Blast: self.job.model_name is None

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\Users\JUAN\Downloads\robetta_models_521138.pdb format pdb

Summary of feedback from opening
C:\Users\JUAN\Downloads\robetta_models_521138.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK ID 521138 MODEL 1 GarvML  
  
Ignored bad PDB record found on line 2  
PFRMAT TS  
  
Ignored bad PDB record found on line 3  
TARGET GarvML  
  
Ignored bad PDB record found on line 5  
METHOD ROSETTA provides both ab initio and  
  
Ignored bad PDB record found on line 6  
METHOD comparative models of protein domains.  
  
75 messages similar to the above omitted  
  
Chain information for robetta_models_521138.pdb  
---  
Chain | Description  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A | No description available  
  

> hide #1.5 models

> hide #1.4 models

> hide #1.3 models

> hide #1.2 models

> set bgColor white

> ui tool show "Build Structure"

> select sidechain

3210 atoms, 2935 bonds, 300 residues, 5 models selected  

> bond sel

Created 0 bonds  

> bond sel

Created 0 bonds  

> ~bond sel

[Repeated 1 time(s)]

> ui tool show "Build Structure"

FYI: command is replacing existing command: "build invert"  
FYI: command is replacing existing command: "build join peptide"  
FYI: command is replacing existing command: "build modify"  
FYI: command is replacing existing command: "build start"  
FYI: command is replacing existing command: "bond"  
FYI: command is replacing existing command: "~bond"  
FYI: command is replacing existing command: "bond length"  

> build join peptide sel length 1.33 omega 180 phi -120 move small

No carbons named 'C' in specified atoms  

> select ::name="ALA"

755 atoms, 320 bonds, 75 residues, 5 models selected  

> select ligand

Nothing selected  

> select sidechain

1205 atoms, 300 residues, 5 models selected  

> select add #1

4425 atoms, 1510 bonds, 300 residues, 6 models selected  

> select subtract #1

Nothing selected  

> select add #1.1

885 atoms, 302 bonds, 60 residues, 1 model selected  

> ui tool show AlphaFold

> alphafold predict #1.1

Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.  
Running AlphaFold prediction  
[Repeated 4 time(s)]

> matchmaker

Missing or invalid "matchAtoms" argument: empty atom specifier  
AlphaFold prediction finished  
Results in C:\Users\JUAN/Downloads/ChimeraX/AlphaFold/prediction_1  

> open C:\Users\JUAN/Downloads/ChimeraX/AlphaFold/prediction_1\best_model.pdb

AlphaFold prediction matching robetta_models_521138.pdb #1.1/A  
---  
Chain| RMSD| Length| Seen| % Id  
A | 3.13 | 65 | 60 | 25  
  

> lighting simple

> graphics silhouettes true

> lighting simple

> view

> view sel

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 0 maps.  

[Repeated 2 time(s)]

Volume zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic
models, 0 maps.  

> ui mousemode right "link markers"

> hide #2 models

> ui tool show AlphaFold

> alphafold search #1.1

Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json  
Webservices job id: 2A3V5CSBGQ5ITY5C  

> alphafold predict #1.1

Running AlphaFold prediction  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 665, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\job.py", line 97, in on_finish  
BlastProteinResults.from_job(  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 90, in from_job  
return cls(  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 86, in __init__  
self._build_ui()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 229, in _build_ui  
param_str = self._format_param_str()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 201, in _format_param_str  
model_formatted = ''.join([self.job.model_name, chain])  
TypeError: sequence item 0: expected str instance, NoneType found  
  
TypeError: sequence item 0: expected str instance, NoneType found  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 201, in _format_param_str  
model_formatted = ''.join([self.job.model_name, chain])  
  
See log for complete Python traceback.  
  
