Opened 13 months ago

Closed 13 months ago

Last modified 13 months ago

#16013 closed defect (not a bug)

MOLE JSON treated as AlphaFold

Reported by: bcneuman@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
JSON files from ​MOLEonline no longer open and are promted to be a AlphaFold PAE file

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> lighting soft

> set bgColor white

> graphics silhouettes true

> open "D:/OneDrive - UC Irvine/Gonen
> lab/neo1.5/J1568_H_af_fl_neo_real_space_refined_005-coot-0.pdb"

Chain information for J1568_H_af_fl_neo_real_space_refined_005-coot-0.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open "D:/OneDrive - UC Irvine/Gonen
> lab/neo1.5/MoleOnline/J1568/mole_channels_uTDyg8jQUC2FWDZrAjDIw_2/json/data.json"

Opening an AlphaFold PAE file requires specifying the structure to associate.
Did not find an open structure from the same directory. To specify the
structure use menu  
  
Tools / Structure Prediction / AlphaFold Error Plot  
  
or use the open command, for example  
  
open D:/OneDrive - UC Irvine/Gonen
lab/neo1.5/MoleOnline/J1568/mole_channels_uTDyg8jQUC2FWDZrAjDIw_2/json/data.json
format pae structure #1  

> open "D:/OneDrive - UC Irvine/Gonen
> lab/neo1.5/MoleOnline/J1568/mole_channels_uTDyg8jQUC2FWDZrAjDIw_2/mole_channels_uTDyg8jQUC2FWDZrAjDIw_2.json"

Opening an AlphaFold PAE file requires specifying the structure to associate.
Did not find an open structure from the same directory. To specify the
structure use menu  
  
Tools / Structure Prediction / AlphaFold Error Plot  
  
or use the open command, for example  
  
open D:/OneDrive - UC Irvine/Gonen
lab/neo1.5/MoleOnline/J1568/mole_channels_uTDyg8jQUC2FWDZrAjDIw_2/mole_channels_uTDyg8jQUC2FWDZrAjDIw_2.json
format pae structure #1  

> lighting soft

> open "D:/OneDrive - UC Irvine/Gonen
> lab/neo1.5/MoleOnline/J1568/mole_channels_uTDyg8jQUC2FWDZrAjDIw_2/mole_channels_uTDyg8jQUC2FWDZrAjDIw_2_pdb/tunnel_1.pdb"

Summary of feedback from opening D:/OneDrive - UC Irvine/Gonen
lab/neo1.5/MoleOnline/J1568/mole_channels_uTDyg8jQUC2FWDZrAjDIw_2/mole_channels_uTDyg8jQUC2FWDZrAjDIw_2_pdb/tunnel_1.pdb  
---  
warning | Ignored bad PDB record found on line 14  
REMARK ATOM NAM RES TUNID X Y Z Distnm RadiusA  
  

> open "D:/OneDrive - UC Irvine/Gonen
> lab/neo1.5/MoleOnline/J1568/mole_channels_uTDyg8jQUC2FWDZrAjDIw_2/mole_channels_uTDyg8jQUC2FWDZrAjDIw_2.json"

Opening an AlphaFold PAE file requires specifying the structure to associate.
Did not find an open structure from the same directory. To specify the
structure use menu  
  
Tools / Structure Prediction / AlphaFold Error Plot  
  
or use the open command, for example  
  
open D:/OneDrive - UC Irvine/Gonen
lab/neo1.5/MoleOnline/J1568/mole_channels_uTDyg8jQUC2FWDZrAjDIw_2/mole_channels_uTDyg8jQUC2FWDZrAjDIw_2.json
format pae structure #1  

> open "D:/OneDrive - UC Irvine/Gonen
> lab/neo1.5/MoleOnline/J1568/mole_channels_uTDyg8jQUC2FWDZrAjDIw_2/json/data.json"

Opening an AlphaFold PAE file requires specifying the structure to associate.
Did not find an open structure from the same directory. To specify the
structure use menu  
  
Tools / Structure Prediction / AlphaFold Error Plot  
  
or use the open command, for example  
  
open D:/OneDrive - UC Irvine/Gonen
lab/neo1.5/MoleOnline/J1568/mole_channels_uTDyg8jQUC2FWDZrAjDIw_2/json/data.json
format pae structure #1  

> ui tool show "AlphaFold Error Plot"

