AlphFold Error Plot: TypeError: expected str, bytes or os.PathLike object, not NoneType

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-13.5.2-x86_64-i386-64bit
ChimeraX Version: 1.7.dev202309121847 (2023-09-12 18:47:21 UTC)
Description
Browse button on Alphafold Error Plot tool gives an error if the structure is from splitting another structure so has no filename.

Log:
Could not find tool "Tabbed Toolbar"  
UCSF ChimeraX version: 1.7.dev202309121847 (2023-09-12)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7ovv format mmcif fromDatabase pdb

7ovv title:  
Crystal structure of the Arabidopsis thaliana thialysine acetyltransferase
AtNATA2 [more info...]  
  
Chain information for 7ovv #1  
---  
Chain | Description | UniProt  
A B | Probable acetyltransferase NATA1-like | NATAL_ARATH 29-226  
  
Non-standard residues in 7ovv #1  
---  
5NG —
[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-
oxolan-2-yl]methoxy-oxidanyl-phosphoryl]
[(3~{R})-4-[[3-[2-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-
oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-
phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-
butanoyl]amino]propanoylamino]ethyldisulfanyl]ethylamino]-3-oxidanylidene-
propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] hydrogen
phosphate (CoA-disulfide)  
  

> split

Split 7ovv (#1) into 2 models  
Chain information for 7ovv A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 7ovv B #1.2  
---  
Chain | Description  
B | No description available  
  

> ui tool show "AlphaFold Error Plot"

Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 147, in _choose_pae_file  
dir = path.split(s.filename)[0]  
^^^^^^^^^^^^^^^^^^^^^^  
File "<frozen posixpath>", line 103, in split  
TypeError: expected str, bytes or os.PathLike object, not NoneType  
  
TypeError: expected str, bytes or os.PathLike object, not NoneType  
  
File "", line 103, in split  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.14.1
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.2
Locale: 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: iMac
      Model Identifier: iMac18,3
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 4.2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 515.0.0.0.0
      OS Loader Version: 577.140.2~15
      SMC Version (system): 2.41f2

Software:

    System Software Overview:

      System Version: macOS 13.5.2 (22G91)
      Kernel Version: Darwin 22.6.0
      Time since boot: 38 days, 15 hours, 21 minutes

Graphics/Displays:

    Radeon Pro 580:

      Chipset Model: Radeon Pro 580
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c0
      ROM Revision: 113-D000AA-931
      VBIOS Version: 113-D0001A1X-025
      EFI Driver Version: 01.00.931
      Metal Support: Metal 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
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    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
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.2
    charset-normalizer: 3.2.0
    ChimeraX-AddCharge: 1.5.11
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.48
    ChimeraX-AtomicLibrary: 10.1
    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: 2.0.4
    ChimeraX-BugReporter: 1.0.1
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    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
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    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: 1.7.dev202309121847
    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: 1.1.2
    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-IUPAC: 1.0
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    ChimeraX-ListInfo: 1.2
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    ChimeraX-MapData: 2.0
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    ChimeraX-MapSeries: 2.1.1
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    ChimeraX-Meeting: 1.0.1
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    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.4
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    ChimeraX-Mol2: 2.0
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    ChimeraX-Morph: 1.0.2
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    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
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    ChimeraX-OpenCommand: 1.11
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    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBImages: 1.2
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
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    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
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    ChimeraX-RenumberResidues: 1.1
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    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
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    ChimeraX-Segment: 1.0.1
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    ChimeraX-SeqView: 2.9
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    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
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    ChimeraX-SwapRes: 2.2.2
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    ChimeraX-Test: 1.0
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    ChimeraX-Topography: 1.0
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    ChimeraX-Tug: 1.0.1
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    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2.2
    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
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    colorama: 0.4.6
    comm: 0.1.3
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[Tom Goddard]

This was originally reported in #9984.

[Tom Goddard]

Fixed.

The AlphaFold Error Plot Browse button was trying to set the initial directory for the file dialog to the directory of the file that the structure listed in the menu came from. But that structure came from a "split" command and so its filename attribute was None. Made the code check that the filename is not None.