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#6548 closed defect (duplicate)

MatchMaker: wrapped C/C++ object of type QPushButton has been deleted

Reported by:	chimerax-bug-report@…	Owned by:	pett
Priority:	normal	Milestone:
Component:	Structure Analysis	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.18363
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6lgx

6lgx title:  
Structure of Rabies virus glycoprotein at basic pH [more info...]  
  
Chain information for 6lgx #1  
---  
Chain | Description | UniProt  
A B | Glycoprotein,Glycoprotein,Glycoprotein | D8VEC1_9RHAB  
  
6lgx mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> open 6lgw

6lgw title:  
Structure of Rabies virus glycoprotein in complex with neutralizing antibody
523-11 at acidic pH [more info...]  
  
Chain information for 6lgw #2  
---  
Chain | Description | UniProt  
A C | scFv 523-11 VH |  
B D | scFv 523-11 VL |  
E F | Glycoprotein,Glycoprotein,Glycoprotein | D8VEC1_9RHAB  
  
6lgw mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> ui mousemode right zoom

> open 6tou

Summary of feedback from opening 6tou fetched from pdb  
---  
notes | Fetching compressed mmCIF 6tou from
http://files.rcsb.org/download/6tou.cif  
Fetching CCD CA from http://ligand-expo.rcsb.org/reports/C/CA/CA.cif  
Fetching CCD CL from http://ligand-expo.rcsb.org/reports/C/CL/CL.cif  
  
6tou title:  
Rabies virus glycoprotein PH domain in complex with the scFv fragment of
broadly neutralizing human antibody RVC20 [more info...]  
  
Chain information for 6tou #3  
---  
Chain | Description | UniProt  
A | Single-chain Fv |  
G | Glycoprotein,Glycoprotein | Q8JUA9_9RHAB  
  
Non-standard residues in 6tou #3  
---  
CA — calcium ion  
CL — chloride ion  
  

> hide #3.1 models

> select #3/G

559 atoms, 557 bonds, 5 pseudobonds, 83 residues, 3 models selected  

> hide (#!3 & sel) target a

> cartoon hide (#!3 & sel)

Drag select of 31 residues, 866 atoms, 2 pseudobonds  
Drag select of 957 residues, 12 pseudobonds, 9342 atoms  

> preset "initial styles" cartoon

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

> select clear

> select #1/A

2968 atoms, 3048 bonds, 3 pseudobonds, 377 residues, 2 models selected  

> cartoon hide (#!1 & sel)

> select clear

[Repeated 1 time(s)]

> select #2/E

2902 atoms, 2977 bonds, 3 pseudobonds, 368 residues, 2 models selected  

> cartoon hide (#!2 & sel)

> select #1/B

2727 atoms, 2802 bonds, 3 pseudobonds, 348 residues, 2 models selected  

> select #2/E

2902 atoms, 2977 bonds, 3 pseudobonds, 368 residues, 2 models selected  

> select #2/F

2993 atoms, 3072 bonds, 2 pseudobonds, 378 residues, 2 models selected  

> ui mousemode right "clip rotate"

> ui mousemode right zoom

> cartoon hide (#!2 & sel)

> hide #3.2 models

> show #3.1 models

> hide #3.1 models

> select #3.1

3 pseudobonds, 1 model selected  

> ~select #3.1

Nothing selected  

> select #3.1

3 pseudobonds, 1 model selected  

> ~select #3.1

Nothing selected  

> hide #3.2 target m

> close #3.2

> select #2/A

930 atoms, 955 bonds, 118 residues, 1 model selected  

> cartoon hide sel

> select #2/B

790 atoms, 808 bonds, 104 residues, 1 model selected  

> cartoon hide sel

> hide #!3 models

> show #!3 models

> hide #!2 models

> show #!2 models

> show #3.1 models

> select #3.1

3 pseudobonds, 1 model selected  

> ~select #3.1

Nothing selected  

> select #3.1

3 pseudobonds, 1 model selected  

> ~select #3.1

Nothing selected  

> select #3.1

3 pseudobonds, 1 model selected  

> hide #3.1 models

> ~select #3.1

Nothing selected  

> select #3/G:301@CA

1 atom, 1 residue, 1 model selected  

> hide sel target a

> select clear

> select #3/G:409@O

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select #3/G:408@O

1 atom, 1 residue, 1 model selected  

> select clear

[Repeated 1 time(s)]