AlphaFold prediction finished  
Results in C:\Users\JUAN/Downloads/ChimeraX/AlphaFold/prediction_2  

> open C:\Users\JUAN/Downloads/ChimeraX/AlphaFold/prediction_2\best_model.pdb

AlphaFold prediction matching robetta_models_521138.pdb #1.1/A  
---  
Chain| RMSD| Length| Seen| % Id  
A | 18.41 | 60 | 60 | 100  
  

> show #2 models

> hide #2 models

> hide #1.1 models

> hide #3 models

> show #2 models

> ui tool show "Build Structure"

> ui tool show "Show Sequence Viewer"

Alignment identifier is 1.1/A  

> select subtract #1.1

Nothing selected  

> hide #!1 models

> hide #2 models

> show #2 models

> hide #2 models

> show #3 models

> hide #3 models

> show #2 models

Alignment identifier is 1  
Alignment identifier is 2/A  

> bond sel

Must specify two or more atoms  

> show #1.1 models

> open C:/Users/JUAN/Downloads/pdb1o83.ent

pdb1o83.ent title:  
Crystal structure of bacteriocin As-48 At pH 7.5, phosphate bound. Crystal
form I [more info...]  
  
Chain information for pdb1o83.ent #4  
---  
Chain | Description | UniProt  
A B C D | bacteriocin As-48 | Q47765 1-70  
  
Non-standard residues in pdb1o83.ent #4  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
PO4 — phosphate ion  
  

> hide #4 models

> hide #1.1 models

> show #3 models

> hide #2 models

> show #2 models

> hide #3 models

> mlp #2

Map values for surface "best_model.pdb_A SES surface": minimum -25.49, mean
-1.843, maximum 22.91  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic #!2

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #2.1: minimum, -5.28, mean
2.99, maximum 16.48  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic #!2

Coulombic values for best_model.pdb_A SES surface #2.1: minimum, -5.28, mean
2.99, maximum 16.48  
To also show corresponding color key, enter the above coulombic command and
add key true  

> color #!2 bynucleotide

> undo

[Repeated 8 time(s)]

> ui tool show AlphaFold

> alphafold search #1.1

Webservices job id: 0YY1I30XR7683SLP  

> alphafold predict #1.1

Running AlphaFold prediction  

> alphafold predict #1.1

Running AlphaFold prediction  

> alphafold predict #1.1

Running AlphaFold prediction  

> alphafold search #1.1

Webservices job id: S5YXSQ5K6NQGSKM3  

> alphafold predict #1.1

Running AlphaFold prediction  

> alphafold search #1.1

Webservices job id: OJDB7DC0QBI31YVK  

> alphafold predict #1.1

Running AlphaFold prediction  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 665, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\job.py", line 97, in on_finish  
BlastProteinResults.from_job(  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 90, in from_job  
return cls(  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 86, in __init__  
self._build_ui()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 229, in _build_ui  
param_str = self._format_param_str()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 201, in _format_param_str  
model_formatted = ''.join([self.job.model_name, chain])  
TypeError: sequence item 0: expected str instance, NoneType found  
  
TypeError: sequence item 0: expected str instance, NoneType found  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 201, in _format_param_str  
model_formatted = ''.join([self.job.model_name, chain])  
  
See log for complete Python traceback.  
  

> alphafold predict #1.1

Running AlphaFold prediction  

> alphafold search #1.1

Webservices job id: 7XR62WMRLKVU0PZJ  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 665, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\job.py", line 97, in on_finish  
BlastProteinResults.from_job(  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 90, in from_job  
return cls(  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 86, in __init__  
self._build_ui()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 229, in _build_ui  
param_str = self._format_param_str()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 201, in _format_param_str  
model_formatted = ''.join([self.job.model_name, chain])  
TypeError: sequence item 0: expected str instance, NoneType found  
  
TypeError: sequence item 0: expected str instance, NoneType found  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 201, in _format_param_str  
model_formatted = ''.join([self.job.model_name, chain])  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 456.71
OpenGL renderer: GeForce GT 710/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: es_ES.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: System manufacturer
Model: System Product Name
OS: Microsoft Windows 10 Education (Build 19045)
Memory: 34,285,846,528
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-9700KF CPU @ 3.60GHz
OSLanguage: es-ES

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    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: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    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
    ChimeraX-CheckWaters: 1.3.1
    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: 1.6.1
    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: 1.1.1
    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-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    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
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    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
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    comtypes: 1.1.14
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pywin32: 305
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    WMI: 1.5.1
    zipp: 3.15.0

[Zach Pearson]

It's harmless if this line fails and the try... block around it reflects that; just needed to catch TypeError too. Should be fixed in tomorrow's build.