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Opened 3 years ago
Closed 3 years ago
#7747 closed defect (duplicate)
wrapped C/C++ object of type ChainMenuButton has been deleted
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | UI | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19041
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:\Users\daisy\OneDrive - The University of Hong Kong\My
> drive\HKU\PHD\meDNA\Models\Other HDs\Oct4_CpGpal_config2_Hoxb13.cxs" format
> session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Log from Thu Oct 6 14:18:14 2022UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:/Users/daisy/OneDrive - The University of Hong Kong/My
> drive/HKU/PHD/meDNA/Models/Other HDs/Oct4_Hoxb13.cxs"
Log from Tue Sep 13 14:58:06 2022UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:\Users\daisy\OneDrive\OneDrive - connect.hku.hk\My
> drive\HKU\PHD\meDNA\Models\Oct4_HB13.cxs" format session
Log from Mon Aug 8 15:23:06 2022UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:\Users\daisy\OneDrive\OneDrive - connect.hku.hk\My
> drive\HKU\PHD\meDNA\Models\Other HDs\Oct4_other HD compare.cxs" format
> session
Log from Thu Jul 28 12:07:42 2022UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:\Users\daisy\OneDrive\OneDrive - connect.hku.hk\My
> drive\HKU\PHD\meDNA\Models\Other HDs\Oct4_other HD compare.cxs" format
> session
Log from Thu Jul 28 12:06:42 2022UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:\Users\daisy\OneDrive\OneDrive - connect.hku.hk\My
> drive\HKU\PHD\meDNA\Models\Other HDs\Oct4_other HD compare.cxs" format
> session
Log from Mon Jul 25 23:04:14 2022UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open C:\ProgramData\ChimeraX\Oct4_CpGpal.cxs format session
Log from Sat Jun 4 16:40:15 2022UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "G:\My Drive\HKU\PHD\meDNA\Models\Oct4_CPGpal\CpGpal_Oct4.cxs" format
> session
Log from Mon May 30 17:27:44 2022UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "G:\My Drive\HKU\PHD\meDNA\Models\Oct4_CPGpal\CpGpal_Oct4.cxs" format
> session
Log from Fri May 27 15:32:55 2022UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "G:\My Drive\HKU\PHD\meDNA\Models\Oct4_CPGpal\CpGpal_Oct4.cxs" format
> session
Log from Thu May 12 11:13:49 2022UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "G:\My Drive\HKU\PHD\meDNA\Models\Oct4_CPGpal\Oct4_cpgpal_Comb.pdb"
> format pdb
Summary of feedback from opening G:\My
Drive\HKU\PHD\meDNA\Models\Oct4_CPGpal\Oct4_cpgpal_Comb.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Accelrys Discovery Studio PDB file
Ignored bad PDB record found on line 2
REMARK Created: Wed Sep 09 10:13:13 China Standard Time 2015
Ignored bad PDB record found on line 880
REMARK Accelrys Discovery Studio PDB file
Ignored bad PDB record found on line 881
REMARK Created: Wed Sep 09 10:13:13 China Standard Time 2015
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
864 messages similar to the above omitted
Ignored bad PDB record found on line 1759
END
Chain information for Oct4_cpgpal_Comb.pdb #1
---
Chain | Description
A | No description available
B | No description available
C D | No description available
> close session
> open "G:/My Drive/HKU/PHD/meDNA/Models/Oct4_CPGpal/PDB
> files/Oct4_CpGpal_control_unmethylated.pdb"
Summary of feedback from opening G:/My
Drive/HKU/PHD/meDNA/Models/Oct4_CPGpal/PDB
files/Oct4_CpGpal_control_unmethylated.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Accelrys Discovery Studio PDB file
Ignored bad PDB record found on line 2
REMARK Created: Wed Sep 09 10:13:13 China Standard Time 2015
Ignored bad PDB record found on line 3289
END
Chain information for Oct4_CpGpal_control_unmethylated.pdb #1
---
Chain | Description
A B | No description available
C D | No description available
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> nucleotides atoms
> style nucleic stick
Changed 1140 atom styles
> delete H
> ui tool show "Color Actions"
> color gold
> color orange
> color goldenrod
> color goldenrod
> color goldenrod
> select up
366 atoms, 410 bonds, 18 residues, 1 model selected
> select up
732 atoms, 820 bonds, 36 residues, 1 model selected
> color sel dark gray
> show sel surfaces
> transparency (#!1 & sel) 40
