[phenixbb] phenix.real_space_correlation

Fri Aug 4 16:09:47 PDT 2017

Hi Bill,

That's embarrassing, having missed the difference in cell size. The Reciprocal space variant (mtz) is now working. Thanks for the help.

Best wishes,

Reza

Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031
________________________________
From: Billy Poon <bkpoon at lbl.gov>
Sent: Friday, August 4, 2017 4:24 PM
To: Reza Khayat
Cc: PHENIX user mailing list
Subject: Re: [phenixbb] phenix.real_space_correlation

Hi Reza,

For the first error, phenix.map_model_cc should be used when you have a model and a map in real space.

For the second error, the unit cell in the model (592.359, 589.659, 590.506, 90, 90, 90) is different than the unit cell in the reflections file (278.528, 278.528, 278.528, 90, 90, 90).

--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
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On Fri, Aug 4, 2017 at 1:10 PM, Reza Khayat <rkhayat at ccny.cuny.edu<mailto:rkhayat at ccny.cuny.edu>> wrote:

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

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