alphafold pae: JSONDecodeError (DropBox)

[davidfay@…]

The following bug report has been submitted:
Platform:        macOS-15.5-arm64-arm-64bit
ChimeraX Version: 1.10rc202506232245 (2025-06-23 22:45:10 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.10rc202506232245 (2025-06-23)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/david/Fay Lab DropBox/Fay Lab
> Folder/DSF_Alphafold/NEKL–MLT_AF_PL_tests/AF_PL_Candidates/NEKL-2_PL_candidates/NEKL2_frm4_2ef53.result/NEKL2_frm4_2ef53/NEKL2_frm4_2ef53_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb"

Chain information for
NEKL2_frm4_2ef53_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
#1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file "/Users/david/Fay Lab DropBox/Fay Lab
> Folder/DSF_Alphafold/NEKL–MLT_AF_PL_tests/AF_PL_Candidates/NEKL-2_PL_candidates/NEKL2_frm4_2ef53.result/NEKL2_frm4_2ef53/NEKL2_frm4_2ef53_scores_rank_001_alphafold2_multimer_v3_model_4_seed_000.json"

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10-rc2025.06.24.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 186, in _open_pae  
self._open_pae_from_file(s)  
File
"/Applications/ChimeraX-1.10-rc2025.06.24.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 212, in _open_pae_from_file  
run(self.session, cmd)  
File
"/Applications/ChimeraX-1.10-rc2025.06.24.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.06.24.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.06.24.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1462, in alphafold_pae  
pae = AlphaFoldPAE(file, structure)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.06.24.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 980, in __init__  
self._pae_matrix = read_pae_matrix(pae_path)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.06.24.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1224, in read_pae_matrix  
return read_json_pae_matrix(path)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.06.24.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1239, in read_json_pae_matrix  
j = json.load(f)  
^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.06.24.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/json/__init__.py",
line 293, in load  
return loads(fp.read(),  
^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.06.24.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/json/__init__.py",
line 346, in loads  
return _default_decoder.decode(s)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.06.24.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/json/decoder.py",
line 337, in decode  
obj, end = self.raw_decode(s, idx=_w(s, 0).end())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.06.24.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/json/decoder.py",
line 355, in raw_decode  
raise JSONDecodeError("Expecting value", s, err.value) from None  
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)  
  
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)  
  
File
"/Applications/ChimeraX-1.10-rc2025.06.24.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/json/decoder.py",
line 355, in raw_decode  
raise JSONDecodeError("Expecting value", s, err.value) from None  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac16,5
      Model Number: Z1FS0008QLL/A
      Chip: Apple M4 Max
      Total Number of Cores: 16 (12 performance and 4 efficiency)
      Memory: 64 GB
      System Firmware Version: 11881.121.1
      OS Loader Version: 11881.121.1

Software:

    System Software Overview:

      System Version: macOS 15.5 (24F74)
      Kernel Version: Darwin 24.5.0
      Time since boot: 16 hours, 12 minutes

Graphics/Displays:

    Apple M4 Max:

      Chipset Model: Apple M4 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 40
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        Studio Display:
          Display Type: Retina LCD
          Resolution: 5120 x 2880 Retina
          Display Serial Number: VK6VF0K67H
          Display Firmware Version: Version 17.0 (Build 21A329)
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.4.0
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.18
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10rc202506232245
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.3
    ChimeraX-ProfileGrids: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.45.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.9.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.58.4
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
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    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
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    tcia_utils: 1.5.1
    tifffile: 2025.3.13
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    tzdata: 2025.2
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    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14

[DavidFay@…]

This seems to be a dropbox issue and not a ChimeraX issue.

[Eric Pettersen]

Reported by David Fay

[Tom Goddard]

This ChimeraX error reading file

/Users/david/Fay Lab DropBox/Fay Lab Folder/DSF_Alphafold/NEKL–MLT_AF_PL_tests/AF_PL_Candidates/NEKL-2_PL_candidates/NEKL2_frm4_2ef53.result/NEKL2_frm4_2ef53/NEKL2_frm4_2ef53_scores_rank_001_alphafold2_multimer_v3_model_4_seed_000.json

json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0) 

means the .json file was empty. I suspect that file is not actually empty and the problem is it is coming from DropBox and somehow dropbox has not synced the file contents so ChimeraX reads it and finds it empty. I believe I've seen this happen before with DropBox. You could try opening the .json file in a text editor to make sure DropBox has copied it. Or copy the entire AlphaFold results from DropBox to a different place on your local disk so DropBox isn't mirroring it.

[Tom Goddard]

No response from reporter.