[phenixbb] map_to_model space group symbol not recognized

Terwilliger, Thomas Charles terwilliger at lanl.gov
Fri Mar 3 14:39:41 PST 2017

Hi Charles,
I'm sorry for the trouble!  I think I fixed this bug ...Could you try updating it and try again?  The use of map_to_model with mtz data is not as developed as using it with a map input file.  Another approach is use phenix.cut_out_density to cut out density for your structure which will then be in space group P1 and use cutout.mtz as input which should work more easily.


From: phenixbb-bounces at phenix-online.org <phenixbb-bounces at phenix-online.org> on behalf of CPMAS Chen <cpmasmit at gmail.com>
Sent: Friday, March 3, 2017 3:15 PM
To: PHENIX user mailing list (phenixbb at phenix-online.org)
Subject: [phenixbb] map_to_model space group symbol not recognized

Hi, All

when I try to using map_to_model tool to optimize my model from low-resolution map,

phenix.map_to_model refine_2.mtz seq_from_pdb.dat

I got the following error, even though I did not provide ncs file,

Space group symmetry written as NCS operators to ncs_from_symmetry.ncs_spec

Traceback (most recent call last):

  File "/usr/local/phenix-1.11-2567/build/../modules/phenix/phenix/command_line/map_to_model.py", line 9, in <module>


  File "/usr/local/phenix-1.11-2567/modules/phenix/phenix/autosol/map_to_model.py", line 5729, in run


  File "/usr/local/phenix-1.11-2567/modules/phenix/phenix/autosol/map_to_model.py", line 4931, in run_segment_and_split_map


  File "/usr/local/phenix-1.11-2567/modules/cctbx_project/cctbx/maptbx/segment_and_split_map.py", line 5795, in run


  File "/usr/local/phenix-1.11-2567/modules/cctbx_project/cctbx/maptbx/segment_and_split_map.py", line 2055, in get_params


  File "/usr/local/phenix-1.11-2567/modules/cctbx_project/cctbx/maptbx/segment_and_split_map.py", line 2051, in get_params_from_args

    return command_line.work.extract()

  File "/usr/local/phenix-1.11-2567/modules/cctbx_project/libtbx/phil/__init__.py", line 1757, in extract

    value = object.extract(parent=result)

  File "/usr/local/phenix-1.11-2567/modules/cctbx_project/libtbx/phil/__init__.py", line 1757, in extract

    value = object.extract(parent=result)

  File "/usr/local/phenix-1.11-2567/modules/cctbx_project/libtbx/phil/__init__.py", line 1122, in extract

    return self._type_from_words()(self.words, master=self)

  File "/usr/local/phenix-1.11-2567/modules/cctbx_project/iotbx/phil.py", line 40, in from_words

    return sgtbx.space_group_info(symbol=str(symbol))

  File "/usr/local/phenix-1.11-2567/modules/cctbx_project/cctbx/sgtbx/__init__.py", line 97, in __init__

    symbols = space_group_symbols(symbol)

RuntimeError: cctbx Error: Space group symbol not recognized: <cctbx_sgtbx_ext.space_group object at 0x101836e20>

Would this be a bug or I simply missed something?





Charles Chen

Research Associate

University of Pittsburgh School of Medicine

Department of Anesthesiology

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