![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#9155 closed defect (can't reproduce)
Crash in garbage collection while importing networkx for alphafold pae
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Prediction | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-12.2.1-arm64-arm-64bit
ChimeraX Version: 1.6rc202304252053 (2023-04-25 20:53:05 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x0000000100f60580 (most recent call first):
File "/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/networkx/algorithms/tree/branchings.py", line 853 in ArborescenceIterator
File "/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/networkx/algorithms/tree/branchings.py", line 831 in
File "", line 228 in _call_with_frames_removed
File "", line 850 in exec_module
File "", line 680 in _load_unlocked
File "", line 986 in _find_and_load_unlocked
File "", line 1007 in _find_and_load
File "/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/networkx/algorithms/tree/__init__.py", line 1 in
File "", line 228 in _call_with_frames_removed
File "", line 850 in exec_module
File "", line 680 in _load_unlocked
File "", line 986 in _find_and_load_unlocked
File "", line 1007 in _find_and_load
File "", line 228 in _call_with_frames_removed
File "", line 972 in _find_and_load_unlocked
File "", line 1007 in _find_and_load
File "/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/networkx/algorithms/approximation/traveling_salesman.py", line 39 in
File "", line 228 in _call_with_frames_removed
File "", line 850 in exec_module
File "", line 680 in _load_unlocked
File "", line 986 in _find_and_load_unlocked
File "", line 1007 in _find_and_load
File "/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/networkx/algorithms/approximation/__init__.py", line 21 in
File "", line 228 in _call_with_frames_removed
File "", line 850 in exec_module
File "", line 680 in _load_unlocked
File "", line 986 in _find_and_load_unlocked
File "", line 1007 in _find_and_load
File "", line 228 in _call_with_frames_removed
File "", line 1058 in _handle_fromlist
File "/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/networkx/algorithms/__init__.py", line 62 in
File "", line 228 in _call_with_frames_removed
File "", line 850 in exec_module
File "", line 680 in _load_unlocked
File "", line 986 in _find_and_load_unlocked
File "", line 1007 in _find_and_load
File "", line 228 in _call_with_frames_removed
File "", line 1058 in _handle_fromlist
File "/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/networkx/__init__.py", line 81 in
File "", line 228 in _call_with_frames_removed
File "", line 850 in exec_module
File "", line 680 in _load_unlocked
File "", line 986 in _find_and_load_unlocked
File "", line 1007 in _find_and_load
File "/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/alphafold/pae.py", line 1100 in pae_domains
File "/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/alphafold/pae.py", line 902 in color_domains
File "/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/alphafold/pae.py", line 545 in _color_domains
File "/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
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"incident" : "6798EF5A-FBD1-4056-8FEC-1520E18AF3E4",
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"ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 4306566999\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100b10000-100b14000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
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===== Log before crash start =====
UCSF ChimeraX version: 1.6rc202304252053 (2023-04-25)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/diakinmeji-3/Documents/Chimera X pdb/CREPT CCT with
> PRTCggg-2.cxs" format session
opened ChimeraX session
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /A:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A
1195 atoms, 1204 bonds, 154 residues, 1 model selected
> close
> ui tool show AlphaFold
> alphafold predict
> AMGSTEELIKALQDLENAASGDATVRQKIASLPQEVQDVSLLEKITDKEAAERLSKTVDEACLLLAEYNGRLAAELEDRRQLARMLVEYTQNQKDVLSEKEKKLEEYKQKLARVTQVRKELKSHIQSLPDLSLLPNVTGGLAPLPSAGDLFSTD,AMGSTEELIKALQDLENAASGDATVRQKIASLPQEVQDVSLLEKITDKEAAERLSKTVDEACLLLAEYNGRLAAELEDRRQLARMLVEYTQNQKDVLSEKEKKLEEYKQKLARVTQVRKELKSHIQSLPDLSLLPNVTGGLAPLPSAGDLFSTD,KDVLSEKEKKLEEYKQKLARV
Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.
