UnicodeDecodeError from numpy checking for SVE

[ff20042004a@…]

The following bug report has been submitted:
Platform:        Linux-5.15.0-107-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
RuntimeError: delayed command registration for 'isolde' failed (register_command() failed for command isolde in bundle ChimeraX-ISOLDE:
'ascii' codec can't decode byte 0xe6 in position 0: ordinal not in range(128))

File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2229, in lazy_register
raise RuntimeError("delayed command registration for %r failed (%s)" % (cmd_name, e))

See log for complete Python traceback.



Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open refined_028-delH-delUD1.pdb

Chain information for refined_028-delH-delUD1.pdb #1  
---  
Chain | Description  
A | No description available  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 330, in _register_cmd  
api._api_caller.register_command(api, self, ci, logger)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1286, in register_command  
return cls._get_func(api, "register_command")(ci.name, logger)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/user/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/__init__.py", line 170, in register_command  
cmd.register_isolde(logger)  
File "/home/user/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/cmd/cmd.py", line 478, in register_isolde  
from chimerax.isolde.manipulations.cmd import register_manip_commands  
File "/home/user/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/manipulations/__init__.py", line 12, in <module>  
from .register_shift import ProteinRegisterShifter  
File "/home/user/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/manipulations/register_shift.py", line 15, in
<module>  
from scipy import interpolate  
File "<frozen importlib._bootstrap>", line 1231, in _handle_fromlist  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/scipy/__init__.py",
line 189, in __getattr__  
return _importlib.import_module(f'scipy.{name}')  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/importlib/__init__.py", line 126,
in import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/scipy/interpolate/__init__.py", line 167, in <module>  
from ._interpolate import *  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/scipy/interpolate/_interpolate.py", line 12, in <module>  
from . import _fitpack_py  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/scipy/interpolate/_fitpack_py.py", line 10, in <module>  
from ._bsplines import BSpline  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/scipy/interpolate/_bsplines.py", line 9, in <module>  
from scipy.optimize import minimize_scalar  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/scipy/optimize/__init__.py", line 410, in <module>  
from ._minimize import *  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/scipy/optimize/_minimize.py", line 27, in <module>  
from ._trustregion_constr import _minimize_trustregion_constr  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/scipy/optimize/_trustregion_constr/__init__.py", line 4, in <module>  
from .minimize_trustregion_constr import _minimize_trustregion_constr  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/scipy/optimize/_trustregion_constr/minimize_trustregion_constr.py",
line 5, in <module>  
from .._constraints import (  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/scipy/optimize/_constraints.py", line 8, in <module>  
from numpy.testing import suppress_warnings  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/numpy/testing/__init__.py", line 11, in <module>  
from ._private.utils import *  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/numpy/testing/_private/utils.py", line 1253, in <module>  
_SUPPORTS_SVE = check_support_sve()  
^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/numpy/testing/_private/utils.py", line 1247, in check_support_sve  
output = subprocess.run(cmd, capture_output=True, text=True)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/subprocess.py", line 550, in run  
stdout, stderr = process.communicate(input, timeout=timeout)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/subprocess.py", line 1207, in
communicate  
stdout, stderr = self._communicate(input, endtime, timeout)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/subprocess.py", line 2097, in
_communicate  
stdout = self._translate_newlines(stdout,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/subprocess.py", line 1084, in
_translate_newlines  
data = data.decode(encoding, errors)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
UnicodeDecodeError: 'ascii' codec can't decode byte 0xe6 in position 0:
ordinal not in range(128)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2227, in lazy_register  
deferred.call()  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2158, in call  
return self.proxy()  
^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 320, in cb  
s._register_cmd(ci, logger)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 332, in _register_cmd  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: register_command() failed for command
isolde in bundle ChimeraX-ISOLDE:  
'ascii' codec can't decode byte 0xe6 in position 0: ordinal not in range(128)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1302, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/user/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/__init__.py", line 183, in run_provider  
toolbar_command(session, name)  
File "/home/user/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/toolbar.py", line 19, in toolbar_command  
run(session, 'isolde start')  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2843, in run  
self._find_command_name(final, used_aliases=_used_aliases)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2579, in _find_command_name  
what.lazy_register(cmd_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2229, in lazy_register  
raise RuntimeError("delayed command registration for %r failed (%s)" %
(cmd_name, e))  
RuntimeError: delayed command registration for 'isolde' failed
(register_command() failed for command isolde in bundle ChimeraX-ISOLDE:  
'ascii' codec can't decode byte 0xe6 in position 0: ordinal not in range(128))  
  
