Opened 9 months ago

Closed 9 months ago

Last modified 9 months ago

#16703 closed defect (fixed)

ISOLDE/OpenMM in 1.10

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc: Greg Couch, Tom Goddard, Tristan Croll
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-15.2-arm64-arm-64bit
ChimeraX Version: 1.10.dev202501242328 (2025-01-24 23:28:17 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.10.dev202501242328 (2025-01-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/hot4cryo/Desktop/Proteasome_in_Halle_Jan2025/cryosparc_P85_J121_006_volume_map_sharp.mrc

Opened cryosparc_P85_J121_006_volume_map_sharp.mrc as #1, grid size
640,640,640, pixel 0.467, shown at level 0.0534, step 4, values float32  

> open
> /Users/hot4cryo/Desktop/Proteasome_in_Halle_Jan2025/Test_P20S_R25_real_space_refined_032.pdb

Chain information for Test_P20S_R25_real_space_refined_032.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I W | No description available  
J X | No description available  
K | No description available  
L | No description available  
M a | No description available  
N b | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
Y | No description available  
Z | No description available  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1403, in register_command  
return cls._get_func(api, "register_command")(ci.name, logger)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/hot4cryo/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/isolde/__init__.py",
line 170, in register_command  
cmd.register_isolde(logger)  
File "/Users/hot4cryo/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/isolde/cmd/cmd.py",
line 462, in register_isolde  
register_isolde_set()  
File "/Users/hot4cryo/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/isolde/cmd/cmd.py",
line 343, in register_isolde_set  
from chimerax.isolde.openmm.sim_param_mgr import fidelity_modes  
File "/Users/hot4cryo/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/openmm/__init__.py", line 12, in <module>  
from .openmm_interface import SimManager, SimHandler, OpenmmThreadHandler, \  
File "/Users/hot4cryo/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 24, in <module>  
from chimerax.isolde._openmm_async import OpenmmThreadHandler as
_OpenmmThreadHandlerBase  
ImportError: dlopen(/Users/hot4cryo/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/_openmm_async.cpython-311-darwin.so, 0x0002): Library
not loaded: @rpath/libOpenMM.8.0.dylib  
Referenced from: <5B912790-F8B3-3EB5-8165-758BE6829F1E>
/Users/hot4cryo/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/_openmm_async.cpython-311-darwin.so  
Reason: tried: '/Users/hot4cryo/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/libOpenMM.8.0.dylib' (no such file),
'/Users/hot4cryo/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/libOpenMM.8.0.dylib' (no such file),
'/Applications/ChimeraX_Daily.app/Contents/lib/libOpenMM.8.0.dylib' (no such
file),
'/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/libOpenMM.8.0.dylib'
(no such file), '/usr/lib/libOpenMM.8.0.dylib' (no such file, not in dyld
cache)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.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_Daily.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_Daily.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_Daily.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(/Users/hot4cryo/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/_openmm_async.cpython-311-darwin.so, 0x0002): Library
not loaded: @rpath/libOpenMM.8.0.dylib  
Referenced from: <5B912790-F8B3-3EB5-8165-758BE6829F1E>
/Users/hot4cryo/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/_openmm_async.cpython-311-darwin.so  
Reason: tried: '/Users/hot4cryo/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/libOpenMM.8.0.dylib' (no such file),
'/Users/hot4cryo/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/libOpenMM.8.0.dylib' (no such file),
'/Applications/ChimeraX_Daily.app/Contents/lib/libOpenMM.8.0.dylib' (no such
file),
'/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/libOpenMM.8.0.dylib'
(no such file), '/usr/lib/libOpenMM.8.0.dylib' (no such file, not in dyld
cache)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 215, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1419, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/hot4cryo/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/isolde/__init__.py",
line 183, in run_provider  
toolbar_command(session, name)  
File "/Users/hot4cryo/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/isolde/toolbar.py",
line 19, in toolbar_command  
run(session, 'isolde start')  
File
"/Applications/ChimeraX_Daily.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_Daily.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_Daily.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_Daily.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(/Users/hot4cryo/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/_openmm_async.cpython-311-darwin.so, 0x0002): Library
not loaded: @rpath/libOpenMM.8.0.dylib  
Referenced from: <5B912790-F8B3-3EB5-8165-758BE6829F1E>
/Users/hot4cryo/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/_openmm_async.cpython-311-darwin.so  
Reason: tried: '/Users/hot4cryo/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/libOpenMM.8.0.dylib' (no such file),
'/Users/hot4cryo/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/libOpenMM.8.0.dylib' (no such file),
'/Applications/ChimeraX_Daily.app/Contents/lib/libOpenMM.8.0.dylib' (no such
file),
'/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/libOpenMM.8.0.dylib'
(no such file), '/usr/lib/libOpenMM.8.0.dylib' (no such file, not in dyld
cache))  
  
