id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8291 Crash in event loop after using XMAS chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x0000000118f48600 (most recent call first): File ""/private/var/folders/kw/dhwh7gkn3pgd7mqr8lnmqm880000gn/T/AppTranslocation/1F088D71-324C-4BB5-BC2C-55C446CD4176/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 283 in event_loop File ""/private/var/folders/kw/dhwh7gkn3pgd7mqr8lnmqm880000gn/T/AppTranslocation/1F088D71-324C-4BB5-BC2C-55C446CD4176/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 884 in init File ""/private/var/folders/kw/dhwh7gkn3pgd7mqr8lnmqm880000gn/T/AppTranslocation/1F088D71-324C-4BB5-BC2C-55C446CD4176/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 1035 in File ""/private/var/folders/kw/dhwh7gkn3pgd7mqr8lnmqm880000gn/T/AppTranslocation/1F088D71-324C-4BB5-BC2C-55C446CD4176/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/private/var/folders/kw/dhwh7gkn3pgd7mqr8lnmqm880000gn/T/AppTranslocation/1F088D71-324C-4BB5-BC2C-55C446CD4176/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 197 in _run_module_as_main {""app_name"":""ChimeraX"",""timestamp"":""2023-01-11 14:04:55.00 +0100"",""app_version"":""1.5.0"",""slice_uuid"":""5df621ee-554e-36a8-b448-93b2334e5480"",""build_version"":""1.5.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 12.6.2 (21G320)"",""incident_id"":""2E3F6DE5-A72E-4ECC-87DB-8E19F60B1A9C"",""name"":""ChimeraX""} { ""uptime"" : 85000, ""procLaunch"" : ""2023-01-11 14:01:10.0163 +0100"", ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro11,4"", ""procStartAbsTime"" : 85163791123717, ""coalitionID"" : 4548, ""osVersion"" : { ""train"" : ""macOS 12.6.2"", ""build"" : ""21G320"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2023-01-11 14:04:55.1699 +0100"", ""incident"" : ""2E3F6DE5-A72E-4ECC-87DB-8E19F60B1A9C"", ""bug_type"" : ""309"", ""pid"" : 18203, ""procExitAbsTime"" : 85388942249967, ""cpuType"" : ""X86-64"", ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Volumes\/VOLUME\/*\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.5.0"",""CFBundleVersion"":""1.5.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""6AFAD35F-EE20-56D3-874B-BA84BCEB3FBA"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""D854A99D-C1C2-8C75-860D-7851247F6672"", ""wakeTime"" : 514, ""sleepWakeUUID"" : ""E99B8A3A-E023-4C70-BFCA-04BB86C782F5"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x2370b30a46c8 is not in any region. 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5220K 41 \nFoundation 16K 1 \nKernel Alloc Once 8K 1 \nMALLOC 442.3M 706 \nMALLOC guard page 32K 7 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nMach message 16K 2 \nObjC additional data 15K 1 \nOpenGL GLSL 384K 4 \nSTACK GUARD 148K 37 \nStack 146.8M 38 \nStack Guard 56.0M 1 \nVM_ALLOCATE 140.9M 127 \nVM_ALLOCATE (reserved) 96.0M 2 reserved VM address space (unallocated)\n__CTF 756 1 \n__DATA 50.4M 825 \n__DATA_CONST 31.2M 341 \n__DATA_DIRTY 1641K 213 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 697.8M 280 \n__TEXT 899.1M 804 \n__UNICODE 592K 1 \ndyld private memory 1280K 3 \nmapped file 187.1M 46 \nshared memory 2980K 27 \n=========== ======= ======= \nTOTAL 3.1G 3654 \nTOTAL, minus reserved VM space 2.6G 3654 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""60356660bbe37970735c5624"", ""factorPackIds"" : { }, ""deploymentId"" : 240000027 }, { ""rolloutId"" : ""5fc94383418129005b4e9ae0"", ""factorPackIds"" : { }, ""deploymentId"" : 240000562 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/jumping/Desktop/F1_20230106_MxR_Praktikum_Hemoglobin_Test_stepHCDMS2_Crosslinks_1,2.pb Failed opening file /Users/jumping/Desktop/F1_20230106_MxR_Praktikum_Hemoglobin_Test_stepHCDMS2_Crosslinks_1,2.pb: Line 0 ""#1/A:40@CA #2/B:2@CA "", got 0 atoms for spec ""#1/A:40@CA"", require exactly 1 > ui tool show XMAS > open /Users/jumping/Desktop/1g08.pdb 1g08.pdb title: Carbonmonoxy liganded bovine hemoglobin pH 5.0 [more info...] Chain information for 1g08.pdb #1 --- Chain | Description | UniProt A C | hemoglobin α chain | HBA_BOVIN B D | hemoglobin β chain | HBB_BOVIN Non-standard residues in 1g08.pdb #1 --- CMO — carbon monoxide HEM — protoporphyrin IX containing Fe (HEME) Peptide pair mapping of XlinkX evidence file: /Users/jumping/Desktop/F1_20230106_MxR_Praktikum_Hemoglobin_Test_stepHCDMS2_Crosslinks.txt Unique peptide pairs: 20 out of 20 Unique peptide pairs with pseudobonds: 20 Pseudobonds are stored in /Users/jumping/Desktop/F1_20230106_MxR_Praktikum_Hemoglobin_Test_stepHCDMS2_Crosslinks_1.pb Mapping information is stored in /Users/jumping/Desktop/F1_20230106_MxR_Praktikum_Hemoglobin_Test_stepHCDMS2_Crosslinks_1.tsv Please select pseudobonds ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-18.8.5 OpenGL renderer: Intel Iris Pro OpenGL Engine OpenGL vendor: Intel Inc. Python: 3.9.11 Locale: 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: MacBook Pro Model Identifier: MacBookPro11,4 Processor Name: Quad-Core Intel Core i7 Processor Speed: 2.2 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 476.0.0.0.0 OS Loader Version: 540.120.3~22 SMC Version (system): 2.29f24 Software: System Software Overview: System Version: macOS 12.6.2 (21G320) Kernel Version: Darwin 21.6.0 Time since boot: 7 days 22:21 Graphics/Displays: Intel Iris Pro: Chipset Model: Intel Iris Pro Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x0d26 Revision ID: 0x0008 Metal Family: Supported, Metal GPUFamily macOS 1 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2880 x 1800 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.1.0 Babel: 2.11.0 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.4 ChimeraX-AddH: 2.2.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.6 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.41.5 ChimeraX-AtomicLibrary: 8.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.4 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.5 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 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-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.8 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.8 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 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: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 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 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.7.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.24.3 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-XMAS: 1.1.2 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.4 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 et-xmlfile: 1.1.0 executing: 1.2.0 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.7.31 imagesize: 1.4.1 importlib-metadata: 5.1.0 ipykernel: 6.15.3 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 5.1.0 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.4 numpy: 1.23.1 openpyxl: 3.0.10 openvr: 1.23.701 packaging: 21.3 pandas: 1.5.2 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.2.0 pip: 22.2.2 pkginfo: 1.8.3 platformdirs: 2.5.4 prompt-toolkit: 3.0.33 psutil: 5.9.1 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 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: 2022.6 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.3.0 QtRangeSlider: 0.1.5 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.0 seaborn: 0.12.2 setuptools: 65.1.1 setuptools-scm: 7.0.5 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 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 stack-data: 0.6.2 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 typing-extensions: 4.4.0 urllib3: 1.26.13 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 zipp: 3.11.0 }}} " defect closed normal Core can't reproduce Tom Goddard r.a.scheltema@… all ChimeraX