Ramachandran plot accessing deleted widgets

[DLMLEN001@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22000
ChimeraX Version: 0.93 (2020-04-03)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\Users\Lenye\Dropbox\CryoEM-
> NitAEBC191-Frankfurt\CynD-C1-WT\WT_model_high_res_superimposed.mrc format
> mrc

Opened WT_model_high_res_superimposed.mrc, grid size 300,300,300, pixel 1.05,
shown at level 0.0119, step 2, values float32  

> volume #1 step 1

> open2 C:/Users/Lenye/Desktop/Truncated_S29AI88F_CynD.pdb

Summary of feedback from opening <_io.textiowrapper
name="C:/Users/Lenye/Desktop/Truncated_S29AI88F_CynD.pdb" mode="rt"
encoding="utf-8">  
---  
warnings | Ignored bad PDB record found on line 284  
DEVIATIONS FROM IDEAL VALUES.  
  
Ignored bad PDB record found on line 285  
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2  
  
Ignored bad PDB record found on line 286  
MOLPROBITY STATISTICS.  
  
Ignored bad PDB record found on line 59464  
END  
  
Chain information for Truncated_S29AI88F_CynD.pdb #2  
---  
Chain | Description  
A | No description available  
B H J M O | No description available  
C D E G I K | No description available  
  

> select all

59166 atoms, 60006 bonds, 3 models selected  

> addh

Summary of feedback from adding hydrogens to Truncated_S29AI88F_CynD.pdb #2  
---  
notes | No usable SEQRES records for Truncated_S29AI88F_CynD.pdb (#2) chain A;
guessing termini instead  
No usable SEQRES records for Truncated_S29AI88F_CynD.pdb (#2) chain B;
guessing termini instead  
No usable SEQRES records for Truncated_S29AI88F_CynD.pdb (#2) chain C;
guessing termini instead  
No usable SEQRES records for Truncated_S29AI88F_CynD.pdb (#2) chain D;
guessing termini instead  
No usable SEQRES records for Truncated_S29AI88F_CynD.pdb (#2) chain E;
guessing termini instead  
7 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A SER 3, /B SER 3, /C SER
3, /D SER 3, /E SER 3, /G SER 3, /H SER 3, /I SER 3, /J SER 3, /K SER 3, /M
SER 3, /O SER 3  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A ILE 319, /B ILE 319, /C
ILE 319, /D ILE 319, /E ILE 319, /G ILE 319, /H ILE 319, /I ILE 319, /J ILE
319, /K ILE 319, /M ILE 319, /O ILE 319  
3247 hydrogen bonds  
/A ILE 319 is not terminus, removing H atom from 'C'  
/B ILE 319 is not terminus, removing H atom from 'C'  
/C ILE 319 is not terminus, removing H atom from 'C'  
/D ILE 319 is not terminus, removing H atom from 'C'  
/E ILE 319 is not terminus, removing H atom from 'C'  
7 messages similar to the above omitted  
120 hydrogens added  
  

Expected an objects specifier or a keyword  

Expected an objects specifier or a keyword  

> select ::name="PHE"

3600 atoms, 3600 bonds, 1 model selected  

> select clear

Expected an objects specifier or a keyword  

> style stick

Changed 59286 atom styles  

> show cartoons

> hide atoms

> select /D:83

19 atoms, 18 bonds, 1 model selected  

> select up

199 atoms, 199 bonds, 1 model selected  

> toolshed show ISOLDE

> set selectionWidth 4

Chain information for Truncated_S29AI88F_CynD.pdb  
---  
Chain | Description  
2.2/A | No description available  
2.2/B 2.2/H 2.2/J 2.2/M 2.2/O | No description available  
2.2/C 2.2/D 2.2/E 2.2/G 2.2/I 2.2/K | No description available  
  
Done loading forcefield  

> select up

199 atoms, 199 bonds, 1 model selected  

QWidget::repaint: Recursive repaint detected  

> select /A

4949 atoms, 5019 bonds, 1 model selected  

> select /B:83

19 atoms, 18 bonds, 1 model selected  

> select up

199 atoms, 199 bonds, 1 model selected  

> toolshed show ISOLDE

> set selectionWidth 4

Done loading forcefield  

QWindowsWindow::setGeometry: Unable to set geometry 1920x1035+0+29 (frame:
1938x1082-9-9) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x991+0+29 (frame: 1938x1038-9-9) margins: 9, 38, 9, 9
minimum size: 422x1035 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=440,1082
maxtrack=0,0)  

> select clear

> select up

199 atoms, 199 bonds, 1 model selected  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\validation\ramaplot.py", line 275, in
_model_changed_cb  
self.update_scatter()  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\validation\ramaplot.py", line 372, in update_scatter  
if not self.visible:  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\validation\ramaplot.py", line 283, in visible  
return self.parent.isVisible()  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\validation\ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\validation\ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 2198, in
_update_selected_residue_info_live  
self.iw._rebuild_sel_res_pep_info.setText(pep_type)  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 2198, in
_update_selected_residue_info_live  
self.iw._rebuild_sel_res_pep_info.setText(pep_type)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\validation\ramaplot.py", line 275, in
_model_changed_cb  
self.update_scatter()  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\validation\ramaplot.py", line 372, in update_scatter  
if not self.visible:  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\validation\ramaplot.py", line 283, in visible  
return self.parent.isVisible()  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\validation\ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\validation\ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  

[a _lot_ of this deleted]

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 2198, in
_update_selected_residue_info_live  
self.iw._rebuild_sel_res_pep_info.setText(pep_type)  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 2198, in
_update_selected_residue_info_live  
self.iw._rebuild_sel_res_pep_info.setText(pep_type)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\validation\ramaplot.py", line 275, in
_model_changed_cb  
self.update_scatter()  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\validation\ramaplot.py", line 372, in update_scatter  
if not self.visible:  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\validation\ramaplot.py", line 283, in visible  
return self.parent.isVisible()  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\validation\ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\validation\ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 2198, in
_update_selected_residue_info_live  
self.iw._rebuild_sel_res_pep_info.setText(pep_type)  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 2198, in
_update_selected_residue_info_live  
self.iw._rebuild_sel_res_pep_info.setText(pep_type)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\validation\ramaplot.py", line 275, in
_model_changed_cb  
self.update_scatter()  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\validation\ramaplot.py", line 372, in update_scatter  
if not self.visible:  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\validation\ramaplot.py", line 283, in visible  
return self.parent.isVisible()  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\validation\ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\validation\ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 2198, in
_update_selected_residue_info_live  
self.iw._rebuild_sel_res_pep_info.setText(pep_type)  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 2198, in
_update_selected_residue_info_live  
self.iw._rebuild_sel_res_pep_info.setText(pep_type)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\validation\ramaplot.py", line 275, in
_model_changed_cb  
self.update_scatter()  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\validation\ramaplot.py", line 372, in update_scatter  
if not self.visible:  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\validation\ramaplot.py", line 283, in visible  
return self.parent.isVisible()  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\validation\ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\validation\ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 2198, in
_update_selected_residue_info_live  
self.iw._rebuild_sel_res_pep_info.setText(pep_type)  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "C:\Users\Lenye\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 2198, in
_update_selected_residue_info_live  
self.iw._rebuild_sel_res_pep_info.setText(pep_type)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 441.37
OpenGL renderer: GeForce RTX 2080 with Max-Q Design/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Acer
Model: Predator PT515-51
OS: Microsoft Windows 11 Home Single Language (Build 22000)
Memory: 17,098,264,576
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz"

[Eric Pettersen]

Reported by Lenye Diamini