id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6364 Qt6 shell tab-completion crash Eric Pettersen Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.15.7-x86_64-i386-64bit ChimeraX Version: 1.4.dev202203090340 (2022-03-09 03:40:10 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x0000700013450000 (most recent call first): File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py"", line 562 in select File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/asyncio/base_events.py"", line 1854 in _run_once File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/asyncio/base_events.py"", line 596 in run_forever File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/tornado/platform/asyncio.py"", line 199 in start File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ipykernel/iostream.py"", line 81 in _thread_main File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000070001244d000 (most recent call first): File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 312 in wait File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 574 in wait File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/IPython/core/history.py"", line 829 in run File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/IPython/core/history.py"", line 58 in needs_sqlite File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/decorator.py"", line 232 in fun File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Current thread 0x000000010eee5dc0 (most recent call first): File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/qtconsole/console_widget.py"", line 1696 in _get_block_plain_text File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/qtconsole/frontend_widget.py"", line 70 in highlightBlock File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/qtconsole/console_widget.py"", line 1089 in _fill_temporary_buffer File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/qtconsole/completion_html.py"", line 350 in _update_list File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/qtconsole/completion_html.py"", line 323 in show_items File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/qtconsole/console_widget.py"", line 1078 in _complete_with_items File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/qtconsole/jupyter_widget.py"", line 179 in _handle_complete_reply File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/qtconsole/base_frontend_mixin.py"", line 138 in _dispatch File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/qtconsole/inprocess.py"", line 46 in call_handlers File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/qtconsole/inprocess.py"", line 42 in File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 318 in event_loop File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 867 in init File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 1018 in File ""/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/Users/pett/src/chimerax/ChimeraX.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"":""2022-03-11 11:27:49.00 -0800"",""app_version"":""1.4.0"",""slice_uuid"":""2847c4a6-fa64-3ae9-8f1f-bf5e32542c6b"",""build_version"":""1.4.0.0"",""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":1,""is_first_party"":1,""bug_type"":""309"",""os_version"":""Mac OS X 10.15.7 (19H1715)"",""incident_id"":""D8F6A297-39B4-42B3-8876-F181575DC735"",""name"":""ChimeraX""} { ""uptime"" : 11000, ""procLaunch"" : ""2022-03-11 11:27:02.4600 -0800"", ""procRole"" : ""Foreground"", ""exception"" : { ""type"" : ""EXC_BAD_ACCESS"", ""signal"" : ""SIGSEGV"", ""subtype"" : ""KERN_INVALID_ADDRESS at 0x00000000"" }, ""userID"" : 501, ""modelCode"" : ""iMac16,2"", ""coalitionID"" : 370, ""osVersion"" : { ""train"" : ""Mac OS X 10.15.7"", ""build"" : ""19H1715"", ""releaseType"" : """" }, ""captureTime"" : ""2022-03-11 11:27:32.0281 -0800"", ""incident"" : ""D8F6A297-39B4-42B3-8876-F181575DC735"", ""pid"" : 2522, ""cpuType"" : ""X86-64"", ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Users\/USER\/*\/ChimeraX.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.4.0"",""CFBundleVersion"":""1.4.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""parentProc"" : ""tcsh"", ""parentPid"" : 597, ""coalitionName"" : ""com.apple.Terminal"", ""crashReporterKey"" : ""1001EC17-01AB-23EF-FBAF-2E1668FB0851"", ""responsiblePid"" : 494, ""responsibleProc"" : ""Terminal"", ""sip"" : ""enabled"", ""vmregioninfo"" : ""0 is not in any region. Bytes before following region: 4511379456\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 000000010ce63000-000000010ce67000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX"", ""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"":6249},""targeted"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":0},""warnings"":0}, ""threads"" : 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""\/Users\/USER\/*\/ChimeraX.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore"", ""name"" : ""QtWebEngineCore"" }, { ""size"" : 1064960, ""arch"" : ""x86_64"", ""path"" : ""\/Users\/USER\/*\/ChimeraX.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/zmq\/.dylibs\/libzmq.5.dylib"", ""name"" : ""libzmq.5.dylib"" }, { ""size"" : 20480, ""arch"" : ""x86_64"", ""path"" : ""\/Users\/USER\/*\/ChimeraX.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/lib-dynload\/select.cpython-39-darwin.so"", ""name"" : ""select.cpython-39-darwin.so"" } ], ""threadTriggered"" : { ""index"" : 0, ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } } } ===== Log before crash start ===== UCSF ChimeraX version: 1.4.dev202203090340 (2022-03-09) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show Shell Populating font family aliases took 263 ms. Replace uses of missing font family ""Monaco"" with one that exists to avoid this cost. ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.4.dev202203090340 (2022-03-09) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-14.7.22 OpenGL renderer: Intel(R) Iris(TM) Pro Graphics 6200 OpenGL vendor: Intel Inc. Locale: en_US.UTF-8 Qt version: PyQt6 6.2.2, Qt 6.2.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac16,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2.8 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 4 MB Memory: 16 GB Boot ROM Version: 428.60.3.0.0 SMC Version (system): 2.32f21 Software: System Software Overview: System Version: macOS 10.15.7 (19H1715) Kernel Version: Darwin 19.6.0 Time since boot: 3:20 Graphics/Displays: Intel Iris Pro Graphics 6200: Chipset Model: Intel Iris Pro Graphics 6200 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x1622 Revision ID: 0x000a Metal: Supported, feature set macOS GPUFamily1 v4 Displays: iMac: Display Type: LCD Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.5.30 cftime: 1.5.2 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 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: 1.36.2 ChimeraX-AtomicLibrary: 6.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.1 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: 1.5.1 ChimeraX-CommandLine: 1.2.1 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4.dev202203090340 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-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: 1.1.5 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: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.2 ChimeraX-ModelPanel: 1.3.2 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-NIHPresets: 1.0.5 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.8 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-Phenix: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 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: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.16.2 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 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: 0.29.26 debugpy: 1.5.1 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.29.1 funcparserlib: 1.0.0a0 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.26 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.9.2 kiwisolver: 1.3.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.0 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.4 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.0 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.0 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.28 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.7 PyQt6: 6.2.2 PyQt6-Qt6: 6.2.3 PyQt6-sip: 13.2.0 PyQt6-WebEngine: 6.2.1 PyQt6-WebEngine-Qt6: 6.2.3 python-dateutil: 2.8.2 pytz: 2021.3 pyzmq: 22.3.0 qtconsole: 5.2.2 QtPy: 2.0.1 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 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 suds-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.8 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect closed normal Window Toolkit duplicate all ChimeraX