> select #3/G:408@O

1 atom, 1 residue, 1 model selected  

> cartoon hide sel

> hide sel target a

> select #3/G:194@OD1

1 atom, 1 residue, 1 model selected  

> select #3/G:194@OD1

1 atom, 1 residue, 1 model selected  

> select clear

[Repeated 2 time(s)]

> color sel hot pink

> select clear

> ui tool show Matchmaker

No reference and/or match structure/chain chosen  

> matchmaker #!2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6lgx, chain A (#1) with 6lgw, chain F (#2), sequence alignment
score = 1971.4  
RMSD between 23 pruned atom pairs is 1.228 angstroms; (across all 355 pairs:
33.765)  
  

> matchmaker #!1 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6lgw, chain F (#2) with 6lgx, chain A (#1), sequence alignment
score = 1971.4  
RMSD between 23 pruned atom pairs is 1.228 angstroms; (across all 355 pairs:
33.765)  
  

> matchmaker #!1 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6lgw, chain F (#2) with 6lgx, chain A (#1), sequence alignment
score = 1971.4  
RMSD between 23 pruned atom pairs is 1.228 angstroms; (across all 355 pairs:
33.765)  
  

> matchmaker #!3 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6lgw, chain F (#2) with 6tou, chain G (#3), sequence alignment
score = 358.8  
RMSD between 50 pruned atom pairs is 0.770 angstroms; (across all 70 pairs:
11.902)  
  

> ui mousemode right "move picked models"

Drag select of 2 residues  

> select clear

> matchmaker #!1 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6lgw, chain F (#2) with 6lgx, chain A (#1), sequence alignment
score = 1971.4  
RMSD between 23 pruned atom pairs is 1.228 angstroms; (across all 355 pairs:
33.765)  
  

> matchmaker #!2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6lgx, chain A (#1) with 6lgw, chain F (#2), sequence alignment
score = 1971.4  
RMSD between 23 pruned atom pairs is 1.228 angstroms; (across all 355 pairs:
33.765)  
  

> matchmaker #!1 to #2/A pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6lgw, chain A (#2) with 6lgx, chain A (#1), sequence alignment
score = 22.4  
RMSD between 3 pruned atom pairs is 0.882 angstroms; (across all 89 pairs:
23.865)  
  

> matchmaker #!1 to #2/B pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6lgw, chain B (#2) with 6lgx, chain B (#1), sequence alignment
score = 24.7  
RMSD between 5 pruned atom pairs is 0.882 angstroms; (across all 96 pairs:
22.026)  
  

> matchmaker #!1 to #2/C pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6lgw, chain C (#2) with 6lgx, chain A (#1), sequence alignment
score = 30.8  
RMSD between 8 pruned atom pairs is 1.706 angstroms; (across all 84 pairs:
23.809)  
  

> matchmaker #!1 to #2/D pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6lgw, chain D (#2) with 6lgx, chain B (#1), sequence alignment
score = 30.6  
RMSD between 6 pruned atom pairs is 1.667 angstroms; (across all 96 pairs:
22.928)  
  

> matchmaker #!1 to #3/A pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6tou, chain A (#3) with 6lgx, chain B (#1), sequence alignment
score = 14.2  
RMSD between 3 pruned atom pairs is 0.625 angstroms; (across all 149 pairs:
29.326)  
  

> matchmaker #!1 to #3/A pairing bs alg Smith-Waterman cutoffDistance none

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Smith-Waterman  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
No iteration  
  
Matchmaker 6tou (#3) with 6lgx (#1), sequence alignment score = 46.5  
RMSD between 75 atom pairs is 17.017 angstroms  
  

> matchmaker #!1 to #3/A pairing bs alg Smith-Waterman cutoffDistance none

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Smith-Waterman  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
No iteration  
  
Matchmaker 6tou (#3) with 6lgx (#1), sequence alignment score = 46.5  
RMSD between 75 atom pairs is 17.017 angstroms  
  

> matchmaker #!1 to #3/A pairing bs cutoffDistance none

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
No iteration  
  
Matchmaker 6tou, chain A (#3) with 6lgx, chain B (#1), sequence alignment
score = 14.2  
RMSD between 149 atom pairs is 22.042 angstroms  
  

