[phenixbb] map_to_model space group symbol not recognized
CPMAS Chen
cpmasmit at gmail.com
Mon Mar 6 13:22:29 PST 2017
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*:
<cctbx_sgtbx_ext.space_group object at 0x102805220>
On Fri, Mar 3, 2017 at 5:39 PM, Terwilliger, Thomas Charles <
terwilliger at lanl.gov> 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:* 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>
>
> 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:
> <cctbx_sgtbx_ext.space_group object at 0x101836e20>
>
>
> 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
>
> ******************************************************
>
>
--
***************************************************
Charles Chen
Research Associate
University of Pittsburgh School of Medicine
Department of Anesthesiology
******************************************************
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