ISOLDE: wrapped C/C++ object of type QToolButton has been deleted

[jheld@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Started isolde

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/jasonheld/Data/Franzi/UNC49_StructureAnalysis/NeuroSnap_Homopentamer_6HUGTemplate_64d063947e35db5dcd26692f/G5EBQ0_UNC49B_LT_SQPARAA_Template_6HUG_rank_1_ISOLDE_5_FinishedRefinement_SH_9169815053/gromacs/step5_input.pdb

Summary of feedback from opening
/Users/jasonheld/Data/Franzi/UNC49_StructureAnalysis/NeuroSnap_Homopentamer_6HUGTemplate_64d063947e35db5dcd26692f/G5EBQ0_UNC49B_LT_SQPARAA_Template_6HUG_rank_1_ISOLDE_5_FinishedRefinement_SH_9169815053/gromacs/step5_input.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
54575 messages similar to the above omitted  
  
Chain information for step5_input.pdb #1  
---  
Chain | Description  
? | No description available  
  

> ui tool show Registration

Thank you for registering your copy of ChimeraX. By providing the information
requested you will be helping us document the impact this software is having
in the scientific community. The information you supplied will only be used
for reporting summary usage statistics; no individual data will be released.  

Failed to subscribed jheld@wustl.edu to the ChimeraX announcements list: HTTP
Error 404: Not Found  

> select disulfide

Nothing selected  

> isolde start

> set selectionWidth 4

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 22 residues in model #1 to IUPAC-IUB
standards.  
Chain information for step5_input.pdb  
---  
Chain | Description  
1.2/? | No description available  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 134, in
_new_frame_cb  
self._rebuild_tree_if_necessary(tname, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 158, in
_rebuild_tree_if_necessary  
if self.container.is_collapsed:  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
Error processing trigger "new frame":  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 134, in
_new_frame_cb  
self._rebuild_tree_if_necessary(tname, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 158, in
_rebuild_tree_if_necessary  
if self.container.is_collapsed:  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
Error processing trigger "new frame":  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 134, in
_new_frame_cb  
self._rebuild_tree_if_necessary(tname, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 158, in
_rebuild_tree_if_necessary  
if self.container.is_collapsed:  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
Error processing trigger "new frame":  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 134, in
_new_frame_cb  
self._rebuild_tree_if_necessary(tname, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 158, in
_rebuild_tree_if_necessary  
if self.container.is_collapsed:  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
Error processing trigger "new frame":  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 134, in
_new_frame_cb  
self._rebuild_tree_if_necessary(tname, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 158, in
_rebuild_tree_if_necessary  
if self.container.is_collapsed:  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
Error processing trigger "new frame":  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 134, in
_new_frame_cb  
self._rebuild_tree_if_necessary(tname, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 158, in
_rebuild_tree_if_necessary  
if self.container.is_collapsed:  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
Error processing trigger "new frame":  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 134, in
_new_frame_cb  
self._rebuild_tree_if_necessary(tname, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 158, in
_rebuild_tree_if_necessary  
if self.container.is_collapsed:  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
Error processing trigger "new frame":  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 134, in
_new_frame_cb  
self._rebuild_tree_if_necessary(tname, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 158, in
_rebuild_tree_if_necessary  
if self.container.is_collapsed:  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
Error processing trigger "new frame":  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 134, in
_new_frame_cb  
self._rebuild_tree_if_necessary(tname, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 158, in
_rebuild_tree_if_necessary  
if self.container.is_collapsed:  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
Error processing trigger "new frame":  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 134, in
_new_frame_cb  
self._rebuild_tree_if_necessary(tname, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 158, in
_rebuild_tree_if_necessary  
if self.container.is_collapsed:  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
Error processing trigger "new frame":  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 134, in
_new_frame_cb  
self._rebuild_tree_if_necessary(tname, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 158, in
_rebuild_tree_if_necessary  
if self.container.is_collapsed:  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
Error processing trigger "new frame":  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 134, in
_new_frame_cb  
self._rebuild_tree_if_necessary(tname, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 158, in
_rebuild_tree_if_necessary  
if self.container.is_collapsed:  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
Error processing trigger "new frame":  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 134, in
_new_frame_cb  
self._rebuild_tree_if_necessary(tname, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 158, in
_rebuild_tree_if_necessary  
if self.container.is_collapsed:  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
Error processing trigger "new frame":  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 134, in
_new_frame_cb  
self._rebuild_tree_if_necessary(tname, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 158, in
_rebuild_tree_if_necessary  
if self.container.is_collapsed:  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
Error processing trigger "new frame":  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 134, in
_new_frame_cb  
self._rebuild_tree_if_necessary(tname, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 158, in
_rebuild_tree_if_necessary  
if self.container.is_collapsed:  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
Error processing trigger "new frame":  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 134, in
_new_frame_cb  
self._rebuild_tree_if_necessary(tname, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 158, in
_rebuild_tree_if_necessary  
if self.container.is_collapsed:  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
Error processing trigger "new frame":  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 134, in
_new_frame_cb  
self._rebuild_tree_if_necessary(tname, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 158, in
_rebuild_tree_if_necessary  
if self.container.is_collapsed:  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
Error processing trigger "new frame":  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 134, in
_new_frame_cb  
self._rebuild_tree_if_necessary(tname, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 158, in
_rebuild_tree_if_necessary  
if self.container.is_collapsed:  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
Error processing trigger "new frame":  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 134, in
_new_frame_cb  
self._rebuild_tree_if_necessary(tname, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 158, in
_rebuild_tree_if_necessary  
if self.container.is_collapsed:  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
Error processing trigger "new frame":  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 134, in
_new_frame_cb  
self._rebuild_tree_if_necessary(tname, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 158, in
_rebuild_tree_if_necessary  
if self.container.is_collapsed:  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
Error processing trigger "new frame":  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 134, in
_new_frame_cb  
self._rebuild_tree_if_necessary(tname, data)  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/general_tab/map_settings.py", line 158, in
_rebuild_tree_if_necessary  
if self.container.is_collapsed:  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
Error processing trigger "new frame":  
RuntimeError: wrapped C/C++ object of type QToolButton has been deleted  
  
File "/Users/jasonheld/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/collapse_button.py", line 56, in is_collapsed  
return not self.toggle_button.isChecked()  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.12.7
OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 6-Core Intel Core i7
      Processor Speed: 2.6 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 12 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1968.120.12.0.0 (iBridge: 20.16.5060.0.0,0)
      OS Loader Version: 577~170

Software:

    System Software Overview:

      System Version: macOS 13.4.1 (c) (22F770820d)
      Kernel Version: Darwin 22.5.0
      Time since boot: 3 days, 4 hours, 18 minutes

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0000
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3

    AMD Radeon Pro 5300M:

      Chipset Model: AMD Radeon Pro 5300M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0043
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32207P1-020
      Option ROM Version: 113-D32207P1-020
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        VX2453 Series:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: SDA122203488
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 7.26


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.21.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.6.0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBImages: 1.1
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PhenixUI: 1.1.13
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-QScore: 1.0
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StarMap: 1.2.15
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    pyqtgraph: 0.13.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    Send2Trash: 1.8.2
    SEQCROW: 1.7.3
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

[Eric Pettersen]

Reported by Jason Held