Re: [phenixbb] phenix.real_space_correlation

Hi Reza, Great! Those error messages are not the most helpful, but it's something we're trying to improve. Let us know of any other issues! -- 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 Web: https://phenix-online.org On Fri, Aug 4, 2017 at 4:09 PM, Reza Khayat wrote:

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 *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 Web: https://phenix-online.org https://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline.org&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=_kfHIIMR3VGLnuYe30Zr0ZFScLJL022yfZrkMqxcp6U&s=zFvWTkDsiaht30qxwR4S_hrkO_PpnTKvG61139Ch-2E&e=

On Fri, Aug 4, 2017 at 1:10 PM, Reza Khayat 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_pr oject/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_pr oject/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/cct bx/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/cct bx/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/cct bx/xray/structure_factors/manager.py", line 233, in __init__ assert xray_structure.unit_cell().is_similar_to(miller_set.unit_cel l()) 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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