id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15413 Crash when waking from sleep, Mac M2 goddard@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.5-arm64-arm-64bit ChimeraX Version: 1.9.dev202405132341 (2024-05-13 23:41:14 UTC) Description Last time you used ChimeraX it crashed. I was running this development build of ChimeraX and left the computer for 2 hours. The computer locked the screen and probably went into sleep mode. When I returned after 2 hours and logged in I saw it immediately crash. This is a Mac Studio with a single display connected and there was no change in the display connection. Fatal Python error: Segmentation fault Thread 0x000000041dd07000 (most recent call first): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Users/goddard/Library/Application Support/ChimeraX/1.9/lib/python/site-packages/tqdm/_monitor.py"", line 60 in run File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000002042d4c00 (most recent call first): File 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the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/goddard/ucsf/people/howard/ClassA_ogr1_human_Active_AF_2022-08-16_GPCRdb.pdb > format pdb Chain information for ClassA_ogr1_human_Active_AF_2022-08-16_GPCRdb.pdb #1 --- Chain | Description A | No description available > open /Users/goddard/ucsf/people/howard/gpr68_scores_processed.csv format dms Opened deep mutational scan data for 7128 mutations of 364 residues, assigned to 364 of 365 residues of chain /A, score column names score_ph55, score_ph65, score_surface. > usage dms label dms label residues columnName a text string [subtractFit a text string] [range range] [palette a colormap] [noDataColor a color] [height a number] [offset offset] [onTop true or false] — Show color-coded labels for deep mutation scan scores range: some numbers or full offset: some numbers > dms label /A:269,20,174,102 : show /A:269,20,174,102 > hide /A:269,20,174,102 > label delete > dms label /A:269,20,102 : label delete > dms label /A:269,20 : show /A:269,20 : select /A:269,20 : show /A:269,20 : dms label /A:269,20 : select clear > label delete > hide > dms label /A:269,20 : show /A:269,20 : label delete > hide > show /A:269,20 : dms label /A:269,20 : preset cartoons/nucleotides cylinders/stubs Using preset: Cartoons/Nucleotides / Cylinders/Stubs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > show /A:269,20 : preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > show /A:269,20 : ui tool show ""Side View"" > set bgColor white > graphics silhouettes true > save /Users/goddard/Desktop/image1.png supersample 3 > usage dms scatter dms scatterplot chain xColumnName a text string yColumnName a text string [correlation true or false] [subtractXFit a text string] [subtractYFit a text string] [type type] [above a number] [below a number] [replace true or false] — Show scatter plot of residues using two phenotype deep mutational scan scores type: one of all_mutations, sum, sum_absolute, or synonymous > dms scatterplot /A xColumnName score_ph55 yColumnName score_ph65 correlation > true Plotted 7073 mutations in chain /A with score_ph55 on x-axis and score_ph65 on y-axis, least squares fit slope 0.225, intercept 0.0311, R squared 0.0564 > view /A:104 > clip off > select /A:104 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel > color /A:104 lime > label hide Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a keyword > label delete > hide > show sel > lighting soft > save /Users/goddard/Desktop/image1.png supersample 3 > label :104 > label :104 height 5 > label :104 height 3 > label :104 height 3 bgColor white > ui mousemode right ""move label"" > label :104 height 3 bgColor lightyellow > save /Users/goddard/Desktop/image1.png supersample 3 > dms histogram /A columnName score_ph55 type synonymous Plotted 234 scores of chain /A for score_ph55 > usage dms stat dms statistics chain columnName a text string [subtractFit a text string] [type type] — Compute mean and standard deviation of deep mutation scan scores type: one of all or synonymous > dms statistics /A columnName score_ph55 type synonymous Column score_ph55, 234 synonymous mutations, mean = 0.0857, standard deviation = 0.618, mean -/+ 2*SD = -1.15 to 1.32 > dms statistics /A columnName score_ph55 type all Column score_ph55, 7092 all mutations, mean = -0.298, standard deviation = 1, mean -/+ 2*SD = -2.3 to 1.7 > dms statistics /A columnName score_surface type synonymous Column score_surface, 234 synonymous mutations, mean = 0.106, standard deviation = 0.668, mean -/+ 2*SD = -1.23 to 1.44 > dms histogram /A columnName score_surface type synonymous Plotted 234 