id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7410 Crash creating SEQCROW QMenuBar in ARM tech preview chimerax-bug-report@… Tony Schaefer "{{{ The following bug report has been submitted: Platform: macOS-12.5-arm64-arm-64bit ChimeraX Version: 1.5.dev202208030611 (2022-08-03 06:11:58 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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""ffede77c-d90b-366b-96f2-665c2f50ee59"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.3G resident=0K(0%) swapped_out_or_unallocated=1.3G(100%)\nWritable regions: Total=2.8G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.8G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 1152K 9 \nActivity Tracing 256K 1 \nCG backing stores 4480K 8 \nCG image 3168K 57 \nCG raster data 256K 1 \nColorSync 624K 27 \nCoreAnimation 6592K 66 \nCoreGraphics 48K 3 \nCoreUI image data 4768K 40 \nFoundation 32K 2 \nKernel Alloc Once 48K 2 \nMALLOC 443.5M 90 \nMALLOC guard page 192K 11 \nMALLOC_MEDIUM (reserved) 1.1G 10 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.5M 35 \nStack 153.3M 35 \nVM_ALLOCATE 170.0M 374 \nVM_ALLOCATE (reserved) 512.0M 4 reserved VM address space (unallocated)\n__AUTH 2624K 311 \n__AUTH_CONST 20.6M 509 \n__CTF 756 1 \n__DATA 25.3M 714 \n__DATA_CONST 28.3M 712 \n__DATA_DIRTY 1804K 216 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 612.8M 202 \n__OBJC_CONST 3665K 282 \n__OBJC_RO 83.0M 1 \n__OBJC_RW 3168K 1 \n__TEXT 756.7M 730 \n__UNICODE 592K 1 \ndyld private memory 1216K 3 \nmapped file 186.6M 55 \nshared memory 3168K 25 \n=========== ======= ======= \nTOTAL 4.5G 4548 \nTOTAL, minus reserved VM space 2.5G 4548 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""5fb4245a1bbfe8005e33a1e1"", ""factorPackIds"" : { }, ""deploymentId"" : 240000015 }, { ""rolloutId"" : ""6112dda2fc54bc3389840642"", ""factorPackIds"" : { ""SIRI_DICTATION_ASSETS"" : ""628bd2fda5168570b594bb52"" }, ""deploymentId"" : 240000137 } ], ""experiments"" : [ ] } } System Profile: Network Service: Wi-Fi, AirPort, en0 Thunderbolt Bus: MacBook Pro, Apple Inc. Thunderbolt Bus: MacBook Pro, Apple Inc. Thunderbolt Bus: MacBook Pro, Apple Inc. Boot Volume File System Type: apfs Memory Module: LPDDR5 USB Device: USB31Bus USB Device: USB31Bus USB Device: USB31Bus Display: Color LCD, 3024 x 1964 Retina, Main, MirrorOff, Online Display: P24h-10, 2560 x 1440 (QHD/WQHD - Wide Quad High Definition), MirrorOff, Online Model: MacBookPro18,3, BootROM 7459.141.1, proc 10:8:2 processors, 16 GB, SMC Graphics: Apple M1 Pro, Apple M1 Pro, Built-In AirPort: Wi-Fi, wl0: Apr 6 2022 05:55:54 version 20.90.45.0.8.7.118 FWID 01-e7138ff2 Bluetooth: Version (null), 0 services, 0 devices, 0 incoming serial ports ===== Log before crash start ===== UCSF ChimeraX version: 1.5.dev202208030611 (2022-08-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Successfully installed 'SEQCROW==1.2.2' Found existing installation: SEQCROW 1.2.2 Uninstalling SEQCROW-1.2.2: Successfully uninstalled SEQCROW-1.2.2 > toolshed install /Users/tylerbenton/Downloads/SEQCROW-1.5a1-py3-none-any.whl Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing /Users/tylerbenton/Downloads/SEQCROW-1.5a1-py3-none-any.whl Requirement already satisfied: scipy in /private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from SEQCROW==1.5a1) (1.9.0) Requirement already satisfied: psutil in /private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from SEQCROW==1.5a1) (5.9.1) Requirement already satisfied: Send2Trash in /Users/tylerbenton/Library/Application Support/ChimeraX/1.5/site-packages (from SEQCROW==1.5a1) (1.8.0) ERROR: Could not find a version that satisfies the requirement ChimeraX-Core=1.2 (from seqcrow) (from versions: none) ERROR: No matching distribution found for ChimeraX-Core=1.2 WARNING: You are using pip version 21.3.1; however, version 22.2.2 is available. You should consider upgrading via the '/private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/MacOS/ChimeraX -m pip install --upgrade pip' command. > toolshed show > toolshed install /Users/tylerbenton/SEQCROW-1.4.4-py3-none-any.whl Errors may have occurred when running pip: pip standard error: \--- WARNING: Value for scheme.platlib does not match. Please report this to distutils: /Users/tylerbenton/Library/Application Support/ChimeraX/1.5/site- packages sysconfig: /Users/tylerbenton/Library/Python/3.9/lib/python/site-packages WARNING: Value for scheme.purelib does not match. Please report this to distutils: /Users/tylerbenton/Library/Application Support/ChimeraX/1.5/site- packages sysconfig: /Users/tylerbenton/Library/Python/3.9/lib/python/site-packages WARNING: Value for scheme.headers does not match. Please report this to distutils: /Users/tylerbenton/Library/Application Support/ChimeraX/include/python3.9/SEQCROW sysconfig: /Users/tylerbenton/Library/Python/3.9/include/SEQCROW WARNING: Value for scheme.scripts does not match. Please report this to distutils: /Users/tylerbenton/Library/Application Support/ChimeraX/bin sysconfig: /Users/tylerbenton/Library/Python/3.9/bin WARNING: Value for scheme.data does not match. Please report this to