id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8356 Crash in event loop chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x000070000e71d000 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 316 in wait File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 574 in wait File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 1284 in run File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Current thread 0x00007ff8471d64c0 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 301 in event_loop File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 867 in init File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 1018 in File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/Applications/ChimeraX-1.3.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"":""2023-01-23 12:56:56.00 +0100"",""app_version"":""1.3.0"",""slice_uuid"":""9596eff5-d2be-396c-9c4e-6177235c3dae"",""build_version"":""1.3.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 13.0.1 (22A400)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""C3911FB0-6ABD-4C72-8B49-AC76A85076EF""} { ""uptime"" : 11000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 2094024781, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro15,1"", ""coalitionID"" : 510, ""osVersion"" : { ""train"" : ""macOS 13.0.1"", ""build"" : ""22A400"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2023-01-23 12:56:43.6013 +0100"", ""incident"" : ""C3911FB0-6ABD-4C72-8B49-AC76A85076EF"", ""pid"" : 51623, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2023-01-23 12:56:17.6016 +0100"", ""procStartAbsTime"" : 11773825673764, ""procExitAbsTime"" : 11799819381853, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.3.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.3.0"",""CFBundleVersion"":""1.3.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""867BEA85-3F23-570E-9E73-07F114627557"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""4C88F093-0D3B-643F-5D86-B4144A026E00"", ""bridgeVersion"" : {""build"":""20P420"",""train"":""7.0""}, ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x27 is not in any region. 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\n__LINKEDIT 274.0M 135 \n__OBJC_RO 65.1M 1 \n__OBJC_RW 1982K 2 \n__TEXT 865.2M 730 \ndyld private memory 256K 1 \nmapped file 404.7M 59 \nshared memory 3512K 30 \n=========== ======= ======= \nTOTAL 3.5G 3238 \nTOTAL, minus reserved VM space 3.0G 3238 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""62699e1ec1ff2978b47f6c3b"", ""factorPackIds"" : { ""SIRI_FIND_MY_CONFIGURATION_FILES"" : ""631f72d1de559130376df1fb"" }, ""deploymentId"" : 240000023 }, { ""rolloutId"" : ""60da5e84ab0ca017dace9abf"", ""factorPackIds"" : { }, ""deploymentId"" : 240000008 } ], ""experiments"" : [ ] }, ""reportNotes"" : [ ""dyld_process_snapshot_create_for_process failed with 5"" ] } ===== Log before crash start ===== UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/au627181/Dropbox/ncr1_shared/manuscript_pH_changes/final_models/1.NCR1-GDN-5.5/Figure1c.cxc > open 1.NCR1-GDN_55_ed_real_space_refined_005.pdb Chain information for 1.NCR1-GDN_55_ed_real_space_refined_005.pdb #1 --- Chain | Description A | No description available > set bgColor white > hide ligand > hide atoms > lighting soft > select #1:1-279 3980 atoms, 4039 bonds, 259 residues, 1 model selected > color sel medium blue > select #1:308-336 456 atoms, 461 bonds, 29 residues, 1 model selected > color sel cadet blue > select #1:337-369 #1:558-735 3297 atoms, 3329 bonds, 204 residues, 1 model selected > color sel orange > select #1:370-389 #1:800-991 3344 atoms, 3399 bonds, 212 residues, 1 model selected > color sel forest green > select #1:390-557 #1:774-799 3124 atoms, 3166 bonds, 194 residues, 1 model selected > color sel yellow > select #1:736-748 236 atoms, 239 bonds, 13 residues, 1 model selected > color sel dark cyan > select #1:749-773 #1:992-1156 3091 atoms, 3121 bonds, 190 residues, 1 model selected > color sel tan > open > /Users/au627181/Dropbox/ncr1_shared/manuscript_pH_changes/final_models/1.NCR1-GDN-5.5/cryosparc_P324_J508_007_volume_map_sharp.mrc Opened cryosparc_P324_J508_007_volume_map_sharp.mrc as #2, grid size 250,250,250, pixel 1.07, shown at level 0.257, step 1, values float32 > volume #2 level 0.4637 > surface dust #2 size 10.7 > ui tool show ""Color Zone"" > color zone #2 near #1 distance 6.43 executed Figure1c.cxc > open > ""/Users/au627181/Dropbox/ncr1_shared/manuscript_pH_changes/figures_v2/fig1/Figure > 1A-B.cxs"" opened ChimeraX session ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/au627181/Dropbox/ncr1_shared/manuscript_pH_changes/final_models/1.NCR1-GDN-5.5/Figure1c.cxc > open 1.NCR1-GDN_55_ed_real_space_refined_005.pdb Chain information for 1.NCR1-GDN_55_ed_real_space_refined_005.pdb #1 --- Chain | Description A | No description available > set bgColor white > hide ligand > hide atoms > lighting soft > select #1:1-279 3980 atoms, 4039 bonds, 259 residues, 1 model selected > color sel medium blue > select #1:308-336 456 atoms, 461 bonds, 29 residues, 1 model selected > color sel cadet blue > select #1:337-369 #1:558-735 3297 atoms, 3329 bonds, 204 residues, 1 model selected > color sel orange > select #1:370-389 #1:800-991 3344 atoms, 3399 bonds, 212 residues, 1 model selected > color sel forest green > select #1:390-557 #1:774-799 3124 atoms, 3166 bonds, 194 residues, 1 model selected > color sel yellow > select #1:736-748 236 atoms, 239 bonds, 13 residues, 1 model selected > color sel dark cyan > select #1:749-773 #1:992-1156 3091 atoms, 3121 bonds, 190 residues, 1 model selected > color sel tan > open > /Users/au627181/Dropbox/ncr1_shared/manuscript_pH_changes/final_models/1.NCR1-GDN-5.5/cryosparc_P324_J508_007_volume_map_sharp.mrc Opened cryosparc_P324_J508_007_volume_map_sharp.mrc as #2, grid size 250,250,250, pixel 1.07, shown at level 0.257, step 1, values float32 > volume #2 level 0.4637 > surface dust #2 size 10.7 > ui tool show ""Color Zone"" > color zone #2 near #1 distance 6.43 executed Figure1c.cxc OpenGL version: 4.1 ATI-4.9.48 OpenGL renderer: AMD Radeon Pro 555X OpenGL Engine OpenGL vendor: ATI Technologies Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro15,1 Processor Name: 6-Core Intel Core i7 Processor Speed: 2,2 GHz Number of Processors: 1 Total Number of Cores: 6 L2 Cache (per Core): 256 KB L3 Cache: 9 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1916.40.8.0.0 (iBridge: 20.16.420.0.0,0) OS Loader Version: 564.40.4~27 Software: System Software Overview: System Version: macOS 13.0.1 (22A400) Kernel Version: Darwin 22.1.0 Time since boot: 3 hours, 18 minutes Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0000 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 Radeon Pro 555X: Chipset Model: Radeon Pro 555X Type: GPU Bus: PCIe PCIe Lane Width: x8 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x67ef Revision ID: 0x00e3 ROM Revision: 113-C980AL-075 VBIOS Version: 113-C97501P-005 EFI Driver Version: 01.A1.075 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2880 x 1800 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL U2412M: Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: Y1H5T2AQ098L Mirror: Off Online: Yes Rotation: Supported Adapter Type: Analog VGA or Analog Over DVI-I 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: 2021.5.30 cftime: 1.5.1.1 charset-normalizer: 2.0.9 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 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: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 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 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 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: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 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 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6.1 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: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.7 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 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: 0.4.4 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.8.0 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.3 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 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 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 }}} " defect closed normal Core can't reproduce all ChimeraX