Matchmaker change matrix: wrapped C/C++ object of type QPushButton has been deleted

[yoav@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
Occurs when trying to change the matrix in the matchmaker GUI 

Log:
Startup Messages  
---  
warning | No presets found in custom preset folder
C:/ProgramData/ChimeraX/Presets  
  

> graphics quality 3

> lighting qualityOfShadows finer

> graphics rate true

> graphics rate maxFrameRate 144

> graphics rate waitForVsync false

UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3cmt

3cmt title:  
Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures
[more info...]  
  
Chain information for 3cmt #1  
---  
Chain | Description  
A D | Protein recA  
B E | DNA
(5'-D(*DTP*DTP*DTP*DTP*DTP*DCP*DCP*DCP*dap*DCP*DCP*DTP*DTP*DTP*DT)-3')  
C F | DNA (5'-D(P*DGP*DGP*DTP*DGP*DGP*DG)-3')  
  
Non-standard residues in 3cmt #1  
---  
ADP — adenosine-5'-diphosphate  
ALF — tetrafluoroaluminate ion  
MG — magnesium ion  
  
3cmt mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> preset "initial styles" cartoon

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> lighting full

> lighting shadows false

> lighting shadows true

> lighting simple

> lighting full

> set bgColor black

> lighting shadows false

> lighting shadows true

> color bychain

> color byhetero

> nucleotides atoms

> style nucleic stick

Changed 732 atom styles  

> select /B

236 atoms, 260 bonds, 12 residues, 1 model selected  

> select /A

12290 atoms, 12429 bonds, 16 pseudobonds, 1624 residues, 3 models selected  

> select /B

236 atoms, 260 bonds, 12 residues, 1 model selected  

> view sel

> ui mousemode right clip

> view sel

> sequence chain /B

Alignment identifier is 1/B  

> select clear

> view /B

> select /B:999

Nothing selected  

> select /B:1002

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select clear

> select clear

> view sel

> open

Missing or invalid "fileNames" argument: Expected a file name  

> close #1

> open 3cmt maxAssemblies 1

'maxAssemblies' has no suffix  

> open maxAssemblies 1 3cmt

'maxAssemblies' has no suffix  

> open fromDatabase rcsb_bio 3cmt maxAssemblies 1

'fromDatabase' has no suffix  

> open 3cmt fromDatabase rcsb_bio maxAssemblies 1

Summary of feedback from opening 3cmt fetched from rcsb_bio  
---  
warnings | Start residue of secondary structure not found: HELIX 61 61 SER D
44 LEU D 51 1 8  
Start residue of secondary structure not found: HELIX 62 62 GLY D 71 ARG D 85
1 15  
Start residue of secondary structure not found: HELIX 63 63 ASP D 100 LEU D
107 1 8  
Start residue of secondary structure not found: HELIX 64 64 THR D 121 GLY D
136 1 16  
Start residue of secondary structure not found: HELIX 65 65 PRO D 151 GLY D
157 1 7  
137 messages similar to the above omitted  
Cannot find LINK/SSBOND residue THR (73 )  
Cannot find LINK/SSBOND residue THR (1073 )  
Cannot find LINK/SSBOND residue THR (2073 )  
Cannot find LINK/SSBOND residue THR (3073 )  
Cannot find LINK/SSBOND residue THR (4073 )  
5 messages similar to the above omitted  
note | Fetching compressed 3cmt bioassembly 1 from
https://files.rcsb.org/download/3cmt.pdb1.gz  
  
3cmt bioassembly 1 title:  
Mechanism of homologous recombination from the reca-ssDNA/dsDNA structures
[more info...]  
  
Chain information for 3cmt bioassembly 1 #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  
Non-standard residues in 3cmt bioassembly 1 #1  
---  
ADP — adenosine-5'-diphosphate  
ALF — tetrafluoroaluminate ion  
MG — magnesium ion  
  
Opened 1 biological assemblies for 3cmt  

> select #1.2

12 pseudobonds, 1 model selected  

> ~select #1.2

Nothing selected  

> select nucleic

366 atoms, 406 bonds, 18 residues, 1 model selected  

> select /A:37-4328

12257 atoms, 12396 bonds, 24 pseudobonds, 1621 residues, 3 models selected  

> select /B:1002-1013

236 atoms, 260 bonds, 12 residues, 1 model selected  

> select /C:2007-2012

130 atoms, 146 bonds, 6 residues, 1 model selected  

> select /B

236 atoms, 260 bonds, 12 residues, 1 model selected  

> split /B

Split 3cmt bioassembly 1 (#1) into 3 models  
Chain information for 3cmt bioassembly 1 A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 3cmt bioassembly 1 B #1.2  
---  
Chain | Description  
B | No description available  
  
