Updated ChimeraX but not ISOLDE

[jliu321@…]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-12-04)
Description
still has the same problem with opening isolde. Just re-downloaded chimerax from the website. How can I solve it? 

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.91 (2019-12-04)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show ISOLDE

> set selectionWidth 4

Traceback (most recent call last):  
File
"/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 627, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File
"/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1612, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "/Users/jingliu/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/__init__.py", line 48, in start_tool  
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True)  
File
"/Users/jingliu/Desktop/ChimeraX_Daily.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/jingliu/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/tool.py", line 168, in __init__  
self.isolde = isolde.Isolde(self)  
File "/Users/jingliu/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 307, in __init__  
self._start_gui(gui)  
File "/Users/jingliu/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 444, in _start_gui  
self._populate_menus_and_update_params()  
File "/Users/jingliu/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 543, in
_populate_menus_and_update_params  
self._update_model_list(None, None, force=True)  
File "/Users/jingliu/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 945, in _update_model_list  
from chimerax.clipper.symmetry import Symmetry_Manager  
ImportError: cannot import name 'Symmetry_Manager' from
'chimerax.clipper.symmetry' (/Users/jingliu/Library/Application
Support/ChimeraX/0.91/site-packages/chimerax/clipper/symmetry.py)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1315, in <lambda>  
run(ses, "toolshed show %s" % StringArg.unparse(tool_name)))  
File
"/Users/jingliu/Desktop/ChimeraX_Daily.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
"/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File
"/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/toolshed.py", line 339, in toolshed_show  
bi.start_tool(session, name)  
File
"/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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:  
cannot import name 'Symmetry_Manager' from 'chimerax.clipper.symmetry'
(/Users/jingliu/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py)  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
cannot import name 'Symmetry_Manager' from 'chimerax.clipper.symmetry'
(/Users/jingliu/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py)  
  
File
"/Users/jingliu/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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: 4.1 INTEL-12.10.12
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.

[Tristan Croll]

If you go to the ToolShed (Tools/More Tools...), click on the ISOLDE link and then click the "Install" button on the right, this should fix it. Please let me know if it doesn't.

[jliu321@…]

Thanks. Yes, re-install isolde fixes the problem.

Thank you.

Jing
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Thursday, December 5, 2019 12:29 AM
Cc: Jing Liu <jliu321@stanford.edu>; tic20@cam.ac.uk <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #2647: Updated ChimeraX but not ISOLDE

#2647: Updated ChimeraX but not ISOLDE
----------------------------------+---------------------------
          Reporter:  jliu321@…    |      Owner:  Tristan Croll
              Type:  defect       |     Status:  assigned
          Priority:  normal       |  Milestone:
         Component:  Third Party  |    Version:
        Resolution:               |   Keywords:
        Blocked By:               |   Blocking:
Notify when closed:               |   Platform:  all
           Project:  ChimeraX     |
----------------------------------+---------------------------

Comment (by Tristan Croll):

 If you go to the ToolShed (Tools/More Tools...), click on the ISOLDE link
 and then click the "Install" button on the right, this should fix it.
 Please let me know if it doesn't.

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2647#comment:2>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
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