> color (#!1 & sel) dark gray
> transparency (#!1 & sel) 40
> select clear
> select clear
Alignment identifier is 1
Alignment identifier is 2
> color (#!1 & sel) red
> nucleotides sel atoms
> style nucleic & sel stick
Changed 82 atom styles
> color (#!1 & sel) blue
> color (#!1 & sel) black
> select clear
> select clear
> select clear
> show sel atoms
> select clear
> select /C:119
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
162 atoms, 160 bonds, 18 residues, 1 model selected
> select down
22 atoms, 11 bonds, 2 residues, 1 model selected
> select up
162 atoms, 160 bonds, 18 residues, 1 model selected
> color sel byhetero
> select clear
> select clear
> select clear
> save "G:/My Drive/HKU/PHD/meDNA/Models/Oct4_CPGpal/Oct4 CpGpal.png" width
> 1297 height 856 supersample 3
> save "G:/My Drive/HKU/PHD/meDNA/Models/Oct4_CPGpal/CpGpal_Oct4.cxs"
opened ChimeraX session
> select up
110 atoms, 110 bonds, 13 residues, 1 model selected
> select up
502 atoms, 508 bonds, 60 residues, 1 model selected
> select clear
> select up
110 atoms, 110 bonds, 13 residues, 1 model selected
> select up
502 atoms, 508 bonds, 60 residues, 1 model selected
> color sel light sea green
> color sel #00aa7fff
> color sel byhetero
> select clear
> select up
89 atoms, 89 bonds, 11 residues, 1 model selected
> select up
502 atoms, 508 bonds, 60 residues, 1 model selected
> ui tool show "Color Actions"
> color sel sea green
> color sel byhetero
> select clear
> select clear
> undo
> save "G:/My Drive/HKU/PHD/meDNA/Models/Oct4_CPGpal/CpGpal_Oct4.cxs"
opened ChimeraX session
> select /B:194@O3'
1 atom, 1 residue, 1 model selected
> select /A:19@N3
1 atom, 1 residue, 1 model selected
> select /A:14@N4
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 20 bonds, 1 residue, 2 models selected
> select up
366 atoms, 410 bonds, 18 residues, 2 models selected
> select up
387 atoms, 433 bonds, 19 residues, 3 models selected
> select up
732 atoms, 820 bonds, 36 residues, 3 models selected
> select /A:20@C4'
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 20 bonds, 1 residue, 2 models selected
> select up
366 atoms, 410 bonds, 18 residues, 2 models selected
> select up
367 atoms, 410 bonds, 19 residues, 3 models selected
> select up
387 atoms, 433 bonds, 19 residues, 3 models selected
> select up
732 atoms, 820 bonds, 36 residues, 3 models selected
> hide sel surfaces
> color (#!1 & sel) byhetero
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 2 models selected
> select up
366 atoms, 410 bonds, 18 residues, 2 models selected
> select down
22 atoms, 24 bonds, 1 residue, 2 models selected
> select /B:4
19 atoms, 20 bonds, 1 residue, 1 model selected
> select clear
> ui tool show Distances
> distance /B:5@N3 /D:293@NH1
Distance between /B DA 5 N3 and /D ARG 293 NH1: 6.600Å
Exactly two atoms must be selected!
> select clear
> distance /A:19@N2 /D:293@NH1
Distance between /A DG 19 N2 and /D ARG 293 NH1: 4.122Å
> select /A:20@O2
1 atom, 1 residue, 1 model selected
> select clear
> distance /A:20@O2 /D:293@NH1
Distance between /A DC 20 O2 and /D ARG 293 NH1: 2.723Å
> save "G:/My Drive/HKU/PHD/meDNA/Models/Oct4_CPGpal/CpGpal_Oct4.cxs"
opened ChimeraX session
> select up
52 atoms, 55 bonds, 3 residues, 2 models selected
> select up
447 atoms, 490 bonds, 27 residues, 2 models selected
> select up
813 atoms, 900 bonds, 45 residues, 3 models selected
> show sel surfaces
> undo
> hide sel surfaces
> select clear
> select clear
> select up
366 atoms, 410 bonds, 18 residues, 2 models selected
> select up
732 atoms, 820 bonds, 36 residues, 3 models selected
> show sel surfaces
> color (#!1 & sel) gray
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> hide sel surfaces
> select clear
> select up
110 atoms, 110 bonds, 13 residues, 1 model selected
> select up
502 atoms, 508 bonds, 60 residues, 1 model selected
> select up
595 atoms, 601 bonds, 71 residues, 1 model selected
> select up
1004 atoms, 1016 bonds, 120 residues, 2 models selected
> show sel surfaces
> select clear
> hide #!2 models
> save ./Oct4_CpGpal.cxs
opened ChimeraX session
> hide surfaces
> open "C:/Users/daisy/OneDrive/OneDrive - connect.hku.hk/My
> drive/HKU/PHD/meDNA/Models/Other HDs/5ego.pdb"
5ego.pdb title:
HOXB13-MEIS1 heterodimer bound to methylated DNA [more info...]
