id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20440 Item chooser: name 'self' is not defined christian.biertuempfel@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Linux-6.8.0-110-generic-x86_64-with-glibc2.39 ChimeraX Version: 1.12rc202605280043 (2026-05-28 00:43:25 UTC) Description modified ArtiaX plugin according to issue #44 to fix relion star file import. imported tomo and particle list from star file Log: Startup Messages --- warning | GBM is not supported with the current configuration. Fallback to Vulkan rendering in Chromium. UCSF ChimeraX version: 1.12rc202605280043 (2026-05-28) © 2016-2026 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > artiax start Using preset: ArtiaX / Artiax Default Preset expands to these ChimeraX commands: set bgColor black lighting depthCue false camera ortho Opened rec_984-3_tomo51.mrc as #1.1.1, grid size 512,720,232, pixel 10.9,10.9,10.9, shown at level 6.5, step 2, values float32 > artiax clip off > artiax tomo #1.1.1 sliceDirection 0,0,1 > artiax view xy > open /project/chiem/rbc/job060_run_data_51.star format star Summary of feedback from opening /project/chiem/rbc/job060_run_data_51.star --- notes | Processed as relion Processed as relion Processed as relion5 Using sizes: X: 512, Y: 720, Z: 232 Using pixelsize: 10.920000076293945 Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/triggerset.py"", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 464, in _items_change self.set_value(next_val, delayed=True) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 404, in set_value _when_all_updated(self, self.value_changed.emit) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 534, in _when_all_updated timer, old_func = self._wau_timer_info ^^^^ NameError: name 'self' is not defined Error processing trigger ""model id changed"": NameError: name 'self' is not defined File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 534, in _when_all_updated timer, old_func = self._wau_timer_info ^^^^ See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/triggerset.py"", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 464, in _items_change self.set_value(next_val, delayed=True) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 404, in set_value _when_all_updated(self, self.value_changed.emit) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 534, in _when_all_updated timer, old_func = self._wau_timer_info ^^^^ NameError: name 'self' is not defined Error processing trigger ""add models"": NameError: name 'self' is not defined File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 534, in _when_all_updated timer, old_func = self._wau_timer_info ^^^^ See log for complete Python traceback. > artiax clip off Opened Particle list job060_run_data_51.star with 2059 particles. OpenGL version: 3.3.0 NVIDIA 580.126.20 OpenGL renderer: NVIDIA GeForce RTX 2080 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.13 Locale: en_US.UTF-8 Qt version: PyQt6 6.10.2, Qt 6.10.0 Qt runtime version: 6.10.2 Qt platform: xcb XDG_SESSION_TYPE=x11 DESKTOP_SESSION= XDG_SESSION_DESKTOP= XDG_CURRENT_DESKTOP=GNOME DCV_GL_DISPLAY=:0.0 DISPLAY=:0 Manufacturer: Supermicro Model: SYS-4029GP-TRT OS: Ubuntu 24.04 Architecture: 64bit ELF Virtual Machine: none CPU: 80 Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz Cache Size: 28160 KB Memory: total used free shared buff/cache available Mem: 503Gi 21Gi 2.8Gi 155Mi 483Gi 481Gi Swap: 8.0Gi 8.0Gi 25Mi Graphics: 03:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41) DeviceName: Aspeed Video 2500 Subsystem: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] Installed Packages: accessible-pygments: 0.0.5 aiohappyeyeballs: 2.6.2 aiohttp: 3.13.4 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.13.0 appdirs: 1.4.4 asttokens: 3.0.1 attrs: 26.1.0 babel: 2.18.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 4.3.3 bs4: 0.0.2 build: 1.3.0 certifi: 2026.5.20 cftime: 1.6.5 charset-normalizer: 3.4.7 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.2 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-ArtiaX: 0.6.1 ChimeraX-Atomic: 1.67.1 ChimeraX-AtomicLibrary: 14.4 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4.1 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.4 ChimeraX-Cluster: 1.0 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.1 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.12rc202605280043 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.2.1 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: 1.4.1 ChimeraX-Hbonds: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.8.2 ChimeraX-Label: 1.5 ChimeraX-LightingGUI: 1.0 ChimeraX-LinuxSupport: 1.0.1 ChimeraX-ListInfo: 1.3.1 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.3 ChimeraX-Map: 1.3 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-MatchAlign: 1.2 ChimeraX-MatchMaker: 2.4.1 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.2.0 ChimeraX-MDcrds: 2.19 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.9 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.23 ChimeraX-ModelPanel: 1.6.1 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: 1.0.1 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.15.4 ChimeraX-OpenFold: 1.0 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.13 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.6 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.8.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.12 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.18 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SNFG: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.4 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.50.7 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.6.2 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: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.4.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.14.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.2.4 debugpy: 1.8.20 decorator: 5.3.1 distro: 1.9.0 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.63.0 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 geomdl: 5.4.0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.16.0 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.16 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 2.0.0 iniconfig: 2.3.0 ipykernel: 7.1.0 ipython: 9.9.0 ipython_pygments_lexers: 1.1.1 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.8.0 jupyter_core: 5.9.1 kiwisolver: 1.5.0 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.2 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.1 narwhals: 2.21.2 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 nvidia-nvjitlink-cu12: 12.9.86 OpenMM: 8.4.0 OpenMM-CUDA-12: 8.4.0 openvr: 1.26.701 packaging: 25.0 pandas: 3.0.3 ParmEd: 4.2.2 parso: 0.8.7 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.10.0 plotly: 6.7.0 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.5.2 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pyarrow: 24.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.13.4 pydantic-settings: 2.14.1 pydantic_core: 2.46.4 pydata-sphinx-theme: 0.18.0 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.5.1 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6: 6.10.2 PyQt6-Qt6: 6.10.2 PyQt6-WebEngine: 6.10.0 PyQt6-WebEngine-Qt6: 6.10.2 PyQt6_sip: 13.10.3 pytest: 9.0.3 pytest-cov: 7.1.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.2 python-multipart: 0.0.29 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.1.0 sortedcontainers: 2.4.0 soupsieve: 2.8.4 Sphinx: 9.0.4 sphinx-autodoc-typehints: 3.6.1 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 sse-starlette: 3.4.4 stack-data: 0.6.3 starfile: 0.5.13 starlette: 1.1.0 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 3.2.1 threadpoolctl: 3.6.0 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.6 tqdm: 4.67.3 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 Unidecode: 1.4.0 urllib3: 2.7.0 uvicorn: 0.48.0 wcwidth: 0.7.0 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 yarl: 1.24.2 }}} " defect accepted normal UI all ChimeraX