id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7995 Crash in color chooser afrance2@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.5.dev202206100131 (2022-06-10 01:31:06 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Aborted Thread 0x0000700016693000 (most recent call first): File ""/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 316 in wait File ""/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 574 in wait File ""/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 1297 in run File ""/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000070002a6d2000 (most recent call first): File 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\nFoundation 16K 1 \nKernel Alloc Once 8K 1 \nMALLOC 799.5M 978 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)\nMach message 16K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 228K 57 \nStack 481.9M 58 \nStack Guard 56.0M 1 \nVM_ALLOCATE 185.8M 166 \nVM_ALLOCATE (reserved) 128.0M 1 reserved VM address space (unallocated)\n__DATA 56.0M 660 \n__DATA_CONST 30.0M 340 \n__DATA_DIRTY 1621K 213 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 666.0M 142 \n__OBJC_RO 81.5M 1 \n__OBJC_RW 3120K 2 \n__TEXT 776.8M 662 \n__UNICODE 588K 1 \ndyld private memory 1184K 3 \nmapped file 188.4M 48 \nshared memory 2980K 27 \n=========== ======= ======= \nTOTAL 3.5G 3564 \nTOTAL, minus reserved VM space 3.3G 3564 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""601d9415f79519000ccd4b69"", ""factorPackIds"" : { ""SIRI_TEXT_TO_SPEECH"" : ""61ef3bd729647d394933a0a6"" }, ""deploymentId"" : 240000416 }, { ""rolloutId"" : ""602ad4dac86151000cf27e46"", ""factorPackIds"" : { ""SIRI_DICTATION_ASSETS"" : ""614a34c5eae97a2111628dc5"" }, ""deploymentId"" : 240000305 }, { ""rolloutId"" : ""60da5e84ab0ca017dace9abf"", ""factorPackIds"" : { }, ""deploymentId"" : 240000008 }, { ""rolloutId"" : ""607844aa04477260f58a8077"", ""factorPackIds"" : { ""SIRI_MORPHUN_ASSETS"" : ""6103050cbfe6dc472e1c982a"" }, ""deploymentId"" : 240000066 }, { ""rolloutId"" : ""60186475825c62000ccf5450"", ""factorPackIds"" : { }, ""deploymentId"" : 240000026 }, { ""rolloutId"" : ""60f8ddccefea4203d95cbeef"", ""factorPackIds"" : { }, ""deploymentId"" : 240000021 }, { ""rolloutId"" : ""5ffde50ce2aacd000d47a95f"", ""factorPackIds"" : { }, ""deploymentId"" : 240000215 }, { ""rolloutId"" : ""5fc94383418129005b4e9ae0"", ""factorPackIds"" : { }, ""deploymentId"" : 240000537 }, { ""rolloutId"" : ""5fb4245a1bbfe8005e33a1e1"", ""factorPackIds"" : { }, ""deploymentId"" : 240000020 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.5.dev202206100131 (2022-06-10) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/amandaghilardi/Desktop/orai/for Anh Tuan/AE-13/ae-13.mol2"" Summary of feedback from opening /Users/amandaghilardi/Desktop/orai/for Anh Tuan/AE-13/ae-13.mol2 --- warnings | line 10: ignoring section 'DICT' line 24893: bad substructure data line 24893: ignore unexpected line '1 UNK 1 GROUP 0 **** 0 ROOT' Chain information for Model of AAH15369.2 based on 7KR5 - prepared_A, 7KR5 - prepared_B, 7KR5 - prepared_C, 7KR5 - prepared_D, 7KR5 - prepared_E, 7KR5 - prepared_F-1 - prepared #1.1 --- Chain | Description A B C D E F | No description available Opened ae-13.mol2 containing 2 structures (11981 atoms, 12127 bonds) > set bgColor white > style stick Changed 11981 atom styles > show cartoons > hide protein > select #1.1/A 1992 atoms, 2016 bonds, 127 residues, 1 model selected > delete atoms sel > delete bonds sel > select #1.1/B 1990 atoms, 2014 bonds, 127 residues, 1 model selected > delete atoms sel > delete bonds sel > select #.12 Expected an objects specifier or a keyword > select #1.2 36 atoms, 38 bonds, 1 residue, 1 model selected > select sel : show sel > select clear > hide H > select protein 7963 atoms, 8059 bonds, 508 residues, 1 model selected > show sel surfaces > select #1.1/D 1990 atoms, 2014 bonds, 127 residues, 1 model selected > color (#!1.1 & sel) #fcfff4ff > color (#!1.1 & sel) #fdfff4ff > color (#!1.1 & sel) #fffff5ff > color (#!1.1 & sel) #fff7f2ff > color (#!1.1 & sel) #fff4f0ff > color (#!1.1 & sel) #ffebeaff > color (#!1.1 & sel) #ffe4e6ff > color (#!1.1 & sel) #ffdfe3ff > color (#!1.1 & sel) #ffdde2ff > color (#!1.1 & sel) #ffdce2ff > color (#!1.1 & sel) #ffd8e1ff > color (#!1.1 & sel) #ffd6e1ff > color (#!1.1 & sel) #ffcfddff > color (#!1.1 & sel) #ffcdddff > color (#!1.1 & sel) #ffccdcff > color (#!1.1 & sel) #ffc9dbff > color (#!1.1 & sel) #ffc5d9ff > color (#!1.1 & sel) #ffc2d7ff > color (#!1.1 & sel) #ffbfd6ff > color (#!1.1 & sel) #ffefffff > undo > color (#!1.1 & sel) #fff1ffff > color (#!1.1 & sel) #fff0ffff > color (#!1.1 & sel) #ffefffff > color (#!1.1 & sel) #ffedfeff > color (#!1.1 & sel) #ffecffff > color (#!1.1 & sel) #ffebffff > color (#!1.1 & sel) #ffeaffff > color (#!1.1 & sel) #ffe8ffff > color (#!1.1 & sel) #ffe7ffff > color (#!1.1 & sel) #ffe6ffff > color (#!1.1 & sel) #ffe3ffff > color (#!1.1 & sel) #ffe0feff > color (#!1.1 & sel) #ffdefeff > color (#!1.1 & sel) #ffdbfdff > color (#!1.1 & sel) #ffd8fdff > color (#!1.1 & sel) #ffd4fdff > color (#!1.1 & sel) #ffd3fdff > color (#!1.1 & sel) #ffd2fdff > color (#!1.1 & sel) #ffd0fdff > color (#!1.1 & sel) #ffcdfdff > color (#!1.1 & sel) #ffc9fdff > color (#!1.1 & sel) #ffc6feff > color (#!1.1 & sel) #ffc3feff > color (#!1.1 & sel) #ffc2feff > color (#!1.1 & sel) #ffc0feff > color (#!1.1 & sel) #ffbffeff > color (#!1.1 & sel) #ffbdfeff > color (#!1.1 & sel) #ffbcfeff > color (#!1.1 & sel) #ffb9feff > color (#!1.1 & sel) #ffb6feff > color (#!1.1 & sel) #ffb1fdff > color (#!1.1 & sel) #ffaffdff > color (#!1.1 & sel) #ffaefdff > color (#!1.1 & sel) #ffaefcff > color (#!1.1 & sel) #ffb0faff > color (#!1.1 & sel) #ffb3f8ff > color (#!1.1 & sel) #ffb6f7ff > color (#!1.1 & sel) #ffb9f6ff > color (#!1.1 & sel) #ffbbf6ff > color (#!1.1 & sel) #ffbbf5ff > color (#!1.1 & sel) #ffbcf5ff > color (#!1.1 & sel) #ffbcf4ff > color (#!1.1 & sel) #ffbdf4ff > color (#!1.1 & sel) #ffbef3ff > color (#!1.1 & sel) #ffbff3ff > color (#!1.1 & sel) #ffc0f2ff > color (#!1.1 & sel) #ffc1f1ff > color (#!1.1 & sel) #ffc3f0ff > color (#!1.1 & sel) #ffc5f0ff > color (#!1.1 & sel) #ffc6efff > color (#!1.1 & sel) #ffc7eeff > color (#!1.1 & sel) #ffc8edff > color (#!1.1 & sel) #ffc8ecff > color (#!1.1 & sel) #ffc8ebff > color (#!1.1 & sel) #ffc8eaff > color (#!1.1 & sel) #ffc9e7ff > color (#!1.1 & sel) #ffcae2ff > color (#!1.1 & sel) #ffcae1ff > color (#!1.1 & sel) #ffcae0ff > color (#!1.1 & sel) #ffcae1ff ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.5.dev202206100131 (2022-06-10) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-4.7.29 OpenGL renderer: AMD Radeon Pro 5500 XT OpenGL Engine OpenGL vendor: ATI Technologies 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: iMac Model Identifier: iMac20,1 Processor Name: 8-Core Intel Core i7 Processor Speed: 3.8 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 1715.40.15.0.0 (iBridge: 19.16.10549.0.0,0) OS Loader Version: 540.40.4~45 Software: System Software Overview: System Version: macOS 12.0.1 (21A559) Kernel Version: Darwin 21.1.0 Time since boot: 17:09 Graphics/Displays: AMD Radeon Pro 5500 XT: Chipset Model: AMD Radeon Pro 5500 XT Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 8 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0041 ROM Revision: 113-D3220I-231 VBIOS Version: 113-D322A1XT-011 Option ROM Version: 113-D322A1XT-011 EFI Driver Version: 01.01.231 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: iMac: Display Type: Built-In Retina LCD Resolution: Retina 5K (5120 x 2880) 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 build: 0.7.0 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: 1.39.2 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: 1.2 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: 1.5.2 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.5.dev202206100131 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: 1.1.6 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: 2.2 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-RenumberResidues: 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: 2.6.2 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: 1.20.4 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 MolecularDynamicsViewer: 1.4 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 pep517: 0.12.0 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 tomli: 2.0.1 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 feedback normal Platform Tom Goddard all ChimeraX