Chain information for 5ego.pdb #3
---
Chain | Description
A | homeobox protein MEIS1
B | homeobox protein hox-B13
D | DNA (5'-D(P*GP*TP*TP*GP*ap*CP*ap*GP*TP*TP*TP*TP*ap*(5CM) P*GP*ap*GP*G)-3')
E | DNA (5'-D(*CP*CP*TP*(5CM) P*GP*TP*ap*ap*ap*ap*CP*TP*GP*TP*CP*ap*ap*C)-3')
Non-standard residues in 5ego.pdb #3
---
5CM — 5-methyl-2'-deoxy-cytidine-5'-monophosphate
> ui tool show Matchmaker
> matchmaker #3 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 Oct4_CpGpal_control_unmethylated.pdb, chain D (#1) with 5ego.pdb,
chain B (#3), sequence alignment score = 115.7
RMSD between 49 pruned atom pairs is 0.999 angstroms; (across all 59 pairs:
1.673)
> save "C:/Users/daisy/OneDrive/OneDrive - connect.hku.hk/My
> drive/HKU/PHD/meDNA/Models/Other HDs/Oct4_other HD compare.cxs"
opened ChimeraX session
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
375 atoms, 420 bonds, 18 residues, 1 model selected
> select down
20 atoms, 21 bonds, 1 residue, 1 model selected
> color sel black
> color sel byhetero
> select #1/D:333
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/B:260
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:258
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select clear
> select #1/D:331
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/D:330
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/D:331
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/D:332
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/D:331
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/D:333
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> show sel atoms
> color (#!1 & sel) byhetero
> select clear
> ui tool show Matchmaker
> matchmaker #3/B to #1/D pairing ss
Parameters
---
Chain pairing | ss
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 Oct4_CpGpal_control_unmethylated.pdb, chain D (#1) with 5ego.pdb,
chain B (#3), sequence alignment score = 115.7
RMSD between 49 pruned atom pairs is 0.999 angstroms; (across all 59 pairs:
1.673)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> matchmaker #3 to #1/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 Oct4_CpGpal_control_unmethylated.pdb, chain D (#1) with 5ego.pdb,
chain B (#3), sequence alignment score = 115.7
RMSD between 49 pruned atom pairs is 0.999 angstroms; (across all 59 pairs:
1.673)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> select clear
> select clear
> ui tool show Matchmaker
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\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 "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\options\options.py", line 272, 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 "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\options\options.py", line 272, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\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 "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\options\options.py", line 272, 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 "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\options\options.py", line 272, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
> matchmaker #1/D to #3/B pairing ss
Parameters
---
Chain pairing | ss
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 5ego.pdb, chain B (#3) with Oct4_CpGpal_control_unmethylated.pdb,
chain D (#1), sequence alignment score = 115.7
RMSD between 49 pruned atom pairs is 0.999 angstroms; (across all 59 pairs:
1.673)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> matchmaker #1/D to #3/B pairing ss
Parameters
---
Chain pairing | ss
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 5ego.pdb, chain B (#3) with Oct4_CpGpal_control_unmethylated.pdb,
chain D (#1), sequence alignment score = 115.7
RMSD between 49 pruned atom pairs is 0.999 angstroms; (across all 59 pairs:
1.673)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> matchmaker #1/D to #3/B pairing ss
Parameters
---
Chain pairing | ss
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 5ego.pdb, chain B (#3) with Oct4_CpGpal_control_unmethylated.pdb,
chain D (#1), sequence alignment score = 115.7
RMSD between 49 pruned atom pairs is 0.999 angstroms; (across all 59 pairs:
1.673)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> matchmaker #1/D to #3/B pairing ss
Parameters
---
Chain pairing | ss
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 5ego.pdb, chain B (#3) with Oct4_CpGpal_control_unmethylated.pdb,
chain D (#1), sequence alignment score = 115.7
RMSD between 49 pruned atom pairs is 0.999 angstroms; (across all 59 pairs:
1.673)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> matchmaker #1/D to #3/B pairing ss
Parameters
---
Chain pairing | ss
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 5ego.pdb, chain B (#3) with Oct4_CpGpal_control_unmethylated.pdb,
chain D (#1), sequence alignment score = 115.7
RMSD between 49 pruned atom pairs is 0.999 angstroms; (across all 59 pairs:
1.673)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\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 "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\options\options.py", line 272, 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 "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\options\options.py", line 272, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
