ISOLDE: The specified module could not be found

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Successfully installed 'ChimeraX_ISOLDE-1.0-cp37-cp37m-win_amd64.whl'  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing
c:\users\dahailuo\appdata\local\ucsf\chimerax\cache\1.0\installers\chimerax_isolde-1.0-cp37-cp37m-win_amd64.whl  
Requirement already satisfied, skipping upgrade: ChimeraX-Clipper~=0.13.0 in
c:\users\dahailuo\appdata\local\ucsf\chimerax\1.0\site-packages (from
ChimeraX-ISOLDE==1.0) (0.13.0)  
Requirement already satisfied, skipping upgrade: ChimeraX-Atomic~=1.0.0 in
c:\program files\chimerax 1.0\bin\lib\site-packages (from ChimeraX-
ISOLDE==1.0) (1.0)  
Requirement already satisfied, skipping upgrade: ChimeraX-Core~=1.0.0 in
c:\program files\chimerax 1.0\bin\lib\site-packages (from ChimeraX-
ISOLDE==1.0) (1.0)  
Requirement already satisfied, skipping upgrade: ChimeraX-Arrays~=1.0 in
c:\program files\chimerax 1.0\bin\lib\site-packages (from ChimeraX-
ISOLDE==1.0) (1.0)  
Requirement already satisfied, skipping upgrade: ChimeraX-Graphics~=1.0 in
c:\program files\chimerax 1.0\bin\lib\site-packages (from ChimeraX-
Atomic~=1.0.0->ChimeraX-ISOLDE==1.0) (1.0)  
Requirement already satisfied, skipping upgrade: ChimeraX-Geometry~=1.0 in
c:\program files\chimerax 1.0\bin\lib\site-packages (from ChimeraX-
Atomic~=1.0.0->ChimeraX-ISOLDE==1.0) (1.0)  
Installing collected packages: ChimeraX-ISOLDE  
Attempting uninstall: ChimeraX-ISOLDE  
Found existing installation: ChimeraX-ISOLDE 1.0  
Uninstalling ChimeraX-ISOLDE-1.0:  
Successfully uninstalled ChimeraX-ISOLDE-1.0  
Successfully installed ChimeraX-ISOLDE-1.0  
Lock 1748436340232 acquired on
C:\Users\dahailuo\AppData\Local\UCSF\ChimeraX\Cache\1.0\toolshed\bundle_info.cache.lock  
Lock 1748436340232 released on
C:\Users\dahailuo\AppData\Local\UCSF\ChimeraX\Cache\1.0\toolshed\bundle_info.cache.lock  
  

WARNING: You are using pip version 20.1; however, version 20.2.1 is available.  
You should consider upgrading via the 'C:\Program Files\ChimeraX
1.0\bin\ChimeraX.exe -m pip install --upgrade pip' command.  
  

> ui tool show ISOLDE

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 531, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1587, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "C:\Users\dahailuo\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\\__init__.py", line 132, in start_tool  
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\tools.py", line 193, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File "C:\Users\dahailuo\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\tool.py", line 185, in __init__  
from . import isolde  
File "C:\Users\dahailuo\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\isolde.py", line 30, in <module>  
from .constants import defaults, sim_outcomes, control  
File "C:\Users\dahailuo\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\constants.py", line 14, in <module>  
from simtk.openmm import VariableLangevinIntegrator, CustomGBForce  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\simtk\openmm\\__init__.py", line 19, in <module>  
from simtk.openmm.openmm import *  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\simtk\openmm\openmm.py", line 28, in <module>  
_openmm = swig_import_helper()  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\simtk\openmm\openmm.py", line 24, in swig_import_helper  
_mod = imp.load_module('_openmm', fp, pathname, description)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\imp.py", line 242, in load_module  
return load_dynamic(name, filename, file)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\imp.py", line 342, in load_dynamic  
return _load(spec)  
ImportError: DLL load failed: The specified module could not be found.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py",
line 1468, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\cmd.py",
line 187, in ui_tool_show  
bi.start_tool(session, name)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 537, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
DLL load failed: The specified module could not be found.  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
DLL load failed: The specified module could not be found.  
  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 537, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\dahailuo\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\ui\util.py", line 19, in showPopup  
if self._width_update_needed:  
AttributeError: 'WinAutoResizeQComboBox' object has no attribute
'_width_update_needed'  
  
