id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19317 Crash on Mac waking from sleep ellen_goodall@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.7.1-arm64-arm-64bit ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. 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""CFBundleVersion"" : ""3603"" } ], ""sharedCache"" : { ""base"" : 6975488000, ""size"" : 5039341568, ""uuid"" : ""e93019e7-f1c3-3ee2-9cac-6c6940bee5d1"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=12.9G written=431.4M(3%) resident=7340K(0%) swapped_out=424.2M(3%) unallocated=12.5G(97%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 512K 25 \nColorSync 624K 33 \nCoreAnimation 1968K 102 \nCoreGraphics 64K 4 \nCoreServices 624K 2 \nCoreUI image data 3600K 28 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 11.9G 164 \nMALLOC guard page 288K 18 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.6M 38 \nStack 199.8M 38 \nVM_ALLOCATE 802.7M 433 \n__AUTH 5517K 696 \n__AUTH_CONST 77.4M 943 \n__CTF 824 1 \n__DATA 37.3M 1079 \n__DATA_CONST 37.2M 1097 \n__DATA_DIRTY 2777K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 647.7M 148 \n__OBJC_RO 61.4M 1 \n__OBJC_RW 2396K 1 \n__TEXT 1.3G 1112 \n__TEXT (graphics) 352K 5 \n__TPRO_CONST 128K 2 \ndyld private memory 1840K 17 \nmapped file 577.5M 91 \npage table in kernel 7340K 1 \nshared memory 3152K 23 \n=========== ======= ======= \nTOTAL 15.7G 6459 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""64e7b9fe40ababbd0af794c0ed3ad9701cf88160"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""645197bf528fbf3c3af54105"", ""factorPackIds"" : { ""SIRI_VALUE_INFERENCE_PERVASIVE_ENTITY_RESOLUTION"" : ""663e65b4a1526e1ca0e288a1"" }, ""deploymentId"" : 240000002 }, { ""rolloutId"" : ""639124e81d92412bfb4880b3"", ""factorPackIds"" : { }, ""deploymentId"" : 240000012 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/Ellen/HMS Dropbox/Ellen > Goodall/DataShare_FBXO7_20S_SchulmanHarper/ChimeraX/EAG_PI31_withDeMartinoLimap.cxs"" > format session Opened cryosparc_P175_J828_009_volume_map_sharp.mrc as #3, grid size 392,392,392, pixel 0.851, shown at level 0.8, step 1, values float32 Opened cryosparc_P175_J828_009_volume_map.mrc as #4, grid size 392,392,392, pixel 0.851, shown at level 0.433, step 1, values float32 Opened emd_29604.map as #6, grid size 352,352,352, pixel 0.828, shown at level 0.369, step 2, values float32 > view name session-start opened ChimeraX session > ui tool show ""Side View"" > show #!3 models > show #!4 models > show #!5 models > hide #!5 models > hide #!4 models > hide #!3 models > hide #!2 models > hide #5.1 models > show #!6 models > hide #!6 models > hide #7 models > show #7 models > show #!5 models > close #5 > show #!6 models > hide #!6 models > open ""/Users/Ellen/HMS Dropbox/Ellen Goodall/Ellen_raw > data/c20S_AF3/PI31_FBXO7_20S_comparisons.cxs"" Opened cryosparc_P175_J828_009_volume_map_sharp.mrc as #3, grid size 392,392,392, pixel 0.851, shown at level 0.8, step 1, values float32 Opened cryosparc_P175_J828_009_volume_map.mrc as #4, grid size 392,392,392, pixel 0.851, shown at level 0.433, step 1, values float32 Opened emd_29604.map as #6, grid size 352,352,352, pixel 0.828, shown at level 0.369, step 2, values float32 > view name session-start opened ChimeraX session > hide #!1 models > hide #!8 models > hide #!9 models > hide #9.1 models > hide #!10 models > hide #!16 models > hide #!15 models > show #!16 models > rename #16 7teo_sc20S_fub1 > rename #15 8adn_vn20S_PI31L > rename #14 4r67_hs20S_carfilzomib > close #13 > close #12 > close #11 > rename #10 5lf0_hs20S_epoxomicin > hide #!16 models > show #7 models > rename #7 8fz6_Bt20S_hsPI31 > show #!6 models > rename #6 emd_29604_Bt20S_hsPI31.map > close #5 > hide #7 models > hide #!6 models > show #!4 models > hide #!4 models > show #!3 models > rename #3 cryosparc_P175_J828_009_volume_map_sharp_PI31_OG20S.mrc > rename #4 cryosparc_P175_J828_009_volume_map_PI31_OG20S.mrc > hide #!3 models > show #!3 models > open ""/Users/Ellen/HMS Dropbox/Ellen Goodall/Ellen_raw > data/c20S_AF3/20SOG_Fbxo7.pdb"" Chain information for 20SOG_Fbxo7.pdb #5 --- Chain | Description A O | No description available B P | No description available C Q | No description available D R | No description available E S | No description available F T | No description available G U | No description available H V | No description available I W | No description available J X | No description available K Y | No description available L Z | No description available M a | No description available N b | No description available c d | No description available > open ""/Users/Ellen/HMS Dropbox/Ellen Goodall/Ellen_raw > data/c20S_AF3/cryosparc_P571_J19_009.mrc"" Opened cryosparc_P571_J19_009.mrc as #11, grid size 384,384,384, pixel 0.851, shown at level 0.0933, step 2, values float32 > open ""/Users/Ellen/HMS Dropbox/Ellen Goodall/Ellen_raw > data/c20S_AF3/cryosparc_P571_J19_009_sharp.mrc"" Opened cryosparc_P571_J19_009_sharp.mrc as #12, grid size 384,384,384, pixel 0.851, shown at level 0.137, step 2, values float32 > hide #!3 models > hide #!5 models > show #!5 models > color #5 dim grey > hide #!11 models > hide #!12 models > ~display #5 > ribbon #5 > select