Running AlphaFold prediction
AlphaFold prediction finished
Results in /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_20
Downloaded prediction file not found:
/Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_20/best_model.pdb
> open
> /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_5/best_model.pdb
> format pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> close
> open "/Users/diakinmeji-3/Documents/Chimera X pdb/CREPT CCT with PRTC-1.cxs"
> format session
opened ChimeraX session
> select /B:21
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B
179 atoms, 179 bonds, 21 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /A:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A
1195 atoms, 1204 bonds, 154 residues, 1 model selected
> close
> ui tool show AlphaFold
> alphafold predict
> KDVLSEKEKKLEEYKQKLARV,AMGSTEELIKALQDLENAASGDATVRQKIASLPQEVQDVSLLEKITDKEAAERLSKTVDEACLLLAEYNGRLAAELEDRRQLARMLVEYTQNQKDVLSEKEKKLEEYKQKLARVTQVRKELKSHIQSLPDLSLLPNVTGGLAPLPSAGDLFSTD,AMGSTEELIKALQDLENAASGDATVRQKIASLPQEVQDVSLLEKITDKEAAERLSKTVDEACLLLAEYNGRLAAELEDRRQLARMLVEYTQNQKDVLSEKEKKLEEYKQKLARVTQVRKELKSHIQSLPDLSLLPNVTGGLAPLPSAGDLFSTD
Running AlphaFold prediction
AlphaFold prediction finished
Results in /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_21
Downloaded prediction file not found:
/Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_21/best_model.pdb
> alphafold predict
> KDVLSEKEKKLEEYKQKLARV,AMGSTEELIKALQDLENAASGDATVRQKIASLPQEVQDVSLLEKITDKEAAERLSKTVDEACLLLAEYNGRLAAELEDRRQLARMLVEYTQNQKDVLSEKEKKLEEYKQKLARVTQVRKELKSHIQSLPDLSLLPNVTGGLAPLPSAGDLFSTD,AMGSTEELIKALQDLENAASGDATVRQKIASLPQEVQDVSLLEKITDKEAAERLSKTVDEACLLLAEYNGRLAAELEDRRQLARMLVEYTQNQKDVLSEKEKKLEEYKQKLARVTQVRKELKSHIQSLPDLSLLPNVTGGLAPLPSAGDLFSTD
Running AlphaFold prediction
AlphaFold prediction finished
Results in /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_22
Downloaded prediction file not found:
/Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_22/best_model.pdb
> close
> ui tool show AlphaFold
> alphafold predict
> KDVLSEKEKKLEEYKQKLARV,AMGSTEELIKALQDLENAASGDATVRQKIASLPQEVQDVSLLEKITDKEAAERLSKTVDEACLLLAEYNGRLAAELEDRRQLARMLVEYTQNQKDVLSEKEKKLEEYKQKLARVTQVRKELKSHIQSLPDLSLLPNVTGGLAPLPSAGDLFSTD
Running AlphaFold prediction
AlphaFold prediction finished
Results in /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_23
> open
> /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_23/best_model.pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
> close
> ui tool show AlphaFold
> alphafold predict
> KDVLSEKEKKLEEYKQKLARV,AMGSTEELIKALQDLENAASGDATVRQKIASLPQEVQDVSLLEKITDKEAAERLSKTVDEACLLLAEYNGRLAAELEDRRQLARMLVEYTQNQKDVLSEKEKKLEEYKQKLARVTQVRKELKSHIQSLPDLSLLPNVTGGLAPLPSAGDLFSTD,AMGSTEELIKALQDLENAASGDATVRQKIASLPQEVQDVSLLEKITDKEAAERLSKTVDEACLLLAEYNGRLAAELEDRRQLARMLVEYTQNQKDVLSEKEKKLEEYKQKLARVTQVRKELKSHIQSLPDLSLLPNVTGGLAPLPSAGDLFSTD
Running AlphaFold prediction
AlphaFold prediction finished
Results in /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_24
Downloaded prediction file not found:
/Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_24/best_model.pdb
> help help:user/tools/alphafold.html
> open
> /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_13/best_model.pdb
> format pdb
Chain information for best_model.pdb #1
---
Chain | Description
A B | No description available
C | No description available
> close
> open "/Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_2/Full
> CREPT_Ma-Ligand-1.cxs" format session
opened ChimeraX session
> close
> open
> /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_3/best_model.pdb
> format pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
> close
> open
> /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_1/best_model.pdb
> format pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
> close
> open "/Users/diakinmeji-3/Documents/Chimera X pdb/Ligand7_CREPT-PRTC-
> competitive.cxs" format session
opened ChimeraX session
> close
> open
> /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_9/af550_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
> format pdb
Chain information for
af550_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1
---
Chain | Description
A | No description available
B | No description available
> close
> open
> /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_9/best_model.pdb
> format pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
> close
> open "/Users/diakinmeji-3/Documents/Chimera X pdb/CREPT CCT with
> PRTCggg-2.cxs" format session
opened ChimeraX session
> close
> open "/Users/diakinmeji-3/Documents/Chimera X pdb/CREPT CCT with PRTC-1.cxs"
> format session
opened ChimeraX session
> close
> open
> /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_23/best_model.pdb
> format pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
> close
> open
> /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_23/best_model.pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
> close
> open
> /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_13/best_model.pdb
Chain information for best_model.pdb #1
---
Chain | Description
A B | No description available
C | No description available
> open
> /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_13/query.fasta
Sequence '3' differs in length from preceding sequences, and it is therefore
impossible to open these sequences as an alignment. If you want to open the
sequences individually, specify 'false' as the value of the 'alignment'
keyword in the 'open' command.
> close
> open
> /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_13/query.fasta
Sequence '3' differs in length from preceding sequences, and it is therefore
impossible to open these sequences as an alignment. If you want to open the
sequences individually, specify 'false' as the value of the 'alignment'
keyword in the 'open' command.
> open
> /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_12/best_model.pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
> close
> open
> /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_13/best_model.pdb
Chain information for best_model.pdb #1
---
Chain | Description
A B | No description available
C | No description available
> color byattribute sequence
No known/registered numeric attribute sequence
> color /a blue
> color /a skyblue
> color /b skyblue
> color /b blue
> color /c orange
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file
> /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_13/best_model_pae.json
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6rc202304252053 (2023-04-25)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 7429.81.3
OS Loader Version: 7429.81.3
Software:
System Software Overview:
System Version: macOS 12.2.1 (21D62)
Kernel Version: Darwin 21.3.0
Time since boot: 3 days 2:04
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
LG ULTRAFINE:
Resolution: 4608 x 2592
UI Looks like: 2304 x 1296 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: Yes
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.4
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
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: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6rc202304252053
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
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: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
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-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
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: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
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: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Structure Prediction |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in alphafold pae |
comment:2 by , 2 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
| Summary: | Crash in alphafold pae → Crash in garbage collection while importing networkx for alphafold pae |
Note:
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This isn't related to networkx or alphafold pae.
The alphafold PAE domains algorithm imports networkx. It was executing "import networkx" which triggered Python garbage collection which crashed in tupletraverse, a crash we have seen probably 50 times.