Various Clipper problems

[urska.rovsnik@…]

The following bug report has been submitted:
Platform:        Linux-5.4.0-125-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Errors  
---  
error | Bundle 'ChimeraX-Registration' custom initialization failed  
warning | Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/registration/nag.py", line 278, in _strptime  
month = _months.index(month_name)  
ValueError: tuple.index(x): x not in tuple  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/registration/nag.py", line 289, in _strptime  
return datetime.strptime(TimeFormat, value)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/_strptime.py", line 568, in
_strptime_datetime  
tt, fraction, gmtoff_fraction = _strptime(data_string, format)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/_strptime.py", line 349, in
_strptime  
raise ValueError("time data %r does not match format %r" %  
ValueError: time data '%a %b %d %H:%M:%S %Y' does not match format 'fre maj 10
15:30:22 2019'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 365, in initialize  
api._api_caller.initialize(api, session, self)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1278, in initialize  
return cls._get_func(api, "initialize")(session, bi)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/registration/__init__.py", line 41, in initialize  
nag(session)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/registration/nag.py", line 38, in nag  
_check_usage(session)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/registration/nag.py", line 192, in _check_usage  
usage = _get_usage()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/registration/nag.py", line 240, in _get_usage  
usage["dates"].append(_strptime(value))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/registration/nag.py", line 291, in _strptime  
raise ValueError("time data does not match format")  
ValueError: time data does not match format  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/urovsnik/Desktop/Work/GLIC_model_building/GLIC_Alcohol/MapToStructureFactors_1/map_to_structure_factors.mtz

Install the Clipper bundle to open "MTZ" format files.  
Opener for format 'MTZ' is not installed; see log for more info  
Downloading bundle ChimeraX_Clipper-0.18.0-cp39-cp39-manylinux_2_17_x86_64.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
WARNING: Value for scheme.platlib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/urovsnik/.local/share/ChimeraX/1.4/site-packages  
sysconfig: /home/urovsnik/.local/lib/python3.9/site-packages  
WARNING: Value for scheme.purelib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/urovsnik/.local/share/ChimeraX/1.4/site-packages  
sysconfig: /home/urovsnik/.local/lib/python3.9/site-packages  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/urovsnik/.local/share/ChimeraX/include/python3.9/ChimeraX-
Clipper  
sysconfig: /home/urovsnik/.local/include/python3.9/ChimeraX-Clipper  
WARNING: Value for scheme.scripts does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/urovsnik/.local/share/ChimeraX/bin  
sysconfig: /home/urovsnik/.local/bin  
WARNING: Value for scheme.data does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/urovsnik/.local/share/ChimeraX  
sysconfig: /home/urovsnik/.local  
WARNING: Additional context:  
user = True  
home = None  
root = None  
prefix = None  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/urovsnik/.local/share/ChimeraX/include/python3.9/UNKNOWN  
sysconfig: /home/urovsnik/.local/include/python3.9/UNKNOWN  
WARNING: You are using pip version 21.3.1; however, version 22.2.2 is
available.  
You should consider upgrading via the '/usr/bin/chimerax -m pip install
--upgrade pip' command.  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing
./Downloads/ChimeraX_Clipper-0.18.0-cp39-cp39-manylinux_2_17_x86_64.whl  
Requirement already satisfied: ChimeraX-Core~=1.4.dev202203030220 in
/usr/lib/ucsf-chimerax/lib/python3.9/site-packages (from ChimeraX-
Clipper==0.18.0) (1.4)  
Requirement already satisfied: ChimeraX-AtomicLibrary~=7.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Clipper==0.18.0) (7.0)  
Requirement already satisfied: ChimeraX-Atomic~=1.36 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Clipper==0.18.0) (1.39.1)  
Requirement already satisfied: ChimeraX-Arrays~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Clipper==0.18.0) (1.0)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.18.0) (1.2)  
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.18.0) (2.7)  
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.18.0) (2.0.2)  
Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.18.0) (1.0.2)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.18.0) (1.1)  
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in
/usr/lib/ucsf-chimerax/lib/python3.9/site-packages (from ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.18.0) (2.0.1)  
Requirement already satisfied: ChimeraX-PDB~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.18.0) (2.6.6)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.2.2)  
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.5.1)  
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.9)  
Requirement already satisfied: ChimeraX-UI~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.18.3)  
Requirement already satisfied: ChimeraX-Surface~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.0)  
Requirement already satisfied: ChimeraX-IO~=1.0.1 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-PDB~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.0.1)  
Requirement already satisfied: ChimeraX-Map~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.1)  
Requirement already satisfied: ChimeraX-StdCommands~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.8)  
Requirement already satisfied: ChimeraX-MapData~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (2.0)  
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-UI~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.0)  
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-UI~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.1)  
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.18.0) (2.1)  
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-
Clipper==0.18.0) (2.0)  
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-
SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.18.0) (1.0)  
Requirement already satisfied: ChimeraX-MapFit~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.18.0) (2.0)  
Requirement already satisfied: ChimeraX-Dssp~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.36->ChimeraX-Clipper==0.18.0) (2.0)  
Installing collected packages: ChimeraX-Clipper  
Successfully installed ChimeraX-Clipper-0.18.0  
\---  

