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@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:
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
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@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:
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
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@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:
-------------------------------------------------------------------------------
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@lbl.gov
phenixbb@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'