RuntimeError: delayed command registration for 'isolde' failed
(register_command() failed for command isolde in bundle ChimeraX-ISOLDE:  
dlopen(/Users/hot4cryo/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/_openmm_async.cpython-311-darwin.so, 0x0002): Library
not loaded: @rpath/libOpenMM.8.0.dylib  
Referenced from: <5B912790-F8B3-3EB5-8165-758BE6829F1E>
/Users/hot4cryo/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/_openmm_async.cpython-311-darwin.so  
Reason: tried: '/Users/hot4cryo/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/libOpenMM.8.0.dylib' (no such file),
'/Users/hot4cryo/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/libOpenMM.8.0.dylib' (no such file),
'/Applications/ChimeraX_Daily.app/Contents/lib/libOpenMM.8.0.dylib' (no such
file),
'/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/libOpenMM.8.0.dylib'
(no such file), '/usr/lib/libOpenMM.8.0.dylib' (no such file, not in dyld
cache))  
  
File
"/Applications/ChimeraX_Daily.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.  
  
FYI: command is replacing existing command: "isolde start"  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1403, in register_command  
return cls._get_func(api, "register_command")(ci.name, logger)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/hot4cryo/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/isolde/__init__.py",
line 170, in register_command  
cmd.register_isolde(logger)  
File "/Users/hot4cryo/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/isolde/cmd/cmd.py",
line 482, in register_isolde  
from chimerax.isolde.openmm.cmd import register_ff_cmd  
File "/Users/hot4cryo/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/openmm/__init__.py", line 12, in <module>  
from .openmm_interface import SimManager, SimHandler, OpenmmThreadHandler, \  
File "/Users/hot4cryo/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 24, in <module>  
from chimerax.isolde._openmm_async import OpenmmThreadHandler as
_OpenmmThreadHandlerBase  
ImportError: dlopen(/Users/hot4cryo/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/_openmm_async.cpython-311-darwin.so, 0x0002): Library
not loaded: @rpath/libOpenMM.8.0.dylib  
Referenced from: <5B912790-F8B3-3EB5-8165-758BE6829F1E>
/Users/hot4cryo/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/_openmm_async.cpython-311-darwin.so  
Reason: tried: '/Users/hot4cryo/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/libOpenMM.8.0.dylib' (no such file),
'/Users/hot4cryo/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/libOpenMM.8.0.dylib' (no such file),
'/Applications/ChimeraX_Daily.app/Contents/lib/libOpenMM.8.0.dylib' (no such
file),
'/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/libOpenMM.8.0.dylib'
(no such file), '/usr/lib/libOpenMM.8.0.dylib' (no such file, not in dyld
cache)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.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_Daily.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_Daily.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_Daily.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(/Users/hot4cryo/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/_openmm_async.cpython-311-darwin.so, 0x0002): Library
not loaded: @rpath/libOpenMM.8.0.dylib  
Referenced from: <5B912790-F8B3-3EB5-8165-758BE6829F1E>
/Users/hot4cryo/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/_openmm_async.cpython-311-darwin.so  
Reason: tried: '/Users/hot4cryo/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/libOpenMM.8.0.dylib' (no such file),
'/Users/hot4cryo/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/libOpenMM.8.0.dylib' (no such file),
'/Applications/ChimeraX_Daily.app/Contents/lib/libOpenMM.8.0.dylib' (no such
file),
'/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/libOpenMM.8.0.dylib'
(no such file), '/usr/lib/libOpenMM.8.0.dylib' (no such file, not in dyld
cache)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 215, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1419, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/hot4cryo/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/isolde/__init__.py",
line 183, in run_provider  
toolbar_command(session, name)  
File "/Users/hot4cryo/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/isolde/toolbar.py",
line 19, in toolbar_command  
run(session, 'isolde start')  
File
"/Applications/ChimeraX_Daily.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_Daily.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_Daily.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_Daily.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(/Users/hot4cryo/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/_openmm_async.cpython-311-darwin.so, 0x0002): Library
not loaded: @rpath/libOpenMM.8.0.dylib  
Referenced from: <5B912790-F8B3-3EB5-8165-758BE6829F1E>
/Users/hot4cryo/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/_openmm_async.cpython-311-darwin.so  
Reason: tried: '/Users/hot4cryo/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/libOpenMM.8.0.dylib' (no such file),
'/Users/hot4cryo/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/libOpenMM.8.0.dylib' (no such file),
'/Applications/ChimeraX_Daily.app/Contents/lib/libOpenMM.8.0.dylib' (no such
file),
'/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/libOpenMM.8.0.dylib'
(no such file), '/usr/lib/libOpenMM.8.0.dylib' (no such file, not in dyld
cache))  
  
