id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2352 ISOLDE environment preparation -- running a command: Expected a keyword chimerax-bug-report@… Tristan Croll "{{{ 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 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. }}} " defect closed normal Third Party not a bug all ChimeraX