id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7184 Crash in Qt event loop running AlphaFold prediction chimerax-bug-report@… Tom Goddard "{{{ 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. 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""rolloutId"" : ""5fc94383418129005b4e9ae0"", ""factorPackIds"" : { }, ""deploymentId"" : 240000385 }, { ""rolloutId"" : ""5ffde50ce2aacd000d47a95f"", ""factorPackIds"" : { }, ""deploymentId"" : 240000167 } ], ""experiments"" : [ ] } } ===== 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 Successfully installed 'SEQCROW==1.4.4' Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Collecting SEQCROW==1.4.4 Downloading https://cxtoolshed.rbvi.ucsf.edu/media/seqcrow/releases/1.4.4/SEQCROW-1.4.4-py3-none- any.whl (5.4 MB) Requirement already satisfied: psutil in ./ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from SEQCROW==1.4.4) (5.8.0) Requirement already satisfied: ChimeraX-Core=1.2 in ./ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from SEQCROW==1.4.4) (1.3) Requirement already satisfied: jinja2 in ./ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from SEQCROW==1.4.4) (3.0.1) Requirement already satisfied: Send2Trash in /Users/jaredford/Library/Application Support/ChimeraX/1.3/site-packages (from SEQCROW==1.4.4) (1.8.0) Requirement already satisfied: scipy in ./ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from SEQCROW==1.4.4) (1.7.1) Requirement already satisfied: MarkupSafe>=2.0 in ./ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from jinja2->SEQCROW==1.4.4) (2.0.1) Requirement already satisfied: numpy=1.16.5 in ./ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from scipy->SEQCROW==1.4.4) (1.21.2) Installing collected packages: SEQCROW Attempting uninstall: SEQCROW Found existing installation: SEQCROW 1.3.2 Uninstalling SEQCROW-1.3.2: Successfully uninstalled SEQCROW-1.3.2 Successfully installed SEQCROW-1.4.4 WARNING: Value for scheme.platlib does not match. Please report this to distutils: /Users/jaredford/Library/Application Support/ChimeraX/1.3/site- packages sysconfig: /Users/jaredford/Library/Python/3.9/lib/python/site-packages WARNING: Value for scheme.purelib does not match. Please report this to distutils: /Users/jaredford/Library/Application Support/ChimeraX/1.3/site- packages sysconfig: /Users/jaredford/Library/Python/3.9/lib/python/site-packages WARNING: Value for scheme.headers does not match. Please report this to distutils: /Users/jaredford/Library/Application Support/ChimeraX/include/python3.9/SEQCROW sysconfig: /Users/jaredford/Library/Python/3.9/include/SEQCROW WARNING: Value for scheme.scripts does not match. Please report this to distutils: /Users/jaredford/Library/Application Support/ChimeraX/bin sysconfig: /Users/jaredford/Library/Python/3.9/bin WARNING: Value for scheme.data does not match. Please report this to distutils: /Users/jaredford/Library/Application Support/ChimeraX sysconfig: /Users/jaredford/Library/Python/3.9 WARNING: Additional context: user = True home = None root = None prefix = None WARNING: Value for scheme.headers does not match. Please report this to distutils: /Users/jaredford/Library/Application Support/ChimeraX/include/python3.9/UNKNOWN sysconfig: /Users/jaredford/Library/Python/3.9/include/UNKNOWN WARNING: You are using pip version 21.2.4; however, version 22.1.2 is available. You should consider upgrading via the '/Users/jaredford/Desktop/ChimeraX-1.3.app/Contents/MacOS/ChimeraX -m pip install --upgrade pip' command. > open 1DNP 1dnp title: Structure of deoxyribodipyrimidine photolyase [more info...] Chain information for 1dnp #1 --- Chain | Description | UniProt A B | DNA photolyase | PHR_ECOLI Non-standard residues in 1dnp #1 --- FAD — flavin-adenine dinucleotide MHF — 5,10-methenyl-6,7,8-trihydrofolic acid 1dnp mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > ui tool show AlphaFold > alphafold predict #1/A Running AlphaFold prediction > open ""/Users/jaredford/Desktop/Chimera runs/Photolyase with alphafold > predict and R344K.cxs"" opened ChimeraX session Traceback (most recent call last): File ""/Users/jaredford/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py"", line 629, in changeEvent self.hide_floating_tools = self.isMinimized() File ""/Users/jaredford/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py"", line 734, in hide_floating_tools tw._mw_set_shown(True) File ""/Users/jaredford/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py"", line 2187, in _mw_set_shown self.__toolkit.shown = shown AttributeError: 'NoneType' object has no attribute 'shown' AttributeError: 'NoneType' object has no attribute 'shown' File ""/Users/jaredford/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py"", line 2187, in _mw_set_shown self.__toolkit.shown = shown See log for complete Python traceback. > hide #3 models > close #3 > close #2 > alphafold predict > TTHLVWFRQDLRLHDNLALAAACRNSSARVLALYIATPRQWATHNMSPRQAELINAQLNGLQIALAEKGIPLLFREVDDFVASVEIVKQVCAENSVTHLFYNYQYEVNERARDVEVERALRNVVCEGFDDSVILPPGAVMTGNHEMYKVFTPFKNAWLKRLREGMPECVAAPKVRSSGSIEPSPSITLNYPRQSFDTAHFPVEEKAAIAQLRQFCQNGAGEYEQQRDFPAVEGTSRLSASLATGGLSPRQCLHRLLAEQPQALDGGAGSVWLNELIWREFYRHLITYHPSLCKHRPFIAWTDRVQWQSNPAHLQAWQEGKTGYPIVDAAMRQLNSTGWMHNRLRMITASFLVKDLLIDWREGERYFMSQLIDGDLAANNGGWQWAASTGTDAAPYFRIFNPTTQGEKFDHEGEFIRQWLPELRDVPGKVVHEPWKWAQKAGVTLDYPQPIVEHKEARVQTLAAYEAARKGK Using the same data path for profile, may corrupt the data. Running AlphaFold prediction > ui tool show AlphaFold > alphafold predict #1/A Using the same data path for profile, may corrupt the data. Running AlphaFold prediction ===== 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 Back buffer dpr of 1 doesn't match <_NSViewBackingLayer: 0x7ff5e31f1860> contents scale of 2 - updating layer to match. Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x7ff5e31f1860> contents scale of 1 - updating layer to match. OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 OpenGL vendor: AppleHardware: 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: 21 days 11:25 Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: HISENSE: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 3840 x 2160 @ 30.00Hz Main Display: Yes Mirror: On Mirror Status: Master Mirror Online: Yes Automatically Adjust Brightness: Yes Television: Yes Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Mirror: On Mirror Status: Hardware Mirror Online: Yes Automatically Adjust Brightness: No Connection Type: Internal 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 Send2Trash: 1.8.0 SEQCROW: 1.4.4 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 Structure Prediction can't reproduce all ChimeraX