QWindowsWindow::setGeometry: Unable to set geometry 558x125+2121+1326 (frame:
576x172+2112+1288) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 556x117+2122+1333 (frame:
574x164+2113+1295) margins: 9, 38, 9, 9 minimum size: 446x99 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=576, y=171)))  

Must choose path to predicted aligned file  

> alphafold pae #1 file "D:/OneDrive - UC Irvine/Gonen
> lab/neo1.5/MoleOnline/J1568/mole_channels_uTDyg8jQUC2FWDZrAjDIw_2/json/data.json"

JSON file "D:/OneDrive - UC Irvine/Gonen
lab/neo1.5/MoleOnline/J1568/mole_channels_uTDyg8jQUC2FWDZrAjDIw_2/json/data.json"
is not AlphaFold predicted aligned error data, expected a top level list  

> alphafold pae #1 file "D:/OneDrive - UC Irvine/Gonen
> lab/neo1.5/MoleOnline/J1568/mole_channels_uTDyg8jQUC2FWDZrAjDIw_2/json/data.json"

JSON file "D:/OneDrive - UC Irvine/Gonen
lab/neo1.5/MoleOnline/J1568/mole_channels_uTDyg8jQUC2FWDZrAjDIw_2/json/data.json"
is not AlphaFold predicted aligned error data, expected a top level list  

> help help:user/tools/alphafold.html#pae

QWindowsWindow::setGeometry: Unable to set geometry 1058x1104+1871+838 (frame:
1076x1151+1862+800) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1056x1096+1872+845 (frame:
1074x1143+1863+807) margins: 9, 38, 9, 9 minimum size: 840x877 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=1068, y=1143)))  

> open "D:/OneDrive - UC Irvine/Gonen
> lab/neo1.5/MoleOnline/J1568/mole_channels_uTDyg8jQUC2FWDZrAjDIw_2/json/data.json"

Opening an AlphaFold PAE file requires specifying the structure to associate.
Did not find an open structure from the same directory. To specify the
structure use menu  
  
Tools / Structure Prediction / AlphaFold Error Plot  
  
or use the open command, for example  
  
open D:/OneDrive - UC Irvine/Gonen
lab/neo1.5/MoleOnline/J1568/mole_channels_uTDyg8jQUC2FWDZrAjDIw_2/json/data.json
format pae structure #1  

> open "D:/OneDrive - UC Irvine/Gonen
> lab/neo1.5/MoleOnline/J1568/mole_channels_uTDyg8jQUC2FWDZrAjDIw_2/mole_channels_uTDyg8jQUC2FWDZrAjDIw_2.json"

Opening an AlphaFold PAE file requires specifying the structure to associate.
Did not find an open structure from the same directory. To specify the
structure use menu  
  
Tools / Structure Prediction / AlphaFold Error Plot  
  
or use the open command, for example  
  
open D:/OneDrive - UC Irvine/Gonen
lab/neo1.5/MoleOnline/J1568/mole_channels_uTDyg8jQUC2FWDZrAjDIw_2/mole_channels_uTDyg8jQUC2FWDZrAjDIw_2.json
format pae structure #1  

> open D:/OneDrive - UC Irvine/Gonen
> lab/neo1.5/MoleOnline/J1568/mole_channels_uTDyg8jQUC2FWDZrAjDIw_2/mole_channels_uTDyg8jQUC2FWDZrAjDIw_2.json

'D:/OneDrive' has no suffix  

> hide #2 models

> show #2 models

> close #2

> open D:/OneDrive - UC Irvine/Gonen
> lab/neo1.5/MoleOnline/J1568/mole_channels_uTDyg8jQUC2FWDZrAjDIw_2/mole_channels_uTDyg8jQUC2FWDZrAjDIw_2.json

'D:/OneDrive' has no suffix  

> open C:\Users\b-neu\Desktop\mole_channels_uTDyg8jQUC2FWDZrAjDIw_2.json

Opening an AlphaFold PAE file requires specifying the structure to associate.
Did not find an open structure from the same directory. To specify the
structure use menu  
  
Tools / Structure Prediction / AlphaFold Error Plot  
  
or use the open command, for example  
  
open C:\Users\b-neu\Desktop\mole_channels_uTDyg8jQUC2FWDZrAjDIw_2.json format
pae structure #1  

> toolshed show

QWindowsWindow::setGeometry: Unable to set geometry 1058x1104+1871+838 (frame:
1076x1151+1862+800) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1056x1096+1872+845 (frame:
1074x1143+1863+807) margins: 9, 38, 9, 9 minimum size: 840x877 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=1068, y=1143)))  

