id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6679 Unknown crash chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.15.7-x86_64-i386-64bit ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. {""app_name"":""ChimeraX"",""timestamp"":""2022-04-21 14:53:34.00 +0800"",""app_version"":""1.2.5"",""slice_uuid"":""74b1c996-e1f3-331c-8c86-116411356099"",""build_version"":""1.2.5.0"",""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":1,""bug_type"":""309"",""os_version"":""Mac OS X 10.15.7 (19H1615)"",""incident_id"":""51872D9E-5E7B-4713-BAC0-4F3D4D5C48DB"",""name"":""ChimeraX""} { ""uptime"" : 200000, ""procLaunch"" : ""2022-04-21 14:49:08.8217 +0800"", ""procRole"" : ""Foreground"", ""exception"" : { ""type"" : ""EXC_BAD_ACCESS"", ""signal"" : ""SIGSEGV"", ""subtype"" : ""KERN_INVALID_ADDRESS at 0x5e87a360"" }, ""userID"" : 501, ""modelCode"" : ""MacBookPro15,2"", ""coalitionID"" : 32292, ""osVersion"" : { ""train"" : ""Mac OS X 10.15.7"", ""build"" : ""19H1615"", ""releaseType"" : """" }, ""captureTime"" : ""2022-04-21 14:53:04.3048 +0800"", ""incident"" : ""51872D9E-5E7B-4713-BAC0-4F3D4D5C48DB"", ""pid"" : 67570, ""cpuType"" : ""X86-64"", ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.2.5.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.2.5"",""CFBundleVersion"":""1.2.5.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""C6C3E8A4-6727-9870-8970-EC4AA6F74003"", ""wakeTime"" : 1806, ""bridgeVersion"" : {""build"":""19P647"",""train"":""6.1""}, ""sleepWakeUUID"" : ""37460234-2DB5-4312-91B6-432D310D9DB1"", ""sip"" : ""enabled"", ""vmregioninfo"" : ""0x7f8d5e87a360 is not in any region. Bytes after previous region: 877409 Bytes before following region: 44192\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_LARGE 00007f8d5e5a4000-00007f8d5e7a4000 [ 2048K] rw-\/rwx SM=PRV \n---> GAP OF 0xe1000 BYTES\n MALLOC_LARGE 00007f8d5e885000-00007f8d5e8b2000 [ 180K] rw-\/rwx SM=PRV "", ""is_corpse"" : 1, ""extMods"" : {""caller"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":0},""system"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":177083},""targeted"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":3},""warnings"":0}, ""threads"" : 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""threadState"" : { ""r13"" : 3126, ""rax"" : 0, ""rflags"" : 582, ""cpu"" : 0, ""r14"" : 11, ""rsi"" : 11, ""r8"" : 140245405622088, ""cr2"" : 140245405622088, ""rdx"" : 0, ""r10"" : 4494093760, ""r9"" : 1844494853665879581, ""r15"" : 22, ""rbx"" : 4494093760, ""trap"" : 133, ""err"" : 33554760, ""r11"" : 582, ""rip"" : 140735121847098, ""rbp"" : 140245405620864, ""rsp"" : 140245405620824, ""r12"" : 775, ""rcx"" : 140245405620824, ""flavor"" : ""x86_THREAD_STATE"", ""rdi"" : 775 }, ""usedImages"" : [ [ ""77699c5a-e7df-3cf4-b9c8-e00de1b2c117"", 140735121817600, ""P"" ], [ ""62cb1a98-0b8f-31e7-a02b-a1139927f61d"", 140735122595840, ""P"" ], [ ""bcd3f031-4a3f-32cf-ab9a-d6ee7a7499d4"", 140735120830464, ""P"" ], [ ""009a7c1f-313a-318e-b9f2-30f4c06fea5c"", 140735122558976, ""P"" ], [ ""00000000-0000-0000-0000-000000000000"", 0, ""A"" ], [ ""cb6173b9-de92-343c-a0dd-2abc40cd0ddd"", 4474097664, ""P"" ], [ ""52fb4bb8-2a2d-32cb-a317-31062700b23f"", 4419043328, ""P"" ], [ 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""libsystem_platform.dylib"" }, { ""size"" : 0 }, { ""size"" : 1441792, ""arch"" : ""x86_64"", ""path"" : ""\/Applications\/ChimeraX-1.2.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.8\/lib\/python3.8\/site-packages\/PyQt5\/QtCore.abi3.so"", ""name"" : ""QtCore.abi3.so"" }, { ""size"" : 2322432, ""arch"" : ""x86_64"", ""path"" : ""\/Applications\/ChimeraX-1.2.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.8\/Python"", ""name"" : ""Python"" }, { ""size"" : 4096, ""arch"" : ""x86_64"", ""path"" : ""\/Applications\/ChimeraX-1.2.5.app\/Contents\/MacOS\/ChimeraX"", ""name"" : ""ChimeraX"" }, { ""size"" : 225280, ""arch"" : ""x86_64"", ""path"" : ""\/usr\/lib\/system\/libdyld.dylib"", ""name"" : ""libdyld.dylib"" }, { ""size"" : 61177856, ""arch"" : ""x86_64"", ""path"" : ""\/Applications\/ChimeraX-1.2.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.8\/lib\/python3.8\/site-packages\/numpy\/.dylibs\/libopenblas.0.dylib"", ""name"" : ""libopenblas.0.dylib"" }, { ""size"" : 131002368, ""arch"" : ""x86_64"", ""path"" : ""\/Applications\/ChimeraX-1.2.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.8\/lib\/python3.8\/site-packages\/PyQt5\/Qt\/lib\/QtWebEngineCore.framework\/Versions\/5\/QtWebEngineCore"", ""name"" : ""QtWebEngineCore"" }, { ""size"" : 4726784, ""arch"" : ""x86_64h"", ""path"" : ""\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation"", ""name"" : ""CoreFoundation"" }, { ""size"" : 14413824, ""arch"" : ""x86_64"", ""path"" : ""\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit"", ""name"" : ""AppKit"" } ], ""threadTriggered"" : { ""index"" : 0, ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } } } Log: UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-14.7.21 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655 OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro15,2 Processor Name: Quad-Core Intel Core i7 Processor Speed: 2.8 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 8 MB Hyper-Threading Technology: Enabled Memory: 16 GB Boot ROM Version: 1715.60.5.0.0 (iBridge: 19.16.10647.0.0,0) Software: System Software Overview: System Version: macOS 10.15.7 (19H1615) Kernel Version: Darwin 19.6.0 Time since boot: 15 days 23:02 Graphics/Displays: Intel Iris Plus Graphics 655: Chipset Model: Intel Iris Plus Graphics 655 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3ea5 Revision ID: 0x0001 Metal: Supported, feature set macOS GPUFamily2 v1 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No 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 Tom Goddard all ChimeraX