After session restore: wrapped C/C++ object of type ChainListWidget has been deleted

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "/Users/chiduzg/Dropbox (The Francis Crick)/ToozeS/ATG9B
> paper/Figures/Figure 3/Working/Protomer alignments.cxs"

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type AtomicStructureListWidget has been
deleted  
  
Error processing trigger "remove models":  
RuntimeError: wrapped C/C++ object of type AtomicStructureListWidget has been
deleted  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type AtomicStructureListWidget has been
deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type AtomicStructureListWidget has been
deleted  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type AtomicStructureListWidget has been
deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type AtomicStructureListWidget has been
deleted  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type AtomicStructureListWidget has been
deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type AtomicStructureListWidget has been
deleted  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type AtomicStructureListWidget has been
deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type AtomicStructureListWidget has been
deleted  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  
Log from Mon Feb 13 17:00:24 2023UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/chiduzg/Dropbox (The Francis Crick)/George Chiduza/Structural
> Bioinformatics/Structure prediction/atg9b/alphafold/9B_no_loops_monomer.pdb"

Summary of feedback from opening /Users/chiduzg/Dropbox (The Francis
Crick)/George Chiduza/Structural Bioinformatics/Structure
prediction/atg9b/alphafold/9B_no_loops_monomer.pdb  
---  
warnings | End residue of secondary structure not found: HELIX 26 26 GLY A 722
ARG A 748 1 27  
Start residue of secondary structure not found: HELIX 29 29 GLY A 816 ALA A
821 1 6  
Start residue of secondary structure not found: HELIX 31 31 ALA A 854 ALA A
856 1 3  
  
9B_no_loops_monomer.pdb title:  
Alphafold V2.0 prediction for autophagy-related protein 9B (Q674R7) [more
info...]  
  
Chain information for 9B_no_loops_monomer.pdb #1  
---  
Chain | Description | UniProt  
A | autophagy-related protein 9B | ATG9B_HUMAN  
  

> set bgColor white

> open "/Users/chiduzg/Dropbox (The Francis Crick)/George Chiduza/Structural
> Bioinformatics/ATG9A structure analysis/State A (6wqz)/protomer.pdb"

Summary of feedback from opening /Users/chiduzg/Dropbox (The Francis
Crick)/George Chiduza/Structural Bioinformatics/ATG9A structure analysis/State
A (6wqz)/protomer.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ASN C 42
LYS C 56 1 15  
Start residue of secondary structure not found: HELIX 2 2 GLY C 58 CYS C 86 1
29  
Start residue of secondary structure not found: HELIX 3 3 ASP C 88 ALA C 94 1
7  
Start residue of secondary structure not found: HELIX 4 4 THR C 111 ALA C 115
1 5  
Start residue of secondary structure not found: HELIX 5 5 PRO C 118 LEU C 168
1 51  
51 messages similar to the above omitted  
  
protomer.pdb title:  
Structure of human ATG9A, the ONLY transmembrane protein of the core autophagy
machinery [more info...]  
  
Chain information for protomer.pdb #2  
---  
Chain | Description | UniProt  
A | autophagy-related protein 9A | ATG9A_HUMAN  
  

> open "/Users/chiduzg/Dropbox (The Francis Crick)/George Chiduza/Structural
> Bioinformatics/ATG9A structure analysis/State B (6wr4)/protomer_state_b.pdb"

Summary of feedback from opening /Users/chiduzg/Dropbox (The Francis
Crick)/George Chiduza/Structural Bioinformatics/ATG9A structure analysis/State
B (6wr4)/protomer_state_b.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 21 21 ASN B
42 LYS B 56 1 15  
Start residue of secondary structure not found: HELIX 22 22 GLY B 58 CYS B 86
1 29  
Start residue of secondary structure not found: HELIX 23 23 ASP B 88 ALA B 94
1 7  
Start residue of secondary structure not found: HELIX 24 24 THR B 111 ALA B
115 1 5  
Start residue of secondary structure not found: HELIX 25 25 PRO B 118 SER B
123 1 6  
43 messages similar to the above omitted  
  
protomer_state_b.pdb title:  
Structure of human ATG9A, the ONLY transmembrane protein of the core autophagy
machinery [more info...]  
  
