[phenixbb] mtriage error

[Sara Weaver]

Hi all,

I'm trying to process some cryoEM data that goes to 2.9 angstroms in
phenix.  I can't seem to run mtriage on several different builds.  Any
ideas?  I've put the errors below.  I've tried making my input map a .mrc,
or a .ccp4 and get the same errors.

Thanks!
Sara

[sjweaver at brmaster job099]$
/hotdata/sbgrid/programs/x86_64-linux/phenix/1.12-2829/phenix-1.12-2829/build/bin/phenix.mtriage
map_file_name=run_class001.mrc
-------------------------------------------------------------------------------

phenix.mtriage:
  Given map file and optionally model and half-map files compute map
statistics.

How to run:
  phenix.mtriage model_file_name=m.pdb map_file_name=m.map
half_map_file_name_1=m1.map half_map_file_name_2=m2.map

Optional: model_file_name=, half_map_file_name_1=, half_map_file_name_2=

Feedback:
  PAfonine at lbl.gov
  phenixbb at phenix-online.org

-------------------------------------------------------------------------------

-------------------------------------------------------------------------------

Input model:
************
No model specified.
-------------------------------------------------------------------------------

Box (unit cell) info:
*********************
Unit cell: (255.948, 255.948, 255.948, 90, 90, 90)
Space group: P 1 (No. 1)
Traceback (most recent call last):
  File
"/hotdata/sbgrid/programs/x86_64-linux/phenix/1.12-2829/phenix-1.12-2829/build/../modules/cctbx_project/mmtbx/command_line/mtriage.py",
line 277, in <module>
    run(args=sys.argv[1:])
  File
"/hotdata/sbgrid/programs/x86_64-linux/phenix/1.12-2829/phenix-1.12-2829/build/../modules/cctbx_project/mmtbx/command_line/mtriage.py",
line 190, in run
    task_obj.run()
  File
"/hotdata/sbgrid/programs/x86_64-linux/phenix/1.12-2829/phenix-1.12-2829/modules/cctbx_project/mmtbx/maps/mtriage.py",
line 174, in run
    self._shift_origin()
  File
"/hotdata/sbgrid/programs/x86_64-linux/phenix/1.12-2829/phenix-1.12-2829/modules/cctbx_project/mmtbx/maps/mtriage.py",
line 204, in _shift_origin
    crystal_symmetry = self.crystal_symmetry)
  File
"/hotdata/sbgrid/programs/x86_64-linux/phenix/1.12-2829/phenix-1.12-2829/modules/cctbx_project/cctbx/maptbx/__init__.py",
line 112, in shift_origin_if_needed
    assert [sites_cart, crystal_symmetry].count(None) in [0, 2]
AssertionError

[sjweaver at brmaster job099]$
/hotdata/sbgrid/programs/x86_64-linux/phenix/1.13-2998/phenix-1.13-2998/build/bin/phenix.mtriage
map_file_name=run_class001.mrc
-------------------------------------------------------------------------------

phenix.mtriage:
  Given map file and optionally model and half-map files compute map
statistics.

How to run:
  phenix.mtriage model_file_name=m.pdb map_file_name=m.map
half_map_file_name_1=m1.map half_map_file_name_2=m2.map

Optional: model_file_name=, half_map_file_name_1=, half_map_file_name_2=

Feedback:
  PAfonine at lbl.gov
  phenixbb at phenix-online.org

-------------------------------------------------------------------------------

-------------------------------------------------------------------------------

Input model:
************
No model specified.
-------------------------------------------------------------------------------

