Opened 3 years ago
Closed 3 years ago
#7519 closed defect (can't reproduce)
Mismatch between Cocoa and Carbon for virtual key
Reported by: | Owned by: | pett | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Window Toolkit | Version: | |
Keywords: | Cc: | Tom Goddard | |
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.4 (2022-06-03 23:39:42 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 0x000000010a779600 (most recent call first): File "/Users/gaojieyu/Desktop/ChimeraX-1.4.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/gaojieyu/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 870 in init File "/Users/gaojieyu/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1021 in File "/Users/gaojieyu/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code File "/Users/gaojieyu/Desktop/ChimeraX-1.4.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":"2022-08-26 17:36:13.00 -0400","app_version":"1.4.0","slice_uuid":"9596eff5-d2be-396c-9c4e-6177235c3dae","build_version":"1.4.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.5.1 (21G83)","incident_id":"6A14BF8A-1EB6-4565-B57B-745B3DEFE605","name":"ChimeraX"} { "uptime" : 150000, "procLaunch" : "2022-08-26 16:58:09.8860 -0400", "procRole" : "Foreground", "version" : 2, "userID" : 501, "deployVersion" : 210, "modelCode" : "MacBookPro16,2", "procStartAbsTime" : 149736125779739, "coalitionID" : 15712, "osVersion" : { "train" : "macOS 12.5.1", "build" : "21G83", "releaseType" : "User" }, "captureTime" : "2022-08-26 17:36:13.0722 -0400", "incident" : "6A14BF8A-1EB6-4565-B57B-745B3DEFE605", "bug_type" : "309", "pid" : 22184, "procExitAbsTime" : 151830921313291, "cpuType" : "X86-64", "procName" : "ChimeraX", "procPath" : "\/Users\/USER\/Desktop\/ChimeraX-1.4.app\/Contents\/MacOS\/ChimeraX", "bundleInfo" : {"CFBundleShortVersionString":"1.4.0","CFBundleVersion":"1.4.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"}, "storeInfo" : {"deviceIdentifierForVendor":"22E35AEF-2DED-58BB-8C3E-160F4F986DC6","thirdParty":true}, "parentProc" : "launchd", "parentPid" : 1, "coalitionName" : "edu.ucsf.cgl.ChimeraX", "crashReporterKey" : "D83B9353-741E-879B-0C74-F3B785A7F01E", "wakeTime" : 329, "bridgeVersion" : {"build":"19P6066","train":"6.6"}, "sleepWakeUUID" : "70FF21F1-5FC5-4DD3-AC44-3BB072DACEDB", "sip" : "enabled", "vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 140737486946280\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n VM_ALLOCATE 7fffffea8000-7fffffea9000 [ 4K] r-x\/r-x SM=ALI ", "isCorpse" : 1, "exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"}, "vmregioninfo" : "0x18 is not in any region. 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240000008 } ], "experiments" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/gaojieyu/Downloads/1i0z.pdb format pdb 1i0z.pdb title: Human heart L-lactate dehydrogenase H chain, ternary complex with nadh and oxamate [more info...] Chain information for 1i0z.pdb #1 --- Chain | Description | UniProt A B | LDH-B | LDHB_HUMAN Non-standard residues in 1i0z.pdb #1 --- NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH) OXM — oxamic acid > select /A/B 5522 atoms, 5292 bonds, 986 residues, 1 model selected > hide sel cartoons > hide sel atoms > select ::name="OXM" 12 atoms, 10 bonds, 2 residues, 1 model selected > show sel atoms > ui mousemode right zone > select sel : select sel : select sel : select /A-B:67 20 atoms, 20 bonds, 2 residues, 1 model selected > select /A-B:67 20 atoms, 20 bonds, 2 residues, 1 model selected > select sel : select sel : select /A/B 5522 atoms, 5292 bonds, 986 residues, 1 model selected > select sel : select sel : select ::name="OXM" 12 atoms, 10 bonds, 2 residues, 1 model selected > select sel : select /A-B:67 20 atoms, 20 bonds, 2 residues, 1 model selected > ui mousemode right select > ui mousemode right label > select sel : select clear > select ::name="OXM" 12 atoms, 10 bonds, 2 residues, 1 model selected > select sel : show sel atoms > select > /A-B:2-8,29-42,54-72,82-87,105-128,139-152,154-156,163-179,181-185,201-203,211-215,226-246,249-265,309-328 2782 atoms, 2808 bonds, 350 residues, 1 model selected > select /A-B:106 22 atoms, 20 bonds, 2 residues, 1 model selected > label delete residues > ui mousemode right select > select > /A-B:2-8,29-42,54-72,82-87,105-128,139-152,154-156,163-179,181-185,201-203,211-215,226-246,249-265,309-328 2782 atoms, 2808 bonds, 350 residues, 1 model selected > ui mousemode right select Drag select of 1 atoms > ui mousemode right distance > select clear Mismatch between Cocoa '\x0' and Carbon 'z' for virtual key 6 with QFlags(NoModifier) Mismatch between Cocoa '\x0' and Carbon 'Z' for virtual key 6 with QFlags(ShiftModifier) Mismatch between Cocoa '\x0' and Carbon 'z' for virtual key 6 with QFlags(ControlModifier) Mismatch between Cocoa '\x0' and Carbon 'Z' for virtual key 6 with QFlags(ShiftModifier|ControlModifier) Mismatch between Cocoa '\x0' and Carbon '\u03a9' for virtual key 6 with QFlags(AltModifier) Mismatch between Cocoa '\x0' and Carbon '\u00b8' for virtual key 6 with QFlags(ShiftModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\u03a9' for virtual key 6 with QFlags(ControlModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\u00b8' for virtual key 6 with QFlags(ShiftModifier|ControlModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with QFlags(MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with QFlags(ShiftModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with QFlags(ControlModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with QFlags(ShiftModifier|ControlModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with QFlags(AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with QFlags(ShiftModifier|AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with