Failure importing clipper_python

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Errors  
---  
error | Bundle 'ChimeraX-Clipper' custom initialization failed  
warning | Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 501, in get_module  
m = importlib.import_module(self.package_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\importlib\\__init__.py", line 126,
in import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "<frozen importlib._bootstrap>", line 1204, in _gcd_import  
File "<frozen importlib._bootstrap>", line 1176, in _find_and_load  
File "<frozen importlib._bootstrap>", line 1147, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 690, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 940, in exec_module  
File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed  
File "C:\Users\86139\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\clipper\\__init__.py", line 39, in <module>  
from .clipper_python import (  
ImportError: DLL load failed while importing clipper_python: 找不到指定的模块。  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 375, in initialize  
api = self._get_api(session.logger)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 520, in _get_api  
m = self.get_module()  
^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 503, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-
Clipper's module: DLL load failed while importing clipper_python: 找不到指定的模块。  
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  

> open D:\GYY\GYY-
> work\hainanU\manuscripts\2_DCE\DCE_作图/ae46_refine_73-coot-9_refmac1.pdb

Summary of feedback from opening D:\GYY\GYY-
work\hainanU\manuscripts\2_DCE\DCE_作图/ae46_refine_73-coot-9_refmac1.pdb  
---  
warnings | Ignored bad PDB record found on line 95  
MODRES NAG E 1 NAG-b-D RENAME  
  
Ignored bad PDB record found on line 96  
MODRES FUC E 2 FUC-b-L RENAME  
  
Ignored bad PDB record found on line 97  
MODRES MAN E 3 MAN-b-D RENAME  
  
Ignored bad PDB record found on line 98  
MODRES NAG F 1 NAG-b-D RENAME  
  
Ignored bad PDB record found on line 99  
MODRES MAN F 2 MAN-b-D RENAME  
  
20 messages similar to the above omitted  
  
Chain information for ae46_refine_73-coot-9_refmac1.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C D | No description available  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 501, in get_module  
m = importlib.import_module(self.package_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\importlib\\__init__.py", line 126,
in import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "<frozen importlib._bootstrap>", line 1204, in _gcd_import  
File "<frozen importlib._bootstrap>", line 1176, in _find_and_load  
File "<frozen importlib._bootstrap>", line 1147, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 690, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 940, in exec_module  
File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed  
File "C:\Users\86139\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\clipper\\__init__.py", line 39, in <module>  
from .clipper_python import (  
ImportError: DLL load failed while importing clipper_python: 找不到指定的模块。  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 329, in _register_cmd  
api = self._get_api(logger)  
^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 520, in _get_api  
m = self.get_module()  
^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 503, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-
Clipper's module: DLL load failed while importing clipper_python: 找不到指定的模块。  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2475, in lazy_register  
deferred.call()  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2403, in call  
return self.proxy()  
^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 320, in cb  
s._register_cmd(ci, logger)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 332, in _register_cmd  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: register_command() failed for command
clipper in bundle ChimeraX-Clipper:  
Error importing bundle ChimeraX-Clipper's module: DLL load failed while
importing clipper_python: 找不到指定的模块。  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3139, in run  
self._find_command_name(final, used_aliases=_used_aliases)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2863, in _find_command_name  
what.lazy_register(cmd_name)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2477, in lazy_register  
raise RuntimeError(  
RuntimeError: delayed command registration for 'clipper' failed
(register_command() failed for command clipper in bundle ChimeraX-Clipper:  
Error importing bundle ChimeraX-Clipper's module: DLL load failed while
importing clipper_python: 找不到指定的模块。)  
  
RuntimeError: delayed command registration for 'clipper' failed
(register_command() failed for command clipper in bundle ChimeraX-Clipper:  
Error importing bundle ChimeraX-Clipper's module: DLL load failed while
importing clipper_python: 找不到指定的模块。)  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2477, in lazy_register  
raise RuntimeError(  
  
See log for complete Python traceback.  
  

> isolde start

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1306, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\86139\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\\__init__.py", line 184, in run_provider  
toolbar_command(session, name)  
File "C:\Users\86139\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\toolbar.py", line 19, in toolbar_command  
run(session, 'isolde start')  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\86139\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\cmd\cmd.py", line 29, in isolde_start  
get_singleton(session, show_splash=show_splash)  
File "C:\Users\86139\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\cmd\cmd.py", line 20, in get_singleton  
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=create,
show_splash=show_splash)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\tools.py", line 216, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\86139\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\tool.py", line 29, in __init__  
isolde = Isolde(session)  
^^^^^^^^^^^^^^^  
File "C:\Users\86139\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\isolde.py", line 301, in __init__  
self._prepare_environment()  
File "C:\Users\86139\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\isolde.py", line 321, in _prepare_environment  
from chimerax.clipper import symmetry  
File "C:\Users\86139\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\clipper\\__init__.py", line 39, in <module>  
from .clipper_python import (  
ImportError: DLL load failed while importing clipper_python: 找不到指定的模块。  
  
ImportError: DLL load failed while importing clipper_python: 找不到指定的模块。  
  
File "C:\Users\86139\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\clipper\\__init__.py", line 39, in  
from .clipper_python import (  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 560.94
OpenGL renderer: NVIDIA GeForce RTX 3070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: zh_CN.cp936
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows

Manufacturer: Dell Inc.
Model: XPS 8940
OS: Microsoft Windows 11 家庭中文版 (Build 22621)
Memory: 34,005,581,824
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i7-10700K CPU @ 3.80GHz
OSLanguage: zh-CN

Installed Packages:
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    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
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    certifi: 2024.6.2
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    ChimeraX-AddCharge: 1.5.17
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    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
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    ChimeraX-BugReporter: 1.0.1
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    ChimeraX-ConnectStructure: 2.0.1
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    ChimeraX-Core: 1.8
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    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
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    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
    WMI: 1.5.1

[pett]

The Chinese translates to: The specified module could not be found

[Tristan Croll]

This is the sort of issue that in my experience is near-impossible to diagnose without sitting down on the offending system (and even then Python can make it unduly hard). Python has a habit of returning that generic message even if the compiled library *exists* and is *found*, but fails to *load*... and figuring out *why* it fails to load can be enormously painful.