Successfully installed ChimeraX-Clipper-0.18.0  
Installed ChimeraX-Clipper (0.18.0)  
Installed ChimeraX-Registration (1.1)  

QWebEngineUrlScheme::registerScheme: Scheme "cxreg" already registered  

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/registration/nag.py", line 278, in _strptime  
month = _months.index(month_name)  
ValueError: tuple.index(x): x not in tuple  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/registration/nag.py", line 289, in _strptime  
return datetime.strptime(TimeFormat, value)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/_strptime.py", line 568, in
_strptime_datetime  
tt, fraction, gmtoff_fraction = _strptime(data_string, format)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/_strptime.py", line 349, in
_strptime  
raise ValueError("time data %r does not match format %r" %  
ValueError: time data '%a %b %d %H:%M:%S %Y' does not match format 'fre maj 10
15:30:22 2019'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 365, in initialize  
api._api_caller.initialize(api, session, self)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1278, in initialize  
return cls._get_func(api, "initialize")(session, bi)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/registration/__init__.py", line 41, in initialize  
nag(session)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/registration/nag.py", line 38, in nag  
_check_usage(session)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/registration/nag.py", line 192, in _check_usage  
usage = _get_usage()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/registration/nag.py", line 240, in _get_usage  
usage["dates"].append(_strptime(value))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/registration/nag.py", line 291, in _strptime  
raise ValueError("time data does not match format")  
ValueError: time data does not match format  
  

ChimeraX-Registration (installed) [version: 1.1] [api package:
chimerax.registration] [category: Utilities] [tool: Registration [categories:
Utilities] [synopsis: Register ChimeraX with RBVI]] [command: registration
status [categories: Utilities] [synopsis: Report registration status]]
[command: registration file [categories: Utilities] [synopsis: Report
registration file location or apply registration file]]: custom initialization
failed  

> open
> /home/urovsnik/Desktop/Work/GLIC_model_building/GLIC_Alcohol/MapToStructureFactors_1/map_to_structure_factors.mtz

Install the Clipper bundle to open "MTZ" format files.  
Opener for format 'MTZ' is not installed; see log for more info  
Downloading bundle ChimeraX_Clipper-0.18.0-cp39-cp39-manylinux_2_17_x86_64.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
WARNING: Value for scheme.platlib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/urovsnik/.local/share/ChimeraX/1.4/site-packages  
sysconfig: /home/urovsnik/.local/lib/python3.9/site-packages  
WARNING: Value for scheme.purelib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/urovsnik/.local/share/ChimeraX/1.4/site-packages  
sysconfig: /home/urovsnik/.local/lib/python3.9/site-packages  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/urovsnik/.local/share/ChimeraX/include/python3.9/ChimeraX-
Clipper  
sysconfig: /home/urovsnik/.local/include/python3.9/ChimeraX-Clipper  
WARNING: Value for scheme.scripts does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/urovsnik/.local/share/ChimeraX/bin  
sysconfig: /home/urovsnik/.local/bin  
WARNING: Value for scheme.data does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/urovsnik/.local/share/ChimeraX  
sysconfig: /home/urovsnik/.local  
WARNING: Additional context:  
user = True  
home = None  
root = None  
prefix = None  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/urovsnik/.local/share/ChimeraX/include/python3.9/UNKNOWN  
sysconfig: /home/urovsnik/.local/include/python3.9/UNKNOWN  
WARNING: You are using pip version 21.3.1; however, version 22.2.2 is
available.  
You should consider upgrading via the '/usr/bin/chimerax -m pip install
--upgrade pip' command.  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing
./Downloads/ChimeraX_Clipper-0.18.0-cp39-cp39-manylinux_2_17_x86_64.whl  
Installing collected packages: ChimeraX-Clipper  
Attempting uninstall: ChimeraX-Clipper  
Found existing installation: ChimeraX-Clipper 0.18.0  
Uninstalling ChimeraX-Clipper-0.18.0:  
Successfully uninstalled ChimeraX-Clipper-0.18.0  
Successfully installed ChimeraX-Clipper-0.18.0  
\---  

