<div dir="ltr">Hi all,<div><br></div><div>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. </div><div><br></div><div>Thanks!</div><div>Sara</div><div><br></div><div><div>[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
</div><div>-------------------------------------------------------------------------------
</div><div>phenix.mtriage:
</div><div> Given map file and optionally model and half-map files compute map statistics.
</div><div><br clear="none"></div><div>How to run:
</div><div> 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
</div><div><br clear="none"></div><div>Optional: model_file_name=, half_map_file_name_1=, half_map_file_name_2=
</div><div><br clear="none"></div><div>Feedback:
</div><div> <a href="mailto:PAfonine@lbl.gov">PAfonine@lbl.gov</a>
</div><div> <a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
</div><div>
</div><div>-------------------------------------------------------------------------------
</div><div>-------------------------------------------------------------------------------
</div><div>Input model:
</div><div>************
</div><div>No model specified.
</div><div>-------------------------------------------------------------------------------
</div><div>Box (unit cell) info:
</div><div>*********************
</div><div>Unit cell: (255.948, 255.948, 255.948, 90, 90, 90)
</div><div>Space group: P 1 (No. 1)
</div><div>Traceback (most recent call last):
</div><div> 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>
</div><div> run(args=sys.argv[1:])
</div><div> 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
</div><div> task_obj.run()
</div><div> 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
</div><div> self._shift_origin()
</div><div> 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
</div><div> crystal_symmetry = self.crystal_symmetry)
</div><div> 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
</div><div> assert [sites_cart, crystal_symmetry].count(None) in [0, 2]
</div><div>AssertionError </div></div><div><br></div><div><div>[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
</div><div>-------------------------------------------------------------------------------
</div><div>phenix.mtriage:
</div><div> Given map file and optionally model and half-map files compute map statistics.
</div><div><br clear="none"></div><div>How to run:
</div><div> 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
</div><div><br clear="none"></div><div>Optional: model_file_name=, half_map_file_name_1=, half_map_file_name_2=
</div><div><br clear="none"></div><div>Feedback:
</div><div> <a href="mailto:PAfonine@lbl.gov">PAfonine@lbl.gov</a>
</div><div> <a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
</div><div>
</div><div>-------------------------------------------------------------------------------
</div><div>-------------------------------------------------------------------------------
</div><div>Input model:
</div><div>************
</div><div>No model specified.
</div><div>-------------------------------------------------------------------------------
</div><div>Box (unit cell) info:
</div><div>*********************
</div><div>Unit cell: (255.948, 255.948, 255.948, 90, 90, 90)
</div><div>Space group: P 1 (No. 1)
</div><div>Traceback (most recent call last):
</div><div> 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>
</div><div> run(args=sys.argv[1:])
</div><div> 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
</div><div> task_obj.run()
</div><div> 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
</div><div> self.call(func=self._compute_d_model_b0, prefix="Compute d_model_b0")
</div><div> 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
</div><div> func()
</div><div> 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
</div><div> map_data = self.box.map_data,
</div><div>AttributeError: 'NoneType' object has no attribute 'map_data' </div></div><div><br></div><div><div>[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
</div><div>-------------------------------------------------------------------------------
</div><div>phenix.mtriage:
</div><div> Given map file and optionally model and half-map files compute map statistics.
