over_step_size) File "/opt/X-tal_suite/phenix-1.12-2829/modules/cctbx_project/cctbx/miller/__init__.py", line 1515, in structure_factors_from_scatterers algorithm=algorithm) File "/opt/X-tal_suite/phenix-1.12-2829/modules/cctbx_project/cctbx/xray/structure_factors/from_scatterers.py", line 53, in __call__ algorithm=algorithm) # passing algorithm allows f to decide on CPU/GPU implementation File "/opt/X-tal_suite/phenix-1.12-2829/modules/cctbx_project/cctbx/xray/structure_factors/from_scatterers_fft.py", line 18, in __init__ manager, xray_structure, miller_set, algorithm="fft") File "/opt/X-tal_suite/phenix-1.12-2829/modules/cctbx_project/cctbx/xray/structure_factors/manager.py", line 233, in __init__ assert xray_structure.unit_cell().is_similar_to(miller_set.unit_cell()) AssertionError Any suggestions would be appreciated. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031