RuntimeError: delayed command registration for 'isolde' failed
(register_command() failed for command isolde in bundle ChimeraX-ISOLDE:  
'ascii' codec can't decode byte 0xe6 in position 0: ordinal not in range(128))  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2229, in lazy_register  
raise RuntimeError("delayed command registration for %r failed (%s)" %
(cmd_name, e))  
  
See log for complete Python traceback.  
  
FYI: command is replacing existing command: "isolde start"  
FYI: command is replacing existing command: "isolde set"  
FYI: command is replacing existing command: "isolde select"  
FYI: command is replacing existing command: "isolde sim"  
FYI: command is replacing existing command: "isolde report"  
FYI: command is replacing existing command: "isolde ignore"  
FYI: command is replacing existing command: "isolde ~ignore"  
FYI: command is replacing existing command: "isolde tutorial"  
FYI: command is replacing existing command: "isolde demo"  
FYI: command is replacing existing command: "isolde stepto"  
FYI: command is replacing existing command: "isolde jumpto"  
FYI: command is replacing existing command: "isolde adjust bfactors"  
FYI: command is replacing existing command: "isolde shorthand"  
FYI: command is replacing existing command: "isolde remote xmlrpc"  
FYI: command is replacing existing command: "isolde remote rest start"  
FYI: command is replacing existing command: "isolde remote rest info"  
FYI: command is replacing existing command: "isolde remote rest stop"  
FYI: command is replacing existing command: "isolde restrain distances"  
FYI: command is replacing existing command: "isolde restrain single distance"  
FYI: command is replacing existing command: "isolde release distances"  
FYI: command is replacing existing command: "isolde restrain basepairs"  
FYI: command is replacing existing command: "isolde adjust distances"  
FYI: command is replacing existing command: "isolde restrain ligands"  
FYI: command is replacing existing command: "isolde restrain torsions"  
FYI: command is replacing existing command: "isolde adjust torsions"  
FYI: command is replacing existing command: "isolde release torsions"  
FYI: command is replacing existing command: "isolde restrain talosNMR"  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 330, in _register_cmd  
api._api_caller.register_command(api, self, ci, logger)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1286, in register_command  
return cls._get_func(api, "register_command")(ci.name, logger)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/user/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/__init__.py", line 170, in register_command  
cmd.register_isolde(logger)  
File "/home/user/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/cmd/cmd.py", line 478, in register_isolde  
from chimerax.isolde.manipulations.cmd import register_manip_commands  
File "/home/user/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/manipulations/__init__.py", line 12, in <module>  
from .register_shift import ProteinRegisterShifter  
File "/home/user/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/manipulations/register_shift.py", line 15, in
<module>  
from scipy import interpolate  
File "<frozen importlib._bootstrap>", line 1231, in _handle_fromlist  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/scipy/__init__.py",
line 189, in __getattr__  
return _importlib.import_module(f'scipy.{name}')  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/importlib/__init__.py", line 126,
in import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/scipy/interpolate/__init__.py", line 167, in <module>  
from ._interpolate import *  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/scipy/interpolate/_interpolate.py", line 12, in <module>  
from . import _fitpack_py  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/scipy/interpolate/_fitpack_py.py", line 10, in <module>  
from ._bsplines import BSpline  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/scipy/interpolate/_bsplines.py", line 9, in <module>  
from scipy.optimize import minimize_scalar  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/scipy/optimize/__init__.py", line 410, in <module>  
from ._minimize import *  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/scipy/optimize/_minimize.py", line 27, in <module>  
from ._trustregion_constr import _minimize_trustregion_constr  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/scipy/optimize/_trustregion_constr/__init__.py", line 4, in <module>  
from .minimize_trustregion_constr import _minimize_trustregion_constr  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/scipy/optimize/_trustregion_constr/minimize_trustregion_constr.py",
line 5, in <module>  
from .._constraints import (  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/scipy/optimize/_constraints.py", line 8, in <module>  
from numpy.testing import suppress_warnings  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/numpy/testing/__init__.py", line 11, in <module>  
from ._private.utils import *  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/numpy/testing/_private/utils.py", line 1253, in <module>  
_SUPPORTS_SVE = check_support_sve()  
^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/numpy/testing/_private/utils.py", line 1247, in check_support_sve  
output = subprocess.run(cmd, capture_output=True, text=True)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/subprocess.py", line 550, in run  
stdout, stderr = process.communicate(input, timeout=timeout)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/subprocess.py", line 1207, in
communicate  
stdout, stderr = self._communicate(input, endtime, timeout)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/subprocess.py", line 2097, in
_communicate  
stdout = self._translate_newlines(stdout,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/subprocess.py", line 1084, in
_translate_newlines  
data = data.decode(encoding, errors)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
UnicodeDecodeError: 'ascii' codec can't decode byte 0xe6 in position 0:
ordinal not in range(128)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2227, in lazy_register  
deferred.call()  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2158, in call  
return self.proxy()  
^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 320, in cb  
s._register_cmd(ci, logger)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 332, in _register_cmd  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: register_command() failed for command
isolde in bundle ChimeraX-ISOLDE:  
'ascii' codec can't decode byte 0xe6 in position 0: ordinal not in range(128)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1302, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/user/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/__init__.py", line 183, in run_provider  
toolbar_command(session, name)  
File "/home/user/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/toolbar.py", line 19, in toolbar_command  
run(session, 'isolde start')  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2843, in run  
self._find_command_name(final, used_aliases=_used_aliases)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2579, in _find_command_name  
what.lazy_register(cmd_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2229, in lazy_register  
raise RuntimeError("delayed command registration for %r failed (%s)" %
(cmd_name, e))  
RuntimeError: delayed command registration for 'isolde' failed
(register_command() failed for command isolde in bundle ChimeraX-ISOLDE:  
'ascii' codec can't decode byte 0xe6 in position 0: ordinal not in range(128))  
  