> matchmaker #!1 to #3 cutoffDistance none

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
No iteration  
  
Matchmaker 6tou, chain G (#3) with 6lgx, chain A (#1), sequence alignment
score = 358.8  
RMSD between 70 atom pairs is 11.038 angstroms  
  

> matchmaker #!1 to #3 alg Smith-Waterman cutoffDistance none

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Smith-Waterman  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
No iteration  
  
Matchmaker 6tou (#3) with 6lgx (#1), sequence alignment score = 371.3  
RMSD between 63 atom pairs is 1.435 angstroms  
  

> view matrix models
> #1,0.76833,0.18371,0.61313,-2.8064,0.012062,0.9536,-0.30084,14.726,-0.63994,0.23854,0.73046,44.756

> view matrix models
> #2,-0.6164,-0.47863,0.62527,58.219,0.52848,-0.84012,-0.1221,-38.812,0.58374,0.25518,0.7708,41.294

> view matrix models
> #3,-0.10473,0.29275,0.95044,92.102,-0.92437,-0.38118,0.015555,-38.047,0.36684,-0.87692,0.31053,-25.701

> view matrix models
> #1,0.76833,0.18371,0.61313,-44.99,0.012062,0.9536,-0.30084,7.3601,-0.63994,0.23854,0.73046,19.57

> cartoon #1-2#!3

> hide #!1 models

> hide #!2 models

> show #3.1 models

> hide #3.1 models

> cartoon #!3

> show #!2 models

> view matrix models
> #2,-0.6164,-0.47863,0.62527,23.617,0.52848,-0.84012,-0.1221,-30.876,0.58374,0.25518,0.7708,9.3856

> select clear

> ui mousemode right zoom

> hide #!2 models

> show #!1 models

> select #1/A

2968 atoms, 3048 bonds, 3 pseudobonds, 377 residues, 2 models selected  

> cartoon hide (#!1 & sel)

> ui tool show Matchmaker

> matchmaker #!1 to #3 alg Smith-Waterman cutoffDistance none

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Smith-Waterman  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
No iteration  
  
Matchmaker 6tou (#3) with 6lgx (#1), sequence alignment score = 371.3  
RMSD between 63 atom pairs is 1.435 angstroms  
  

> ui mousemode right "translate selected atoms"

> ui mousemode right "move picked models"

> matchmaker #!3 to #1 alg Smith-Waterman cutoffDistance none

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Smith-Waterman  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
No iteration  
  
Matchmaker 6lgx (#1) with 6tou (#3), sequence alignment score = 371.3  
RMSD between 63 atom pairs is 1.435 angstroms  
  
Traceback (most recent call last):  
File "F:\crystal\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "F:\crystal\ChimeraX 1.3\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 "F:\crystal\ChimeraX 1.3\bin\lib\site-
packages\chimerax\ui\options\options.py", line 343, 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 "F:\crystal\ChimeraX 1.3\bin\lib\site-
packages\chimerax\ui\options\options.py", line 343, in set_value  
self.widget.setText(value)  
  
See log for complete Python traceback.  
  

> matchmaker #!3 to #1 cutoffDistance none

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
No iteration  
  
Matchmaker 6lgx, chain A (#1) with 6tou, chain G (#3), sequence alignment
score = 358.8  
RMSD between 70 atom pairs is 11.038 angstroms  
  
Traceback (most recent call last):  
File "F:\crystal\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "F:\crystal\ChimeraX 1.3\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 "F:\crystal\ChimeraX 1.3\bin\lib\site-
packages\chimerax\ui\options\options.py", line 451, in set_value  
self._float_widget.set_text("")  
File "F:\crystal\ChimeraX 1.3\bin\lib\site-
packages\chimerax\ui\widgets\slider.py", line 362, in set_text  
self._value_text.setText(text)  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
Error processing trigger "setting changed":  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File "F:\crystal\ChimeraX 1.3\bin\lib\site-
packages\chimerax\ui\widgets\slider.py", line 362, in set_text  
self._value_text.setText(text)  
  
See log for complete Python traceback.  
  

