Missing log messages in second AlphaFold prediction

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-12.6-arm64-arm-64bit
ChimeraX Version: 1.5.dev202210072043 (2022-10-07 20:43:13 UTC)
Description
The second time an AlphaFold prediction is run where the same Google Colab session is still alive it does not print the model numbers and scores as each model is computed.  It seems that the second run setup of the logging somehow disables that log output.

Log:
UCSF ChimeraX version: 1.5.dev202210072043 (2022-10-07)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6oug format mmcif fromDatabase pdb

6oug title:  
Structure of drug-resistant V27A mutant of the influenza M2 proton channel
bound to spiroadamantyl amine inhibitor, TM + cytosolic helix construct [more
info...]  
  
Chain information for 6oug #1  
---  
Chain | Description | UniProt  
A B C D E F G H | Matrix protein 2 | M2_I71A1  
  
Non-standard residues in 6oug #1  
---  
E01 —
(1r,1'S,3'S,5'S,7'S)-spiro[cyclohexane-1,2'-tricyclo[3.3.1.1~3,7~]decan]-4-amine  
  
6oug mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> ui tool show AlphaFold

> alphafold predict #1/A templates true

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/goddard/Downloads/ChimeraX/AlphaFold/prediction_57  

> open
> /Users/goddard/Downloads/ChimeraX/AlphaFold/prediction_57/best_model.pdb

AlphaFold chains matching chain A  
---  
Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id  
A |  |  | 6.92 | 41 | 35 | 100  
  

> alphafold predict
> DSSDPLAVAASIIGILHLILWILDRLFFKSIYRFFEHGLKR,DSSDPLAVAASIIGILHLILWILDRLFFKSIYRFFEHGLKR

Running AlphaFold prediction  

> hide atoms

> show cartoons

AlphaFold prediction finished  
Results in /Users/goddard/Downloads/ChimeraX/AlphaFold/prediction_58  

> open
> /Users/goddard/Downloads/ChimeraX/AlphaFold/prediction_58/best_model.pdb

Chain information for best_model.pdb #3  
---  
Chain | Description  
B C | No description available  
  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.9.11
Locale: en_US.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: MacBookPro18,2
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 7459.141.1
      OS Loader Version: 7459.141.1

Software:

    System Software Overview:

      System Version: macOS 12.6 (21G115)
      Kernel Version: Darwin 21.6.0
      Time since boot: 16 days 11:21

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      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: No
          Connection Type: Internal


Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.0.8
    Babel: 2.10.3
    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
    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-ArtiaX: 0.1
    ChimeraX-Atomic: 1.41.4
    ChimeraX-AtomicLibrary: 8.0.2
    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-Clipper: 0.19.0.dev0
    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.dev202210072043
    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-ISOLDE: 1.5.dev0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
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    ChimeraX-Map: 1.1.1
    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
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    ChimeraX-MDcrds: 2.6
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    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
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    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PhenixUI: 1.0.4
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
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    ChimeraX-ReadPbonds: 1.0.1
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    ChimeraX-RemoteControl: 1.0
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    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
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    ChimeraX-SelInspector: 1.0
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    ChimeraX-Shell: 1.0.1
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    ChimeraX-ShowSequences: 1.0.1
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    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
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    ChimeraX-UI: 1.24.2
    ChimeraX-uniprot: 2.2.1
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    ChimeraX-ViewDockX: 1.1.3
    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
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    Deprecated: 1.2.13
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.1.0
    filelock: 3.7.1
    fonttools: 4.37.4
    funcparserlib: 1.0.0
    future: 0.18.2
    grako: 3.16.5
    graphtools: 1.5.2
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.2.22
    imageio: 2.22.1
    imagesize: 1.4.1
    importlib-metadata: 5.0.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
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    Jinja2: 3.1.2
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