'ObjectLabels' object has no attribute '_structure_change_handler'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-11.4-arm64-arm-64bit
ChimeraX Version: 1.9rc202412030631 (2024-12-03 06:31:08 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9rc202412030631 (2024-12-03)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open XP_011519262.1

Unrecognized file suffix '.1'  

> open XP_0519262.1

Unrecognized file suffix '.1'  

> open XP_0519262

'XP_0519262' has no suffix  

> close #

Expected a models specifier or a keyword  

> open SEC7

'SEC7' has no suffix  

> close #

Expected a models specifier or a keyword  

> open iqsec3

'iqsec3' has no suffix  

> close #

Expected a models specifier or a keyword  

> open 2bbv

2bbv title:  
The refined three-dimensional structure of an insect virus At 2.8 angstroms
resolution [more info...]  
  
Chain information for 2bbv #1  
---  
Chain | Description | UniProt  
A B C | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV 1-363  
D E F | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV 364-407  
N | RNA (5'-R(*UP*CP*UP*UP*AP*UP*AP*UP*CP*U)-3') |   
  
Non-standard residues in 2bbv #1  
---  
CA — calcium ion  
  
2bbv mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
6| crystal asymmetric unit, crystal frame  
  

> open sec7

'sec7' has no suffix  

> hide target m

> open q9upp2

'q9upp2' has no suffix  

> open arf1

'arf1' has no suffix  

> open 5nlv

Summary of feedback from opening 5nlv fetched from pdb  
---  
notes | Fetching compressed mmCIF 5nlv from http://files.rcsb.org/download/5nlv.cif  
Fetching CCD CME from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/CME/CME.cif  
  
5nlv title:  
Brag2 Sec7-PH (390-763) [more info...]  
  
Chain information for 5nlv #2  
---  
Chain | Description | UniProt  
A | IQ motif and SEC7 domain-containing protein 1 | IQEC1_HUMAN 390-763  
  
14 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> ui windowfill toggle

> open 5nlv format mmcif fromDatabase pdb

5nlv title:  
Brag2 Sec7-PH (390-763) [more info...]  
  
Chain information for 5nlv #3  
---  
Chain | Description | UniProt  
A | IQ motif and SEC7 domain-containing protein 1 | IQEC1_HUMAN 390-763  
  
14 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> show #!2-3 cartoons

> coulombic #!2-3

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue CME (net charge +0) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/bin/amber20/bin/antechamber
-ek qm_theory='AM1', -i
/var/folders/z4/296t1sm966g7lk2v1ljrvknw0000gn/T/tmppuybstam/ante.in.mol2 -fi
mol2 -o
/var/folders/z4/296t1sm966g7lk2v1ljrvknw0000gn/T/tmppuybstam/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n  
(CME) ``  
(CME) `Welcome to antechamber 20.0: molecular input file processor.`  
(CME) ``  
(CME) `Info: Finished reading file
(/var/folders/z4/296t1sm966g7lk2v1ljrvknw0000gn/T/tmppuybstam/ante.in.mol2);
atoms read (31), bonds read (30).`  
(CME) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(CME) `Running:
/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/bin/amber20/bin/bondtype
-j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(CME) ``  
(CME) ``  
(CME) `Running:
/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/bin/amber20/bin/atomtype
-i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(CME) `Info: Total number of electrons: 134; net charge: 0`  
(CME) ``  
(CME) `Running:
/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/bin/amber20/bin/sqm -O -i
sqm.in -o sqm.out`  
(CME) ``  
(CME) `Running:
/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(CME) ``  
(CME) `Running:
/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/bin/amber20/bin/atomtype
-f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(CME) ``  
Charges for residue CME determined  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 215, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1419, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider  
shortcuts.run_provider(session, name)  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1386, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 402, in try_shortcut  
self.run_shortcut(keys)  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 420, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 339, in run  
f(s)  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 72, in func_plus_tip  
func(cmd + " %s")(session)  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 593, in run_expanded_command  
run(session, cmd)  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 536, in run  
run_command(session, command, **kw)  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/coulombic/cmd.py", line 102, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/coulombic/coulombic.py", line 136, in assign_charges  
charged_struct.delete()  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 130, in delete  
Model.delete(self) # Delete children (pseudobond groups) before deleting
structure  
^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 115, in delete  
Drawing.delete(self)  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1239, in delete  
self.remove_all_drawings()  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 373, in remove_all_drawings  
self.remove_drawings(cd, delete)  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 366, in remove_drawings  
d.delete()  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/pbgroup.py", line 58, in delete  
Model.delete(self)  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 115, in delete  
Drawing.delete(self)  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1239, in delete  
self.remove_all_drawings()  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 373, in remove_all_drawings  
self.remove_drawings(cd, delete)  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 366, in remove_drawings  
d.delete()  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/label/label3d.py", line 408, in delete  
h = self._structure_change_handler  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'ObjectLabels' object has no attribute
'_structure_change_handler'  
  