Successfully installed ChimeraX-Clipper-0.18.0  
Installed ChimeraX-Clipper (0.18.0)  
Replacing data format 'MTZ' as defined by ChimeraX-Clipper with definition
from ChimeraX-Clipper  

> open
> /home/urovsnik/Desktop/Work/GLIC_model_building/GLIC_Alcohol/MapToStructureFactors_1/map_to_structure_factors.mtz

Install the Clipper bundle to open "MTZ" format files.  
Opener for format 'MTZ' is not installed; see log for more info  

> open
> /home/urovsnik/Desktop/Work/GLIC_model_building/GLIC_Alcohol/MapToStructureFactors_1/map_to_structure_factors.mtz
> format mtz

Summary of feedback from opening
/home/urovsnik/Desktop/Work/GLIC_model_building/GLIC_Alcohol/MapToStructureFactors_1/map_to_structure_factors.mtz  
---  
notes |  
  
  
| Chain information for fixed01_real_space_refined_008.pdb #1  
  
---  
  
  
Chain  
| Description  
  
  
  
  
  
  
A B C D E  
| No description available  
  
  
  
  
  
Discarding unrecognised/unsupported data array /crystal/dataset/HLA A  
Discarding unrecognised/unsupported data array /crystal/dataset/HLB A  
Discarding unrecognised/unsupported data array /crystal/dataset/HLC A  
Discarding unrecognised/unsupported data array /crystal/dataset/HLD A  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 457, in collated_open  
return remember_data_format()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/home/urovsnik/.local/share/ChimeraX/1.4/site-
packages/chimerax/clipper/__init__.py", line 240, in open  
return open_structure_factors(session, data, **kw)  
File "/home/urovsnik/.local/share/ChimeraX/1.4/site-
packages/chimerax/clipper/cmd.py", line 52, in open_structure_factors  
raise e  
File "/home/urovsnik/.local/share/ChimeraX/1.4/site-
packages/chimerax/clipper/cmd.py", line 32, in open_structure_factors  
xmapset = mmgr.add_xmapset_from_file(path, oversampling_rate=over_sampling,  
File "/home/urovsnik/.local/share/ChimeraX/1.4/site-
packages/chimerax/clipper/maps/map_mgr.py", line 324, in add_xmapset_from_file  
return XmapSet(self, mtzdata)  
File "/home/urovsnik/.local/share/ChimeraX/1.4/site-
packages/chimerax/clipper/maps/xmapset.py", line 185, in __init__  
self.init_maps(use_static_maps, use_live_maps,  
File "/home/urovsnik/.local/share/ChimeraX/1.4/site-
packages/chimerax/clipper/maps/xmapset.py", line 257, in init_maps  
self._launch_live_xmap_mgr(crystal_data, fsigf_data)  
File "/home/urovsnik/.local/share/ChimeraX/1.4/site-
packages/chimerax/clipper/maps/xmapset.py", line 442, in _launch_live_xmap_mgr  
xm = self._live_xmap_mgr = Xtal_thread_mgr(self.hklinfo,  
RuntimeError: Cannot determine the correct value for the free reflections in
the given FreeR_flag array. Please convert your reflection file to CCP4 or
PHENIX format using sftools or phenix.reflection_file_editor.  
  
RuntimeError: Cannot determine the correct value for the free reflections in
the given FreeR_flag array. Please convert your reflection file to CCP4 or
PHENIX format using sftools or phenix.reflection_file_editor.  
  
File "/home/urovsnik/.local/share/ChimeraX/1.4/site-
packages/chimerax/clipper/maps/xmapset.py", line 442, in _launch_live_xmap_mgr  
xm = self._live_xmap_mgr = Xtal_thread_mgr(self.hklinfo,  
  
See log for complete Python traceback.  
  