QFlags(ControlModifier|AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x1a' for virtual key 6 with QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier) Drag select of 1 atoms > ui mousemode right distance > ui mousemode right select > ui mousemode right distance > ui tool show Distances > distance /A:193@NE2 /A:402@O1 Distance between /A HIS 193 NE2 and OXM 402 O1: 2.818Å > save /Users/gaojieyu/Desktop/image14.png supersample 3 Drag select of 1 atoms Exactly two atoms must be selected! > select clear > undo Drag select of 1 atoms Exactly two atoms must be selected! Drag select of 1 atoms > distance /A:169@NH2 /A:402@O3 Distance between /A ARG 169 NH2 and OXM 402 O3: 2.948Å > ui mousemode right select Drag select of 1 atoms > distance /A:169@NH1 /A:402@O2 Distance between /A ARG 169 NH1 and OXM 402 O2: 2.908Å > select clear Drag select of 5 atoms, 5 bonds Drag select of 7 atoms, 7 bonds > hide sel atoms Drag select of 1 atoms > hide sel atoms Drag select of 1 atoms > hide sel atoms Drag select of 6 atoms, 6 bonds > hide sel atoms Drag select of 7 atoms, 6 bonds > hide sel atoms Drag select of 2 atoms, 1 bonds > hide sel atoms Drag select of 5 atoms, 4 bonds > hide sel atoms > save /Users/gaojieyu/Desktop/image15.png supersample 3 > undo > select clear Drag select of 7 atoms, 6 bonds > hide sel atoms Drag select of 7 atoms, 6 bonds > hide sel atoms Drag select of 1 atoms > hide sel atoms Drag select of 1 atoms > ui tool show H-Bonds > ui mousemode right distance Exactly two atoms must be selected! Drag select of 1 atoms Exactly two atoms must be selected! > ui mousemode right select > ui mousemode right distance Exactly two atoms must be selected! Drag select of 1 atoms > ui mousemode right distance Exactly two atoms must be selected! Drag select of 1 atoms > ui mousemode right distance > distance /B:412@O2 /B:169@NH1 Distance between /B OXM 412 O2 and ARG 169 NH1: 2.863Å Drag select of 1 atoms Exactly two atoms must be selected! > ui mousemode right select Drag select of 1 atoms Exactly two atoms must be selected! Drag select of 1 atoms > ui mousemode right distance Exactly two atoms must be selected! Drag select of 1 atoms Exactly two atoms must be selected! > ui mousemode right select Drag select of 1 atoms > distance /B:193@NE2 /B:412@O1 Distance between /B HIS 193 NE2 and OXM 412 O1: 2.781Å > ui mousemode right select Drag select of 1 atoms > distance /B:412@O3 /B:169@NH2 Distance between /B OXM 412 O3 and ARG 169 NH2: 2.838Å > select clear > save /Users/gaojieyu/Desktop/image16.png supersample 3 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/gaojieyu/Downloads/1i0z.pdb format pdb 1i0z.pdb title: Human heart L-lactate dehydrogenase H chain, ternary complex with nadh and oxamate [more info...] Chain information for 1i0z.pdb #1 --- Chain | Description | UniProt A B | LDH-B | LDHB_HUMAN Non-standard residues in 1i0z.pdb #1 --- NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH) OXM — oxamic acid OpenGL version: 4.1 INTEL-18.8.4 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine OpenGL vendor: Intel Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 512 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1731.140.2.0.0 (iBridge: 19.16.16066.0.0,0) OS Loader Version: 540.120.3~19 Software: System Software Overview: System Version: macOS 12.5.1 (21G83) Kernel Version: Darwin 21.6.0 Time since boot: 6 days 2:29 Graphics/Displays: Intel Iris Plus Graphics: Chipset Model: Intel Iris Plus Graphics Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x8a53 Revision ID: 0x0007 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) 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 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.10.8 cftime: 1.6.0 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: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.1 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 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: 2.2.4 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4 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: 1.1 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: 1.2 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: 1.1.1 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: 1.5.5 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-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.9 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 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: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.6 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: 1.1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.18.3 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: 1.1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.33.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 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: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.5 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: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 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: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 23.1.0 qtconsole: 5.3.0 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.2 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: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0
Change History (3)
comment:1 by , 3 years ago
Cc: | added |
---|---|
Component: | Unassigned → Window Toolkit |
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → Mismatch between Cocoa and Carbon for virtual key |
comment:2 by , 3 years ago
comment:3 by , 3 years ago
Resolution: | → can't reproduce |
---|---|
Status: | accepted → closed |
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