RuntimeError: delayed command registration for 'isolde' failed
(register_command() failed for command isolde in bundle ChimeraX-ISOLDE:  
dlopen(/Users/hot4cryo/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/_openmm_async.cpython-311-darwin.so, 0x0002): Library
not loaded: @rpath/libOpenMM.8.0.dylib  
Referenced from: <5B912790-F8B3-3EB5-8165-758BE6829F1E>
/Users/hot4cryo/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/_openmm_async.cpython-311-darwin.so  
Reason: tried: '/Users/hot4cryo/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/libOpenMM.8.0.dylib' (no such file),
'/Users/hot4cryo/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/libOpenMM.8.0.dylib' (no such file),
'/Applications/ChimeraX_Daily.app/Contents/lib/libOpenMM.8.0.dylib' (no such
file),
'/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/libOpenMM.8.0.dylib'
(no such file), '/usr/lib/libOpenMM.8.0.dylib' (no such file, not in dyld
cache))  
  
File
"/Applications/ChimeraX_Daily.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 - 89.3
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,9
      Model Number: MPHE3GR/A
      Chip: Apple M2 Pro
      Total Number of Cores: 10 (6 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.61.3
      OS Loader Version: 11881.61.3

Software:

    System Software Overview:

      System Version: macOS 15.2 (24C101)
      Kernel Version: Darwin 24.2.0
      Time since boot: 3 days, 19 hours, 21 minutes

Graphics/Displays:

    Apple M2 Pro:

      Chipset Model: Apple M2 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.8.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.2.0
    autocommand: 2.2.2
    babel: 2.16.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.1
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.18
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    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: 2.3
    ChimeraX-Clipper: 0.23.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.dev202501242328
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.7
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ISOLDE: 1.8.dev0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.5.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    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-MutationScores: 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: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.7
    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: 1.1.2
    ChimeraX-ProfileGrids: 1.0.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.15
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    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: 2.5.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.43
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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: 1.3.1
    coverage: 7.6.10
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.12
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.15.4
    fonttools: 4.55.6
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
    importlib_resources: 6.4.0
    inflect: 7.3.1
    iniconfig: 2.0.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    jedi: 0.19.1
    Jinja2: 3.1.5
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.8
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    more-itertools: 10.3.0
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    ordered-set: 4.1.0
    packaging: 23.2
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    platformdirs: 4.2.2
    pluggy: 1.5.0
    prompt_toolkit: 3.0.50
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.1
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    pytest: 8.3.4
    pytest-cov: 6.0.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4.2
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.12.2
    typing_extensions: 4.12.2
    tzdata: 2025.1
    urllib3: 2.3.0
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    zipp: 3.19.2

Change History (4)

comment:1 by Eric Pettersen, 9 months ago

Cc: Greg Couch Tom Goddard Tristan Croll added
Component: Unassigned → Third Party
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → ISOLDE/OpenMM in 1.10

Should we edit the ISOLDE Toolshed requirements to add <1.10?

comment:2 by Tristan Croll, 9 months ago 

That sounds like the best solution. Sorry for the hassle.

On Mon, 27 Jan 2025 at 19:15, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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comment:3 by Eric Pettersen, 9 months ago

Resolution: → fixed
Status: accepted → closed

There are _lot_ of ISOLDE releases. Added the requirement to the 1.9 and 1.8 releases.

comment:4 by Tristan Croll, 9 months ago 

:)

I’m pretty sure all the older ones are safe. Will double check tomorrow.

On Mon, 27 Jan 2025 at 20:00, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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