ISOLDER: Scipy symbol not found while registering command

[jean-marc.jeckelmann@…]

The following bug report has been submitted:
Platform:        macOS-11.7.10-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1290, in register_command  
return cls._get_func(api, "register_command")(ci.name, logger)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/__init__.py", line 171, in register_command  
cmd.register_isolde(logger)  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/cmd/cmd.py", line 479, in register_isolde  
from chimerax.isolde.manipulations.cmd import register_manip_commands  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/manipulations/__init__.py", line 12, in <module>  
from .register_shift import ProteinRegisterShifter  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/manipulations/register_shift.py", line 15, in
<module>  
from scipy import interpolate  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/__init__.py", line 134, in __getattr__  
return _importlib.import_module(f'scipy.{name}')  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/importlib/__init__.py",
line 126, in import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/interpolate/__init__.py", line 167, in <module>  
from ._interpolate import *  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/interpolate/_interpolate.py", line 10, in <module>  
import scipy.special as spec  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/__init__.py", line 777, in <module>  
from . import _ufuncs  
File "scipy/special/_ufuncs.pyx", line 1, in init scipy.special._ufuncs  
ImportError:
dlopen(/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/_ufuncs_cxx.cpython-311-darwin.so, 2): Symbol not
found:
__ZTTNSt3__118basic_stringstreamIcNS_11char_traitsIcEENS_9allocatorIcEEEE  
Referenced from:
/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/_ufuncs_cxx.cpython-311-darwin.so (which was built for
Mac OS X 12.0)  
Expected in: /usr/lib/libc++.1.dylib  
in
/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/_ufuncs_cxx.cpython-311-darwin.so  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2475, in lazy_register  
deferred.call()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2403, in call  
return self.proxy()  
^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 320, in cb  
s._register_cmd(ci, logger)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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:  
dlopen(/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/_ufuncs_cxx.cpython-311-darwin.so, 2): Symbol not
found:
__ZTTNSt3__118basic_stringstreamIcNS_11char_traitsIcEENS_9allocatorIcEEEE  
Referenced from:
/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/_ufuncs_cxx.cpython-311-darwin.so (which was built for
Mac OS X 12.0)  
Expected in: /usr/lib/libc++.1.dylib  
in
/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/_ufuncs_cxx.cpython-311-darwin.so  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1306, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/__init__.py", line 184, in run_provider  
toolbar_command(session, name)  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/toolbar.py", line 19, in toolbar_command  
run(session, 'isolde start')  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3139, in run  
self._find_command_name(final, used_aliases=_used_aliases)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2863, in _find_command_name  
what.lazy_register(cmd_name)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2477, in lazy_register  
raise RuntimeError(  
RuntimeError: delayed command registration for 'isolde' failed
(register_command() failed for command isolde in bundle ChimeraX-ISOLDE:  
dlopen(/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/_ufuncs_cxx.cpython-311-darwin.so, 2): Symbol not
found:
__ZTTNSt3__118basic_stringstreamIcNS_11char_traitsIcEENS_9allocatorIcEEEE  
Referenced from:
/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/_ufuncs_cxx.cpython-311-darwin.so (which was built for
Mac OS X 12.0)  
Expected in: /usr/lib/libc++.1.dylib  
in
/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/_ufuncs_cxx.cpython-311-darwin.so)  
  
RuntimeError: delayed command registration for 'isolde' failed
(register_command() failed for command isolde in bundle ChimeraX-ISOLDE:  
dlopen(/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/_ufuncs_cxx.cpython-311-darwin.so, 2): Symbol not
found:
__ZTTNSt3__118basic_stringstreamIcNS_11char_traitsIcEENS_9allocatorIcEEEE  
Referenced from:
/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/_ufuncs_cxx.cpython-311-darwin.so (which was built for
Mac OS X 12.0)  
Expected in: /usr/lib/libc++.1.dylib  
in
/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/_ufuncs_cxx.cpython-311-darwin.so)  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2477, in lazy_register  
raise RuntimeError(  
  
See log for complete Python traceback.  
  