Chain information for 3cmt bioassembly 1 C #1.3  
---  
Chain | Description  
C | No description available  
  

> select #1.1

12290 atoms, 12429 bonds, 27 pseudobonds, 1624 residues, 3 models selected  

> ~select #1.1

Nothing selected  

> select #1.2

236 atoms, 260 bonds, 12 residues, 1 model selected  

> ~select #1.2

Nothing selected  

> hide #1.3 models

> hide #!1.1 models

> select #1.2

236 atoms, 260 bonds, 12 residues, 1 model selected  

> select /C

130 atoms, 146 bonds, 6 residues, 1 model selected  

> show /C

> show #1.2 cartoons

> show #1.2 atoms

> select clear

> show #1.2 cartoons

> show #!1.1 models

> show #1.3 models

> el /C

Unknown command: el /C  

> select /C

130 atoms, 146 bonds, 6 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> show sel atoms

> show sel cartoons

> hide #!1.1 models

> hide #1.3 models

> show #1.2 target m

> hide #1.2 target m

> show #1.2 target m

> show #1.3

> show #1.3 target m

> hide #1.3 target m

> show /C target m

> hide #1.3 models

> ui tool show "Color Actions"

> ui tool show "Color Actions"

> color sel cyan target c

> undo

> select #1.2

236 atoms, 260 bonds, 12 residues, 1 model selected  

> color sel cyan target c

> color sel cyan target ac

> color sel byhetero

> open "D:/OneDrive/OneDrive - mail.tau.ac.il/University/Year C/Int. to
> Structural Biology/Final Exam/Section 1/BForm-Template.pdb"

Chain information for BForm-Template.pdb #2  
---  
Chain | Description  
| No description available  
  

> sequence chain #2

Alignment identifier is 2/  

> select #2:11

32 atoms, 33 bonds, 1 residue, 1 model selected  

> select #2:12

33 atoms, 34 bonds, 1 residue, 1 model selected  

> select #2:11

32 atoms, 33 bonds, 1 residue, 1 model selected  

> select #2:12

33 atoms, 34 bonds, 1 residue, 1 model selected  

> select clear

> select #2:11

32 atoms, 33 bonds, 1 residue, 1 model selected  

> select #2:12

33 atoms, 34 bonds, 1 residue, 1 model selected  

> select #2:11

32 atoms, 33 bonds, 1 residue, 1 model selected  

> view #2 clip false

> view sel

> view

> select #2

761 atoms, 819 bonds, 24 residues, 1 model selected  

> view sel

> select clear

> select #2:12

33 atoms, 34 bonds, 1 residue, 1 model selected  

> select reverse

Expected an objects specifier or a keyword  

> select ~sel

13044 atoms, 13257 bonds, 27 pseudobonds, 1654 residues, 7 models selected  

> hide #1.2 models

> select ~sel

13044 atoms, 13257 bonds, 27 pseudobonds, 1654 residues, 7 models selected  

> select #2:1-12

373 atoms, 397 bonds, 12 residues, 1 model selected  

> select #2:1-12

373 atoms, 397 bonds, 12 residues, 1 model selected  

> select #2

761 atoms, 819 bonds, 24 residues, 1 model selected  

> select subtract #2:1-12

388 atoms, 422 bonds, 12 residues, 1 model selected  

> delete sel

> select clear

> sequence chain #2

Alignment identifier is 2/  

> select clear

> select #1.2

236 atoms, 260 bonds, 12 residues, 1 model selected  

> select #2

373 atoms, 397 bonds, 12 residues, 1 model selected  

> view sel

> show #1.2 models

> select #1.2

236 atoms, 260 bonds, 12 residues, 1 model selected  

> select #2

373 atoms, 397 bonds, 12 residues, 1 model selected  

> select #2#1.2

609 atoms, 657 bonds, 24 residues, 2 models selected  

> view sel

> select #2

373 atoms, 397 bonds, 12 residues, 1 model selected  

> color sel byhetero

> nucleotides sel atoms

> style nucleic & sel stick

Changed 373 atom styles  

> color sel red target ac

> select #1.2

236 atoms, 260 bonds, 12 residues, 1 model selected  

> color sel dodger blue target ac

> select #2

373 atoms, 397 bonds, 12 residues, 1 model selected  

> color sel coral target ac

> color sel orange target ac

> color sel dark orange target ac

> color sel byhetero

> select #1.2

236 atoms, 260 bonds, 12 residues, 1 model selected  

> color sel byhetero

> ui tool show Matchmaker

> help help:user

> align #1.2 toAtoms #2

Unequal number of atoms to pair, 236 and 373  

> sequence chain #1.2

Alignment identifier is 1.2/B  

> sequence chain #2

Alignment identifier is 2/  

> close #2

> open "D:/OneDrive/OneDrive - mail.tau.ac.il/University/Year C/Int. to
> Structural Biology/Final Exam/Section 1/Bdna.pdb"

