Opened 4 years ago

Closed 4 years ago

#5381 closed defect (fixed)

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

Reported by: rsr2169@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by pett) 

The following bug report has been submitted:
Platform:        macOS-10.14.6-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
Tried to run an ISOLDE simulation

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show

Downloading bundle ChimeraX_ISOLDE-1.2.2-cp38-cp38-macosx_10_13_x86_64.whl  
Successfully installed ChimeraX-Clipper-0.16.1 ChimeraX-ISOLDE-1.2.2  
Installed ChimeraX-Clipper (0.16.1)  
Installed ChimeraX-ISOLDE (1.2.2)  

> ui tool show ISOLDE

/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/simtk/openmm/app/desmonddmsfile.py:411: SyntaxWarning: "is" with a
literal. Did you mean "=="?  
if implicitSolvent is 'AGBNP3':  
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/simtk/openmm/app/desmonddmsfile.py:433: SyntaxWarning: "is" with a
literal. Did you mean "=="?  
if implicitSolvent is 'GVolSA':  
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/simtk/openmm/app/desmonddmsfile.py:440: SyntaxWarning: "is" with a
literal. Did you mean "=="?  
if implicitSolvent is 'AGBNP':  

> set selectionWidth 4

Cached rama8000-cispro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-transpro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-gly-sym data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-prepro-noGP data not found. Regenerating from text file. This
is normal if running ISOLDE for the first time  
Cached rama8000-ileval-nopreP data not found. Regenerating from text file.
This is normal if running ISOLDE for the first time  
Cached rama8000-general-noGPIVpreP data not found. Regenerating from text
file. This is normal if running ISOLDE for the first time  
Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.  
Done loading forcefield  

> open "/Users/ryroark/Documents/Shapiro Lab/SHIV samples/41328_A1 and BG505
> v2/RealSpaceRefine_18/J139_008_zflip.mrc"

Opened J139_008_zflip.mrc as #1, grid size 384,384,384, pixel 0.83, shown at
level 0.0791, step 2, values float32  

> open "/Users/ryroark/Documents/Shapiro Lab/SHIV samples/41328_A1 and BG505
> v2/RealSpaceRefine_24/41328_BG505_refined_V-coot-X.pdb"

Chain information for 41328_BG505_refined_V-coot-X.pdb #2  
---  
Chain | Description  
A E I | No description available  
B F J | No description available  
L | No description available  
M | No description available  
  
Chain information for 41328_BG505_refined_V-coot-X.pdb  
---  
Chain | Description  
2.2/A 2.2/E 2.2/I | No description available  
2.2/B 2.2/F 2.2/J | No description available  
2.2/L | No description available  
2.2/M | No description available  
  
Cached rota8000-val data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-leu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ile data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-pro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-phe data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-tyr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-trp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ser data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-thr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-cys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-met data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-lys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-his data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-arg data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asn data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-gln data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-glu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  

> ui tool show ISOLDE

> set selectionWidth 4

Done loading forcefield  

> select #2.2

16913 atoms, 17387 bonds, 8 pseudobonds, 2062 residues, 6 models selected  

> select #2.2

16913 atoms, 17387 bonds, 8 pseudobonds, 2062 residues, 6 models selected  

> addh

Summary of feedback from adding hydrogens to 41328_BG505_refined_V-coot-X.pdb
#2.2  
---  
notes | No usable SEQRES records for 41328_BG505_refined_V-coot-X.pdb (#2.2)
chain A; guessing termini instead  
No usable SEQRES records for 41328_BG505_refined_V-coot-X.pdb (#2.2) chain B;
guessing termini instead  
No usable SEQRES records for 41328_BG505_refined_V-coot-X.pdb (#2.2) chain E;
guessing termini instead  
No usable SEQRES records for 41328_BG505_refined_V-coot-X.pdb (#2.2) chain F;
guessing termini instead  
No usable SEQRES records for 41328_BG505_refined_V-coot-X.pdb (#2.2) chain I;
guessing termini instead  
3 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A ASN 33, /B LEU 520, /E
ASN 33, /F LEU 520, /I ASN 33, /J LEU 520, /L GLN 1, /M GLN 1  
Chain-initial residues that are not actual N termini: /A HIS 66, /A ASN 186,
/B GLN 563, /E HIS 66, /F GLN 563, /I HIS 66, /I ASN 186, /J GLN 563  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A VAL 505, /A ASP 57, /A
ILE 184, /B ASP 664, /B LEU 545, /E VAL 505, /E ASP 57, /F ASP 664, /F LEU
545, /I VAL 505, /I ASP 57, /I ILE 184, /J ASP 664, /J LEU 545, /L LEU 104, /M
SER 113  
1370 hydrogen bonds  
Adding 'H' to /A HIS 66  
Adding 'H' to /A ASN 186  
Adding 'H' to /B GLN 563  
Adding 'H' to /E HIS 66  
Adding 'H' to /F GLN 563  
3 messages similar to the above omitted  
/A VAL 505 is not terminus, removing H atom from 'C'  
/B ASP 664 is not terminus, removing H atom from 'C'  
/E VAL 505 is not terminus, removing H atom from 'C'  
/F ASP 664 is not terminus, removing H atom from 'C'  
/I VAL 505 is not terminus, removing H atom from 'C'  
3 messages similar to the above omitted  
16567 hydrogens added  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  

