Sequence realignment error

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-12.3.1-arm64-arm-64bit
ChimeraX Version: 1.4.dev202203271748 (2022-03-27 17:48:18 UTC)
Description
Tried Sequence Viewer menu Edit / Realign using Clustal Omega on the attached 2 sequence fasta file and got this error.

Log:
UCSF ChimeraX version: 1.4.dev202203271748 (2022-03-27)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/goddard/Desktop/align.fasta

Summary of feedback from opening /Users/goddard/Desktop/align.fasta  
---  
notes | Alignment identifier is align.fasta  
Showing conservation header ("seq_conservation" residue attribute) for
alignment align.fasta  
  
Opened 2 sequences from align.fasta  

> sequence align align.fasta program clustalOmega

Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 210, in _run_thread  
self.run(*args, **kw)  
TypeError: run() got an unexpected keyword argument 'blocking'  
  
Exception in thread:  
TypeError: run() got an unexpected keyword argument 'blocking'  
  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 210, in _run_thread  
self.run(*args, **kw)  
  
See log for complete Python traceback.  
  
Alignment identifier is 1  
Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq-view/tool.py", line 540, in <lambda>  
run(self.session, "seq align %s program %s" % (unparse(self.alignment.ident),
unparse(arg))))  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/cmd.py", line 313, in seqalign_align  
return session.alignments.new_alignment(realigned, None, name=title)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/manager.py", line 243, in new_alignment  
alignment = Alignment(self.session, seqs, identify_as, attrs, markups,
auto_destroy,  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 111, in __init__  
self._headers = [hdr_class(self) for hdr_class in
session.alignments.headers()]  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 111, in <listcomp>  
self._headers = [hdr_class(self) for hdr_class in
session.alignments.headers()]  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/consensus.py", line 25, in __init__  
self.conserved = [False] * len(alignment.seqs[0])  
IndexError: list index out of range  
  

Populating font family aliases took 69 ms. Replace uses of missing font family
".AppleSystemUIFont" with one that exists to avoid this cost.  

IndexError: list index out of range  
  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/consensus.py", line 25, in __init__  
self.conserved = [False] * len(alignment.seqs[0])  
  
See log for complete Python traceback.  
  




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

Locale: UTF-8
Qt version: PyQt6 6.2.3, Qt 6.2.3
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: 7459.101.3
      OS Loader Version: 7459.101.3

Software:

    System Software Overview:

      System Version: macOS 12.3.1 (21E258)
      Kernel Version: Darwin 21.4.0
      Time since boot: 15 days 9:53

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: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    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: 2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.36.3
    ChimeraX-AtomicLibrary: 6.1.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.2
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4.dev202203271748
    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: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    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
    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: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    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-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
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.5
    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
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.16.3
    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: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
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    idna: 3.3
    ihm: 0.27
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    ipykernel: 6.6.1
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    Jinja2: 3.0.3
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    kiwisolver: 1.4.0
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    lxml: 4.7.1
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    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.4
    networkx: 2.6.3
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.28
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.7
    PyQt6: 6.2.3
    PyQt6-Qt6: 6.2.4
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    PyQt6-WebEngine: 6.2.1
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    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
File attachment: align.fasta

align.fasta​

[goddard@…]

Added by email2trac

[Tom Goddard]

Works in daily build.

[Tom Goddard]

Works in daily build.