Chain information for protomer_state_b.pdb #3  
---  
Chain | Description | UniProt  
A | autophagy-related protein 9A | ATG9A_HUMAN  
  

> open "/Users/chiduzg/Dropbox (The Francis Crick)/George Chiduza/Cryo-
> EM/ATG9B/maps_for_model_building_atg9b/Best model
> 041122/9B_coot-22_real_space_refined_monomer_trimer_ABC_real_space_refined_007.pdb"

Chain information for
9B_coot-22_real_space_refined_monomer_trimer_ABC_real_space_refined_007.pdb #4  
---  
Chain | Description  
A B C | No description available  
  

> hide #!1 models

> hide #!2 models

> hide #!3 models

> view

> select #4/A

3679 atoms, 3776 bonds, 4 pseudobonds, 461 residues, 2 models selected  

> color (#!4 & sel) orange red

> select ~sel

20464 atoms, 21016 bonds, 18 pseudobonds, 2538 residues, 8 models selected  

> hide sel & #!4 cartoons

> ui tool show Matchmaker

> matchmaker #!1-3 to #4/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
9B_coot-22_real_space_refined_monomer_trimer_ABC_real_space_refined_007.pdb,
chain A (#4) with 9B_no_loops_monomer.pdb, chain A (#1), sequence alignment
score = 2233.1  
RMSD between 377 pruned atom pairs is 0.979 angstroms; (across all 461 pairs:
2.730)  
  
Matchmaker
9B_coot-22_real_space_refined_monomer_trimer_ABC_real_space_refined_007.pdb,
chain A (#4) with protomer.pdb, chain A (#2), sequence alignment score =
1468.7  
RMSD between 315 pruned atom pairs is 1.152 angstroms; (across all 453 pairs:
2.974)  
  
Matchmaker
9B_coot-22_real_space_refined_monomer_trimer_ABC_real_space_refined_007.pdb,
chain A (#4) with protomer_state_b.pdb, chain A (#3), sequence alignment score
= 1349.3  
RMSD between 304 pruned atom pairs is 1.117 angstroms; (across all 448 pairs:
3.293)  
  

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> select #4/A

3679 atoms, 3776 bonds, 4 pseudobonds, 461 residues, 2 models selected  

> show sel atoms

> save "/Users/chiduzg/Dropbox (The Francis Crick)/George Chiduza/Structural
> Bioinformatics/ATG9B paper/atg9b_protomer.pdb" models #4 displayedOnly true
> selectedOnly true

> close session

> open "/Users/chiduzg/Dropbox (The Francis Crick)/George Chiduza/Structural
> Bioinformatics/ATG9B paper/atg9b_protomer.pdb" format pdb

Summary of feedback from opening /Users/chiduzg/Dropbox (The Francis
Crick)/George Chiduza/Structural Bioinformatics/ATG9B paper/atg9b_protomer.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 24 24 LEU B
192 ARG B 205 1 14  
Start residue of secondary structure not found: HELIX 25 25 PHE B 208 ARG B
234 1 27  
Start residue of secondary structure not found: HELIX 26 26 TYR B 238 PHE B
242 1 5  
Start residue of secondary structure not found: HELIX 27 27 LEU B 261 ALA B
264 1 4  
Start residue of secondary structure not found: HELIX 28 28 SER B 268 SER B
277 1 10  
45 messages similar to the above omitted  
  
Chain information for atg9b_protomer.pdb #1  
---  
Chain | Description  
A | No description available  
  

> set bgColor white

> color orange red

> open "/Users/chiduzg/Dropbox (The Francis Crick)/George Chiduza/Structural
> Bioinformatics/ATG9A structure analysis/State A (6wqz)/protomer.pdb" format
> pdb

