Re: [phenixbb] map_to_model space group symbol not recognized

Thanks, Tom. I downloaded 1.11.1-2575. the same error is still there as seen by the error msg attached at the end. Maybe you mean the nightly-build version? Let me try that too. Actually, my real problem is to fit my data (3.75A) to my protein model. The Rwork/Rfree is about 0.4/0.45 and I can improve it to about 0.37/0.42. However, I can see there are quite some residues not fitting to the density. So, I am trying some methods provided in phenix to improve my fitting. Currently, what I am working is 1) phenix-rosetta, 2) map_to_model, 3) morph_model. Any other suggestions? Thanks! Charles Traceback (most recent call last): File "/usr/local/phenix-1.11.1-2575/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-1.11.1-2575/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-1.11.1-2575/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-1.11.1-2575/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-1.11.1-2575/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-1.11.1-2575/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-1.11.1-2575/modules/cctbx_project/libtbx/phil/__init__.py", line 1757, in extract value = object.extract(parent=result) File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/libtbx/phil/__init__.py", line 1757, in extract value = object.extract(parent=result) File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/libtbx/phil/__init__.py", line 1122, in extract return self._type_from_words()(self.words, master=self) File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/iotbx/phil.py", line 40, in from_words return sgtbx.space_group_info(symbol=str(symbol)) File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/cctbx/sgtbx/__init__.py", line 97, in __init__ symbols = space_group_symbols(symbol) RuntimeError: cctbx Error: *Space group symbol not recognized*: On Fri, Mar 3, 2017 at 5:39 PM, Terwilliger, Thomas Charles < [email protected]> wrote:

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

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-- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************