> matchmaker #!3 to #1 ssFraction 0.0888 cutoffDistance none

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.0888  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
No iteration  
  
Matchmaker 6lgx, chain A (#1) with 6tou, chain G (#3), sequence alignment
score = 394.155  
RMSD between 71 atom pairs is 1.420 angstroms  
  
Traceback (most recent call last):  
File "F:\crystal\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "F:\crystal\ChimeraX 1.3\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 "F:\crystal\ChimeraX 1.3\bin\lib\site-
packages\chimerax\ui\options\options.py", line 339, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "F:\crystal\ChimeraX 1.3\bin\lib\site-
packages\chimerax\ui\options\options.py", line 339, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  

> ui mousemode right zoom

> select #3/A

1856 atoms, 1825 bonds, 312 residues, 1 model selected  

> select #3/A

1856 atoms, 1825 bonds, 312 residues, 1 model selected  

> cartoon sel

> select clear

> select #3/A

1856 atoms, 1825 bonds, 312 residues, 1 model selected  

> select #3/G

559 atoms, 557 bonds, 3 pseudobonds, 83 residues, 2 models selected  

> ui tool show Matchmaker

> matchmaker #!1 to #3/G pairing bs ssFraction 0.0888 cutoffDistance none

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.0888  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
No iteration  
  
Matchmaker 6tou, chain G (#3) with 6lgx, chain A (#1), sequence alignment
score = 394.155  
RMSD between 71 atom pairs is 1.420 angstroms  
  

> matchmaker #!1 to #3/G pairing bs ssFraction 0.0888 cutoffDistance none

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.0888  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
No iteration  
  
Matchmaker 6tou, chain G (#3) with 6lgx, chain A (#1), sequence alignment
score = 394.155  
RMSD between 71 atom pairs is 1.420 angstroms  
  

> matchmaker #!1 to #3/G pairing bs ssFraction 0.0888 cutoffDistance none

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.0888  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
No iteration  
  
Matchmaker 6tou, chain G (#3) with 6lgx, chain A (#1), sequence alignment
score = 394.155  
RMSD between 71 atom pairs is 1.420 angstroms  
  

> matchmaker #!1 to #3/G pairing bs ssFraction 0.0888 cutoffDistance none

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.0888  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
No iteration  
  
Matchmaker 6tou, chain G (#3) with 6lgx, chain A (#1), sequence alignment
score = 394.155  
RMSD between 71 atom pairs is 1.420 angstroms  
  
Traceback (most recent call last):  
File "F:\crystal\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "F:\crystal\ChimeraX 1.3\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 "F:\crystal\ChimeraX 1.3\bin\lib\site-
packages\chimerax\ui\options\options.py", line 309, in set_value  
self.widget.setChecked(value)  
RuntimeError: wrapped C/C++ object of type QCheckBox has been deleted  
  
Error processing trigger "setting changed":  
RuntimeError: wrapped C/C++ object of type QCheckBox has been deleted  
  
File "F:\crystal\ChimeraX 1.3\bin\lib\site-
packages\chimerax\ui\options\options.py", line 309, in set_value  
self.widget.setChecked(value)  
  
See log for complete Python traceback.  
  

> matchmaker #!1 to #3/G pairing bs ssFraction 0.0888 cutoffDistance none
> showAlignment true

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.0888  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
No iteration  
  
Matchmaker 6tou, chain G (#3) with 6lgx, chain A (#1), sequence alignment
score = 394.155  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: 6lgx #1/A, 6tou #3/G  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 71 atom pairs is 1.420 angstroms  
  
Traceback (most recent call last):  
File "F:\crystal\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "F:\crystal\ChimeraX 1.3\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 "F:\crystal\ChimeraX 1.3\bin\lib\site-
packages\chimerax\ui\options\options.py", line 343, 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 "F:\crystal\ChimeraX 1.3\bin\lib\site-
packages\chimerax\ui\options\options.py", line 343, in set_value  
self.widget.setText(value)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 27.20.100.8477
OpenGL renderer: Intel(R) HD Graphics 620
OpenGL vendor: Intel
Manufacturer: ASUSTeK COMPUTER INC.
Model: X405UA
OS: Microsoft Windows 10 教育版 (Build 18363)
Memory: 17,059,831,808
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-7200U CPU @ 2.50GHz
OSLanguage: zh-CN
Locale: ('zh_CN', 'cp936')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by pett, 4 years ago

Component:	Unassigned → Structure Analysis
Owner:	set to pett
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → MatchMaker: wrapped C/C++ object of type QPushButton has been deleted

comment:2 by pett, 4 years ago

Resolution:	→ duplicate
Status:	accepted → closed

Duplicate of #6151

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