> matchmaker #!1 to #3
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 5ego.pdb, chain B (#3) with Oct4_CpGpal_control_unmethylated.pdb,
chain D (#1), sequence alignment score = 115.7
RMSD between 49 pruned atom pairs is 0.999 angstroms; (across all 59 pairs:
1.673)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> matchmaker #!1 to #3
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 5ego.pdb, chain B (#3) with Oct4_CpGpal_control_unmethylated.pdb,
chain D (#1), sequence alignment score = 115.7
RMSD between 49 pruned atom pairs is 0.999 angstroms; (across all 59 pairs:
1.673)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> matchmaker #!1 to #3
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 5ego.pdb, chain B (#3) with Oct4_CpGpal_control_unmethylated.pdb,
chain D (#1), sequence alignment score = 115.7
RMSD between 49 pruned atom pairs is 0.999 angstroms; (across all 59 pairs:
1.673)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> matchmaker #!1 to #3
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 5ego.pdb, chain B (#3) with Oct4_CpGpal_control_unmethylated.pdb,
chain D (#1), sequence alignment score = 115.7
RMSD between 49 pruned atom pairs is 0.999 angstroms; (across all 59 pairs:
1.673)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> matchmaker #!1 to #3
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 5ego.pdb, chain B (#3) with Oct4_CpGpal_control_unmethylated.pdb,
chain D (#1), sequence alignment score = 115.7
RMSD between 49 pruned atom pairs is 0.999 angstroms; (across all 59 pairs:
1.673)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\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 "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\options\options.py", line 272, 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 "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\options\options.py", line 272, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
> matchmaker #!1 to #3/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 5ego.pdb, chain B (#3) with Oct4_CpGpal_control_unmethylated.pdb,
chain D (#1), sequence alignment score = 115.7
RMSD between 49 pruned atom pairs is 0.999 angstroms; (across all 59 pairs:
1.673)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> matchmaker #!1 to #3/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 5ego.pdb, chain B (#3) with Oct4_CpGpal_control_unmethylated.pdb,
chain D (#1), sequence alignment score = 115.7
RMSD between 49 pruned atom pairs is 0.999 angstroms; (across all 59 pairs:
1.673)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> matchmaker #!1 to #3/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 5ego.pdb, chain B (#3) with Oct4_CpGpal_control_unmethylated.pdb,
chain D (#1), sequence alignment score = 115.7
RMSD between 49 pruned atom pairs is 0.999 angstroms; (across all 59 pairs:
1.673)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> save "C:/Users/daisy/OneDrive/OneDrive - connect.hku.hk/My
> drive/HKU/PHD/meDNA/Models/Other HDs/Oct4_other HD compare.cxs"
opened ChimeraX session
> select up
26 atoms, 14 bonds, 3 residues, 3 models selected
> select up
26 atoms, 24 bonds, 3 residues, 3 models selected
> label (#3#!1 & sel) text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> save "C:/Users/daisy/OneDrive/OneDrive - connect.hku.hk/My
> drive/HKU/PHD/meDNA/Models/Other HDs/Oct4_other HD compare.cxs"
opened ChimeraX session
> show sel atoms
> select #3/D:34
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #3/B:265
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
165 atoms, 167 bonds, 18 residues, 1 model selected
> select up
540 atoms, 543 bonds, 66 residues, 1 model selected
Alignment identifier is 3/B
> select clear
> select #3/B:258@CB
1 atom, 1 residue, 1 model selected
> show sel atoms
> show sel atoms
> select #1/D:342
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel atoms
> show sel atoms
> show sel atoms
> show sel atoms
> show sel atoms
> show sel atoms
> show sel atoms
> show sel atoms
> hide #!3 models
> color (#!1 & sel) lime
> select clear
> show #!3 models
> select up
10 atoms, 8 bonds, 2 residues, 1 model selected
> select up
16 atoms, 14 bonds, 2 residues, 1 model selected
> select clear
> select #3/B:262
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel yellow
> select #1/D:335
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:177
22 atoms, 24 bonds, 1 residue, 1 model selected
> save "C:/Users/daisy/OneDrive/OneDrive - connect.hku.hk/My
> drive/HKU/PHD/meDNA/Models/Oct4_HB13.cxs"
opened ChimeraX session
> select clear
> select clear
> select up
110 atoms, 110 bonds, 13 residues, 2 models selected
> select up
502 atoms, 508 bonds, 60 residues, 2 models selected
> color (#!1 & sel) forest green
> select #1/D:324
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
89 atoms, 89 bonds, 11 residues, 2 models selected
> select up
502 atoms, 508 bonds, 60 residues, 2 models selected
> color (#!1 & sel) orange
> select up
877 atoms, 928 bonds, 78 residues, 3 models selected
> select up
885 atoms, 928 bonds, 86 residues, 3 models selected
> select up
