id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8387 Unknown crash chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC) Description Last time you used ChimeraX it crashed. 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(unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nMach message 24K 6 \nOpenGL GLSL 256K 3 \nRosetta Arena 4096K 2 \nRosetta Generic 3924K 978 \nRosetta IndirectBranch 2048K 1 \nRosetta JIT 128.0M 1 \nRosetta Return Stack 680K 68 \nRosetta Thread Context 680K 68 \nSTACK GUARD 36K 9 \nStack 138.6M 37 \nStack Guard 56.1M 28 \nVM_ALLOCATE 111.5M 223 \nVM_ALLOCATE (reserved) 224.1M 8 reserved VM address space (unallocated)\n__CTF 756 1 \n__DATA 44.2M 751 \n__DATA_CONST 39.6M 378 \n__DATA_DIRTY 1829K 223 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 260.2M 147 \n__OBJC_RO 65.4M 1 \n__OBJC_RW 1987K 2 \n__TEXT 849.9M 741 \ndyld private memory 256K 1 \nmapped file 4.9G 1681 \nshared memory 3016K 24 \nunshared pmap 14.4M 10 \n=========== ======= ======= \nTOTAL 9.3G 5733 \nTOTAL, minus reserved VM space 7.6G 5733 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""61fd92db295c182621ececc3"", ""factorPackIds"" : { ""SIRI_DIALOG_ASSETS"" : ""63c94f2e30a095237b822e36"" }, ""deploymentId"" : 240000292 }, { ""rolloutId"" : ""610d52e1fc54bc3389840408"", ""factorPackIds"" : { ""SIRI_UNDERSTANDING_ASR_ASSISTANT"" : ""63c7a8807b814a4e084bc5d3"", ""SIRI_UNDERSTANDING_MORPHUN"" : ""62ec7220c682040ba94e6a20"" }, ""deploymentId"" : 240000600 } ], ""experiments"" : [ ] }, ""reportNotes"" : [ ""dyld_process_snapshot_create_for_process failed with 5"" ] } Log: UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. > open > /Users/rasmus/Desktop/Paper.AdvFunctMat_deadline_20230131/Text+Figures/20230129/movie_1/movie_1.cxs Opened MASK_Stack.tif as #1, grid size 1708,1564,14, pixel 1,1,20, shown at step 1, values uint8 Opened Site8stk_defect_segmented.tif as #2, grid size 1708,1564,14, pixel 1,1,20, shown at level 167, step 1, values uint8 Log from Sun Jan 29 12:15:35 2023UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. > open > /Users/rasmus/Desktop/Paper.AdvFunctMat_deadline_20230131/3D.Visualisierung/20230122/planes+movie- > orientation_003.cxs format session Opened MASK_Stack.tif as #1, grid size 1708,1564,14, pixel 1,1,20, shown at step 1, values uint8 Opened Site8stk_defect_segmented.tif as #2, grid size 1708,1564,14, pixel 1,1,20, shown at level 167, step 1, values uint8 Log from Sun Jan 22 19:07:42 2023UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/rasmus/Desktop/Paper.AdvFunctMat_deadline_20230131/3D.Visualisierung/20230122/help2/MASK_Stack.tif > format images Opened MASK_Stack.tif as #1, grid size 1708,1564,14, pixel 1, shown at step 2, values uint8 > volume #1 region 0,0,6,1707,1563,6 step 1 showOutlineBox true > volume #1 region 0,0,1,1707,1563,1 > volume #1 level 0,0 level 25.5,0.8 level 255,1 > volume #1 level 0,0 level 96.14,1 level 255,1 > volume #1 region 0,0,1,1707,1563,1 > volume #1 region 0,0,1,1707,1563,1 > volume #1 region 0,0,1,1707,1563,2 > volume #1 region 0,0,1,1707,1563,3 > volume #1 region 0,0,3,1707,1563,3 > volume #1 region 0,0,1,1707,1563,1 > toolshed show > volume #1 region 0,0,1,1707,1563,1 > volume #1 region 0,0,2,1707,1563,2 > volume #1 region 0,0,3,1707,1563,3 > volume #1 region 0,0,0,1707,1563,13 step 2 > volume #1 region 0,0,0,1707,1563,13 step 2 > volume #1 imageMode ""tilted slab"" tiltedSlabAxis -0.5083,0.4522,0.7329 > tiltedSlabOffset -76.57 > volume #1 region 0,0,0,1707,1563,13 step 1 colorMode opaque8 orthoplanes xyz > positionPlanes 853,781,6 imageMode orthoplanes > volume #1 orthoplanes xyz positionPlanes 853,781,0 > volume #1 orthoplanes xyz positionPlanes 853,781,13 > volume #1 region 0,0,6,1707,1563,6 step 1 colorMode auto8 imageMode ""full > region"" > volume #1 region 0,0,0,1707,1563,0 > save > /Users/rasmus/Desktop/Paper.AdvFunctMat_deadline_20230131/3D.Visualisierung/20230122/planes+movie- > orientation_001.cxs > volume #1 region 0,0,8,1707,1563,8 > volume #1 region 0,0,13,1707,1563,13 > volume #1 style image region all imageMode ""tilted slab"" tiltedSlabAxis > 0,0,1 tiltedSlabOffset 7 tiltedSlabSpacing 1 tiltedSlabPlaneCount 10 > mousemode rightMode ""rotate slab"" > volume #1 orthoplanes xyz positionPlanes 854,782,7 style image region all > mousemode rightMode ""move planes"" > volume region all imageMode ""full region"" > volume unzone > mousemode rightMode ""crop volume"" Volume zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic models, 1 maps. > volume region all imageMode ""full region"" > volume unzone > mousemode rightMode ""crop volume"" > volume planes z style image imageMode ""full region"" > mousemode rightMode ""move planes"" > transparency 50 > volume region all imageMode ""full region"" > volume unzone > mousemode rightMode ""crop volume"" > transparency 50 > volume style image > volume style surface > volume style surface > volume style image > movie record > turn y 2 180 > wait 180 > movie encode /Users/rasmus/Desktop/movie3.mp4 Movie saved to /Users/rasmus/Desktop/movie3.mp4 > movie record > turn y 2 180 > wait 180 > movie encode /Users/rasmus/Desktop/movie4.mp4 Movie saved to /Users/rasmus/Desktop/movie4.mp4 > movie record > turn y 2 180 > wait 180 > movie encode /Users/rasmus/Desktop/movie5.mp4 Movie saved to /Users/rasmus/Desktop/movie5.mp4 > volume #1 region 0,0,3,1707,1563,3 > volume #1 level 0,0 level 83.78,0.9559 level 255,1 > volume #1 level 0,0 level 118.6,1 level 255,1 > volume #1 level 79.66,0 level 118.6,1 level 255,1 > volume #1 level 79.66,0 level 248.6,0 level 255,1 > volume #1 level 79.66,0 level 248.6,0 level 255,1 > volume #1 color #ffffff80 color #ffffff80 color #ffffff80 > volume #1 color #ffffff80 color #ffffff80 color #ffffff80 > volume #1 color #ffffff80 color #ffffff80 color white > volume #1 region 0,0,0,1707,1563,13 step 2 > volume #1 region 0,0,0,1707,1563,13 step 2 > volume #1 style image region all imageMode ""tilted slab"" tiltedSlabAxis > 0,0,1 tiltedSlabOffset 7 tiltedSlabSpacing 1 tiltedSlabPlaneCount 10 > mousemode rightMode ""rotate slab"" > volume #1 tiltedSlabAxis 0.003558,0.007404,1 tiltedSlabOffset 10.65 > volume #1 tiltedSlabAxis -0.05888,0.04939,0.997 tiltedSlabOffset -12.91 > volume #1 tiltedSlabAxis -0.05888,0.04939,0.997 tiltedSlabOffset -12.91 > volume #1 tiltedSlabAxis -0.03619,0.02836,0.9989 tiltedSlabOffset -8.601 > volume #1 tiltedSlabAxis -0.03576,0.03474,0.9988 tiltedSlabOffset -4.531 > volume #1 step 1 > volume #1 step 4 > volume #1 step 2 > save > /Users/rasmus/Desktop/Paper.AdvFunctMat_deadline_20230131/3D.Visualisierung/20230122/planes+movie- > orientation_002.cxs > open > /Users/rasmus/Desktop/Paper.AdvFunctMat_deadline_20230131/3D.Visualisierung/20230122/defectzone.segmented/Site8stk_defect_segmented.tif Opened Site8stk_defect_segmented.tif as #2, grid size 1708,1564,14, pixel 1, shown at step 2, values uint8 > volume #1 region 0,0,6,1707,1563,6 step 1 imageMode ""full region"" > volume #2 level 0,0 level 25.5,0.8 level 255,1 > volume #2 > volume #2 step 1 > volume #2 color #6581ff color #ffffb3 color #ffffb3 > volume #2 > volume #2 style mesh > volume #2 color #5e6aff > voxelSize 1,1,20 Unknown command: voxelSize 1,1,20 > volume #1 voxelSize 1,1,20 > volume #2 voxelSize 1,1,20 > volume #1 region 0,0,0,1707,1563,13 step 2 > volume #1 style mesh region 0,0,0,1707,1563,13 step 2 > volume #2 level 16.94 > volume #1 level 195.5 > volume #1 style image imageMode ""tilted slab"" tiltedSlabAxis > 0.4011,0.5996,-0.6926 tiltedSlabOffset 726.7 tiltedSlabPlaneCount 1 > volume #1 tiltedSlabAxis 0.5187,0.227,-0.8242 tiltedSlabOffset 570.8 > volume #2 level 57.68 > volume #2 level 166.6 > volume #1 tiltedSlabAxis 0.1697,0.2469,-0.9541 tiltedSlabOffset 217.3 > volume #1 tiltedSlabAxis 0.07054,-0.1325,-0.9887 tiltedSlabOffset -159.8 > volume #1 region 0,0,6,1707,1563,6 step 1 imageMode ""full region"" > volume #2 region 0,0,0,1707,1563,13 > movie record > turn y 2 180 > wait 180 > movie encode /Users/rasmus/Desktop/movie1.mp4 Movie saved to /Users/rasmus/Desktop/movie1.mp4 > movie record > movie encode Movie saved to /Users/rasmus/Desktop/movie.mp4 > movie record > turn y 2 180 > wait 180 > movie encode /Users/rasmus/Desktop/movie2.mp4 Movie saved to /Users/rasmus/Desktop/movie2.mp4 > movie record > turn y 2 180 > wait 180 > movie encode /Users/rasmus/Desktop/movie2.mp4 Movie saved to /Users/rasmus/Desktop/movie2.mp4 > movie encode No frames have been recorded > movie record > movie encode Movie saved to /Users/rasmus/Desktop/movie.mp4 > save > /Users/rasmus/Desktop/Paper.AdvFunctMat_deadline_20230131/3D.Visualisierung/20230122/planes+movie- > orientation_003.cxs ——— End of log from Sun Jan 22 19:07:42 2023 ——— opened ChimeraX session > hide #!1 models > show #!1 models > show #2.1 models > hide #2.1 models > show #2.1 models > hide #2.2 models > show #2.2 models > hide #2.2 models > show #2.2 models > hide #2.1 models > show #2.1 models > set bgColor white > set bgColor black > lighting full > lighting full > lighting soft > lighting simple > lighting full > lighting simple > save > /Users/rasmus/Desktop/Paper.AdvFunctMat_deadline_20230131/Text+Figures/20230129/movie_1.cxs > volume showOutlineBox false > volume showOutlineBox true > volume showOutlineBox false > save /Users/rasmus/Desktop/image1.png supersample 3 > save /Users/rasmus/Desktop/image1.png supersample 3 > save /Users/rasmus/Desktop/image2.png supersample 3 > save /Users/rasmus/Desktop/image3.png supersample 3 > save /Users/rasmus/Desktop/image4.png supersample 3 > save /Users/rasmus/Desktop/image5.png supersample 3 > save /Users/rasmus/Desktop/image6.png supersample 3 > save /Users/rasmus/Desktop/image7.png supersample 3 > save /Users/rasmus/Desktop/image8.png supersample 3 > save /Users/rasmus/Desktop/image9.png supersample 3 > save /Users/rasmus/Desktop/image10.png supersample 3 > save /Users/rasmus/Desktop/image11.png supersample 3 > save /Users/rasmus/Desktop/image12.png supersample 3 > save /Users/rasmus/Desktop/image13.png supersample 3 > save > /Users/rasmus/Desktop/Paper.AdvFunctMat_deadline_20230131/Text+Figures/20230129/movie_1/movie_1.cxs ——— End of log from Sun Jan 29 12:15:35 2023 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 83 OpenGL renderer: Apple M1 Max OpenGL vendor: AppleHardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,2 Model Number: MK1A3D/A Chip: Unknown Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 32 GB System Firmware Version: 8419.80.7 OS Loader Version: 8419.80.7 Software: System Software Overview: System Version: macOS 13.2 (22D49) Kernel Version: Darwin 22.3.0 Time since boot: 4 hours, 32 minutes Graphics/Displays: Apple M1 Max: Chipset Model: Apple M1 Max Type: GPU Bus: Built-In Total Number of Cores: 32 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.12.5 cftime: 1.5.0 chardet: 3.0.4 ChimeraX-AddCharge: 1.0.1 ChimeraX-AddH: 2.1.6 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.13.2 ChimeraX-AtomicLibrary: 3.1.3 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.5.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.2.1 ChimeraX-CommandLine: 1.1.4 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.5 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.1.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.3 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.0 ChimeraX-Hbonds: 2.1 ChimeraX-Help: 1.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.0.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.2.1 ChimeraX-MDcrds: 2.2 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.3 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.0.1 ChimeraX-ModelPanel: 1.0.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.1 ChimeraX-OpenCommand: 1.5 ChimeraX-PDB: 2.4.1 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.1 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.0.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.4 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.3.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.7.6 ChimeraX-uniprot: 2.1 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.21 decorator: 5.0.9 distlib: 0.3.1 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.17 imagecodecs: 2020.5.30 imagesize: 1.2.0 ipykernel: 5.3.4 ipython: 7.18.1 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.7 jupyter-core: 4.7.1 kiwisolver: 1.3.1 line-profiler: 2.1.2 lxml: 4.6.2 lz4: 3.1.0 MarkupSafe: 2.0.1 matplotlib: 3.3.2 matplotlib-inline: 0.1.2 msgpack: 1.0.0 netCDF4: 1.5.4 networkx: 2.5 numexpr: 2.7.3 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.9 ParmEd: 3.2.0 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 21.0.1 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.18 psutil: 5.7.2 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.7.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 pyzmq: 22.0.3 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 setuptools: 50.3.2 sfftk-rw: 0.6.7.dev1 six: 1.15.0 snowballstemmer: 2.1.0 sortedcontainers: 2.2.2 Sphinx: 3.2.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 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 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.0 wheel-filename: 1.3.0 }}} " defect closed normal Core can't reproduce all ChimeraX