ISOLDE/OpenMM: trouble loading DLL

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 0.92 (2020-01-28)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.92 (2020-01-28)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\Users\alexa\Desktop\NuA4\NuA4-SS-good-2-coot-7.pdb

Chain information for NuA4-SS-good-2-coot-7.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
  

> show cartoons

> hide atoms

> set bgColor white

> open D:/NuA4-Phenix/MapToStructureFactors_20/map_to_structure_factors.mtz

Must specify a structure model to associate with crystallographic data  

> toolshed show ISOLDE

Traceback (most recent call last):  
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 630, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1612, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "C:\Users\alexa\AppData\Local\UCSF\ChimeraX\0.92\site-
packages\chimerax\isolde\\__init__.py", line 128, in start_tool  
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True)  
File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py",
line 214, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File "C:\Users\alexa\AppData\Local\UCSF\ChimeraX\0.92\site-
packages\chimerax\isolde\tool.py", line 183, in __init__  
from . import isolde  
File "C:\Users\alexa\AppData\Local\UCSF\ChimeraX\0.92\site-
packages\chimerax\isolde\isolde.py", line 30, in <module>  
from .constants import defaults, sim_outcomes, control  
File "C:\Users\alexa\AppData\Local\UCSF\ChimeraX\0.92\site-
packages\chimerax\isolde\constants.py", line 14, in <module>  
from simtk.openmm import VariableLangevinIntegrator, CustomGBForce  
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\simtk\openmm\\__init__.py", line 19, in <module>  
from simtk.openmm.openmm import *  
File "D:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py",
line 28, in <module>  
_openmm = swig_import_helper()  
File "D:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py",
line 24, in swig_import_helper  
_mod = imp.load_module('_openmm', fp, pathname, description)  
File "D:\Program Files\ChimeraX\bin\lib\imp.py", line 242, in load_module  
return load_dynamic(name, filename, file)  
File "D:\Program Files\ChimeraX\bin\lib\imp.py", line 342, in load_dynamic  
return _load(spec)  
ImportError: DLL load failed: Le module spécifié est introuvable.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1331, in <lambda>  
run(ses, "toolshed show %s" % StringArg.unparse(tool_name)))  
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\toolshed.py", line 339, in toolshed_show  
bi.start_tool(session, name)  
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 636, 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: Le module spécifié est introuvable.  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
DLL load failed: Le module spécifié est introuvable.  
  
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 636, 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\alexa\AppData\Local\UCSF\ChimeraX\0.92\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\alexa\AppData\Local\UCSF\ChimeraX\0.92\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 436.48
OpenGL renderer: GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Tristan Croll]

This was caused by a bug in the Intel MKL library used by Numpy breaking subsequent dynamic loading of libraries in Windows. Updating to ChimeraX 0.93 and the matching ISOLDE version should fix it.