ISOLDE run from ChimeraX 0.9 daily rather than final

[mgm@…]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-04-09)
Description
(Describe the actions that caused this problem to occur here)Have just installed a fresh copy of ChimeraX and Isolde and get the following message on start up of ISOLDE:chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in bundle ChimeraX-ISOLDE: Expected a keyword File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/toolshed/info.py", line 631, 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.



Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.9 (2019-04-09)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/mgm/.mnt/Suffolk/data/atpase_em/bov_dimer/mgm/processing/rel-
local_DLS-02_state1-k3-class003_fo-a-p-stalk-mask_post-Flat-FSC-
mask_ext2-soft16_autob.mrc

Opened rel-local_DLS-02_state1-k3-class003_fo-a-p-stalk-mask_post-Flat-FSC-
mask_ext2-soft16_autob.mrc, grid size 500,500,500, pixel 1.05, shown at level
0.00474, step 2, values float32  

> toolshed show ISOLDE

Expected a keyword  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 625, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1417, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/isolde/__init__.py", line 31, in start_tool  
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/tools.py", line 214, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/isolde/tool.py", line 168, in __init__  
self.isolde = isolde.Isolde(self)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/isolde/isolde.py", line 320, in __init__  
self._start_gui(gui)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/isolde/isolde.py", line 442, in _start_gui  
self._prepare_environment()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/isolde/isolde.py", line 335, in _prepare_environment  
run(session, 'set selectionWidth
{}'.format(self.params.selection_outline_width))  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2599, in run  
raise UserError(self._error)  
chimerax.core.errors.UserError: Expected a keyword  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1053, in <lambda>  
run(ses, "toolshed show %s" % quote_if_necessary(tool_name)))  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2628, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/toolshed.py", line 337, in toolshed_show  
bi.start_tool(session, tool_name)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 631, 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:  
Expected a keyword  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
Expected a keyword  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 631, 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: 4.1 ATI-2.11.20
OpenGL renderer: AMD Radeon RX Vega 56 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[mgm@…]

Hi Tristan,

Please ignore the bug report I submitted earlier where I was getting an error message on launching isolde.  I had done a fresh install of ChimeraX (June version of 0.9) but had not realised the current version is now called ChimeraX-0.9.app and so after installing, I had simply clicked the existing ChimeraX icon in my dock having assumed the new version had replaced the old version.  This launched the April version of 0.9 which was still in my Applications folder as it is called ChimeraX.app.  I have removed that version and everything is working perfectly in ChimeraX-0.9.app.

Apologies
MGM




Martin G Montgomery
Senior Investigative Scientist
ATP Synthase Group
MRC Mitochondrial Biology Unit
University of Cambridge
The Keith Peters Building
Cambridge Biomedical Campus
Hills Road 
Cambridge
Great Britain
CB2 0XY

www.mrc-mbu.cam.ac.uk