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