scores of chain /A for score_surface > usage dms umap dms umap chain columnName a text string [subtractFit a text string] — Project residues in umap plot according to mutation scores > dms umap /A columnName score_ph55 211 of 364 have 20 mutations > usage dms hist dms histogram chain columnName a text string [subtractFit a text string] [bins an integer] [curve true or false] [smoothWidth a number] [type type] [above a number] [below a number] [replace true or false] — Show histogram of deep mutational scan scores type: one of all_mutations, sum, sum_absolute, or synonymous > dms histogram /A columnName score_ph55 type synonymous subtractFit > score_surface Plotted 234 scores of chain /A for score_ph55 > dms statistics /A columnName score_ph55 type synonymous subtractFit > score_surface Column score_ph55, 234 synonymous mutations, mean = 0.164, standard deviation = 0.459, mean -/+ 2*SD = -0.754 to 1.08 > usage dms Subcommands are: * dms attribute * dms histogram * dms label * dms scatterplot * dms statistics * dms umap > usage dms histogram dms histogram chain columnName a text string [subtractFit a text string] [bins an integer] [curve true or false] [smoothWidth a number] [type type] [above a number] [below a number] [replace true or false] — Show histogram of deep mutational scan scores type: one of all_mutations, sum, sum_absolute, or synonymous ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.9.dev202405132341 (2024-05-13) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M2 Ultra OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: Mac Studio Model Identifier: Mac14,14 Model Number: Z1800003VLL/A Chip: Apple M2 Ultra Total Number of Cores: 24 (16 performance and 8 efficiency) Memory: 64 GB System Firmware Version: 10151.121.1 OS Loader Version: 10151.121.1 Software: System Software Overview: System Version: macOS 14.5 (23F79) Kernel Version: Darwin 23.5.0 Time since boot: 21 days, 19 hours, 30 minutes Graphics/Displays: Apple M2 Ultra: Chipset Model: Apple M2 Ultra Type: GPU Bus: Built-In Total Number of Cores: 60 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: PHL 278B1: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.14.0 beautifulsoup4: 4.12.3 biopython: 1.83 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.6 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57 ChimeraX-AtomicLibrary: 14.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.5 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.3 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: 2.2.4 ChimeraX-Clipper: 0.23.0 ChimeraX-clix: 0.1.4 ChimeraX-ColorActions: 1.0.4 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9.dev202405132341 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-DeepMutationalScan: 1.0 ChimeraX-Dicom: 1.2 ChimeraX-DiffPlot: 1.0 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: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 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-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.15 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-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.4 ChimeraX-PDB: 2.7.5 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: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 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: 1.0.4 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.4 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: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.2 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.1 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: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.51.0 fsspec: 2024.3.1 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.2 jedi: 0.19.1 Jinja2: 3.1.3 joblib: 1.4.2 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.10 kiwisolver: 1.4.5 line-profiler: 4.1.2 llvmlite: 0.42.0 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 mpmath: 1.3.0 mrcfile: 1.5.0 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numba: 0.59.1 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.1 prompt-toolkit: 3.0.43 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynndescent: 0.5.12 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scikit-learn: 1.4.2 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 sympy: 1.12 tables: 3.8.0 tcia-utils: 1.5.1 threadpoolctl: 3.5.0 tifffile: 2024.1.30 tinyarray: 1.2.4 torch: 2.3.0 tornado: 6.4 tqdm: 4.66.4 traitlets: 5.14.2 typing-extensions: 4.11.0 tzdata: 2024.1 umap-learn: 0.5.6 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.10 }}} " defect assigned normal Window Toolkit Eric Pettersen all ChimeraX