> open
> /home/urovsnik/Desktop/Work/GLIC_model_building/GLIC_Alcohol/RealSpaceRefine_8/fixed01_real_space_refined_008.pdb

Chain information for fixed01_real_space_refined_008.pdb #1  
---  
Chain | Description  
A B C D E | No description available  
  

> open
> /home/urovsnik/Desktop/Work/GLIC_model_building/GLIC_Alcohol/MapToStructureFactors_1/map_to_structure_factors.mtz

Install the Clipper bundle to open "MTZ" format files.  
Opener for format 'MTZ' is not installed; see log for more info  

> open
> /home/urovsnik/Desktop/Work/GLIC_model_building/GLIC_Alcohol/MapToStructureFactors_1/map_to_structure_factors.mtz
> format mtz

Summary of feedback from opening
/home/urovsnik/Desktop/Work/GLIC_model_building/GLIC_Alcohol/MapToStructureFactors_1/map_to_structure_factors.mtz  
---  
notes | Discarding unrecognised/unsupported data array /crystal/dataset/HLA A  
Discarding unrecognised/unsupported data array /crystal/dataset/HLB A  
Discarding unrecognised/unsupported data array /crystal/dataset/HLC A  
Discarding unrecognised/unsupported data array /crystal/dataset/HLD A  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 457, in collated_open  
return remember_data_format()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/home/urovsnik/.local/share/ChimeraX/1.4/site-
packages/chimerax/clipper/__init__.py", line 240, in open  
return open_structure_factors(session, data, **kw)  
File "/home/urovsnik/.local/share/ChimeraX/1.4/site-
packages/chimerax/clipper/cmd.py", line 52, in open_structure_factors  
raise e  
File "/home/urovsnik/.local/share/ChimeraX/1.4/site-
packages/chimerax/clipper/cmd.py", line 32, in open_structure_factors  
xmapset = mmgr.add_xmapset_from_file(path, oversampling_rate=over_sampling,  
File "/home/urovsnik/.local/share/ChimeraX/1.4/site-
packages/chimerax/clipper/maps/map_mgr.py", line 324, in add_xmapset_from_file  
return XmapSet(self, mtzdata)  
File "/home/urovsnik/.local/share/ChimeraX/1.4/site-
packages/chimerax/clipper/maps/xmapset.py", line 185, in __init__  
self.init_maps(use_static_maps, use_live_maps,  
File "/home/urovsnik/.local/share/ChimeraX/1.4/site-
packages/chimerax/clipper/maps/xmapset.py", line 257, in init_maps  
self._launch_live_xmap_mgr(crystal_data, fsigf_data)  
File "/home/urovsnik/.local/share/ChimeraX/1.4/site-
packages/chimerax/clipper/maps/xmapset.py", line 442, in _launch_live_xmap_mgr  
xm = self._live_xmap_mgr = Xtal_thread_mgr(self.hklinfo,  
RuntimeError: Cannot determine the correct value for the free reflections in
the given FreeR_flag array. Please convert your reflection file to CCP4 or
PHENIX format using sftools or phenix.reflection_file_editor.  
  
RuntimeError: Cannot determine the correct value for the free reflections in
the given FreeR_flag array. Please convert your reflection file to CCP4 or
PHENIX format using sftools or phenix.reflection_file_editor.  
  
File "/home/urovsnik/.local/share/ChimeraX/1.4/site-
packages/chimerax/clipper/maps/xmapset.py", line 442, in _launch_live_xmap_mgr  
xm = self._live_xmap_mgr = Xtal_thread_mgr(self.hklinfo,  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 450.51.06
OpenGL renderer: GeForce GTX 980 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7A33
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virtual Machine: none
CPU: 16 AMD Ryzen 7 2700 Eight-Core Processor
Cache Size: 512 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           62Gi       7.0Gi        50Gi       157Mi       5.7Gi        54Gi
	Swap:         979Mi          0B       979Mi

Graphics:
	26:00.0 VGA compatible controller [0300]: NVIDIA Corporation GM200 [GeForce GTX 980 Ti] [10de:17c8] (rev a1)	
	Subsystem: PNY GM200 [GeForce GTX 980 Ti] [196e:1511]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.18.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    distro: 1.6.0
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

[Tristan Croll]

Hmm. I’ll see if I can figure out a way to give a more legible error
message, but it looks like the short story here is: don’t use the output
from map_to_structure_factors with ISOLDE. There’s no need - just use the
real-space map.

On Wed, 14 Sep 2022 at 12:08, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[Tom Goddard]

I made a separate ticket #7595 for the start-up error in the ChimeraX registration code. And I noted the Clipper install error on the existing ticket #7343.

[Tristan Croll]

Handling of map_to_structure_factors MTZ files should be greatly improved in the next ISOLDE version.