id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2647 Updated ChimeraX but not ISOLDE jliu321@… Tristan Croll "{{{ 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 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. }}} " defect closed normal Third Party fixed all ChimeraX