ISOLDE: failure registering 'isolde' command

[torquato@…]

The following bug report has been submitted:
Platform:        Linux-5.15.0-97-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
(Describe the actions that caused this problem to occur here)

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 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show

Downloading bundle ChimeraX_PhenixUI-1.2.2-py3-none-any.whl  
Installed ChimeraX-PhenixUI (1.2.2)  
Downloading bundle MolecularDynamicsViewer-1.4-py3-none-any.whl  
Installed MolecularDynamicsViewer (1.4)  
Downloading bundle ChimeraX_TugLigands-1.1-py3-none-any.whl  
Installed ChimeraX-TugLigands (1.1)  
Downloading bundle ChimeraX_PDBImages-1.2-py3-none-any.whl  
Installed ChimeraX-PDBImages (1.2)  

> open
> /home/ricardo/aakz211/alphafold/prediction/aakz211_alphafold_relaxed.pdb_0015.pdb

Summary of feedback from opening
/home/ricardo/aakz211/alphafold/prediction/aakz211_alphafold_relaxed.pdb_0015.pdb  
---  
warnings | Ignored bad PDB record found on line 1026  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 1027  
#BEGIN_POSE_ENERGIES_TABLE aakz211_alphafold_relaxed.pdb_0015.pdb  
  
Ignored bad PDB record found on line 1028  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13
coordinate_constraint omega fa_dun p_aa_pp yhh_planarity ref rama_prepro total  
  
Ignored bad PDB record found on line 1029  
weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.5 0.4 0.7 0.6 0.625 1 0.45 NA  
  
Ignored bad PDB record found on line 1030  
pose -276.16 49.5133 196.04 0.58039 9.86906 -6.8243 -71.2564 5.26504 -12.2395
-10.6681 -14.7577 -3.95274 -2.44072 58.1571 30.0705 73.8135 -4.72605 0.00131
17.9771 32.4543 70.7171  
  
73 messages similar to the above omitted  
  
Chain information for aakz211_alphafold_relaxed.pdb_0015.pdb #1  
---  
Chain | Description  
A | No description available  
  

> show atoms

> hide atoms

> show cartoons

> show atoms

> show cartoons

> style sphere

Changed 1021 atom styles  

> style sphere

Changed 1021 atom styles  

> hide atoms

> hide cartoons

> show atoms

> color byhetero

> hide surfaces

> show surfaces

> hide surfaces

> hide atoms

> show atoms

> style sphere

Changed 1021 atom styles  

> style stick

Changed 1021 atom styles  

> hide atoms

> show atoms

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for aakz211_alphafold_relaxed.pdb_0015.pdb_A SES surface
#1.1: minimum, -9.93, mean 1.50, maximum 12.36  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp

Map values for surface "aakz211_alphafold_relaxed.pdb_0015.pdb_A SES surface":
minimum -27.07, mean -4.717, maximum 21.14  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic

Coulombic values for aakz211_alphafold_relaxed.pdb_0015.pdb_A SES surface
#1.1: minimum, -9.93, mean 1.50, maximum 12.36  
To also show corresponding color key, enter the above coulombic command and
add key true  

> color byhetero

> color bychain

> color bypolymer

> rainbow

> coulombic

Coulombic values for aakz211_alphafold_relaxed.pdb_0015.pdb_A SES surface
#1.1: minimum, -9.93, mean 1.50, maximum 12.36  
To also show corresponding color key, enter the above coulombic command and
add key true  
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/ricardo/.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/ricardo/.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/ricardo/.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/ricardo/.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 0xc3 in position 422:
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 0xc3 in position 422: 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/ricardo/.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/ricardo/.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 0xc3 in position 422: 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 0xc3 in position 422: 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/ricardo/.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/ricardo/.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/ricardo/.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/ricardo/.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 0xc3 in position 422:
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 0xc3 in position 422: 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/ricardo/.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/ricardo/.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 0xc3 in position 422: 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 0xc3 in position 422: 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 535.161.07
OpenGL renderer: NVIDIA GeForce GTX 1060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: pt_BR.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=cinnamon
XDG_SESSION_DESKTOP=cinnamon
XDG_CURRENT_DESKTOP=X-Cinnamon
DISPLAY=:0
Manufacturer: LENOVO
Model: 81CQ
OS: Linux Mint 21.3 Virginia
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz
Cache Size: 6144 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            15Gi       4.6Gi       455Mi       587Mi        10Gi       9.9Gi
	Swap:          2.8Gi          0B       2.8Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation HD Graphics 630 [8086:591b] (rev 04)	
	Subsystem: Lenovo HD Graphics 630 [17aa:38e1]	
	Kernel driver in use: i915

Installed Packages:
    alabaster: 0.7.13
    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: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    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
    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
    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: 1.5.13
    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: 1.0.3
    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-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: 1.12.3
    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-TugLigands: 1.1
    ChimeraX-UI: 1.33.2
    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: 0.2.0
    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: 4.47.0
    funcparserlib: 2.0.0a0
    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: 5.5.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    MolecularDynamicsViewer: 1.4
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    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: 2.2.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    Pillow: 10.0.1
    pip: 23.0
    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: 0.13.2
    Send2Trash: 1.8.2
    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: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    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: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

[Eric Pettersen]

Reported by Ricardo Torquato