KeyError removing tool from _tool_instances dict

[chimerax-bug-report@…]

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 <lambda>  
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: <chimerax.atomic.molobject.Sequence object at 0x14c4fcf10>  
  
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.