> toolshed show

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
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1290, in register_command  
return cls._get_func(api, "register_command")(ci.name, logger)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/__init__.py", line 171, in register_command  
cmd.register_isolde(logger)  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/cmd/cmd.py", line 479, in register_isolde  
from chimerax.isolde.manipulations.cmd import register_manip_commands  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/manipulations/__init__.py", line 12, in <module>  
from .register_shift import ProteinRegisterShifter  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/manipulations/register_shift.py", line 15, in
<module>  
from scipy import interpolate  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/__init__.py", line 134, in __getattr__  
return _importlib.import_module(f'scipy.{name}')  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/importlib/__init__.py",
line 126, in import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/interpolate/__init__.py", line 167, in <module>  
from ._interpolate import *  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/interpolate/_interpolate.py", line 10, in <module>  
import scipy.special as spec  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/__init__.py", line 777, in <module>  
from . import _ufuncs  
File "scipy/special/_ufuncs.pyx", line 1, in init scipy.special._ufuncs  
ImportError:
dlopen(/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/_ufuncs_cxx.cpython-311-darwin.so, 2): Symbol not
found:
__ZTTNSt3__118basic_stringstreamIcNS_11char_traitsIcEENS_9allocatorIcEEEE  
Referenced from:
/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/_ufuncs_cxx.cpython-311-darwin.so (which was built for
Mac OS X 12.0)  
Expected in: /usr/lib/libc++.1.dylib  
in
/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/_ufuncs_cxx.cpython-311-darwin.so  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2475, in lazy_register  
deferred.call()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2403, in call  
return self.proxy()  
^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 320, in cb  
s._register_cmd(ci, logger)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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:  
dlopen(/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/_ufuncs_cxx.cpython-311-darwin.so, 2): Symbol not
found:
__ZTTNSt3__118basic_stringstreamIcNS_11char_traitsIcEENS_9allocatorIcEEEE  
Referenced from:
/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/_ufuncs_cxx.cpython-311-darwin.so (which was built for
Mac OS X 12.0)  
Expected in: /usr/lib/libc++.1.dylib  
in
/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/_ufuncs_cxx.cpython-311-darwin.so  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1306, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/__init__.py", line 184, in run_provider  
toolbar_command(session, name)  
File "/Users/jmjb/Library/Application Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/toolbar.py", line 19, in toolbar_command  
run(session, 'isolde start')  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3139, in run  
self._find_command_name(final, used_aliases=_used_aliases)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2863, in _find_command_name  
what.lazy_register(cmd_name)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2477, in lazy_register  
raise RuntimeError(  
RuntimeError: delayed command registration for 'isolde' failed
(register_command() failed for command isolde in bundle ChimeraX-ISOLDE:  
dlopen(/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/_ufuncs_cxx.cpython-311-darwin.so, 2): Symbol not
found:
__ZTTNSt3__118basic_stringstreamIcNS_11char_traitsIcEENS_9allocatorIcEEEE  
Referenced from:
/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/_ufuncs_cxx.cpython-311-darwin.so (which was built for
Mac OS X 12.0)  
Expected in: /usr/lib/libc++.1.dylib  
in
/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/_ufuncs_cxx.cpython-311-darwin.so)  
  
RuntimeError: delayed command registration for 'isolde' failed
(register_command() failed for command isolde in bundle ChimeraX-ISOLDE:  
dlopen(/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/_ufuncs_cxx.cpython-311-darwin.so, 2): Symbol not
found:
__ZTTNSt3__118basic_stringstreamIcNS_11char_traitsIcEENS_9allocatorIcEEEE  
Referenced from:
/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/_ufuncs_cxx.cpython-311-darwin.so (which was built for
Mac OS X 12.0)  
Expected in: /usr/lib/libc++.1.dylib  
in
/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/_ufuncs_cxx.cpython-311-darwin.so)  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2477, in lazy_register  
raise RuntimeError(  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 71.7.1
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro17,1
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 8422.141.2
      OS Loader Version: 6723.140.2

Software:

    System Software Overview:

      System Version: macOS 11.7.10 (20G1427)
      Kernel Version: Darwin 20.6.0
      Time since boot: 11:42

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Resolution: 2880 x 1800
          UI Looks like: 1440 x 900 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.23.1
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    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: 1.8
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    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: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    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-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    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: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    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
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11