AttributeError: 'WinAutoResizeQComboBox' object has no attribute
'_width_update_needed'  
  
File "C:\Users\dahailuo\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\ui\util.py", line 19, in showPopup  
if self._width_update_needed:  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\dahailuo\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\ui\util.py", line 19, in showPopup  
if self._width_update_needed:  
AttributeError: 'WinAutoResizeQComboBox' object has no attribute
'_width_update_needed'  
  
AttributeError: 'WinAutoResizeQComboBox' object has no attribute
'_width_update_needed'  
  
File "C:\Users\dahailuo\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\ui\util.py", line 19, in showPopup  
if self._width_update_needed:  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\dahailuo\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\ui\util.py", line 19, in showPopup  
if self._width_update_needed:  
AttributeError: 'WinAutoResizeQComboBox' object has no attribute
'_width_update_needed'  
  
AttributeError: 'WinAutoResizeQComboBox' object has no attribute
'_width_update_needed'  
  
File "C:\Users\dahailuo\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\ui\util.py", line 19, in showPopup  
if self._width_update_needed:  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\dahailuo\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\ui\util.py", line 19, in showPopup  
if self._width_update_needed:  
AttributeError: 'WinAutoResizeQComboBox' object has no attribute
'_width_update_needed'  
  
AttributeError: 'WinAutoResizeQComboBox' object has no attribute
'_width_update_needed'  
  
File "C:\Users\dahailuo\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\ui\util.py", line 19, in showPopup  
if self._width_update_needed:  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\dahailuo\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\ui\util.py", line 19, in showPopup  
if self._width_update_needed:  
AttributeError: 'WinAutoResizeQComboBox' object has no attribute
'_width_update_needed'  
  
AttributeError: 'WinAutoResizeQComboBox' object has no attribute
'_width_update_needed'  
  
File "C:\Users\dahailuo\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\ui\util.py", line 19, in showPopup  
if self._width_update_needed:  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\dahailuo\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\ui\util.py", line 19, in showPopup  
if self._width_update_needed:  
AttributeError: 'WinAutoResizeQComboBox' object has no attribute
'_width_update_needed'  
  
AttributeError: 'WinAutoResizeQComboBox' object has no attribute
'_width_update_needed'  
  
File "C:\Users\dahailuo\AppData\Local\UCSF\ChimeraX\1.0\site-
packages\chimerax\isolde\ui\util.py", line 19, in showPopup  
if self._width_update_needed:  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 391.25
OpenGL renderer: Quadro K4200/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision Tower 7810
OS: Microsoft Windows 10 Education (Build 18363)
Memory: 68,640,100,352
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

[pett]

This is a newer version of ChimeraX; was the numpy fix after 6/4?

[Greg Couch]

The problem was with numpy 1.18.1 on January 28th where we reverted to 1.17.4. We updated to 1.18.2 on April 19th. ChimeraX 1.0 has 1.18.4.

The error says that the _openmm DLL was not found. Will need Tristan's help.

[Tristan Croll]

Hmm... crap, sorry. Didn't notice that it's the new version. Will try wiping my Windows installation of ISOLDE and reinstalling afresh from the ToolShed. Hopefully it's something simple like needing to restart ChimeraX after the install...

[Tristan Croll]

I can't reproduce this. I just deleted %localappdata%/UCSF/ChimeraX/cache/1.0 and %localappdata%/UCSF/ChimeraX/1.0, then installed ISOLDE from the ToolShed and ran a simulation. Everything ran fine (log output below). What's confusing me is the pattern of messages at the start of the log... looks like maybe the user clicked the install button twice? Will see what happens when I do that...

Log contents:

Startup Messages
note available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Some installed bundles are out of date. Please update the following bundles:
UI to version 1.2.1 (currently 1.0)
UI to version 1.2 (currently 1.0)