1247 atoms, 1333 bonds, 104 residues, 3 models selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 737 atom styles
> select #1/B:6
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/B:7
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
366 atoms, 410 bonds, 18 residues, 2 models selected
> select up
1736 atoms, 1836 bonds, 156 residues, 2 models selected
> select #1/C:129
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
110 atoms, 110 bonds, 13 residues, 2 models selected
> select up
502 atoms, 508 bonds, 60 residues, 2 models selected
> select #1/D:323
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
89 atoms, 89 bonds, 11 residues, 2 models selected
> select up
502 atoms, 508 bonds, 60 residues, 2 models selected
> color (#!1 & sel) forest green
> select #1/B:7
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
366 atoms, 410 bonds, 18 residues, 2 models selected
> select up
728 atoms, 815 bonds, 36 residues, 3 models selected
> color (#!1,3 & sel) forest green
> color (#!1,3 & sel) byhetero
> select clear
> select #1/A:180
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
366 atoms, 410 bonds, 18 residues, 2 models selected
> select up
741 atoms, 830 bonds, 36 residues, 3 models selected
> color (#!1,3 & sel) forest green
> color (#!1,3 & sel) byhetero
> ~label (#!1,3 & sel) atoms
> ~label (#!1,3 & sel) residues
> select clear
Drag select of 1197 atoms, 312 residues, 1287 bonds
> ~label (#!1,3 & sel) residues
> select clear
> select #3/A:303
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
101 atoms, 100 bonds, 13 residues, 1 model selected
> select up
478 atoms, 489 bonds, 59 residues, 1 model selected
> select up
588 atoms, 599 bonds, 72 residues, 1 model selected
> select up
1018 atoms, 1032 bonds, 125 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #00aaffff
> color sel #aaaa7fff
> color sel #55aaffff
> select clear
> select #1/B:189
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #3/E:18
19 atoms, 20 bonds, 1 residue, 1 model selected
> select up
362 atoms, 405 bonds, 18 residues, 1 model selected
> select #3/D:20
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
737 atoms, 825 bonds, 36 residues, 1 model selected
> color sel cyan
> color sel cornflower blue
> color sel byhetero
> select clear
> select up
110 atoms, 110 bonds, 13 residues, 2 models selected
> select up
502 atoms, 508 bonds, 60 residues, 2 models selected
> select up
591 atoms, 597 bonds, 71 residues, 3 models selected
> select up
591 atoms, 597 bonds, 71 residues, 3 models selected
> select up
1004 atoms, 1016 bonds, 120 residues, 3 models selected
> hide (#!1 & sel) target a
> select clear
Drag select of 1 bonds, 1 atoms
> select #3/B:265
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
165 atoms, 167 bonds, 18 residues, 1 model selected
> select up
540 atoms, 543 bonds, 66 residues, 1 model selected
> hide sel target a
> select clear
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3/A
Alignment identifier is 3/D
Alignment identifier is 3/E
Destroying pre-existing alignment with identifier 3/B
Alignment identifier is 3/B
> color sel gray
> color sel gray
> select up
40 atoms, 42 bonds, 2 residues, 1 model selected
> color sel byhetero
> select clear
> color (#!1 & sel) black
> color (#!1 & sel) byhetero
> select clear
> select clear
> select clear
> select clear
> select clear
> select clear
> select clear
> select up
110 atoms, 110 bonds, 13 residues, 1 model selected
> select up
540 atoms, 543 bonds, 66 residues, 1 model selected
> ui tool show "Color Actions"
> color sel gold
> color sel orange
> color sel goldenrod
> color sel sandy brown
> color sel light salmon
> color sel peru
> color sel peru
> color sel deep sky blue
> color sel dark turquoise
> color sel cornflower blue
> color sel dark cyan
> color sel cornflower blue
> color sel cornflower blue
> color sel dark goldenrod
> select clear
> select up
110 atoms, 110 bonds, 13 residues, 1 model selected
> select up
540 atoms, 543 bonds, 66 residues, 1 model selected
> color sel cornflower blue
> color sel royal blue
> color sel cornflower blue
> color sel royal blue
> color sel cornflower blue
> color sel royal blue
> color sel navy
> color sel royal blue
> color sel indigo
> color sel cornflower blue
> color sel dark violet
> color sel dark violet
> color sel blue violet
> color sel wheat
> color sel burly wood
> color sel cornflower blue
> select clear
> select clear
> select clear
> select clear
> save "C:/Users/daisy/OneDrive/OneDrive - connect.hku.hk/My
> drive/HKU/PHD/meDNA/Models/Other HDs/Oct4_Hoxb13.cxs"
opened ChimeraX session
> close session
> open "C:/Users/daisy/OneDrive - The University of Hong Kong/My
> drive/HKU/PHD/meDNA/Models/Other HDs/5ego.pdb"
5ego.pdb title:
HOXB13-MEIS1 heterodimer bound to methylated DNA [more info...]
Chain information for 5ego.pdb #1
---
Chain | Description
A | homeobox protein MEIS1
B | homeobox protein hox-B13
D | DNA (5'-D(P*GP*TP*TP*GP*ap*CP*ap*GP*TP*TP*TP*TP*ap*(5CM) P*GP*ap*GP*G)-3')
E | DNA (5'-D(*CP*CP*TP*(5CM) P*GP*TP*ap*ap*ap*ap*CP*TP*GP*TP*CP*ap*ap*C)-3')
Non-standard residues in 5ego.pdb #1
---
5CM — 5-methyl-2'-deoxy-cytidine-5'-monophosphate
> show atoms
> nucleotides atoms
> style nucleic stick
Changed 737 atom styles
> select ::name="5CM"::name="HOH"
60 atoms, 42 bonds, 22 residues, 1 model selected
