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Opened 3 years ago
Closed 3 years ago
#8485 closed defect (can't reproduce)
After session restore: wrapped C/C++ object of type ChainListWidget has been deleted
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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: 4.1 INTEL-20.2.44
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.
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
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → After session restore: wrapped C/C++ object of type ChainListWidget has been deleted |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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Would need the session file to have a shot