ISOLDE environment preparation -- running a command: Expected a keyword

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Darwin-18.2.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-04-19)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.9 (2019-04-19)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/maozhouhe/Document/NIDVD/1.
Manuscript_preparation/HPV58-netrulization/20190528-Figure/Complex-
figure/5G9/5G9-MDFF.pdb"

Summary of feedback from opening /Users/maozhouhe/Document/NIDVD/1.
Manuscript_preparation/HPV58-netrulization/20190528-Figure/Complex-
figure/5G9/5G9-MDFF.pdb  
---  
warnings | Ignored bad PDB record found on line 181  
  
  
Ignored bad PDB record found on line 182  
  
  
Ignored bad PDB record found on line 183  
ALLOWED : 7.78 %  
  
Ignored bad PDB record found on line 184  
CIS-PROLINE : 5.02283105023  
  
Ignored bad PDB record found on line 185  
CIS-GENERAL : 0.0334672021419  
  
18 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (427 )  
  
Chain information for 5G9-MDFF.pdb #1  
---  
Chain | Description  
A | No description available  
B C E | No description available  
D | No description available  
H | No description available  
L | No description available  
  

> 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 623, 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 1397, 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 2602, 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 1054, 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 2631, 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 629, 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 629, 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-2.4.9
OpenGL renderer: AMD Radeon Pro 455 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[Tristan Croll]

Looks like an API change? Will sort it out first thing tomorrow.

[Eric Pettersen]

I'm not aware of any command that ISOLDE would be likely to use whose syntax has changed recently. Nonetheless, _something_ happened. Will be interested to hear what changed.

[Tristan Croll]

Oh, I see. It *is* an API change, but in the wrong direction. They're using an old pre-release daily build of ChimeraX 0.9 (2019-04-19 vs 2019-06-06 for the 0.9 stable release). Must be before the set selectionWidth command was implemented. Since it's an anonymous report there's not much to do other than close this.