[phenixbb] phenix.real_space_correlation

[Reza Khayat]

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20170804/b2394fd7/attachment.htm>