[phenixbb] phenix.real_space_correlation

Billy Poon bkpoon at lbl.gov
Fri Aug 4 18:24:27 PDT 2017 

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 <rkhayat at ccny.cuny.edu> 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 <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
> 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 <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_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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