Chain information for Bdna.pdb #2  
---  
Chain | Description  
| No description available  
  

> align #1.2 toAtoms #2

Unequal number of atoms to pair, 236 and 373  

> sequence chain #2

Alignment identifier is 2/  

> select #1.2

236 atoms, 260 bonds, 12 residues, 1 model selected  

> select #2

373 atoms, 397 bonds, 12 residues, 1 model selected  

> ui tool show Matchmaker

Traceback (most recent call last):  
File "D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\triggerset.py", line
130, in invoke  
return self._func(self._name, data)  
File "D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\options\options.py",
line 50, in <lambda>  
data[0] == pself.attr_name and setattr(pself, "value", pself.get_attribute()))  
File "D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\options\options.py",
line 276, in set_value  
self.widget.setText(value)  
RuntimeError: wrapped C/C++ object of type QPushButton has been deleted  
  
Error processing trigger "setting changed":  
RuntimeError: wrapped C/C++ object of type QPushButton has been deleted  
  
File "D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\options\options.py",
line 276, in set_value  
self.widget.setText(value)  
  
See log for complete Python traceback.  
  

> select #2

373 atoms, 397 bonds, 12 residues, 1 model selected  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 373 atom styles  

> ui tool show "Color Actions"

> color sel chocolate target ac

> color sel dark orange target ac

> color sel byhetero

> ui tool show Matchmaker

Traceback (most recent call last):  
File "D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\triggerset.py", line
130, in invoke  
return self._func(self._name, data)  
File "D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\options\options.py",
line 50, in <lambda>  
data[0] == pself.attr_name and setattr(pself, "value", pself.get_attribute()))  
File "D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\options\options.py",
line 276, in set_value  
self.widget.setText(value)  
RuntimeError: wrapped C/C++ object of type QPushButton has been deleted  
  
Error processing trigger "setting changed":  
RuntimeError: wrapped C/C++ object of type QPushButton has been deleted  
  
File "D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\options\options.py",
line 276, in set_value  
self.widget.setText(value)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\triggerset.py", line
130, in invoke  
return self._func(self._name, data)  
File "D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\options\options.py",
line 50, in <lambda>  
data[0] == pself.attr_name and setattr(pself, "value", pself.get_attribute()))  
File "D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\options\options.py",
line 276, in set_value  
self.widget.setText(value)  
RuntimeError: wrapped C/C++ object of type QPushButton has been deleted  
  
Error processing trigger "setting changed":  
RuntimeError: wrapped C/C++ object of type QPushButton has been deleted  
  
File "D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\options\options.py",
line 276, in set_value  
self.widget.setText(value)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\triggerset.py", line
130, in invoke  
return self._func(self._name, data)  
File "D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\options\options.py",
line 50, in <lambda>  
data[0] == pself.attr_name and setattr(pself, "value", pself.get_attribute()))  
File "D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\options\options.py",
line 276, in set_value  
self.widget.setText(value)  
RuntimeError: wrapped C/C++ object of type QPushButton has been deleted  
  
Error processing trigger "setting changed":  
RuntimeError: wrapped C/C++ object of type QPushButton has been deleted  
  
File "D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\options\options.py",
line 276, in set_value  
self.widget.setText(value)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\triggerset.py", line
130, in invoke  
return self._func(self._name, data)  
File "D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\options\options.py",
line 50, in <lambda>  
data[0] == pself.attr_name and setattr(pself, "value", pself.get_attribute()))  
File "D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\options\options.py",
line 276, in set_value  
self.widget.setText(value)  
RuntimeError: wrapped C/C++ object of type QPushButton has been deleted  
  
Error processing trigger "setting changed":  
RuntimeError: wrapped C/C++ object of type QPushButton has been deleted  
  
File "D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\options\options.py",
line 276, in set_value  
self.widget.setText(value)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 460.89
OpenGL renderer: GeForce GTX 1080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: System manufacturer
Model: System Product Name
OS: Microsoft Windows 10 Pro N (Build 19042)
Memory: 17,113,600,000
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 1700 Eight-Core Processor          "
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
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    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
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    certifi: 2020.6.20
    chardet: 3.0.4
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    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
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    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
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    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
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    ChimeraX-Dicom: 1.0
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    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
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    ChimeraX-Help: 1.0
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    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2
    WMI: 1.5.1

[pett]

Hi Yoav,

Thanks for reporting this problem. Unfortunately I am having trouble reproducing it. Can you reproduce it? If you can, could you save a session from just before the problem occurs and send me that? It would help immensely.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab