id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18081 Crash on Mac waking from sleep shiv.sahteli@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.5-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 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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}, ""logWritingSignature"" : ""1f12ffc27354a67358a6ea07ec3b8362997a7e42"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""67fd77fe1f9da9148f70d6ed"", ""factorPackIds"" : { }, ""deploymentId"" : 240000011 }, { ""rolloutId"" : ""60186475825c62000ccf5450"", ""factorPackIds"" : { }, ""deploymentId"" : 240000083 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/sahtelis/Desktop/connexin- > str_analysis/DOGsitescorer/cx43_pocket1_analysis.cxs Opened 7xqj_P_1_gpsAll.ccp4 as #2, grid size 48,55,42, pixel 0.4,0.4,0.4, shown at level 1, step 1, values float32 opened ChimeraX session > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!4 models > show #!4 models > open /Users/sahtelis/Desktop/connexin- > str_analysis/DOGsitescorer/cx43_pocket1_comparisonwithcx43_analysis.cxs opened ChimeraX session > show #!3 models > hide #!3 models > hide #!9 models > show #!9 models > select add #9 2686 atoms, 2724 bonds, 1 pseudobond, 190 residues, 3 models selected > hide sel cartoons > show sel cartoons > hide (#!9 & sel-residues & (protein|nucleic)) target a > cartoon hide (#!9 & sel-residues) > show (#!9 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab > select add #9 2686 atoms, 2724 bonds, 189 pseudobonds, 190 residues, 5 models selected > select subtract #9 1 model selected > hide #!9 models > show #!9 models > select add #9 2686 atoms, 2724 bonds, 189 pseudobonds, 190 residues, 4 models selected > hide sel cartoons > show sel cartoons > hide sel cartoons > hide (#!9 & sel-residues & (protein|nucleic)) target a > cartoon hide (#!9 & sel-residues) > show (#!9 & sel-residues & backbone) target ab > show (#!9 & sel-residues & sidechain) target ab > hide (#!9 & sel-residues & (protein|nucleic)) target a > cartoon hide (#!9 & sel-residues) > show (#!9 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab > select add #9 2686 atoms, 2724 bonds, 189 pseudobonds, 190 residues, 5 models selected > select subtract #9 1 model selected > select add #2 1660 atoms, 1706 bonds, 1 pseudobond, 204 residues, 3 models selected > hide sel cartoons > hide (#!2 & sel-residues & (protein|nucleic)) target a > cartoon hide (#!2 & sel-residues) > show (#!2 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab > select add #2 1660 atoms, 1706 bonds, 203 pseudobonds, 204 residues, 5 models selected > select subtract #2 1 model selected > select #9:A:44,45,46, 47,48,50,51,65,66,69,70,71,72,73,75,76, 195,198,199, > 200, 201, 202, 203, 222,223, 224, 228, 232 488 atoms, 487 bonds, 18 pseudobonds, 28 residues, 2 models selected > style (#!9 & sel) stick Changed 488 atom styles > show sel atoms > select add #9 2686 atoms, 2724 bonds, 151 pseudobonds, 190 residues, 5 models selected > select subtract #9 1 model selected > hide H > hide #!2 models > select #9:A:44,45,46, 47,48,50,51,65,66,69,70,71,72,73,75,76, 195,198,199, > 200, 201, 202, 203, 222,223, 224, 228, 232 488 atoms, 487 bonds, 28 residues, 1 model selected > combine sel > select add #9 2686 atoms, 2724 bonds, 151 pseudobonds, 190 residues, 5 models selected > select subtract #9 1 model selected > hide #!9 models > hide #!10 models > show #!10 models > show #!9 models > select add #10 2686 atoms, 2724 bonds, 151 pseudobonds, 190 residues, 3 models selected > hide sel atoms > hide (#!10 & sel-residues & (protein|nucleic)) target a > cartoon hide (#!10 & sel-residues) > show (#!10 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab > select add #10 2686 atoms, 2724 bonds, 189 pseudobonds, 190 residues, 3 models selected > select subtract #10 Nothing selected > select #9:A:44,45,46, 47,48,50,51,65,66,69,70,71,72,73,75,76, 195,198,199, > 200, 201, 202, 203, 222,223, 224, 228, 232 488 atoms, 487 bonds, 28 residues, 1 model selected > surface (#!9 & sel) > coulombic sel The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: cx45_chainA_refine11_coot3.pdb #9/A GLU 11 cx45_chainA_refine11_coot3.pdb #9/A GLU 12 cx45_chainA_refine11_coot3.pdb #9/A HIS 14 cx45_chainA_refine11_coot3.pdb #9/A HIS 16 cx45_chainA_refine11_coot3.pdb #9/A SER 17 cx45_chainA_refine11_coot3.pdb #9/A THR 18 cx45_chainA_refine11_coot3.pdb #9/A PHE 19 cx45_chainA_refine11_coot3.pdb #9/A LEU 92 cx45_chainA_refine11_coot3.pdb #9/A LYS 101 cx45_chainA_refine11_coot3.pdb #9/A MET 102 cx45_chainA_refine11_coot3.pdb #9/A GLU 103 cx45_chainA_refine11_coot3.pdb #9/A LEU 173 cx45_chainA_refine11_coot3.pdb #9/A MET 174 cx45_chainA_refine11_coot3.pdb #9/A ILE 176 cx45_chainA_refine11_coot3.pdb #9/A LEU 179 cx45_chainA_refine11_coot3.pdb #9/A HIS 252 cx45_chainA_refine11_coot3.pdb #9/A PHE 255 cx45_chainA_refine11_coot3.pdb #9/A ILE 258 cx45_chainA_refine11_coot3.pdb #9/A ARG 259 cx45_chainA_refine11_coot3.pdb #9/A LEU 262 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for cx45_chainA_refine11_coot3.pdb_A SES surface #9.3: minimum, -13.26, mean 0.84, maximum 12.84 To also show corresponding color key, enter the above coulombic command and add key true > select add #9 2686 atoms, 2724 bonds, 151 pseudobonds, 190 residues, 5 models selected > select subtract #9 1 model selected > hide #!9 models > show #!9 models > close #10 > close session > open /Users/sahtelis/Desktop/connexin- > str_analysis/DOGsitescorer/cx43_pocket1_comparisonwithcx43_analysis.cxs opened ChimeraX session > hide #!9 models > show #!1 models > hide #!1 models > show #!3 models > hide #!3 models > select > #2:A:45,46,47,48,49,51,52,66,67,70,71,72,73,74,76,77,172,173,176,177,178,179,180,181,200,201,202,206,210 252 atoms, 252 bonds, 29 residues, 1 model selected > surface style #2 solid > show sel surfaces > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for copy of cx43_hc_7xqj.cif_A SES surface #2.2: minimum, -13.05, mean 0.99, maximum 18.04 To also show corresponding color key, enter the above coulombic command and add key true > select add #2 1660 atoms, 1706 bonds, 1 pseudobond, 204 residues, 4 models selected > select subtract #2 1 model selected > transparency #2 70 > show #!3 models > hide #!3 models > show #!3 models > hide #!2 models > show #!2 models > select > #2:A:45,46,47,48,49,51,52,66,67,70,71,72,73,74,76,77,172,173,176,177,178,179,180,181,200,201,202,206,210 252 atoms, 252 bonds, 29 residues, 1 model selected > hide sel surfaces > transparency #3 90 > select add #2 1660 atoms, 1706 bonds, 1 pseudobond, 204 residues, 4 models selected > select subtract #2 1 model selected > hide #!2 models > hide #!3 models > show #!3 models > hide #!3 models > show #!2 models > show #!3 models > hide #!2 models > hide #!3 models > show #!2 models > hide #!2 models > show #!3 models > show #!2 models > hide #!2 models > hide #3.1 models > hide #3.2 models > hide #!3 models > show #3.2 models > show #3.1 models > hide #3.1 models > show #3.1 models > hide #3.1 models > transparency #3 50 > transparency #3 00 > ui tool show ""Side View"" > show #!2 models > hide #!3 models > show #!3 models > hide #!3 models > view ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 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 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac15,12 Model Number: MC8G4KS/A Chip: Apple M3 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 11881.121.1 OS Loader Version: 11881.121.1 Software: System Software Overview: System Version: macOS 15.5 (24F74) Kernel Version: Darwin 24.5.0 Time since boot: 10 days, 2 minutes Graphics/Displays: Apple M3: Chipset Model: Apple M3 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: LEN T32p-20: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: On Mirror Status: Master Mirror Online: Yes Rotation: Supported Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Mirror: On Mirror Status: Hardware Mirror Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 autocommand: 2.2.2 babel: 2.16.0 backports.tarfile: 1.2.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-Clipper: 0.24.0 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 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: 1.4.1 ChimeraX-Hbonds: 2.5 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-ISOLDE: 1.9 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-locscalesurfer: 0.1 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: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 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 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 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: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 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: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 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: 1.18.1 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 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: 1.41 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 einops: 0.3.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 fsspec: 2025.5.0 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 importlib_metadata: 8.0.0 importlib_resources: 6.4.0 inflect: 7.3.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jaraco.context: 5.3.0 jaraco.functools: 4.0.1 jaraco.text: 3.12.1 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 more-itertools: 10.3.0 mpmath: 1.3.0 mrcfile: 1.3.0 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.24.4 numpy: 1.26.4 openvr: 1.26.701 ordered-set: 4.1.0 packaging: 23.2 packaging: 24.1 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 platformdirs: 4.2.2 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.10.1 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 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: 0.6.3 sympy: 1.14.0 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 timm: 0.4.12 tinyarray: 1.2.4 tomli: 2.0.1 torch: 2.2.2 torchvision: 0.17.2 tornado: 6.4.2 tqdm: 4.66.6 traitlets: 5.14.3 typeguard: 4.3.0 typing_extensions: 4.12.2 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 zipp: 3.19.2 }}} " defect closed normal Window Toolkit duplicate all ChimeraX