id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7050 Crash during color panel drag/drop chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.4rc202206032339 (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: Aborted Thread 0x0000000314eab000 (most recent call first): File ""/private/var/folders/39/nrw5njw91hlbgyqhplqwkqkw0000gn/T/AppTranslocation/83E4C07E-FD68-47CA-95C4-D7425C4700BA/d/ChimeraX-1.4-rc2022.06.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 316 in wait File ""/private/var/folders/39/nrw5njw91hlbgyqhplqwkqkw0000gn/T/AppTranslocation/83E4C07E-FD68-47CA-95C4-D7425C4700BA/d/ChimeraX-1.4-rc2022.06.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 574 in wait File ""/private/var/folders/39/nrw5njw91hlbgyqhplqwkqkw0000gn/T/AppTranslocation/83E4C07E-FD68-47CA-95C4-D7425C4700BA/d/ChimeraX-1.4-rc2022.06.03.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 1297 in run File 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\n__OBJC_RO 81.8M 1 \n__OBJC_RW 3136K 2 \n__TEXT 772.1M 659 \n__UNICODE 588K 1 \ndyld private memory 1184K 3 \nmapped file 5.3G 1099 \nshared memory 3144K 25 \nunshared pmap 10.5M 8 \n=========== ======= ======= \nTOTAL 9.2G 4438 \nTOTAL, minus reserved VM space 8.0G 4438 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""601d9415f79519000ccd4b69"", ""factorPackIds"" : { ""SIRI_TEXT_TO_SPEECH"" : ""622657ce37186c771d5404ad"" }, ""deploymentId"" : 240000416 }, { ""rolloutId"" : ""60356660bbe37970735c5624"", ""factorPackIds"" : { }, ""deploymentId"" : 240000027 }, { ""rolloutId"" : ""602ad4dac86151000cf27e46"", ""factorPackIds"" : { ""SIRI_DICTATION_ASSETS"" : ""61fb0e87c773c43cde3bb80e"" }, ""deploymentId"" : 240000305 }, { ""rolloutId"" : ""60da5e84ab0ca017dace9abf"", ""factorPackIds"" : { }, ""deploymentId"" : 240000008 }, { ""rolloutId"" : ""607844aa04477260f58a8077"", ""factorPackIds"" : { ""SIRI_MORPHUN_ASSETS"" : ""6103050cbfe6dc472e1c982a"" }, ""deploymentId"" : 240000066 }, { ""rolloutId"" : ""5fb4245a1bbfe8005e33a1e1"", ""factorPackIds"" : { }, ""deploymentId"" : 240000015 }, { ""rolloutId"" : ""5fc94383418129005b4e9ae0"", ""factorPackIds"" : { }, ""deploymentId"" : 240000370 }, { ""rolloutId"" : ""5ffde50ce2aacd000d47a95f"", ""factorPackIds"" : { }, ""deploymentId"" : 240000149 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.4rc202206032339 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/lisawilliams/Downloads/7ryc.pdb format pdb 7ryc.pdb title: Oxytocin receptor (otr) bound to oxytocin In complex with A heterotrimeric GQ protein [more info...] Chain information for 7ryc.pdb #1 --- Chain | Description | UniProt C | transducin β chain 1 | GBB1_HUMAN D | guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit γ-2, guanine nucleotide-binding protein G(I) subunit α-2, guanine nucleotide-binding protein G(S) subunit α isoforms short | E | SCFV16 | L | oxytocin | NEU1_HUMAN O | OT-R | OXYR_HUMAN Non-standard residues in 7ryc.pdb #1 --- MG — magnesium ion NH2 — amino group Alignment identifier is 1/L Alignment identifier is 1/O Alignment identifier is 1/D Alignment identifier is 1/C Alignment identifier is 1/E > select /D:11 5 atoms, 4 bonds, 1 residue, 1 model selected > select /D:11-1246 1973 atoms, 2008 bonds, 4 pseudobonds, 263 residues, 2 models selected > show sel surfaces > hide sel surfaces > hide sel cartoons > hide sel atoms > select /C:3 5 atoms, 4 bonds, 1 residue, 1 model selected > select /C:3-243 1727 atoms, 1760 bonds, 241 residues, 1 model selected > select /C:340 9 atoms, 8 bonds, 1 residue, 1 model selected > select /C:3-340 2442 atoms, 2487 bonds, 338 residues, 1 model selected > hide sel surfaces > hide sel cartoons > hide sel atoms > select /E:2 7 atoms, 6 bonds, 1 residue, 1 model selected > select /E:2-247 1695 atoms, 1739 bonds, 2 pseudobonds, 230 residues, 2 models selected > hide sel surfaces > hide sel cartoons > hide sel atoms > select /O:31 7 atoms, 7 bonds, 1 residue, 1 model selected > select /O:31-345 2097 atoms, 2153 bonds, 2 pseudobonds, 285 residues, 2 models selected > show sel cartoons > hide sel atoms > select /L:1 6 atoms, 5 bonds, 1 residue, 1 model selected > select /L:1-10 69 atoms, 71 bonds, 10 residues, 1 model selected > style sel stick Changed 69 atom styles > ui tool show ""Selection Inspector"" > color sel #f67670 atoms > color sel #f6756f atoms > color sel #f6726c atoms > color sel #f66e67 atoms > color sel #f66d66 atoms > color sel #f66b65 atoms > color sel #f66761 atoms > color sel #f6645e atoms > color sel #f6625c atoms > color sel #f6615a atoms > color sel #f65e58 atoms > color sel #f65d56 atoms > color sel #f65a55 atoms > color sel #f65a54 atoms > color sel #f65954 atoms > color sel #f65853 atoms > color sel #f65652 atoms > color sel #f65450 atoms > color sel #f6534f atoms > color sel #f6524e atoms > color sel #f6514e atoms > color sel #f6514d atoms > select /O:31-345 2097 atoms, 2153 bonds, 2 pseudobonds, 285 residues, 2 models