> hide sel target a
Alignment identifier is 1/D
Alignment identifier is 1/E
> show sel atoms
> show sel atoms
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
1013 atoms, 1032 bonds, 120 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> select clear
> select clear
> select up
101 atoms, 100 bonds, 13 residues, 1 model selected
> select up
478 atoms, 489 bonds, 59 residues, 1 model selected
> select clear
> select up
110 atoms, 110 bonds, 13 residues, 1 model selected
> select up
540 atoms, 543 bonds, 66 residues, 1 model selected
> color sel dark gray
> select clear
> select up
110 atoms, 110 bonds, 13 residues, 1 model selected
> select up
540 atoms, 543 bonds, 66 residues, 1 model selected
> color sel cornflower blue
> select clear
> open "C:/Users/daisy/OneDrive - The University of Hong Kong/My
> drive/HKU/PHD/meDNA/Models/Vlad/oct4_oct4_nr5a2_cpg_01_equil_06.pdb"
Chain information for oct4_oct4_nr5a2_cpg_01_equil_06.pdb #2
---
Chain | Description
A B | No description available
C | No description available
D | No description available
> save "C:/Users/daisy/OneDrive - The University of Hong Kong/My
> drive/HKU/PHD/meDNA/Models/Other HDs/Oct4_CpGpal_config1_Hoxb13.cxs"
> ui tool show Matchmaker
> matchmaker #2 to #1/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 5ego.pdb, chain B (#1) with oct4_oct4_nr5a2_cpg_01_equil_06.pdb,
chain B (#2), sequence alignment score = 119.1
RMSD between 41 pruned atom pairs is 1.101 angstroms; (across all 63 pairs:
4.797)
> matchmaker #2 to #1/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 5ego.pdb, chain B (#1) with oct4_oct4_nr5a2_cpg_01_equil_06.pdb,
chain B (#2), sequence alignment score = 119.1
RMSD between 41 pruned atom pairs is 1.101 angstroms; (across all 63 pairs:
4.797)
> color sel cornflower blue
> color sel byhetero
> color sel gray
> color sel dark gray
> color sel byhetero
> color sel byhetero
> nucleotides sel atoms
> style nucleic & sel stick
Changed 42 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 42 atom styles
> select clear
> nucleotides atoms
> style nucleic stick
Changed 3298 atom styles
> select up
737 atoms, 825 bonds, 36 residues, 1 model selected
> color sel cornflower blue
> color sel byhetero
> color sel dark gray
> color sel byhetero
> color sel dark gray
> color sel byhetero
> save "C:/Users/daisy/OneDrive - The University of Hong Kong/My
> drive/HKU/PHD/meDNA/Models/Other HDs/Oct4_CpGpal_config1_Hoxb13.cxs"
> select up
1641 atoms, 1783 bonds, 58 residues, 2 models selected
> select up
1677 atoms, 1821 bonds, 59 residues, 2 models selected
> select up
2923 atoms, 3164 bonds, 98 residues, 2 models selected
> color sel light gray
> color sel gray
> color sel byhetero
> select clear
Alignment identifier is 1/A
Alignment identifier is 1/D
Alignment identifier is 1/E
Alignment identifier is 1/B
Alignment identifier is 1
Alignment identifier is 2/C
Alignment identifier is 2/D
No statusbar messages will be shown due to inadequate OpenGL
No statusbar messages will be shown due to inadequate OpenGL
No statusbar messages will be shown due to inadequate OpenGL
No statusbar messages will be shown due to inadequate OpenGL
No statusbar messages will be shown due to inadequate OpenGL
> select #2/D:399
32 atoms, 33 bonds, 1 residue, 1 model selected
> select up
1282 atoms, 1381 bonds, 40 residues, 1 model selected
> select up
8031 atoms, 8261 bonds, 408 residues, 1 model selected
> select down
1282 atoms, 1381 bonds, 40 residues, 1 model selected
> select up
2561 atoms, 2759 bonds, 80 residues, 1 model selected
Alignment identifier is 2/C
Alignment identifier is 2/D
> color sel black
> color sel dark gray
> color sel black
> color sel byhetero
> color sel black
> color sel byhetero
> select #1/E:1
16 atoms, 17 bonds, 1 residue, 1 model selected
> select up
362 atoms, 405 bonds, 18 residues, 1 model selected
> color sel cornflower blue
Alignment identifier is 1/E
> color sel black
Destroying pre-existing alignment with identifier 1/E
Alignment identifier is 1/E
> select up
737 atoms, 825 bonds, 36 residues, 1 model selected
> select down
84 atoms, 46 bonds, 4 residues, 1 model selected
Alignment identifier is 1/D
Alignment identifier is 1/E
> color sel black
> color sel byhetero
> select clear
> select up
402 atoms, 402 bonds, 22 residues, 1 model selected
> select up
2735 atoms, 2751 bonds, 164 residues, 1 model selected
> select up
3137 atoms, 3153 bonds, 186 residues, 1 model selected
> select up
5470 atoms, 5502 bonds, 328 residues, 1 model selected
> color sel orange
> select clear
> save "C:/Users/daisy/OneDrive - The University of Hong Kong/My
> drive/HKU/PHD/meDNA/Models/Other HDs/Oct4_CpGpal_config1_Hoxb13.cxs"
> close session
> open "C:\Users\daisy\OneDrive - The University of Hong Kong\My
> drive\HKU\PHD\meDNA\Models\Vlad\oct4_oct4_nr5a2_cpg_01_equil_06.pdb" format
> pdb
Chain information for oct4_oct4_nr5a2_cpg_01_equil_06.pdb #1
---
Chain | Description
A B | No description available
C | No description available
D | No description available
> close session
> open "C:\Users\daisy\OneDrive - The University of Hong Kong\My
> drive\HKU\PHD\meDNA\Models\Other HDs\5ego.pdb" format pdb
5ego.pdb title:
HOXB13-MEIS1 heterodimer bound to methylated DNA [more info...]
