ArtiaX: problem loading Star file

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22000
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
> D:\xinglab\paper\data\segmentation\230213_7_003\230213_PDC_7_ts_003_bin8_WBP_corrected.mrc
> format mrc

Opened 230213_PDC_7_ts_003_bin8_WBP_corrected.mrc as #1, grid size
512,512,150, pixel 12,12,12, shown at level 0.158, step 2, values float32  

> volume #1 style image region 0,0,74,511,511,74 step 1 showOutlineBox true

> volume #1 level -0.9809,0 level 0.266,0.8 level 1.361,1

> volume #1 level -0.9809,0 level 0.02238,0.9385 level 1.361,1

> volume #1 level -0.9809,0 level -0.04321,0.9077 level 1.361,1

> artiax start

Using preset: ArtiaX / Artiax Default  
Preset expands to these ChimeraX commands:

    
    
    set bgColor black
    lighting depthCue false
    camera ortho

  

> artiax add tomo #1

Opened 230213_PDC_7_ts_003_bin8_WBP_corrected.mrc as #2.1.1, grid size
512,512,150, pixel 12,12,12, shown at level 0.16, step 1, values float32  

> artiax tomo #2.1.1 sliceDirection 0,0,1

> artiax view xy

> open "D:/xinglab/paper/data/paper figure/230213_PDC_7_ts_003_PDCcore.star"

Traceback (most recent call last):  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 464, in collated_open  
return remember_data_format()  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\artiax\io\formats.py", line 25, in open  
return open_particle_list(session, data, file_name, format_name=self.name,
from_chimx=True)  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\artiax\io\io.py", line 35, in open_particle_list  
data = formats[format_name].particle_data(session, file_name, oripix=1,
trapix=1, additional_files=additional_files)  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\artiax\io\RELION\RELIONParticleData.py", line 120, in
__init__  
super().__init__(session, file_name, oripix=oripix, trapix=trapix,
additional_files=additional_files)  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\artiax\io\ParticleData.py", line 441, in __init__  
self.read_file()  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\artiax\io\RELION\RELIONParticleData.py", line 123, in
read_file  
content = starfile.read(self.file_name, always_dict=True)  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\starfile\functions.py", line 24, in read  
star = StarParser(filename, read_n_blocks=read_n_blocks)  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\starfile\parser.py", line 30, in __init__  
self.parse_file()  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\starfile\parser.py", line 38, in parse_file  
self._parse_data_block()  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\starfile\parser.py", line 54, in _parse_data_block  
self._parse_loop_block()  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\starfile\parser.py", line 80, in _parse_loop_block  
df.columns = header  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\pandas\core\generic.py", line 6002, in __setattr__  
return object.__setattr__(self, name, value)  
File "pandas\\_libs\properties.pyx", line 69, in
pandas._libs.properties.AxisProperty.__set__  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\pandas\core\generic.py", line 730, in _set_axis  
self._mgr.set_axis(axis, labels)  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\pandas\core\internals\managers.py", line 225, in set_axis  
self._validate_set_axis(axis, new_labels)  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\pandas\core\internals\base.py", line 70, in _validate_set_axis  
raise ValueError(  
ValueError: Length mismatch: Expected axis has 9 elements, new values have 10
elements  
  
ValueError: Length mismatch: Expected axis has 9 elements, new values have 10
elements  
  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\pandas\core\internals\base.py", line 70, in _validate_set_axis  
raise ValueError(  
  
See log for complete Python traceback.  
  

> open "D:/xinglab/paper/data/paper figure/230213_PDC_7_ts_003_PDCcore.star"
> format star

Traceback (most recent call last):  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\artiax\widgets\ArtiaxOpenDialog.py", line 66, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 464, in collated_open  
return remember_data_format()  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\artiax\io\formats.py", line 25, in open  
return open_particle_list(session, data, file_name, format_name=self.name,
from_chimx=True)  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\artiax\io\io.py", line 35, in open_particle_list  
data = formats[format_name].particle_data(session, file_name, oripix=1,
trapix=1, additional_files=additional_files)  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\artiax\io\RELION\RELIONParticleData.py", line 120, in
__init__  
super().__init__(session, file_name, oripix=oripix, trapix=trapix,
additional_files=additional_files)  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\artiax\io\ParticleData.py", line 441, in __init__  
self.read_file()  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\artiax\io\RELION\RELIONParticleData.py", line 123, in
read_file  
content = starfile.read(self.file_name, always_dict=True)  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\starfile\functions.py", line 24, in read  
star = StarParser(filename, read_n_blocks=read_n_blocks)  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\starfile\parser.py", line 30, in __init__  
self.parse_file()  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\starfile\parser.py", line 38, in parse_file  
self._parse_data_block()  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\starfile\parser.py", line 54, in _parse_data_block  
self._parse_loop_block()  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\starfile\parser.py", line 80, in _parse_loop_block  
df.columns = header  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\pandas\core\generic.py", line 6002, in __setattr__  
return object.__setattr__(self, name, value)  
File "pandas\\_libs\properties.pyx", line 69, in
pandas._libs.properties.AxisProperty.__set__  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\pandas\core\generic.py", line 730, in _set_axis  
self._mgr.set_axis(axis, labels)  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\pandas\core\internals\managers.py", line 225, in set_axis  
self._validate_set_axis(axis, new_labels)  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\pandas\core\internals\base.py", line 70, in _validate_set_axis  
raise ValueError(  
ValueError: Length mismatch: Expected axis has 9 elements, new values have 10
elements  
  
ValueError: Length mismatch: Expected axis has 9 elements, new values have 10
elements  
  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\pandas\core\internals\base.py", line 70, in _validate_set_axis  
raise ValueError(  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 27.20.100.8729
OpenGL renderer: Intel(R) UHD Graphics
OpenGL vendor: Intel

Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: LENOVO
Model: 81TC
OS: Microsoft Windows 11 家庭中文版 (Build 22000)
Memory: 16,966,471,680
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-10710U CPU @ 1.10GHz
OSLanguage: zh-CN

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-ArtiaX: 0.3
    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
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    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
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    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
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    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
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    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
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    numexpr: 2.8.4
    numpy: 1.23.5
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    packaging: 23.1
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    ParmEd: 3.4.3
    parso: 0.8.3
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    PyOpenGL-accelerate: 3.1.5
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    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
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    snowballstemmer: 2.2.0
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    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
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