AlphaFold Error Plot: local variable 'path' referenced before assignment

[hzauzsmj@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.5.dev202206220131 (2022-06-22 01:31:19 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.5.dev202206220131 (2022-06-22)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open D:/FPSrevision0411/pSuT/test_f829b_unrelaxed_rank_1_model_1.pdb
> D:/FPSrevision0411/pSuT/test_f829b_unrelaxed_rank_1_model_1_scores.json

Unrecognized file suffix '.json'  

> open D:/FPSrevision0411/pSuT/test_f829b_unrelaxed_rank_1_model_1.pdb
> D:/FPSrevision0411/pSuT/test_f829b_unrelaxed_rank_1_model_1_scores.json

Unrecognized file suffix '.json'  

> open D:/FPSrevision0411/pSuT/test_f829b_unrelaxed_rank_1_model_1.pdb

Chain information for test_f829b_unrelaxed_rank_1_model_1.pdb #1  
---  
Chain | Description  
A | No description available  
  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file
> D:/FPSrevision0411/pSuT\\\test_f829b_unrelaxed_rank_1_model_1_scores.json

> color bfactor #1 palette alphafold

4111 atoms, 545 residues, atom bfactor range 22.7 to 98.7  

> color #1:34-34 lime

> color #1:33-33 magenta

> color bfactor #1 palette alphafold

4111 atoms, 545 residues, atom bfactor range 22.7 to 98.7  

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

> ui tool show AlphaFold

> alphafold match #1

Unable to reach AlphaFold sequence search web service  
  
https://www.rbvi.ucsf.edu/chimerax/cgi-bin/alphafold_search2_cgi.py  

No AlphaFold model with similar sequence for chain A  

Opened 0 AlphaFold model  

> alphafold match #1

Unable to reach AlphaFold sequence search web service  
  
https://www.rbvi.ucsf.edu/chimerax/cgi-bin/alphafold_search2_cgi.py  

No AlphaFold model with similar sequence for chain A  

Opened 0 AlphaFold model  

> alphafold match #1

Unable to reach AlphaFold sequence search web service  
  
https://www.rbvi.ucsf.edu/chimerax/cgi-bin/alphafold_search2_cgi.py  

No AlphaFold model with similar sequence for chain A  

Opened 0 AlphaFold model  

> open D:/FPSrevision0411/pINV.bmp

Expected array size based on DOCK file size is 3314230 which does not agree
with header array size -1839837886 or byte swapped header array size
1112364690  

> open D:/FPSrevision0411/AF-Q0WWW9-F1-pSuT.pdb

AF-Q0WWW9-F1-pSuT.pdb title:  
Alphafold monomer V2.0 prediction for D-xylose-proton symporter-like 3,
chloroplastic (Q0WWW9) [more info...]  
  
Chain information for AF-Q0WWW9-F1-pSuT.pdb #2  
---  
Chain | Description | UniProt  
A | D-xylose-proton symporter-like 3, chloroplastic | XYLL3_ARATH  
  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file
> D:/FPSrevision0411/AF-Q0WWW9-F1-predicted_aligned_error_v2.json

Number of residues in structure "test_f829b_unrelaxed_rank_1_model_1.pdb #1"
is 545 which does not match PAE matrix size 558.  
  
This can happen if the AlphaFold model has been trimmed to match an
experimental structure, or if residues have been deleted. The full-length
AlphaFold model must be used to show predicted aligned error.  

> ui tool show Matchmaker

> matchmaker #2 to #1 showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker test_f829b_unrelaxed_rank_1_model_1.pdb, chain A (#1) with
AF-Q0WWW9-F1-pSuT.pdb, chain A (#2), sequence alignment score = 2218.8  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1:
test_f829b_unrelaxed_rank_1_model_1.pdb #1/A, AF-Q0WWW9-F1-pSuT.pdb #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 438 pruned atom pairs is 0.410 angstroms; (across all 537 pairs:
12.561)  
  

> color bfactor #1 palette alphafold

4111 atoms, 545 residues, atom bfactor range 22.7 to 98.7  

> color bfactor #1 palette alphafold

4111 atoms, 545 residues, atom bfactor range 22.7 to 98.7  

> hide #2 models

> show #2 models

> hide #1 models

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file
> D:/FPSrevision0411/AF-Q0WWW9-F1-predicted_aligned_error_v2.json

Number of residues in structure "test_f829b_unrelaxed_rank_1_model_1.pdb #1"
is 545 which does not match PAE matrix size 558.  
  
This can happen if the AlphaFold model has been trimmed to match an
experimental structure, or if residues have been deleted. The full-length
AlphaFold model must be used to show predicted aligned error.  

> hide #1 target m

> select add #1

4111 atoms, 4204 bonds, 545 residues, 1 model selected  

> select subtract #1

Nothing selected  

> select add #2

4229 atoms, 4327 bonds, 558 residues, 1 model selected  

> ui tool show "AlphaFold Error Plot"

> show #1 models

> hide #2 models

> show #2 models

> rmsdAlign #1 toModels #2

rmsdAlign is provided by the uninstalled bundle SEQCROW versions 0.1 – 1.2.2  

> colsed

Unknown command: colsed  

> closed

Unknown command: closed  

> close

> open D:/FPSrevision0411/AF-Q0WWW9-F1-pSuT.pdb

AF-Q0WWW9-F1-pSuT.pdb title:  
Alphafold monomer V2.0 prediction for D-xylose-proton symporter-like 3,
chloroplastic (Q0WWW9) [more info...]  
  