QWindowsWindow::setGeometry: Unable to set geometry 750x594+2025+1093 (frame:
768x641+2016+1055) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 748x586+2026+1100 (frame:
766x633+2017+1062) margins: 9, 38, 9, 9 minimum size: 600x321 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=768, y=448)))  

> help help:contact.html

QWindowsWindow::setGeometry: Unable to set geometry 1058x1104+1871+838 (frame:
1076x1151+1862+800) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1056x1096+1872+845 (frame:
1074x1143+1863+807) margins: 9, 38, 9, 9 minimum size: 840x877 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=1068, y=1143)))  

> open "D:/OneDrive - UC Irvine/Gonen lab/Publications/Apo1.8 &
> ProTx-I/MOLEonline/consensus
> map/mole_channels_foioDACXdEeYMcL8jocVuA_1.json"

Opening an AlphaFold PAE file requires specifying the structure to associate.
Did not find an open structure from the same directory. To specify the
structure use menu  
  
Tools / Structure Prediction / AlphaFold Error Plot  
  
or use the open command, for example  
  
open D:/OneDrive - UC Irvine/Gonen lab/Publications/Apo1.8 &
ProTx-I/MOLEonline/consensus map/mole_channels_foioDACXdEeYMcL8jocVuA_1.json
format pae structure #1  




OpenGL version: 3.3.0 NVIDIA 561.09
OpenGL renderer: NVIDIA GeForce RTX 4070 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows

Manufacturer: LENOVO
Model: 83DH
OS: Microsoft Windows 11 Home (Build 22631)
Memory: 33,615,630,336
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 8845HS w/ Radeon 780M Graphics     
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2024.6.2
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    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-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    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: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    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: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    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
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.1
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pywin32: 306
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
    WMI: 1.5.1

Change History (3)

comment:1 by pett, 13 months ago

Component: Unassigned → Input/Output
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → MOLE JSON treated as AlphaFold

Reported by Bryan Neumann

comment:2 by Tom Goddard, 13 months ago

Resolution: → not a bug
Status: assigned → closed

Sorry about that change. AlphaFold PAE json files are much more commonly used in ChimeraX than MOLE json files so I changed the default for file suffix ".json" to assume AlphaFold PAE data. ChimeraX only looks at the file suffix to determine the type of data. It does not try to figure out from the contents of the file. So for common file suffixes like .json that are used for many different kinds of data you will have specify the format if it is not the default. So to read MOLE json file

open mychannels.json format mole

or in the ChimeraX Open File dialog choose format "Mole tunnels".

In the ChimeraX daily build loading a MOLE file as AlphaFold PAE gives an error message that suggests how to open MOLE data with the above command.

comment:3 by bcneuman@…, 13 months ago 

Hi Tom,

Understood, no problem! Thank you for the speedy instructions, everything is working fine.

Best,
Bryan
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Wednesday, September 25, 2024 10:23 AM
To: Bryan Neumann <bcneuman@uci.edu>; goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #16013: MOLE JSON treated as AlphaFold

#16013: MOLE JSON treated as AlphaFold
-----------------------------------+-------------------------
          Reporter:  bcneuman@…    |      Owner:  Tom Goddard
              Type:  defect        |     Status:  closed
          Priority:  normal        |  Milestone:
         Component:  Input/Output  |    Version:
        Resolution:  not a bug     |   Keywords:
        Blocked By:                |   Blocking:
Notify when closed:                |   Platform:  all
           Project:  ChimeraX      |
-----------------------------------+-------------------------
Changes (by Tom Goddard):

 * resolution:   => not a bug
 * status:  assigned => closed

Comment:

 Sorry about that change.  AlphaFold PAE json files are much more commonly
 used in ChimeraX than MOLE json files so I changed the default for file
 suffix ".json" to assume AlphaFold PAE data.  ChimeraX only looks at the
 file suffix to determine the type of data.  It does not try to figure out
 from the contents of the file.  So for common file suffixes like .json
 that are used for many different kinds of data you will have specify the
 format if it is not the default.  So to read MOLE json file

    open mychannels.json format mole

 or in the ChimeraX Open File dialog choose format "Mole tunnels".

 In the ChimeraX daily build loading a MOLE file as AlphaFold PAE gives an
 error message that suggests how to open MOLE data with the above command.
--
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