ISOLDE in old ChimeraX 0.9 daily

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Darwin-15.6.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-04-09)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.9 (2019-04-09)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Downloading bundle ChimeraX_ISOLDE-1.0b3-cp37-cp37m-macosx_10_9_x86_64.whl  
Successfully installed ChimeraX-Clipper-0.9.7 ChimeraX-ISOLDE-1.0b3  
Installed ChimeraX-Clipper (0.9.7)  
Installed ChimeraX-ISOLDE (1.0b3)  
Downloading bundle ChimeraX_ISOLDE-1.0b3-cp37-cp37m-macosx_10_9_x86_64.whl  

> help help:credits.html

> help help:quickstart

unloading module chimerax.isolde  
Successfully installed ChimeraX-ISOLDE-1.0b3  
Installed ChimeraX-ISOLDE (1.0b3)  

> open /Users/hrb/Desktop/bovine/bovine_Active_27_real_space_refined.pdb

Chain information for bovine_Active_27_real_space_refined.pdb #1  
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s | No description available  
  

> open /Users/hrb/Desktop/bovine/active_bov_mask213_mtf.mrc

Opened active_bov_mask213_mtf.mrc, grid size 450,450,450, pixel 1.05, shown at
level 0.0125, step 2, values float32  

> hide #!1.1 models

> hide #!1.2 models

> hide #!1 models

> hide #!2 models

> show #!2 models

> show #!1 models

> hide #!1 models

> show #!1.1 models

> show #!1.2 models

> ui mousemode rightMode "place marker"

> ui mousemode rightMode "place marker"

> preset '"initial styles"' "original look"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset '"initial styles"' "original look"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset '"initial styles"' sticks

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> hbonds selAtoms

5816 hydrogen bonds found  

> color selAtoms byhetero

> ui mousemode rightMode minimize

> style selAtoms stick

Changed 133121 atom styles  

> hbonds selAtoms

5816 hydrogen bonds found  

> hide #!1.3 models

> hide #!1.2 models

> 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 "/Users/hrb/Library/Application Support/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
"/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 "/Users/hrb/Library/Application Support/ChimeraX/0.9/site-
packages/chimerax/isolde/tool.py", line 168, in __init__  
self.isolde = isolde.Isolde(self)  
File "/Users/hrb/Library/Application Support/ChimeraX/0.9/site-
packages/chimerax/isolde/isolde.py", line 320, in __init__  
self._start_gui(gui)  
File "/Users/hrb/Library/Application Support/ChimeraX/0.9/site-
packages/chimerax/isolde/isolde.py", line 442, in _start_gui  
self._prepare_environment()  
File "/Users/hrb/Library/Application Support/ChimeraX/0.9/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 INTEL-10.14.74
OpenGL renderer: Intel(R) Iris(TM) Pro Graphics 6200
OpenGL vendor: Intel Inc.

[Tristan Croll]

Same daily build as #2352, but different user directory. Still, since it's anonymous there's once again not much to do but close the ticket.

[Tristan Croll]

Update: *not* the same daily build (about a week different) and the user in question just came to see me in person. All sorted out.