Chain information for 5ego.pdb #1
---
Chain | Description
A | homeobox protein MEIS1
B | homeobox protein hox-B13
D | DNA (5'-D(P*GP*TP*TP*GP*ap*CP*ap*GP*TP*TP*TP*TP*ap*(5CM) P*GP*ap*GP*G)-3')
E | DNA (5'-D(*CP*CP*TP*(5CM) P*GP*TP*ap*ap*ap*ap*CP*TP*GP*TP*CP*ap*ap*C)-3')
Non-standard residues in 5ego.pdb #1
---
5CM — 5-methyl-2'-deoxy-cytidine-5'-monophosphate
> open "C:/Users/daisy/OneDrive - The University of Hong Kong/My
> drive/HKU/PHD/meDNA/Models/Vlad/oct4_oct4_nr5a2_cpg_02_equil_03.pdb"
Chain information for oct4_oct4_nr5a2_cpg_02_equil_03.pdb #2
---
Chain | Description
A B | No description available
C | No description available
D | No description available
> select clear
> show atoms
> show atoms
> hide atoms
> nucleotides atoms
> style nucleic stick
Changed 3298 atom styles
> show atoms
> nucleotides atoms
> style nucleic stick
Changed 3298 atom styles
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIE"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
6483 atoms, 6534 bonds, 448 residues, 2 models selected
> hide sel atoms
> select
> ::name="5CM"::name="DA3"::name="DC3"::name="DG5"::name="DT5"::name="HOH"
205 atoms, 193 bonds, 26 residues, 2 models selected
> select
> ::name="5CM"::name="DA3"::name="DC3"::name="DG5"::name="DT5"::name="HOH"
205 atoms, 193 bonds, 26 residues, 2 models selected
> hide sel atoms
> hide sel atoms
> select ::name="5CM"
40 atoms, 42 bonds, 2 residues, 1 model selected
> show sel atoms
> select #1/E:7
21 atoms, 23 bonds, 1 residue, 1 model selected
> select up
362 atoms, 405 bonds, 18 residues, 1 model selected
Alignment identifier is 1/D
Alignment identifier is 1/E
> color sel black
> color sel black
> select nucleic-acid
3298 atoms, 3584 bonds, 116 residues, 2 models selected
> color sel byhetero
> select clear
> ui tool show Matchmaker
> matchmaker #2 to #1/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 5ego.pdb, chain A (#1) with oct4_oct4_nr5a2_cpg_02_equil_03.pdb,
chain B (#2), sequence alignment score = 107.8
RMSD between 43 pruned atom pairs is 1.078 angstroms; (across all 54 pairs:
1.769)
> delete H
Alignment identifier is 1/A
Destroying pre-existing alignment with identifier 1/D
Alignment identifier is 1/D
Destroying pre-existing alignment with identifier 1/E
Alignment identifier is 1/E
Alignment identifier is 1/B
Alignment identifier is 1
Alignment identifier is 2/C
Alignment identifier is 2/D
> select clear
> ui tool show Matchmaker
> matchmaker #2 to #1/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 5ego.pdb, chain B (#1) with oct4_oct4_nr5a2_cpg_02_equil_03.pdb,
chain A (#2), sequence alignment score = 119.1
RMSD between 48 pruned atom pairs is 1.070 angstroms; (across all 63 pairs:
3.681)
> matchmaker #2 to #1/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 5ego.pdb, chain B (#1) with oct4_oct4_nr5a2_cpg_02_equil_03.pdb,
chain A (#2), sequence alignment score = 119.1
RMSD between 48 pruned atom pairs is 1.070 angstroms; (across all 63 pairs:
3.681)
> ui tool show Matchmaker
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\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 "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\options\options.py", line 272, 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 "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\options\options.py", line 272, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
> save "C:/Users/daisy/OneDrive - The University of Hong Kong/My
> drive/HKU/PHD/meDNA/Models/Other HDs/Oct4_CpGpal_config2_Hoxb13.cxs"
> matchmaker #2/B to #1/B pairing ss
Parameters
---
Chain pairing | ss
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 5ego.pdb, chain B (#1) with oct4_oct4_nr5a2_cpg_02_equil_03.pdb,
chain B (#2), sequence alignment score = 116.7
RMSD between 43 pruned atom pairs is 0.905 angstroms; (across all 63 pairs:
5.806)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> matchmaker #2/B to #1/B pairing ss
Parameters
---
Chain pairing | ss
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 5ego.pdb, chain B (#1) with oct4_oct4_nr5a2_cpg_02_equil_03.pdb,
chain B (#2), sequence alignment score = 116.7
RMSD between 43 pruned atom pairs is 0.905 angstroms; (across all 63 pairs:
5.806)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> ui tool show Matchmaker
> matchmaker #2/A to #1/B pairing ss
Parameters
---
Chain pairing | ss
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 5ego.pdb, chain B (#1) with oct4_oct4_nr5a2_cpg_02_equil_03.pdb,
chain A (#2), sequence alignment score = 119.1
RMSD between 48 pruned atom pairs is 1.070 angstroms; (across all 63 pairs:
3.681)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> matchmaker #2/B to #1/B pairing ss
Parameters
---
Chain pairing | ss
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 5ego.pdb, chain B (#1) with oct4_oct4_nr5a2_cpg_02_equil_03.pdb,
chain B (#2), sequence alignment score = 116.7
RMSD between 43 pruned atom pairs is 0.905 angstroms; (across all 63 pairs:
5.806)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> color sel black
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> color sel byhetero
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> color sel black
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> color sel byhetero
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> save "C:/Users/daisy/OneDrive - The University of Hong Kong/My
> drive/HKU/PHD/meDNA/Models/Other HDs/Oct4_CpGpal_config2_Hoxb13.cxs"
opened ChimeraX session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> select clear
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> close session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> open "C:/Users/daisy/OneDrive - The University of Hong Kong/My
> drive/HKU/PHD/meDNA/Models/Vlad/oct4_oct4_nr5a2_cpg_02_equil_02.pdb"
> "C:/Users/daisy/OneDrive - The University of Hong Kong/My
> drive/HKU/PHD/meDNA/Models/Vlad/oct4_oct4_nr5a2_cpg_02_equil_03.pdb"
Chain information for oct4_oct4_nr5a2_cpg_02_equil_02.pdb #1
---
Chain | Description
A B | No description available
C | No description available
D | No description available
Chain information for oct4_oct4_nr5a2_cpg_02_equil_03.pdb #2
---
Chain | Description
A B | No description available
C | No description available
D | No description available
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "add models":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> ui tool show Matchmaker
