id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2788 KeyError removing tool from _tool_instances dict chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Darwin-19.3.0-x86_64-i386-64bit ChimeraX Version: 0.91 (2019-12-23) 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: 0.91 (2019-12-23) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/Matus/Documents/Lab/DNA_RNA_Protein-Structures/3D_PDB/mito- > ribosomes/saved-views-ChimeraX/4yyb_T--bS20---5aj3_j-mS34.cxs format session File not found: /Users/Matus/Documents/Lab/DNA_RNA_Protein- Structures/3D_PDB/mito-ribosomes/saved-views-ChimeraX/4yyb_T--bS20---5aj3_j- mS34.cxs > open /Users/Matus/Documents/Lab/DNA_RNA_Protein-Structures/3D_PDB/mito- > ribosomes/saved-views-ChimeraX/4yyb_T--bS20---5aj3_j-mS34.cxs format session File not found: /Users/Matus/Documents/Lab/DNA_RNA_Protein- Structures/3D_PDB/mito-ribosomes/saved-views-ChimeraX/4yyb_T--bS20---5aj3_j- mS34.cxs > open /Volumes/Seagate-Drive/saved-views-ChimeraX/4yyb_T--bS20---5aj3_j- > mS34.cxs Summary of feedback from opening /Volumes/Seagate-Drive/saved-views- ChimeraX/4yyb_T--bS20---5aj3_j-mS34.cxs --- warning | Unable to restore ""SchemesManager"" object opened ChimeraX session > select #2.25 1777 atoms, 1 model selected > hide sel surfaces > show sel cartoons > view > toolshed show ""Side View"" > toolshed show ""Side View"" > view sel > view > lighting flat > lighting shadows true intensity 0.5 > lighting flat > lighting full > lighting soft > lighting simple > lighting soft > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > lighting flat > graphics silhouettes false > graphics silhouettes true > lighting soft > select #2.24 2296 atoms, 1 model selected > lighting flat > lighting soft > view > close session Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 915, in close_action.triggered.connect(lambda arg, s=self, sess=session: s.file_close_cb(sess)) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 645, in file_close_cb run(session, 'close session') File ""/Applications/ChimeraX-0.91.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-0.91.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 ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/std_commands/close.py"", line 60, in close_session session.reset() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/session.py"", line 466, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seqalign/manager.py"", line 259, in reset_state alignment._destroy() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seqalign/alignment.py"", line 501, in _destroy self._notify_observers(""destroyed"", None) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seqalign/alignment.py"", line 541, in _notify_observers recipient.alignment_notification(note_name, note_data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seq-view/tool.py"", line 459, in alignment_notification self.delete() File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seq-view/tool.py"", line 496, in delete ToolInstance.delete(self) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/tools.py"", line 176, in delete self.session.tools.remove([self]) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/tools.py"", line 360, in remove del self._tool_instances[tid] KeyError: 6 KeyError: 6 File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/tools.py"", line 360, in remove del self._tool_instances[tid] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seqalign/alignment.py"", line 524, in _mmap_mod_cb self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True) KeyError: Error processing trigger ""modified"": KeyError: File ""/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/seqalign/alignment.py"", line 524, in _mmap_mod_cb self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True) See log for complete Python traceback. OpenGL version: 4.1 INTEL-14.4.23 OpenGL renderer: Intel Iris Pro OpenGL Engine OpenGL vendor: Intel Inc. }}} " defect closed normal Core 0.91 can't reproduce Conrad Huang all ChimeraX