distutils: /Users/tylerbenton/Library/Application Support/ChimeraX sysconfig: /Users/tylerbenton/Library/Python/3.9 WARNING: Additional context: user = True home = None root = None prefix = None WARNING: Value for scheme.headers does not match. Please report this to distutils: /Users/tylerbenton/Library/Application Support/ChimeraX/include/python3.9/UNKNOWN sysconfig: /Users/tylerbenton/Library/Python/3.9/include/UNKNOWN WARNING: You are using pip version 21.3.1; however, version 22.2.2 is available. You should consider upgrading via the '/private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/MacOS/ChimeraX -m pip install --upgrade pip' command. \--- pip standard output: \--- Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing /Users/tylerbenton/SEQCROW-1.4.4-py3-none-any.whl Requirement already satisfied: scipy in /private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from SEQCROW==1.4.4) (1.9.0) Requirement already satisfied: ChimeraX-Core=1.2 in /private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from SEQCROW==1.4.4) (1.5.dev202208030611) Requirement already satisfied: Send2Trash in /Users/tylerbenton/Library/Application Support/ChimeraX/1.5/site-packages (from SEQCROW==1.4.4) (1.8.0) Requirement already satisfied: psutil in /private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from SEQCROW==1.4.4) (5.9.1) Requirement already satisfied: jinja2 in /private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from SEQCROW==1.4.4) (3.1.2) Requirement already satisfied: MarkupSafe>=2.0 in /private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from jinja2->SEQCROW==1.4.4) (2.1.1) Requirement already satisfied: numpy=1.18.5 in /private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from scipy->SEQCROW==1.4.4) (1.23.1) Installing collected packages: SEQCROW Successfully installed SEQCROW-1.4.4 \--- Successfully installed SEQCROW-1.4.4 Installed SEQCROW (1.4.4) > ui tool show ""Build QM Input"" settings migrated from version 2 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.5.dev202208030611 (2022-08-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.1 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Chip: Apple M1 Pro Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 7459.141.1 OS Loader Version: 7459.141.1 Software: System Software Overview: System Version: macOS 12.5 (21G72) Kernel Version: Darwin 21.6.0 Time since boot: 2 days 23:37 Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal P24h-10: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.0.5 Babel: 2.10.3 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.7.0 certifi: 2021.10.8 cftime: 1.6.1 charset-normalizer: 2.1.0 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: 2.5.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.7 ChimeraX-AtomicLibrary: 7.0.2 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1.1 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: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChangeChains: 1.0 ChimeraX-CheckWaters: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.1 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.4 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.5.dev202208030611 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.1.6 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.2.1 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: 1.1.5 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.7 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-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 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: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.7.2 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: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.21.4 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.2 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 0.9.1 filelock: 3.4.2 fonttools: 4.34.4 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.33 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 4.12.0 ipykernel: 6.15.1 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 4.11.1 kiwisolver: 1.4.4 line-profiler: 3.4.0 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.3 msgpack: 1.0.4 nest-asyncio: 1.5.5 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.3 numpy: 1.23.1 openvr: 1.16.802 packaging: 21.0 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.12.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.2.0 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.30 psutil: 5.9.1 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.1 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.1 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 23.2.0 qtconsole: 5.3.1 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.28.1 scipy: 1.9.0 Send2Trash: 1.8.0 SEQCROW: 1.4.4 setuptools: 62.6.0 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.3.0 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 urllib3: 1.26.11 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.3.0 zipp: 3.8.1 }}} " defect closed normal Window Toolkit fixed chimerax-programmers all ChimeraX