toolshed showDownloading bundle ChimeraX_ISOLDE-1.0-cp37-cp37m-win_amd64.whl
Successfully installed ChimeraX-Clipper-0.13.0 ChimeraX-ISOLDE-1.0
Installed ChimeraX-Clipper (0.13.0)
Installed ChimeraX-ISOLDE (1.0)
isolde start
set selectionWidth 4Cached rama8000-cispro data not found. Regenerating from text file. This is normal if running ISOLDE for the first time
Cached rama8000-transpro data not found. Regenerating from text file. This is normal if running ISOLDE for the first time
Cached rama8000-gly-sym data not found. Regenerating from text file. This is normal if running ISOLDE for the first time
Cached rama8000-prepro-noGP data not found. Regenerating from text file. This is normal if running ISOLDE for the first time
Cached rama8000-ileval-nopreP data not found. Regenerating from text file. This is normal if running ISOLDE for the first time
Cached rama8000-general-noGPIVpreP data not found. Regenerating from text file. This is normal if running ISOLDE for the first time
Forcefield cache not found or out of date. Regenerating from ffXML files. This is normal if running ISOLDE for the first time, or after upgrading OpenMM.
Done loading forcefield
isolde demo crystal_intro
Summary of feedback from opening C:\Users\tic20\AppData\Local\UCSF\ChimeraX\1.0\site-packages\chimerax\isolde\demo_data\3io0\before.pdb
warning Ignored bad PDB record found on line 3841
END
before.pdb title:
Crystal structure of etub from clostridium kluyveri [more info...]

Chain information for before.pdb #1
Chain Description
A predicted microcompartment protein
before.pdb title:
Crystal structure of etub from clostridium kluyveri [more info...]

Chain information for before.pdb
Chain Description
1.2/A predicted microcompartment protein
Cached rota8000-val data not found. Regenerating from text file. This is normal if running ISOLDE for the first time
Cached rota8000-leu data not found. Regenerating from text file. This is normal if running ISOLDE for the first time
Cached rota8000-ile data not found. Regenerating from text file. This is normal if running ISOLDE for the first time
Cached rota8000-pro data not found. Regenerating from text file. This is normal if running ISOLDE for the first time
Cached rota8000-phe data not found. Regenerating from text file. This is normal if running ISOLDE for the first time
Cached rota8000-tyr data not found. Regenerating from text file. This is normal if running ISOLDE for the first time
Cached rota8000-trp data not found. Regenerating from text file. This is normal if running ISOLDE for the first time
Cached rota8000-ser data not found. Regenerating from text file. This is normal if running ISOLDE for the first time
Cached rota8000-thr data not found. Regenerating from text file. This is normal if running ISOLDE for the first time
Cached rota8000-cys data not found. Regenerating from text file. This is normal if running ISOLDE for the first time
Cached rota8000-met data not found. Regenerating from text file. This is normal if running ISOLDE for the first time
Cached rota8000-lys data not found. Regenerating from text file. This is normal if running ISOLDE for the first time
Cached rota8000-his data not found. Regenerating from text file. This is normal if running ISOLDE for the first time
Cached rota8000-arg data not found. Regenerating from text file. This is normal if running ISOLDE for the first time
Cached rota8000-asp data not found. Regenerating from text file. This is normal if running ISOLDE for the first time
Cached rota8000-asn data not found. Regenerating from text file. This is normal if running ISOLDE for the first time
Cached rota8000-gln data not found. Regenerating from text file. This is normal if running ISOLDE for the first time
Cached rota8000-glu data not found. Regenerating from text file. This is normal if running ISOLDE for the first time
WARNING: multiple experimental reflection datasets found:
(dataset) FOBS, SIGFOBS,
(dataset) IOBS, SIGIOBS,
(dataset) DANO, SIGDANO,
(dataset) F(+), SIGF(+), F(-), SIGF(-),
(dataset) I(+), SIGI(+), I(-), SIGI(-)
Automatically choosing "(dataset) IOBS, SIGIOBS".
Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes...
Loaded crystallographic demo: PDB ID 3io0
select clearUpdating bulk solvent parameters...

[Tristan Croll]

OK, the message at the start of the log is simply what it looks like when ISOLDE gets reinstalled after restarting ChimeraX. Fine. Anyway, I just installed ISOLDE twice from the Toolshed after deleting the local toolshed directories again. First time installed, second time got the "Bundle is in use and will be reinstalled after restarting ChimeraX" message. Restarted; installation log looks identical to the user's. ISOLDE runs fine.

The reason I hate debugging this sort of error is that the DLL load failed: The specified module could not be found. message is often very misleading. Often it means that attempting to load the DLL threw an exception due to some missing or incompatible dependency. In order to debug you almost have to be at the offending machine, watching with a debugger like procmon to see exactly what's going on as the DLL tries to resolve its dependencies. That was the only way I tracked down the MKL bug.