selected > select /L:1-10 69 atoms, 71 bonds, 10 residues, 1 model selected > select /O:31-345 2097 atoms, 2153 bonds, 2 pseudobonds, 285 residues, 2 models selected > select /O:288-289 19 atoms, 20 bonds, 2 residues, 1 model selected > select /O:288-289 19 atoms, 20 bonds, 2 residues, 1 model selected > select /O:288-289 19 atoms, 20 bonds, 2 residues, 1 model selected > select > /O:35-67,74-102,108-143,149-168,170-174,195-235,273-299,308-316,320-332,334-345 1675 atoms, 1709 bonds, 225 residues, 1 model selected > select /O:288 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 14 atom styles > ui tool show ""Selection Inspector"" > color sel #f06858 atoms > color sel #f0675c atoms > color sel #f06866 atoms > color sel #f08399 atoms > color sel #f08eb0 atoms > color sel #f099c7 atoms > color sel #efa4f0 atoms > color sel #dda2f0 atoms > color sel #ba96f0 atoms > color sel #a78bf0 atoms > color sel #796cf0 atoms > color sel #655df0 atoms > color sel #4243f0 atoms > color sel #373ef0 atoms > color sel #2d3af0 atoms > color sel #2b39f0 atoms > color sel #293af0 atoms > color sel #283bf0 atoms > color sel #273bf0 atoms > color sel #283df0 atoms > color sel #2c43f0 atoms > color sel #2e46f0 atoms > color sel #3349f0 atoms > color sel #354bf0 atoms > color sel #354af0 atoms > color sel #364af0 atoms > color sel #374bf0 atoms > color sel #384bf0 atoms > color sel #3a4df0 atoms > color sel #3b4ef0 atoms > color sel #3c4ff0 atoms > color sel #3d50f0 atoms > color sel #4153f0 atoms > color sel #4354f0 atoms > color sel #4657f0 atoms > color sel #4658f0 atoms > color sel #4758f0 atoms > color sel #4759f0 atoms > color sel #495bf0 atoms > color sel #5061f0 atoms > color sel #5766f0 atoms > color sel #5b69f0 atoms > color sel #5c69f0 atoms > color sel #5c68f0 atoms > color sel #5e68f0 atoms > color sel #5f67f0 atoms > color sel #6066f0 atoms > color sel #6166f0 atoms > color sel #6266f0 atoms > color sel #6367f0 atoms > color sel #6468f0 atoms > color sel #6165f0 atoms > color sel #5e60f0 atoms > color sel #5858f0 atoms > color sel #5756f0 atoms > color sel #5755f0 atoms > color sel #5654f0 atoms > color sel #5754f0 atoms > color sel #5855f0 atoms > color sel #5c54f0 atoms > color sel #5e54f0 atoms > color sel #6254f0 atoms > color sel #6253f0 atoms > color sel #6254f0 atoms > color sel #6354f0 atoms > color sel #6554f0 atoms > color sel #6654f0 atoms > color sel #6853f0 atoms > color sel #6953f0 atoms > color sel #6853f0 atoms > color sel #6551f0 atoms > color sel #5a4af0 atoms > color sel #5547f0 atoms > color sel #5044f0 atoms > color sel #4c41f0 atoms > color sel #4b41f0 atoms > color sel #4b40f0 atoms > color sel #4a40f0 atoms > color sel #493ff0 atoms > select > /O:35-67,74-102,108-143,149-168,170-174,195-235,273-299,308-316,320-332,334-345 1675 atoms, 1709 bonds, 225 residues, 1 model selected > select /O:235 5 atoms, 4 bonds, 1 residue, 1 model selected > select /O:235 5 atoms, 4 bonds, 1 residue, 1 model selected > style sel stick Changed 5 atom styles > show sel atoms > style sel stick Changed 5 atom styles > style sel stick Changed 5 atom styles > show sel cartoons > show sel atoms > style sel sphere Changed 5 atom styles > style sel stick Changed 5 atom styles > ui tool show ""Selection Inspector"" > color sel #2d2794 atoms > color sel #342da9 atoms > color sel #3831b8 atoms > color sel #3a32be atoms > color sel #3d35c8 atoms > color sel #3f36ce atoms > color sel #4037d0 atoms > color sel #4037d2 atoms > color sel #4038d3 atoms > color sel #4138d3 atoms > color sel #4038d3 atoms > color sel #4038d2 atoms > select > /O:35-67,74-102,108-143,149-168,170-174,195-235,273-299,308-316,320-332,334-345 1675 atoms, 1709 bonds, 225 residues, 1 model selected > select add #1 8277 atoms, 8458 bonds, 9 pseudobonds, 1127 residues, 3 models selected > select subtract #1 1 model selected > select /O:318 5 atoms, 4 bonds, 1 residue, 1 model selected > select /O:318 5 atoms, 4 bonds, 1 residue, 1 model selected > style sel stick Changed 5 atom styles > show sel atoms > ui tool show ""Selection Inspector"" > color sel #4b41f7 atoms ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.4rc202206032339 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 OpenGL vendor: Apple 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 Air Model Identifier: MacBookAir10,1 Processor Name: Unknown Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache: 8 MB Memory: 8 GB Software: System Software Overview: System Version: macOS 12.2.1 (21D62) Kernel Version: Darwin 21.3.0 Time since boot: 34 days 9:56 Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 7 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina 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: 0.1.3 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: 1.4rc202206032339 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 }}} " defect closed normal Window Toolkit can't reproduce Tom Goddard all ChimeraX