Chain information for AF-Q0WWW9-F1-pSuT.pdb #1  
---  
Chain | Description | UniProt  
A | D-xylose-proton symporter-like 3, chloroplastic | XYLL3_ARATH  
  
Associated AF-Q0WWW9-F1-pSuT.pdb chain A to AF-Q0WWW9-F1-pSuT.pdb, chain A
with 0 mismatches  

> open D:/FPSrevision0411/AF-Q0WWW9-F1-predicted_aligned_error_v2.json

Unrecognized file suffix '.json'  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file
> D:/FPSrevision0411\\\AF-Q0WWW9-F1-predicted_aligned_error_v2.json

> color bfactor #1 palette alphafold

4229 atoms, 558 residues, atom bfactor range 21.6 to 98.7  

> open D:/FPSrevision0411/pSuT/test_f829b_unrelaxed_rank_1_model_1.pdb

Chain information for test_f829b_unrelaxed_rank_1_model_1.pdb #2  
---  
Chain | Description  
A | No description available  
  
Associated test_f829b_unrelaxed_rank_1_model_1.pdb chain A to
test_f829b_unrelaxed_rank_1_model_1.pdb, chain A with 0 mismatches  
Chains used in RMSD evaluation for alignment 1: AF-Q0WWW9-F1-pSuT.pdb #1/A,
test_f829b_unrelaxed_rank_1_model_1.pdb #2/A  

> close #1

> close

> open D:/FPSrevision0411/prediction/selected_prediction.pdb

Chain information for selected_prediction.pdb #1  
---  
Chain | Description  
A | No description available  
  

> close

> open D:/FPSrevision0411/AF-Q9FK88-F1-INV-E.pdb

AF-Q9FK88-F1-INV-E.pdb title:  
Alphafold monomer V2.0 prediction for alkaline/neutral invertase E,
chloroplastic (Q9FK88) [more info...]  
  
Chain information for AF-Q9FK88-F1-INV-E.pdb #1  
---  
Chain | Description | UniProt  
A | alkaline/neutral invertase E, chloroplastic | INVE_ARATH  
  

> open D:/FPSrevision0411/prediction/selected_prediction.pdb

Chain information for selected_prediction.pdb #2  
---  
Chain | Description  
A | No description available  
  

> ui tool show Matchmaker

> matchmaker #2 to #1 showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AF-Q9FK88-F1-INV-E.pdb, chain A (#1) with selected_prediction.pdb,
chain A (#2), sequence alignment score = 2461.8  
Alignment identifier is 2  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2  
Hiding conservation header for alignment 2  
Chains used in RMSD evaluation for alignment 2: AF-Q9FK88-F1-INV-E.pdb #1/A,
selected_prediction.pdb #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  
RMSD between 459 pruned atom pairs is 0.431 angstroms; (across all 617 pairs:
17.720)  
  

> hide #2 models

> ui tool show "AlphaFold Error Plot"

Traceback (most recent call last):  
File "D:\ChimeraX 1.5.dev202206220131\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 136, in _choose_pae_file  
dir = path.split(self._pae_file.text())[0]  
UnboundLocalError: local variable 'path' referenced before assignment  
  
UnboundLocalError: local variable 'path' referenced before assignment  
  
File "D:\ChimeraX 1.5.dev202206220131\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 136, in _choose_pae_file  
dir = path.split(self._pae_file.text())[0]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\ChimeraX 1.5.dev202206220131\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 136, in _choose_pae_file  
dir = path.split(self._pae_file.text())[0]  
UnboundLocalError: local variable 'path' referenced before assignment  
  
UnboundLocalError: local variable 'path' referenced before assignment  
  
File "D:\ChimeraX 1.5.dev202206220131\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 136, in _choose_pae_file  
dir = path.split(self._pae_file.text())[0]  
  
See log for complete Python traceback.  
  
Must choose structure to associate with predicted aligned error  
Traceback (most recent call last):  
File "D:\ChimeraX 1.5.dev202206220131\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 136, in _choose_pae_file  
dir = path.split(self._pae_file.text())[0]  
UnboundLocalError: local variable 'path' referenced before assignment  
  
UnboundLocalError: local variable 'path' referenced before assignment  
  
File "D:\ChimeraX 1.5.dev202206220131\bin\lib\site-
packages\chimerax\alphafold\pae.py", line 136, in _choose_pae_file  
dir = path.split(self._pae_file.text())[0]  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 497.09
OpenGL renderer: NVIDIA GeForce MX150/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.1
Qt platform: windows

Manufacturer: Timi
Model: TM1701
OS: Microsoft Windows 10 家庭中文版 (Build 19044)
Memory: 8,468,402,176
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-8550U CPU @ 1.80GHz
OSLanguage: zh-CN

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.3
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.7.0
    certifi: 2022.6.15
    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: 2.5
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.5
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.5.dev202206220131
    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: 1.1
    ChimeraX-DistMonitor: 1.1.6
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.2.1
    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: 1.1.1
    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: 1.5.6
    ChimeraX-ModelPanel: 1.3.4
    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: 1.9
    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-RenumberResidues: 1.1
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.1
    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: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.21.1
    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: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.2
    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: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.3
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.12.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.1
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.1
    python-dateutil: 2.8.2
    pytz: 2022.1
    pywin32: 303
    pyzmq: 23.2.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
    WMI: 1.5.1

[pett]

Reported by Tengfei Liu

[Tom Goddard]

Fixed in tomorrow's daily build.

This error using the Browse button on the ChimeraX AlphaFold PAE Error panel was because you had not chosen a structure, and a path to an error file had been entered, and a mistake in the code made it not able to show the directory containing that path in a file chooser dialog. I've fixed that bug.

Your current ChimeraX will work if you first choose an atomic structure from the menu in the AlphaFold PAE Error panel. That will allow the Browse button to go to the directory containing the file for that structure where the PAE error file probably resides.