> clipper associate #1 toModel #2

Opened J139_008_zflip.mrc as #2.1.1.1, grid size 384,384,384, pixel 0.83,
shown at step 1, values float32  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  

[_many_ of these deleted]

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/ramaplot.py", line 112, in
_selection_changed_cb  
residues = self.current_model.residues  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 61, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 83, in get_attr  
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None  
AttributeError: Execution of 'Structure' object's 'residues' property raised
AttributeError  
  
Error processing trigger "selection changed":  
AttributeError: Execution of 'Structure' object's 'residues' property raised
AttributeError  
  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 83, in get_attr  
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  

> select protein

30304 atoms, 30659 bonds, 8 pseudobonds, 1941 residues, 2 models selected  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 1162, in _changes_done_cb  
self._update_iffy_rota_list()  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes done":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2389, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/ramaplot.py", line 112, in
_selection_changed_cb  
residues = self.current_model.residues  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 61, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 83, in get_attr  
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None  
AttributeError: Execution of 'Structure' object's 'residues' property raised
AttributeError  
  
Error processing trigger "selection changed":  
AttributeError: Execution of 'Structure' object's 'residues' property raised
AttributeError  
  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 83, in get_attr  
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2702, in _start_sim_or_toggle_pause  
for v in mmgr.all_maps:  
AttributeError: 'NoneType' object has no attribute 'all_maps'  
  
AttributeError: 'NoneType' object has no attribute 'all_maps'  
  
File "/Users/ryroark/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2702, in _start_sim_or_toggle_pause  
for v in mmgr.all_maps:  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.11.20
OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,1
      Processor Name: 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: 9 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 1037.0.78.0.0 (iBridge: 17.16.10572.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G103)
      Kernel Version: Darwin 18.7.0
      Time since boot: 343 days 51 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: Supported, feature set macOS GPUFamily2 v1

    Radeon Pro 560X:

      Chipset Model: Radeon Pro 560X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67ef
      Revision ID: 0x00c2
      ROM Revision: 113-C980AL-075
      VBIOS Version: 113-C97501U-005
      EFI Driver Version: 01.01.075
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
        C27F390:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: H4ZR503501  
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 0.00

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.2
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    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
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    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
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    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
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    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
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    ChimeraX-BlastProtein: 1.1
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    ChimeraX-BundleBuilder: 1.1
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    ChimeraX-CageBuilder: 1.0
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    ChimeraX-Centroids: 1.1
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    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
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    ChimeraX-ConnectStructure: 2.0
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    ChimeraX-CoreFormats: 1.0
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    ChimeraX-Crosslinks: 1.0
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    ChimeraX-FunctionKey: 1.0
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    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
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Change History (2)

comment:1 by pett, 4 years ago

Component: Unassigned → Third Party
Description: modified (diff)
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE: wrapped C/C++ object of type QTableWidget has been deleted

Reported by Ryan Roark

comment:2 by Tristan Croll, 4 years ago

Resolution: → fixed
Status: assigned → closed

Forgot to clean up the last selected model's changes trigger on closing ISOLDE. What happened here:

ISOLDE was opened and model was initialised
ISOLDE was closed - old changes trigger wasn't cleaned up
ISOLDE was re-opened
Hydrogens were added, triggering the out-of-date isolde._model_changes_cb(). The fact that atoms were added triggered a second callback to update the rota/rama lists (if visible) - this tried to use the old, deleted tables from the first ISOLDE GUI.

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