AttributeError: 'ObjectLabels' object has no attribute
'_structure_change_handler'  
  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/label/label3d.py", line 408, in delete  
h = self._structure_change_handler  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> coulombic #!2-3

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue CME (net charge +0) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/bin/amber20/bin/antechamber
-ek qm_theory='AM1', -i
/var/folders/z4/296t1sm966g7lk2v1ljrvknw0000gn/T/tmpxm8b2lhz/ante.in.mol2 -fi
mol2 -o
/var/folders/z4/296t1sm966g7lk2v1ljrvknw0000gn/T/tmpxm8b2lhz/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n  
(CME) ``  
(CME) `Welcome to antechamber 20.0: molecular input file processor.`  
(CME) ``  
(CME) `Info: Finished reading file
(/var/folders/z4/296t1sm966g7lk2v1ljrvknw0000gn/T/tmpxm8b2lhz/ante.in.mol2);
atoms read (31), bonds read (30).`  
(CME) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(CME) `Running:
/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/bin/amber20/bin/bondtype
-j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(CME) ``  
(CME) ``  
(CME) `Running:
/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/bin/amber20/bin/atomtype
-i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(CME) `Info: Total number of electrons: 134; net charge: 0`  
(CME) ``  
(CME) `Running:
/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/bin/amber20/bin/sqm -O -i
sqm.in -o sqm.out`  
(CME) ``  
(CME) `Running:
/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(CME) ``  
(CME) `Running:
/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/bin/amber20/bin/atomtype
-f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(CME) ``  
Charges for residue CME determined  
Exception ignored in: <function Drawing.__del__ at 0x1012fd1c0>  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1217, in __del__  
self.delete()  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/label/label3d.py", line 408, in delete  
h = self._structure_change_handler  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'ObjectLabels' object has no attribute
'_structure_change_handler'  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 215, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1419, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider  
shortcuts.run_provider(session, name)  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1386, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 402, in try_shortcut  
self.run_shortcut(keys)  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 420, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 339, in run  
f(s)  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 72, in func_plus_tip  
func(cmd + " %s")(session)  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 593, in run_expanded_command  
run(session, cmd)  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 536, in run  
run_command(session, command, **kw)  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/coulombic/cmd.py", line 102, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/coulombic/coulombic.py", line 136, in assign_charges  
charged_struct.delete()  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 130, in delete  
Model.delete(self) # Delete children (pseudobond groups) before deleting
structure  
^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 115, in delete  
Drawing.delete(self)  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1239, in delete  
self.remove_all_drawings()  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 373, in remove_all_drawings  
self.remove_drawings(cd, delete)  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 366, in remove_drawings  
d.delete()  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/pbgroup.py", line 58, in delete  
Model.delete(self)  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 115, in delete  
Drawing.delete(self)  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1239, in delete  
self.remove_all_drawings()  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 373, in remove_all_drawings  
self.remove_drawings(cd, delete)  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 366, in remove_drawings  
d.delete()  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/label/label3d.py", line 408, in delete  
h = self._structure_change_handler  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'ObjectLabels' object has no attribute
'_structure_change_handler'  
  
AttributeError: 'ObjectLabels' object has no attribute
'_structure_change_handler'  
  
File
"/Applications/ChimeraX-1.9-rc2024.12.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/label/label3d.py", line 408, in delete  
h = self._structure_change_handler  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 71.6.4
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro17,1
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 6723.120.36
      OS Loader Version: 6723.120.36

Software:

    System Software Overview:

      System Version: macOS 11.4 (20F71)
      Kernel Version: Darwin 20.5.0
      Time since boot: 42 days 17:42

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Resolution: 2880 x 1800
          UI Looks like: 1440 x 900 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.7.1
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.7
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.7
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9rc202412030631
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.12
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.1
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h5py: 3.12.1
    html2text: 2024.2.26
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13

[Eric Pettersen]

The changes to handle pseudobond-deletion-while-unopened moved the handler registration. I've moved it back.