read_json_pae_matrix: KeyError: 0

[nandita.bodra@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.4.dev202204010229 (2022-04-01 02:29:39 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4.dev202204010229 (2022-04-01)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/nabo0034/Downloads/SeMakC_0014-01_deposition_xyz.cif

Summary of feedback from opening
C:/Users/nabo0034/Downloads/SeMakC_0014-01_deposition_xyz.cif  
---  
warnings | Atom H is not in the residue template for MET /B:1  
Atom H3 is not in the residue template for GLN /B:108  
Skipping chem_comp category: Missing column 'type' near line 2538  
Skipping chem_comp category: Missing column 'type' near line 2678  
Skipping chem_comp category: Missing column 'type' near line 2840  
Skipping chem_comp category: Missing column 'type' near line 2977  
Skipping chem_comp category: Missing column 'type' near line 3112  
15 messages similar to the above omitted  
  
Chain information for SeMakC_0014-01_deposition_xyz.cif #1  
---  
Chain | Description  
B | No description available  
  

> select /B

2041 atoms, 2026 bonds, 2 pseudobonds, 134 residues, 2 models selected  

> hide sel atoms

> select clear

> select ::name="HOH"

110 atoms, 110 residues, 1 model selected  

> hide sel atoms

> rainbow sel

[Repeated 1 time(s)]

> select /B

2041 atoms, 2026 bonds, 2 pseudobonds, 134 residues, 2 models selected  

> rainbow sel

> ui tool show "Show Sequence Viewer"

> sequence chain /B

Alignment identifier is 1/B  

> select /B:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select /B:1-71

1087 atoms, 1091 bonds, 71 residues, 1 model selected  

> select /B:12-18,22-24,41-43,75-78

231 atoms, 227 bonds, 17 residues, 1 model selected  

> select /B:4-10,25-29,34-36,45-49,53-60,67-73,85-89,92-98

769 atoms, 768 bonds, 47 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> show sel atoms

[Repeated 1 time(s)]

> hide sel atoms

> select clear

> ui tool show "Command Line Interface"

> set bgColor white

> select /B:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select /B:1-73

1121 atoms, 1126 bonds, 73 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain /B

Destroying pre-existing alignment with identifier 1/B  
Alignment identifier is 1/B  

> close session

> ui tool show AlphaFold

> alphafold predict
> MKKIEILIVVDCAGALATTSLISNVYLIDSNQWLGSWDEGTCQLHTVSEDGQFICWRSCAISPDDEVNITGFYGDMIDQKACLPSPVNDAWEGRVQTRGDTGRYLYTISLSINGITMNFSPYLEVQ,MKKVEILMVVDAAAALASRDLQSNIYLIDTNKYMGSGNEGQAELKTACKDGQLLCWRVVAISPDNEVDIVEFNGQMINDRVCIPTKQGLSGDEFWEGRVEAQGQASTQQYNATLSIDGSRLTFDPFLVISL

Running AlphaFold prediction  
[Repeated 2 time(s)]AlphaFold prediction finished  
Results in C:\Users\nabo0034/Downloads\ChimeraX\AlphaFold\prediction_1  
Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file
> C:\\\Users\\\nabo0034/Downloads\\\ChimeraX\\\AlphaFold\\\prediction_1\\\best_model_pae.json

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 158, in _open_pae  
self._open_pae_from_file(s)  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 182, in _open_pae_from_file  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 674, in alphafold_pae  
pae = AlphaFoldPAE(file, structure)  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 477, in __init__  
self._pae_matrix = read_pae_matrix(pae_path)  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 531, in read_pae_matrix  
return read_json_pae_matrix(path)  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 546, in read_json_pae_matrix  
d = j[0]  
KeyError: 0  
  
KeyError: 0  
  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 546, in read_json_pae_matrix  
d = j[0]  
  
See log for complete Python traceback.  
  

> alphafold pae #1 file
> C:\\\Users\\\nabo0034/Downloads\\\ChimeraX\\\AlphaFold\\\prediction_1\\\best_model_pae.json

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 158, in _open_pae  
self._open_pae_from_file(s)  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 182, in _open_pae_from_file  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 674, in alphafold_pae  
pae = AlphaFoldPAE(file, structure)  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 477, in __init__  
self._pae_matrix = read_pae_matrix(pae_path)  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 531, in read_pae_matrix  
return read_json_pae_matrix(path)  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 546, in read_json_pae_matrix  
d = j[0]  
KeyError: 0  
  
KeyError: 0  
  
File "C:\Program Files\ChimeraX 1.4.dev202204010229\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 546, in read_json_pae_matrix  
d = j[0]  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 27.20.100.9664
OpenGL renderer: Intel(R) HD Graphics 630
OpenGL vendor: Intel

Python: 3.9.11
Locale: sv_SE.cp1252
Qt version: PyQt6 6.2.3, Qt 6.2.3
Qt platform: windows

Manufacturer: Dell Inc.
Model: OptiPlex 7050
OS: Microsoft Windows 10 Enterprise (Build 19045)
Memory: 17,036,312,576
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-7700 CPU @ 3.60GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.37
    ChimeraX-AtomicLibrary: 6.1.2
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4.dev202204010229
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.8
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.16.4
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.31.2
    funcparserlib: 1.0.0a0
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
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    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
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    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.7
    PyQt6-commercial: 6.2.3
    PyQt6-sip: 13.2.0
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    pytz: 2022.1
    pywin32: 303
    pyzmq: 22.3.0
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    scipy: 1.7.3
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    wheel-filename: 1.3.0
    WMI: 1.5.1

[Tom Goddard]

This ChimeraX error parsing AlphaFold PAE results is from using an old pre-release ChimeraX 1.4 version. The PAE file produced by Colabfold changed format after that ChimeraX release, so you need to use a newer ChimeraX. Get the ChimeraX 1.6 release or 1.7 release candidate.