clear > select #5/c 113 atoms, 116 bonds, 15 residues, 1 model selected > select #5/c-d 226 atoms, 232 bonds, 30 residues, 1 model selected > color orchid #5/c-d Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #5/c-d orchid > display #5/c-d > style sel stick Changed 226 atom styles > show #!10 models > hide #!10 models > show #!11 models > ui tool show ""Color Zone"" > color zone #11 near #5 distance 5.11 > color zone #12 near #5 distance 5.11 > hide #!11 models > show #!12 models > rename #11 cryosparc_P571_J19_009_Fbxo7_OG20S.mrc > rename #12 cryosparc_P571_J19_009_sharp_Fbxo7_OG20S.mrc > save ""/Users/Ellen/HMS Dropbox/Ellen Goodall/Ellen_raw > data/Chimeracaptures/PSMF1_FBXO7/FBXO7_PI31_carfilzomib_notcolored.cxs"" > volume #12 color darkgrey > color zone #12 near #5 distance 5.11 > save ""/Users/Ellen/HMS Dropbox/Ellen Goodall/Ellen_raw > data/Chimeracaptures/PSMF1_FBXO7/FBXO7_PI31_carfilzomib_notcolored.cxs"" > close #9 > show #!1 models > hide #!1 models > show #!2 models > hide #!2 models > rename #1 20SCP-OG_PI31_splitgroup.pdb > rename #2 20SCP-OG_PI31.pdb > color #2 dimgrey > hide #!5 models > hide #!12 models > show #!2 models > color #2/c lime > color #2/d forestgreen > color zone #3 near #2 distance 5.11 > show #!3 models > hide #!3 models > show #!4 models > color zone #4 near #2 distance 2.5 > save ""/Users/Ellen/HMS Dropbox/Ellen > Goodall/DataShare_FBXO7_20S_SchulmanHarper/ChimeraX/oldmaps_PI31_Fbxo7_comparison.cxs"" > includeMaps true ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M3 OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac15,12 Model Number: Z1G600070LL/A Chip: Apple M3 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 13822.1.2 OS Loader Version: 11881.140.96 Software: System Software Overview: System Version: macOS 15.7.1 (24G231) Kernel Version: Darwin 24.6.0 Time since boot: 22 days, 1 hour, 54 minutes Graphics/Displays: Apple M3: Chipset Model: Apple M3 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.4.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.5.0 build: 1.2.2.post1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.2 ChimeraX-AddCharge: 1.5.19 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.20.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.4 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.7 ChimeraX-AtomicLibrary: 14.1.18 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: 1.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.5.1 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10 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: 1.1.4 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: 2.5.1 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.6.2 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 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-MatchMaker: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.10.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.19 ChimeraX-ModelPanel: 1.5.1 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 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: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.10 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.3 ChimeraX-ProfileGrids: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 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: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.1 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-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 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: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.45.2 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 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 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.2 coverage: 7.9.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.14 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.58.4 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.14.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.1.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.7 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.8.1 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.4.4 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 ndindex: 1.10.0 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.11.0 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 24.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.8 pluggy: 1.6.0 prompt_toolkit: 3.0.51 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.32 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.3 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.4.1 pytest-cov: 6.2.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 27.0.0 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.14.0 setuptools: 78.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.7 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 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 stack-data: 0.6.3 superqt: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.4 tornado: 6.5.1 traitlets: 5.14.3 typing_extensions: 4.14.0 tzdata: 2025.2 urllib3: 2.5.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 }}} " defect closed normal Window Toolkit duplicate all ChimeraX