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.
-Tom
________________________________
From: [email protected] on behalf of CPMAS Chen
Sent: Friday, March 3, 2017 3:15 PM
To: PHENIX user mailing list ([email protected])
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>
run(sys.argv[1:],out=sys.stdout)
File "/usr/local/phenix-1.11-2567/modules/phenix/phenix/autosol/map_to_model.py", line 5729, in run
tracking_data=run_segment_and_split_map(params,out=out)
File "/usr/local/phenix-1.11-2567/modules/phenix/phenix/autosol/map_to_model.py", line 4931, in run_segment_and_split_map
ncs_group_obj,remainder_ncs_group_obj,tracking_data=segment_map(args)
File "/usr/local/phenix-1.11-2567/modules/cctbx_project/cctbx/maptbx/segment_and_split_map.py", line 5795, in run
params,map_data,pdb_hierarchy,tracking_data=get_params(args,out=out)
File "/usr/local/phenix-1.11-2567/modules/cctbx_project/cctbx/maptbx/segment_and_split_map.py", line 2055, in get_params
params=get_params_from_args(args)
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:
Would this be a bug or I simply missed something?
Thanks!
Charles
--
***************************************************
Charles Chen
Research Associate
University of Pittsburgh School of Medicine
Department of Anesthesiology
******************************************************
