core version requirement

[jiwx@…]

The following bug report has been submitted:
Platform:        Windows-8.1-6.3.9600
ChimeraX Version: 0.9 (2019-06-06)
Description
Just open ISOLDE(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: 0.9 (2019-06-06)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
"C:\\\Users\\\Wenxin.Ji\\\Downloads\\\cryosparc_P20_J46_007_volume_map_sharp324.mrc"

Opened cryosparc_P20_J46_007_volume_map_sharp324.mrc, grid size 400,400,400,
pixel 0.82, shown at level 0.0672, step 2, values float32  

> open C:/Users/Wenxin.Ji/Downloads/BNP_20200507_remodeled_v12.pdb

Chain information for BNP_20200507_remodeled_v12.pdb #2  
---  
Chain | Description  
E | No description available  
T | No description available  
Z | No description available  
  

> toolshed show ISOLDE

Traceback (most recent call last):  
File "H:\Download\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 627, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "H:\Download\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1435, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "C:\Users\Wenxin.Ji\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\isolde\\__init__.py", line 31, in start_tool  
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True)  
File "H:\Download\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py", line
214, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File "C:\Users\Wenxin.Ji\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\isolde\tool.py", line 167, in __init__  
from . import isolde  
File "C:\Users\Wenxin.Ji\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\isolde\isolde.py", line 35, in <module>  
from chimerax import clipper  
File "C:\Users\Wenxin.Ji\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\clipper\\__init__.py", line 26, in <module>  
__version__ = _version()  
File "C:\Users\Wenxin.Ji\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\clipper\\__init__.py", line 24, in _version  
return pkg_resources.require('ChimeraX-Clipper')[0].version  
File "H:\Download\ChimeraX\bin\lib\site-packages\pkg_resources\\__init__.py",
line 900, in require  
needed = self.resolve(parse_requirements(requirements))  
File "H:\Download\ChimeraX\bin\lib\site-packages\pkg_resources\\__init__.py",
line 791, in resolve  
raise VersionConflict(dist, req).with_context(dependent_req)  
pkg_resources.ContextualVersionConflict: (ChimeraX-Core 0.9
(h:\download\chimerax\bin\lib\site-packages), Requirement.parse('ChimeraX-
Core==0.93'), {'ChimeraX-Clipper'})  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "H:\Download\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line
1137, in <lambda>  
run(ses, "toolshed show %s" % quote_if_necessary(tool_name)))  
File "H:\Download\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "H:\Download\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2632, in run  
result = ci.function(session, **kw_args)  
File "H:\Download\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\toolshed.py", line 337, in toolshed_show  
bi.start_tool(session, tool_name)  
File "H:\Download\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 633, 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:  
(ChimeraX-Core 0.9 (h:\download\chimerax\bin\lib\site-packages),
Requirement.parse('ChimeraX-Core==0.93'), {'ChimeraX-Clipper'})  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
(ChimeraX-Core 0.9 (h:\download\chimerax\bin\lib\site-packages),
Requirement.parse('ChimeraX-Core==0.93'), {'ChimeraX-Clipper'})  
  
File "H:\Download\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 633, 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.  
  




OpenGL version: 3.3.0 NVIDIA 430.64
OpenGL renderer: Quadro K2200/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Eric Pettersen]

Reported by Wenxin Ji

[Tristan Croll]

Ah. This probably explains #3234. Wenxin, while your initial email said you were using ChimeraX 0.93, your bug report here says you’re actually running 0.9. You need to update to the 0.93 release version of ChimeraX to run ISOLDE.

This suggests a separate bug, though: it looks like “toolshed install isolde” installed ISOLDE despite the version conflict.
 

 

[Tristan Croll]

This looks to be more of a Tool Shed issue.