Summary of feedback from opening /Users/chiduzg/Dropbox (The Francis
Crick)/George Chiduza/Structural Bioinformatics/ATG9A structure analysis/State
A (6wqz)/protomer.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ASN C 42
LYS C 56 1 15  
Start residue of secondary structure not found: HELIX 2 2 GLY C 58 CYS C 86 1
29  
Start residue of secondary structure not found: HELIX 3 3 ASP C 88 ALA C 94 1
7  
Start residue of secondary structure not found: HELIX 4 4 THR C 111 ALA C 115
1 5  
Start residue of secondary structure not found: HELIX 5 5 PRO C 118 LEU C 168
1 51  
51 messages similar to the above omitted  
  
protomer.pdb title:  
Structure of human ATG9A, the ONLY transmembrane protein of the core autophagy
machinery [more info...]  
  
Chain information for protomer.pdb #2  
---  
Chain | Description | UniProt  
A | autophagy-related protein 9A | ATG9A_HUMAN  
  

> open "/Users/chiduzg/Dropbox (The Francis Crick)/George Chiduza/Structural
> Bioinformatics/ATG9A structure analysis/State B (6wr4)/protomer_state_b.pdb"
> format pdb

Summary of feedback from opening /Users/chiduzg/Dropbox (The Francis
Crick)/George Chiduza/Structural Bioinformatics/ATG9A structure analysis/State
B (6wr4)/protomer_state_b.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 21 21 ASN B
42 LYS B 56 1 15  
Start residue of secondary structure not found: HELIX 22 22 GLY B 58 CYS B 86
1 29  
Start residue of secondary structure not found: HELIX 23 23 ASP B 88 ALA B 94
1 7  
Start residue of secondary structure not found: HELIX 24 24 THR B 111 ALA B
115 1 5  
Start residue of secondary structure not found: HELIX 25 25 PRO B 118 SER B
123 1 6  
43 messages similar to the above omitted  
  
protomer_state_b.pdb title:  
Structure of human ATG9A, the ONLY transmembrane protein of the core autophagy
machinery [more info...]  
  
Chain information for protomer_state_b.pdb #3  
---  
Chain | Description | UniProt  
A | autophagy-related protein 9A | ATG9A_HUMAN  
  

> open "/Users/chiduzg/Dropbox (The Francis Crick)/George Chiduza/Structural
> Bioinformatics/Structure prediction/atg9b/alphafold/9B_no_loops_monomer.pdb"
> format pdb

Summary of feedback from opening /Users/chiduzg/Dropbox (The Francis
Crick)/George Chiduza/Structural Bioinformatics/Structure
prediction/atg9b/alphafold/9B_no_loops_monomer.pdb  
---  
warnings | End residue of secondary structure not found: HELIX 26 26 GLY A 722
ARG A 748 1 27  
Start residue of secondary structure not found: HELIX 29 29 GLY A 816 ALA A
821 1 6  
Start residue of secondary structure not found: HELIX 31 31 ALA A 854 ALA A
856 1 3  
  
9B_no_loops_monomer.pdb title:  
Alphafold V2.0 prediction for autophagy-related protein 9B (Q674R7) [more
info...]  
  
Chain information for 9B_no_loops_monomer.pdb #4  
---  
Chain | Description | UniProt  
A | autophagy-related protein 9B | ATG9B_HUMAN  
  

> ui tool show Matchmaker

> matchmaker #!2-4 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 atg9b_protomer.pdb, chain A (#1) with protomer.pdb, chain A (#2),
sequence alignment score = 1460.9  
RMSD between 315 pruned atom pairs is 1.152 angstroms; (across all 453 pairs:
2.974)  
  
Matchmaker atg9b_protomer.pdb, chain A (#1) with protomer_state_b.pdb, chain A
(#3), sequence alignment score = 1349.3  
RMSD between 304 pruned atom pairs is 1.117 angstroms; (across all 448 pairs:
3.293)  
  