</div><div><br clear="none"></div><div>How to run:
</div><div> 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
</div><div><br clear="none"></div><div>Optional: model_file_name=, half_map_file_name_1=, half_map_file_name_2=
</div><div><br clear="none"></div><div>Feedback:
</div><div> <a href="mailto:PAfonine@lbl.gov">PAfonine@lbl.gov</a>
</div><div> <a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
</div><div>
</div><div>-------------------------------------------------------------------------------
</div><div>Traceback (most recent call last):
</div><div> 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>
</div><div> run(args=sys.argv[1:])
</div><div> 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
</div><div> params = inputs.params)
</div><div> File "/hotdata/sbgrid/programs/x86_64-linux/phenix/dev-3063/phenix-dev-3063/modules/cctbx_project/mmtbx/maps/mtriage.py", line 130, in __init__
</div><div> box = self.params.use_box)
</div><div> 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__
</div><div> crystal_symmetry = self._model.crystal_symmetry())
</div><div>AttributeError: 'NoneType' object has no attribute 'crystal_symmetry'</div><div><br></div>
<p class="inbox-inbox-p1"><span class="inbox-inbox-s1">ariel:20180417_lookingatRefinej348_focused sjweaver$ /Applications/phenix-dev-3112/build/bin/phenix.mtriage map_file_name=run_ct8_class001.mrc<span class="inbox-inbox-Apple-converted-space"> </span></span></p>
<p class="inbox-inbox-p1"><span class="inbox-inbox-s1">-------------------------------------------------------------------------------</span></p>
<p class="inbox-inbox-p1"><span class="inbox-inbox-s1">phenix.mtriage:</span></p>
<p class="inbox-inbox-p1"><span class="inbox-inbox-s1"><span class="inbox-inbox-Apple-converted-space"> </span>Given map file and optionally model and half-map files compute map statistics.</span></p>
<p class="inbox-inbox-p2"><span class="inbox-inbox-s1"></span><br></p>
<p class="inbox-inbox-p1"><span class="inbox-inbox-s1">How to run:</span></p>
<p class="inbox-inbox-p1"><span class="inbox-inbox-s1"><span class="inbox-inbox-Apple-converted-space"> </span>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</span></p>
<p class="inbox-inbox-p2"><span class="inbox-inbox-s1"></span><br></p>
<p class="inbox-inbox-p1"><span class="inbox-inbox-s1">Optional: model_file_name=, half_map_file_name_1=, half_map_file_name_2=</span></p>
<p class="inbox-inbox-p2"><span class="inbox-inbox-s1"></span><br></p>
<p class="inbox-inbox-p1"><span class="inbox-inbox-s1">Feedback:</span></p>
<p class="inbox-inbox-p1"><span class="inbox-inbox-s1"><span class="inbox-inbox-Apple-converted-space"> </span><a href="mailto:PAfonine@lbl.gov">PAfonine@lbl.gov</a></span></p>
<p class="inbox-inbox-p1"><span class="inbox-inbox-s1"><span class="inbox-inbox-Apple-converted-space"> </span><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a></span></p>
<p class="inbox-inbox-p2"><span class="inbox-inbox-s1"><span class="inbox-inbox-Apple-converted-space"> </span></span></p>
<p class="inbox-inbox-p1"><span class="inbox-inbox-s1">-------------------------------------------------------------------------------</span></p>
<p class="inbox-inbox-p1"><span class="inbox-inbox-s1">Traceback (most recent call last):</span></p>
<p class="inbox-inbox-p1"><span class="inbox-inbox-s1"><span class="inbox-inbox-Apple-converted-space"> </span>File "/Applications/phenix-dev-3112/build/../modules/cctbx_project/mmtbx/command_line/mtriage.py", line 339, in <module></span></p>
<p class="inbox-inbox-p1"><span class="inbox-inbox-s1"><span class="inbox-inbox-Apple-converted-space"> </span>run(args=sys.argv[1:])</span></p>
<p class="inbox-inbox-p1"><span class="inbox-inbox-s1"><span class="inbox-inbox-Apple-converted-space"> </span>File "/Applications/phenix-dev-3112/build/../modules/cctbx_project/mmtbx/command_line/mtriage.py", line 204, in run</span></p>
<p class="inbox-inbox-p1"><span class="inbox-inbox-s1"><span class="inbox-inbox-Apple-converted-space"> </span>inputs.model.setup_scattering_dictionaries(</span></p>
<div>AttributeError: 'NoneType' object has no attribute 'setup_scattering_dictionaries' </div></div></div>-- <br><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr">Sara J. Weaver<div><div><i>Doctoral Candidate, Jensen Lab</i></div><div><i>California Institute of Technology</i><br></div></div></div></div>