Box (unit cell) info:
*********************
Unit cell: (255.948, 255.948, 255.948, 90, 90, 90)
Space group: P 1 (No. 1)
Traceback (most recent call last):
  File
"/hotdata/sbgrid/programs/x86_64-linux/phenix/1.13-2998/phenix-1.13-2998/build/../modules/cctbx_project/mmtbx/command_line/mtriage.py",
line 287, in <module>
    run(args=sys.argv[1:])
  File
"/hotdata/sbgrid/programs/x86_64-linux/phenix/1.13-2998/phenix-1.13-2998/build/../modules/cctbx_project/mmtbx/command_line/mtriage.py",
line 195, in run
    task_obj.run()
  File
"/hotdata/sbgrid/programs/x86_64-linux/phenix/1.13-2998/phenix-1.13-2998/modules/cctbx_project/mmtbx/maps/mtriage.py",
line 204, in run
    self.call(func=self._compute_d_model_b0, prefix="Compute d_model_b0")
  File
"/hotdata/sbgrid/programs/x86_64-linux/phenix/1.13-2998/phenix-1.13-2998/modules/cctbx_project/mmtbx/maps/mtriage.py",
line 185, in call
    func()
  File
"/hotdata/sbgrid/programs/x86_64-linux/phenix/1.13-2998/phenix-1.13-2998/modules/cctbx_project/mmtbx/maps/mtriage.py",
line 295, in _compute_d_model_b0
    map_data         = self.box.map_data,
AttributeError: 'NoneType' object has no attribute 'map_data'

[sjweaver at brmaster job099]$
/hotdata/sbgrid/programs/x86_64-linux/phenix/dev-3063/phenix-dev-3063/build/bin/phenix.mtriage
map_file_name=run_class001.mrc
-------------------------------------------------------------------------------

phenix.mtriage:
  Given map file and optionally model and half-map files compute map
statistics.

How to run:
  phenix.mtriage model_file_name=m.pdb map_file_name=m.map
half_map_file_name_1=m1.map half_map_file_name_2=m2.map

Optional: model_file_name=, half_map_file_name_1=, half_map_file_name_2=

Feedback:
  PAfonine at lbl.gov
  phenixbb at phenix-online.org

-------------------------------------------------------------------------------

Traceback (most recent call last):
  File
"/hotdata/sbgrid/programs/x86_64-linux/phenix/dev-3063/phenix-dev-3063/build/../modules/cctbx_project/mmtbx/command_line/mtriage.py",
line 274, in <module>
    run(args=sys.argv[1:])
  File
"/hotdata/sbgrid/programs/x86_64-linux/phenix/dev-3063/phenix-dev-3063/build/../modules/cctbx_project/mmtbx/command_line/mtriage.py",
line 158, in run
    params    = inputs.params)
  File
"/hotdata/sbgrid/programs/x86_64-linux/phenix/dev-3063/phenix-dev-3063/modules/cctbx_project/mmtbx/maps/mtriage.py",
line 130, in __init__
    box       = self.params.use_box)
  File
"/hotdata/sbgrid/programs/x86_64-linux/phenix/dev-3063/phenix-dev-3063/modules/cctbx_project/iotbx/map_and_model.py",
line 115, in __init__
    crystal_symmetry = self._model.crystal_symmetry())
AttributeError: 'NoneType' object has no attribute 'crystal_symmetry'

ariel:20180417_lookingatRefinej348_focused sjweaver$
/Applications/phenix-dev-3112/build/bin/phenix.mtriage
map_file_name=run_ct8_class001.mrc

-------------------------------------------------------------------------------

phenix.mtriage:

  Given map file and optionally model and half-map files compute map
statistics.


How to run:

  phenix.mtriage model_file_name=m.pdb map_file_name=m.map
half_map_file_name_1=m1.map half_map_file_name_2=m2.map


Optional: model_file_name=, half_map_file_name_1=, half_map_file_name_2=


Feedback:

  PAfonine at lbl.gov

  phenixbb at phenix-online.org



-------------------------------------------------------------------------------

Traceback (most recent call last):

  File
"/Applications/phenix-dev-3112/build/../modules/cctbx_project/mmtbx/command_line/mtriage.py",
line 339, in <module>

    run(args=sys.argv[1:])

  File
"/Applications/phenix-dev-3112/build/../modules/cctbx_project/mmtbx/command_line/mtriage.py",
line 204, in run

    inputs.model.setup_scattering_dictionaries(
AttributeError: 'NoneType' object has no attribute
'setup_scattering_dictionaries'
-- 
Sara J. Weaver
*Doctoral Candidate, Jensen Lab*
*California Institute of Technology*
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