[phenixbb] phenix.real_space_correlation

Fri Aug 4 13:24:20 PDT 2017

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

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_
> 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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