id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8948 ChimeraX bug report submission Scooter Morris Zach Pearson "{{{ The following bug report has been submitted: Platform: macOS-13.3.1-arm64-arm-64bit ChimeraX Version: 1.7.dev202305040107 (2023-05-04 01:07:28 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Qt fatal error: QThread: Destroyed while thread is still running Fatal Python error: Aborted Thread 0x00000002decf7000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 316 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 574 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 1297 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000016e77b000 (most recent call first): File 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""c28e4ee6-1b08-4f90-8e05-2809e78310a3"", ""experimentId"" : ""6317d2003d24842ff850182a"", ""deploymentId"" : 400000013 }, { ""treatmentId"" : ""6dd670af-0633-45e4-ae5f-122ae4df02be"", ""experimentId"" : ""64406ba83deb637ac8a04419"", ""deploymentId"" : 900000005 } ] } } ===== Log before crash start ===== Startup Messages --- warning | Registration file '/Users/scooter/Library/Application Support/ChimeraX/registration' has expired UCSF ChimeraX version: 1.7.dev202305040107 (2023-05-04) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show ""Download DICOM"" > open 1.3.6.1.4.1.14519.5.2.1.4320.7007.113686129632252779806152571225 > fromDatabase tcia format dicom Summary of feedback from opening 1.3.6.1.4.1.14519.5.2.1.4320.7007.113686129632252779806152571225 fetched from tcia --- note | Opened 2 CT (THORAX W 3.0 B41 Soft Tissue) as #1.1.1, grid size 512,512,130, pixel 0.664,0.664,2.98, shown at step 1, values float32 Images from TCIA may be rotated so that flat planes appear invisible. If the screen looks black but no error message has been issued, try rotating the model into view with your mouse. > open 1.2.276.0.7230010.3.1.3.0.10926.1415313934.845816 fromDatabase tcia > format dicom Summary of feedback from opening 1.2.276.0.7230010.3.1.3.0.10926.1415313934.845816 fetched from tcia --- warning | Merged incoming unique studies with existing patient with same ID note | Opened 1000 SEG (QIN CT challenge: alg02 run1segmentation result) as #1.1.2, grid size 512,512,130, pixel 0.664,0.664,2.98, shown at step 1, values uint8 Images from TCIA may be rotated so that flat planes appear invisible. If the screen looks black but no error message has been issued, try rotating the model into view with your mouse. > open 1.2.276.0.7230010.3.1.3.0.10953.1415313952.202264 fromDatabase tcia > format dicom Summary of feedback from opening 1.2.276.0.7230010.3.1.3.0.10953.1415313952.202264 fetched from tcia --- warning | Merged incoming unique studies with existing patient with same ID note | Opened 1000 SEG (QIN CT challenge: alg02 run2segmentation result) as #1.1.3, grid size 512,512,130, pixel 0.664,0.664,2.98, shown at step 1, values uint8 Images from TCIA may be rotated so that flat planes appear invisible. If the screen looks black but no error message has been issued, try rotating the model into view with your mouse. > open 1.2.276.0.7230010.3.1.3.0.10975.1415313969.658041 fromDatabase tcia > format dicom Summary of feedback from opening 1.2.276.0.7230010.3.1.3.0.10975.1415313969.658041 fetched from tcia --- warning | Merged incoming unique studies with existing patient with same ID note | Opened 1000 SEG (QIN CT challenge: alg02 run3segmentation result) as #1.1.4, grid size 512,512,130, pixel 0.664,0.664,2.98, shown at step 1, values uint8 Images from TCIA may be rotated so that flat planes appear invisible. If the screen looks black but no error message has been issued, try rotating the model into view with your mouse. > open 1.2.276.0.7230010.3.1.3.0.10998.1415313986.834357 fromDatabase tcia > format dicom Summary of feedback from opening 1.2.276.0.7230010.3.1.3.0.10998.1415313986.834357 fetched from tcia --- warning | Merged incoming unique studies with existing patient with same ID note | Opened 1000 SEG (QIN CT challenge: alg03 run1segmentation result) as #1.1.5, grid size 512,512,130, pixel 0.664,0.664,2.98, shown at step 1, values uint8 Images from TCIA may be rotated so that flat planes appear invisible. If the screen looks black but no error message has been issued, try rotating the model into view with your mouse. > open 1.2.276.0.7230010.3.1.3.0.11020.1415314004.305238 fromDatabase tcia > format dicom Summary of feedback from opening 1.2.276.0.7230010.3.1.3.0.11020.1415314004.305238 fetched from tcia --- warning | Merged incoming unique studies with existing patient with same ID note | Opened 1000 SEG (QIN CT challenge: alg03 run2segmentation result) as #1.1.6, grid size 512,512,130, pixel 0.664,0.664,2.98, shown at step 1, values uint8 Images from TCIA may be rotated so that flat planes appear invisible. If the screen looks black but no error message has been issued, try rotating the model into view with your mouse. > open 1.2.276.0.7230010.3.1.3.0.11044.1415314021.713578 fromDatabase tcia > format dicom Summary of feedback from opening 1.2.276.0.7230010.3.1.3.0.11044.1415314021.713578 fetched from tcia --- warning | Merged incoming unique studies with existing patient with same ID note | Opened 1000 SEG (QIN CT challenge: alg03 run3segmentation result) as #1.1.7, grid size 512,512,130, pixel 0.664,0.664,2.98, shown at step 1, values uint8 Images from TCIA may be rotated so that flat planes appear invisible. If the screen looks black but no error message has been issued, try rotating the model into view with your mouse. > open 1.2.276.0.7230010.3.1.3.0.26655.1427919632.692116 fromDatabase tcia > format dicom Summary of feedback from opening 1.2.276.0.7230010.3.1.3.0.26655.1427919632.692116 fetched from tcia --- warning | Merged incoming unique studies with existing patient with same ID note | Opened 1000 SEG (QIN CT challenge: alg01 run01segmentation result) as #1.1.8, grid size 512,512,130, pixel 0.664,0.664,2.98, shown at step 1, values uint8 Images from TCIA may be rotated so that flat planes appear invisible. If the screen looks black but no error message has been issued, try rotating the model into view with your mouse. > open 1.2.276.0.7230010.3.1.3.0.26703.1427919686.825713 fromDatabase tcia > format dicom Summary of feedback from opening 1.2.276.0.7230010.3.1.3.0.26703.1427919686.825713 fetched from tcia --- warning | Merged incoming unique studies with existing patient with same ID note | Opened 1000 SEG (QIN CT challenge: alg01 run03segmentation result) as #1.1.9, grid size 512,512,130, pixel 0.664,0.664,2.98, shown at step 1, values uint8 Images from TCIA may be rotated so that flat planes appear invisible. If the screen looks black but no error message has been issued, try rotating the model into view with your mouse. > open 1.2.276.0.7230010.3.1.3.0.26680.1427919659.772120 fromDatabase tcia > format dicom Summary of feedback from opening 1.2.276.0.7230010.3.1.3.0.26680.1427919659.772120 fetched from tcia --- warning | Merged incoming unique studies with existing patient with same ID note | Opened 1000 SEG (QIN CT challenge: alg01 run02segmentation result) as #1.1.10, grid size 512,512,130, pixel 0.664,0.664,2.98, shown at step 1, values uint8 Images from TCIA may be rotated so that flat planes appear invisible. If the screen looks black but no error message has been issued, try rotating the model into view with your mouse. > volume #1.1.1 region 0,0,0,511,511,129 step 2 > volume #1.1.2 region 0,0,0,511,511,129 step 2 > volume #1.1.3 region 0,0,0,511,511,129 step 2 > volume #1.1.4 region 0,0,0,511,511,129 step 2 > volume #1.1.5 region 0,0,0,511,511,129 step 2 > volume #1.1.6 region 0,0,0,511,511,129 step 2 > volume #1.1.7 region 0,0,0,511,511,129 step 2 > volume #1.1.8 region 0,0,0,511,511,129 step 2 > volume #1.1.9 region 0,0,0,511,511,129 step 2 > volume #1.1.10 region 0,0,0,511,511,129 step 2 > close session > ui tool show ""Download DICOM"" QThread: Destroyed while thread is still running ===== Log before crash end ===== Log: Startup Messages --- warning | Registration file '/Users/scooter/Library/Application Support/ChimeraX/registration' has expired UCSF ChimeraX version: 1.7.dev202305040107 (2023-05-04) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 83.1 OpenGL renderer: Apple M1 Max OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,2 Model Number: Z14W0010BLL/A Chip: Apple M1 Max Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 64 GB System Firmware Version: 8422.100.650 OS Loader Version: 8422.100.650 Software: System Software Overview: System Version: macOS 13.3.1 (a) (22E772610a) Kernel Version: Darwin 22.4.0 Time since boot: 1 day, 1 hour, 12 minutes Graphics/Displays: Apple M1 Max: Chipset Model: Apple M1 Max Type: GPU Bus: Built-In Total Number of Cores: 24 Vendor: Apple (0x106b) Metal Support: Metal 3 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: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 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: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.11 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: 1.45.4 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: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.2 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: 1.7.dev202305040107 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: 1.1.2 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: 1.2 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: 2.1 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: 1.10.2 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: 1.11.1 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: 1.2.2 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2.1 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 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: 2022.2.22 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: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 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 ptyprocess: 0.7.0 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 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 setuptools-scm: 7.0.5 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 zipp: 3.15.0 }}} " defect closed critical 1.6 UI fixed all ChimeraX