ChimeraX bug report submission

[shanyuanyue@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
When I save relion star files, it is reported as keyError:'rlnTomoName', File "C:\Users\86198\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-packages\chimerax\artiax\io\RELION\RELIONParticleData.py", line 317, in write_file data.pop('rlnTomoName')

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed install C:\Users\86198\Desktop\ChimeraX_ArtiaX-0.1-py3-none-any.whl

bundle 'C:\\\Users\\\86198\\\Desktop\\\ChimeraX_ArtiaX-0.1-py3-none-any.whl'
already installed  

> toolshed uninstall C:\Users\86198\Desktop\ChimeraX_ArtiaX-0.1-py3-none-
> any.whl

Missing or invalid "bundleNames" argument: Invalid bundle name  

> toolshed install C:\Users\86198\Desktop\ChimeraX_ArtiaX-0.1-py3-none-any.whl

bundle 'C:\\\Users\\\86198\\\Desktop\\\ChimeraX_ArtiaX-0.1-py3-none-any.whl'
already installed  

> open "E:/WLU-Cell Fate Control Lab-Pei/Training/Cryo-
> ET/原位电镜/北京数据收集/SSY/20250721_Arctis_怀柔/bin2_delete_5nm.star"

Summary of feedback from opening E:/WLU-Cell Fate Control Lab-
Pei/Training/Cryo-ET/原位电镜/北京数据收集/SSY/20250721_Arctis_怀柔/bin2_delete_5nm.star  
---  
notes | Using preset: ArtiaX / Artiax Default  
Preset expands to these ChimeraX commands:

    
    
    set bgColor black  
    lighting depthCue false  
    camera ortho

  
  
  
Opened Particle list bin2_delete_5nm.star with 17286 particles.  

> view orient

> view

> artiax particles #1.2.1 originScaleFactor 3.8

> artiax view xy

> view

> view orient

[Repeated 1 time(s)]Drag select of axes, 1 of 17286 instances, 1 atoms  

> ui mousemode right "delete selected particles"

[Repeated 3 time(s)]

> ui mousemode right "delete picked particle"

[Repeated 2 time(s)]

> ui mousemode right "delete selected particles"

> ui mousemode right "delete picked particle"

> undo

Undo failed, probably because structures have been modified.  

> view orient

[Repeated 1 time(s)]Drag select of axes, 0 of 17286 instances  
[Repeated 1 time(s)]Drag select of axes, 1 of 17286 instances, 1 atoms  

> select clear

[Repeated 1 time(s)]

> save C:/Users/86198/Desktop/1.star partlist #1.2.1

Traceback (most recent call last):  
File "C:\Users\86198\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\artiax\tool.py", line 344, in _save_partlist  
show_save_file_dialog(self.session)  
File "C:\Users\86198\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\artiax\widgets\ArtiaXSaveDialog.py", line 52, in
show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Users\86198\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\artiax\widgets\ArtiaXSaveDialog.py", line 43, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "C:\Users\86198\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\artiax\io\formats.py", line 44, in save  
save_particle_list(session, path, partlist, format_name=self.name)  
File "C:\Users\86198\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\artiax\io\io.py", line 137, in save_particle_list  
save_data.write_file(file_name=file_name, additional_files=additional_files)  
File "C:\Users\86198\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\artiax\io\RELION\RELIONParticleData.py", line 317, in
write_file  
data.pop('rlnTomoName')  
KeyError: 'rlnTomoName'  
  
KeyError: 'rlnTomoName'  
  
File "C:\Users\86198\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\artiax\io\RELION\RELIONParticleData.py", line 317, in
write_file  
data.pop('rlnTomoName')  
  
See log for complete Python traceback.  
  

> save E:/1.star partlist #1.2.1

Traceback (most recent call last):  
File "C:\Users\86198\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\artiax\tool.py", line 344, in _save_partlist  
show_save_file_dialog(self.session)  
File "C:\Users\86198\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\artiax\widgets\ArtiaXSaveDialog.py", line 52, in
show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Users\86198\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\artiax\widgets\ArtiaXSaveDialog.py", line 43, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "C:\Users\86198\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\artiax\io\formats.py", line 44, in save  
save_particle_list(session, path, partlist, format_name=self.name)  
File "C:\Users\86198\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\artiax\io\io.py", line 137, in save_particle_list  
save_data.write_file(file_name=file_name, additional_files=additional_files)  
File "C:\Users\86198\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\artiax\io\RELION\RELIONParticleData.py", line 317, in
write_file  
data.pop('rlnTomoName')  
KeyError: 'rlnTomoName'  
  
KeyError: 'rlnTomoName'  
  
File "C:\Users\86198\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\artiax\io\RELION\RELIONParticleData.py", line 317, in
write_file  
data.pop('rlnTomoName')  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 Core Profile Context 22.20.20.06.231106
OpenGL renderer: AMD Radeon RX 640
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.2
Locale: zh_CN.cp936
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: Vostro 5890
OS: Microsoft Windows 11 家庭中文版 (Build 26100)
Memory: 16,962,883,584
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11700F @ 2.50GHz
OSLanguage: zh-CN

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-ArtiaX: 0.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    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
    ChimeraX-BuildStructure: 2.10.5
    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: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7
    ChimeraX-CoreFormats: 1.2
    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: 1.1.3
    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: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.13
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.3
    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: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.3
    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: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.0
    comtypes: 1.1.14
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.0
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.5.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    pandas: 2.3.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pyarrow: 22.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pywin32: 305
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    starfile: 0.5.13
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9
    WMI: 1.5.1