id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18792 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.5-x86_64-i386-64bit ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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400000012 } ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet still retrieving bundle list from toolshed > isolde shorthand Error running startup command 'isolde shorthand': Unknown command: isolde shorthand UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job068/run_it009_half2_class001.mrc Opened run_it009_half2_class001.mrc as #1, grid size 256,256,256, pixel 2.1, shown at level 0.0252, step 1, values float32 > volume #1 level 0.01219 > volume #1 level 0.005397 > set bgColor black > volume #1 style image colorMode opaque8 showOutlineBox true imageMode ""box > faces"" > volume #1 style surface > volume #1 change image level -0.0004732,0 level 0.02518,0.8 level 0.1018,1 > volume #1 level 0.002999 > volume #1 level 0.002599 > close session > open > /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job064/run_class001.mrc Opened run_class001.mrc as #1, grid size 512,512,512, pixel 1.05, shown at level 0.00278, step 2, values float32 > open > /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job068/run_class001.mrc Opened run_class001.mrc as #2, grid size 256,256,256, pixel 2.1, shown at level 0.0244, step 1, values float32 > volume #2 style image colorMode opaque8 showOutlineBox true imageMode ""box > faces"" > volume #2 style surface > volume #1 style image colorMode opaque8 showOutlineBox true imageMode ""box > faces"" > volume #1 style surface region 0,0,0,511,511,511 step 1 > volume #1 change image level -0.0006178,0 level 0.002778,0.8 level 0.03544,1 > volume #1 level 0.002031 > volume #2 level 0.0203 > volume #2 change image level -0.0008711,0 level 0.02437,0.8 level 0.16,1 > volume #2 level 0.009513 > open > /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job064/j64_recent_sphere2.mrc Opened j64_recent_sphere2.mrc as #3, grid size 512,512,512, pixel 1.05, shown at level 5e-05, step 2, values int8 > volume #2 level 0.00639 > select add #3 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #3,1,0,0,-43.061,0,1,0,-2.1484,0,0,1,17.573 > view matrix models #3,1,0,0,-46.223,0,1,0,-17.375,0,0,1,22.879 > volume #1 level 0.0002312 > volume #1 level 0.0007455 > volume #1 level 0.001602 > volume #1 level 0.001174 > view matrix models #3,1,0,0,-45.062,0,1,0,-18.836,0,0,1,21.486 > view matrix models #3,1,0,0,-41.847,0,1,0,-23.221,0,0,1,16.781 > view matrix models #3,1,0,0,-42.463,0,1,0,-22.421,0,0,1,19.253 > vop resample #3 ongrid #1 Opened j64_recent_sphere2.mrc resampled as #4, grid size 512,512,512, pixel 1.05, shown at step 1, values int8 > select subtract #3 Nothing selected > show #!3 models > hide #!3 models > hide #!4 models > show #!4 models > show #!3 models > hide #!3 models > hide #!4 models > show #!4 models > save /Users/jabrilg/Desktop/j64_recent_sphere3.mrc models #4 > open > /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job064/j64_recent_map2.mrc Opened j64_recent_map2.mrc as #5, grid size 512,512,512, pixel 1.05, shown at level 0.0028, step 2, values float32 > hide #!4 models > hide #!1 models > volume #5 style image colorMode opaque8 showOutlineBox true imageMode ""box > faces"" > volume #5 style surface region 0,0,0,511,511,511 step 1 > volume #5 change image level -0.0005002,0 level 0.002797,0.8 level 0.0316,1 > volume #5 level 0.0007963 > show #!1 models > hide #!1 models > show #!2 models > volume #2 level 0.004308 > hide #!2 models > show #!2 models > hide #!5 models > hide #!2 models > show #!5 models ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet > isolde shorthand Initialising ISOLDE-specific command aliases: Alias Equivalent full command ------------------------------------------------- st isolde step {arguments} aw isolde add water {arguments} awsf isolde add water {arguments} sim false al isolde add ligand {arguments} aa isolde add aa $1 sel {arguments} ht isolde mod his sel {arguments} so setattr sel atoms occupancy {arguments} ab isolde adjust bfactors {arguments} ss isolde sim start sel rt isolde release torsions sel {arguments} rd isolde release distances sel {arguments} ra rd; rt pf isolde pepflip sel cf isolde cisflip sel cbb color bfactor {arguments} cbo color byattr occupancy {arguments} cbc color {arguments} bychain; color {arguments} byhet cs clipper set contourSensitivity {arguments} UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-7.0.3 OpenGL renderer: AMD Radeon Pro 5700 OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.11.2 Locale: en_US.UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac20,2 Processor Name: 8-Core Intel Core i7 Processor Speed: 3,8 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 32 GB System Firmware Version: 2075.120.2.0.0 (iBridge: 22.16.15072.0.0,0) OS Loader Version: 583~1350 Software: System Software Overview: System Version: macOS 15.5 (24F74) Kernel Version: Darwin 24.5.0 Time since boot: 84 days, 21 hours, 51 minutes Graphics/Displays: AMD Radeon Pro 5700: Chipset Model: AMD Radeon Pro 5700 Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 8 GB Vendor: AMD (0x1002) Device ID: 0x731b Revision ID: 0x0040 ROM Revision: 113-D1820Q-231 VBIOS Version: 113-D182A2XG-013 Option ROM Version: 113-D182A2XG-013 EFI Driver Version: 01.01.231 Metal Support: Metal 3 Displays: iMac: Display Type: Built-In Retina LCD Resolution: Retina 5K (5120 x 2880) Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal ROG PG278QR: Resolution: 2048 x 1152 UI Looks like: 2048 x 1152 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: #ASOT2TO5phXd Mirror: Off Online: Yes Rotation: Supported Connection Type: Thunderbolt/DisplayPort Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.3 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: 2.10.5 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: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.22.4 ChimeraX-ColorActions: 1.0.3 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: 1.7 ChimeraX-CoreFormats: 1.2 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: 1.1.3 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-ISOLDE: 1.7.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 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: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.13 ChimeraX-ModelPanel: 1.4 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-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.3 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: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 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-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.3 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: 2.2.2 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: 1.33.2 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 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: 0.2.0 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.0 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.5.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.8 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 Pillow: 10.0.1 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 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: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.3 urllib3: 2.1.0 wcwidth: 0.2.12 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Window Toolkit duplicate all ChimeraX