Matchmaker atg9b_protomer.pdb, chain A (#1) with 9B_no_loops_monomer.pdb,
chain A (#4), sequence alignment score = 2214.5  
RMSD between 377 pruned atom pairs is 0.979 angstroms; (across all 461 pairs:
2.730)  
  

> hide #!1 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> show #!1 models

> show #!4 models

> hide #!4 models

> show #!2 models

> hide #!2 models

> show #!3 models

> view

> close session

> open "/Users/chiduzg/Dropbox (The Francis Crick)/George Chiduza/Cryo-
> EM/ATG9B/maps_for_model_building_atg9b/Best model
> 041122/9B_coot-22_real_space_refined_monomer_trimer_ABC_real_space_refined_007.pdb"
> format pdb

Chain information for
9B_coot-22_real_space_refined_monomer_trimer_ABC_real_space_refined_007.pdb #1  
---  
Chain | Description  
A B C | No description available  
  

> open "/Users/chiduzg/Dropbox (The Francis Crick)/George Chiduza/Structural
> Bioinformatics/ATG9A structure analysis/State B (6wr4)/protomer_state_b.pdb"
> format pdb

Summary of feedback from opening /Users/chiduzg/Dropbox (The Francis
Crick)/George Chiduza/Structural Bioinformatics/ATG9A structure analysis/State
B (6wr4)/protomer_state_b.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 21 21 ASN B
42 LYS B 56 1 15  
Start residue of secondary structure not found: HELIX 22 22 GLY B 58 CYS B 86
1 29  
Start residue of secondary structure not found: HELIX 23 23 ASP B 88 ALA B 94
1 7  
Start residue of secondary structure not found: HELIX 24 24 THR B 111 ALA B
115 1 5  
Start residue of secondary structure not found: HELIX 25 25 PRO B 118 SER B
123 1 6  
43 messages similar to the above omitted  
  
protomer_state_b.pdb title:  
Structure of human ATG9A, the ONLY transmembrane protein of the core autophagy
machinery [more info...]  
  
Chain information for protomer_state_b.pdb #2  
---  
Chain | Description | UniProt  
A | autophagy-related protein 9A | ATG9A_HUMAN  
  

> open "/Users/chiduzg/Dropbox (The Francis Crick)/George Chiduza/Structural
> Bioinformatics/ATG9A structure analysis/State A (6wqz)/protomer.pdb" format
> pdb

Summary of feedback from opening /Users/chiduzg/Dropbox (The Francis
Crick)/George Chiduza/Structural Bioinformatics/ATG9A structure analysis/State
A (6wqz)/protomer.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ASN C 42
LYS C 56 1 15  
Start residue of secondary structure not found: HELIX 2 2 GLY C 58 CYS C 86 1
29  
Start residue of secondary structure not found: HELIX 3 3 ASP C 88 ALA C 94 1
7  
Start residue of secondary structure not found: HELIX 4 4 THR C 111 ALA C 115
1 5  
Start residue of secondary structure not found: HELIX 5 5 PRO C 118 LEU C 168
1 51  
51 messages similar to the above omitted  
  
protomer.pdb title:  
Structure of human ATG9A, the ONLY transmembrane protein of the core autophagy
machinery [more info...]  
  
Chain information for protomer.pdb #3  
---  
Chain | Description | UniProt  
A | autophagy-related protein 9A | ATG9A_HUMAN  
  

> open "/Users/chiduzg/Dropbox (The Francis Crick)/George Chiduza/Structural
> Bioinformatics/Structure prediction/atg9b/alphafold/9B_no_loops_monomer.pdb"
> format pdb

Summary of feedback from opening /Users/chiduzg/Dropbox (The Francis
Crick)/George Chiduza/Structural Bioinformatics/Structure
prediction/atg9b/alphafold/9B_no_loops_monomer.pdb  
---  
warnings | End residue of secondary structure not found: HELIX 26 26 GLY A 722
ARG A 748 1 27  
Start residue of secondary structure not found: HELIX 29 29 GLY A 816 ALA A
821 1 6  
Start residue of secondary structure not found: HELIX 31 31 ALA A 854 ALA A
856 1 3  
  
9B_no_loops_monomer.pdb title:  
Alphafold V2.0 prediction for autophagy-related protein 9B (Q674R7) [more
info...]  
  