> 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 oct4_oct4_nr5a2_cpg_02_equil_03.pdb, chain A (#2) with
oct4_oct4_nr5a2_cpg_02_equil_02.pdb, chain A (#1), sequence alignment score =
805.1
RMSD between 18 pruned atom pairs is 0.494 angstroms; (across all 164 pairs:
13.048)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> matchmaker #1 to #2 matrix Nucleic
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 oct4_oct4_nr5a2_cpg_02_equil_03.pdb, chain C (#2) with
oct4_oct4_nr5a2_cpg_02_equil_02.pdb, chain C (#1), sequence alignment score =
157.2
RMSD between 5 pruned atom pairs is 0.735 angstroms; (across all 40 pairs:
6.417)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> ui tool show Matchmaker
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\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 "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\options\options.py", line 272, 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 "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\options\options.py", line 272, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
> matchmaker #2 to #1/C pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 oct4_oct4_nr5a2_cpg_02_equil_02.pdb, chain C (#1) with
oct4_oct4_nr5a2_cpg_02_equil_03.pdb, chain C (#2), sequence alignment score =
157.2
RMSD between 5 pruned atom pairs is 0.735 angstroms; (across all 40 pairs:
6.417)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> matchmaker #2 to #1/C pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 oct4_oct4_nr5a2_cpg_02_equil_02.pdb, chain C (#1) with
oct4_oct4_nr5a2_cpg_02_equil_03.pdb, chain C (#2), sequence alignment score =
157.2
RMSD between 5 pruned atom pairs is 0.735 angstroms; (across all 40 pairs:
6.417)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> matchmaker #2 to #1/C pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 oct4_oct4_nr5a2_cpg_02_equil_02.pdb, chain C (#1) with
oct4_oct4_nr5a2_cpg_02_equil_03.pdb, chain C (#2), sequence alignment score =
157.2
RMSD between 5 pruned atom pairs is 0.735 angstroms; (across all 40 pairs:
6.417)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> matchmaker #2 to #1/C pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 oct4_oct4_nr5a2_cpg_02_equil_02.pdb, chain C (#1) with
oct4_oct4_nr5a2_cpg_02_equil_03.pdb, chain C (#2), sequence alignment score =
157.2
RMSD between 5 pruned atom pairs is 0.735 angstroms; (across all 40 pairs:
6.417)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> matchmaker #2 to #1/C pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 oct4_oct4_nr5a2_cpg_02_equil_02.pdb, chain C (#1) with
oct4_oct4_nr5a2_cpg_02_equil_03.pdb, chain C (#2), sequence alignment score =
157.2
RMSD between 5 pruned atom pairs is 0.735 angstroms; (across all 40 pairs:
6.417)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> matchmaker #2 to #1/C pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 oct4_oct4_nr5a2_cpg_02_equil_02.pdb, chain C (#1) with
oct4_oct4_nr5a2_cpg_02_equil_03.pdb, chain C (#2), sequence alignment score =
157.2
RMSD between 5 pruned atom pairs is 0.735 angstroms; (across all 40 pairs:
6.417)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> matchmaker #2 to #1/C pairing bs matrix Nucleic
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 oct4_oct4_nr5a2_cpg_02_equil_02.pdb, chain C (#1) with
oct4_oct4_nr5a2_cpg_02_equil_03.pdb, chain C (#2), sequence alignment score =
157.2
RMSD between 5 pruned atom pairs is 0.735 angstroms; (across all 40 pairs:
6.417)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 27.20.100.9664
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: Latitude 3500
OS: Microsoft Windows 10 Enterprise (Build 19042)
Memory: 8,460,267,520
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-8265U CPU @ 1.60GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
chardet: 3.0.4
ChimeraX-AddH: 2.1.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.6.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.0.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.0
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
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: 1.0
ChimeraX-Hbonds: 2.0
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.0
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.0
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.1
ChimeraX-MDcrds: 2.0
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.2.1
ChimeraX-PDB: 2.1
ChimeraX-PDBBio: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0
ChimeraX-PubChem: 2.0
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.0
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.0.4
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.3
ChimeraX-uniprot: 2.0
ChimeraX-ViewDockX: 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: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.20
decorator: 4.4.2
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
gdcm: 2.8.8
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.16
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.0
ipython: 7.15.0
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.3
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.1
MarkupSafe: 1.1.1
matplotlib: 3.2.1
msgpack: 1.0.0
netifaces: 0.10.9
networkx: 2.4
numexpr: 2.7.1
numpy: 1.18.5+mkl
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2.2
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.7
psutil: 5.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.6.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.12.3
PyQt5-sip: 4.19.19
PyQtWebEngine-commercial: 5.12.1
python-dateutil: 2.8.1
pytz: 2020.1
pywin32: 228
pyzmq: 19.0.2
qtconsole: 4.7.4
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.4.1
setuptools: 49.4.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.1.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.6.3
tinyarray: 1.2.2
tornado: 6.0.4
traitlets: 5.0.4
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
WMI: 1.5.1
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → UI |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → wrapped C/C++ object of type ChainMenuButton has been deleted |
comment:2 by , 3 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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