RuntimeError: delayed command registration for 'isolde' failed
(register_command() failed for command isolde in bundle ChimeraX-ISOLDE:  
'ascii' codec can't decode byte 0xe6 in position 0: ordinal not in range(128))  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2229, in lazy_register  
raise RuntimeError("delayed command registration for %r failed (%s)" %
(cmd_name, e))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 535.171.04
OpenGL renderer: NVIDIA RTX A4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: zh_CN.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=xfce
XDG_SESSION_DESKTOP=xfce
XDG_CURRENT_DESKTOP=XFCE
DISPLAY=:0.0
Manufacturer: Dell Inc.
Model: Precision 7920 Tower
OS: Ubuntu 20.04 Focal Fossa
Architecture: 64bit ELF
Virtual Machine: none
CPU: 80 Intel(R) Xeon(R) Gold 5218R CPU @ 2.10GHz
Cache Size: 28160 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:          471Gi       5.1Gi       447Gi       262Mi        19Gi       463Gi
	Swap:         2.0Gi          0B       2.0Gi

Graphics:
	0000:17:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:24b0] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:14ad]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-ArtiaX: 0.3
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.22.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.7.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBImages: 1.2
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PhenixUI: 1.2.2
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-QScore: 1.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RIBFIND: 0.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StarMap: 1.2.15
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-XMAS: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    et-xmlfile: 1.1.0
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    geomdl: 5.3.1
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    MolecularDynamicsViewer: 1.4
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openpyxl: 3.1.2
    openvr: 1.23.701
    packaging: 23.2
    pandas: 2.1.4
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 24.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    pyqtgraph: 0.13.3
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    QtRangeSlider: 0.1.5
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    seaborn: 0.13.1
    SEQCROW: 1.8.7
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    starfile: 0.5.2
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

[Eric Pettersen]

Reported by Feng

[Tom Goddard]

This is a numpy (standard Python numeric library) bug. It may be fixed in newer numpy versions used by the ChimeraX daily build or ChimeraX 1.8 release candidate. You might want to try those newer ChimeraX versions. It happens because a linux utility lscpu is being used by numpy and its output has non-utf8 encoding when a non-English locale is being used on the computer. More details are in bug report #14621

​https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/14721