Chain information for 9B_no_loops_monomer.pdb #4  
---  
Chain | Description | UniProt  
A | autophagy-related protein 9B | ATG9B_HUMAN  
  

> ui tool show Matchmaker

> matchmaker #!2-4 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
9B_coot-22_real_space_refined_monomer_trimer_ABC_real_space_refined_007.pdb,
chain A (#1) with protomer_state_b.pdb, chain A (#2), sequence alignment score
= 1348.1  
RMSD between 304 pruned atom pairs is 1.117 angstroms; (across all 448 pairs:
3.293)  
  
Matchmaker
9B_coot-22_real_space_refined_monomer_trimer_ABC_real_space_refined_007.pdb,
chain A (#1) with protomer.pdb, chain A (#3), sequence alignment score =
1468.7  
RMSD between 315 pruned atom pairs is 1.152 angstroms; (across all 453 pairs:
2.974)  
  
Matchmaker
9B_coot-22_real_space_refined_monomer_trimer_ABC_real_space_refined_007.pdb,
chain A (#1) with 9B_no_loops_monomer.pdb, chain A (#4), sequence alignment
score = 2214.5  
RMSD between 377 pruned atom pairs is 0.979 angstroms; (across all 461 pairs:
2.730)  
  

> select #1/B

3679 atoms, 3776 bonds, 4 pseudobonds, 461 residues, 2 models selected  

> hide sel cartoons

> select #1/C

3679 atoms, 3776 bonds, 4 pseudobonds, 461 residues, 2 models selected  

> hide sel cartoons

> set bgColor white

> view sel

> select #1/A

3679 atoms, 3776 bonds, 4 pseudobonds, 461 residues, 2 models selected  

> view sel

> select clear

> select #3/A

4393 atoms, 4516 bonds, 2 pseudobonds, 536 residues, 2 models selected  

> color (#!3 & sel) magenta

> select add #2

8255 atoms, 8485 bonds, 4 pseudobonds, 1006 residues, 4 models selected  

> select subtract #2

4393 atoms, 4516 bonds, 2 pseudobonds, 536 residues, 2 models selected  

> select #2/A

3862 atoms, 3969 bonds, 2 pseudobonds, 470 residues, 2 models selected  

> color (#!2 & sel) medium blue

> select #1/A

3679 atoms, 3776 bonds, 4 pseudobonds, 461 residues, 2 models selected  

> color (#!1 & sel) orange red

> select clear

> hide #!2 models

> hide #!3 models

> save "/Users/chiduzg/Dropbox (The Francis Crick)/ToozeS/ATG9B
> paper/Figures/Figure 3/Working/Protomer alignments.cxs"

——— End of log from Mon Feb 13 17:00:24 2023 ———

opened ChimeraX session  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainListWidget has been deleted  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 164, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  




OpenGL version: unknown
Could not make opengl context current

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 1916.40.8.0.0 (iBridge: 20.16.420.0.0,0)
      OS Loader Version: 564.40.4~27

Software:

    System Software Overview:

      System Version: macOS 13.0 (22A380)
      Kernel Version: Darwin 22.1.0
      Time since boot: 4 days, 6 hours, 49 minutes

Graphics/Displays:

    Intel Iris Plus Graphics 655:

      Chipset Model: Intel Iris Plus Graphics 655
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea5
      Revision ID: 0x0001
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Mirror: On
          Mirror Status: Hardware Mirror
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL U2415:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 7MT019180A3U
          Main Display: Yes
          Mirror: On
          Mirror Status: Master Mirror
          Online: Yes
          Rotation: Supported
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 41.74


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0