id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5350 faulthandler tracebacks with no ChimeraX crash goddard@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19041 ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC) Description While testing the Open file dialog to see if faulthandler would save any tracebacks while using it, I got other event_loop tracebacks saved in the file that appear unrelated to the open file dialog. I got 3 of these tracebacks in about 10 minutes. They seemed spontaneous. The first one I had left the computer for 5 miniutes and came back it was there, and the next two also arrived after leaving the computer for 5 minutes. Log: UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 3dwt format mmcif fromDatabase pdb 3dwt title: Structure of CabBCII-10 nanobody [more info...] Chain information for 3dwt #1 --- Chain | Description A B C D E F G H | cAbBCII-10 Non-standard residues in 3dwt #1 --- GOL — glycerol (glycerin; propane-1,2,3-triol) 3dwt mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 3| author_and_software_defined_assembly 4| author_and_software_defined_assembly 5| author_and_software_defined_assembly 6| author_and_software_defined_assembly 7| author_and_software_defined_assembly 8| author_and_software_defined_assembly > info path system versioned config directory: C:\ProgramData\UCSF\ChimeraX\1.2 system versioned data directory: C:\ProgramData\UCSF\ChimeraX\1.2 system unversioned config directory: C:\ProgramData\UCSF\ChimeraX system unversioned data directory: C:\ProgramData\UCSF\ChimeraX user versioned cache directory: C:\Users\goddard\AppData\Local\UCSF\ChimeraX\Cache\1.2 user versioned config directory: C:\Users\goddard\AppData\Local\UCSF\ChimeraX\1.2 user versioned data directory: C:\Users\goddard\AppData\Local\UCSF\ChimeraX\1.2 user versioned log directory: C:\Users\goddard\AppData\Local\UCSF\ChimeraX\1.2\Logs user versioned state directory: C:\Users\goddard\AppData\Local\UCSF\ChimeraX\1.2 user unversioned cache directory: C:\Users\goddard\AppData\Local\UCSF\ChimeraX\Cache user unversioned config directory: C:\Users\goddard\AppData\Local\UCSF\ChimeraX user unversioned data directory: C:\Users\goddard\AppData\Local\UCSF\ChimeraX user unversioned log directory: C:\Users\goddard\AppData\Local\UCSF\ChimeraX\Logs user unversioned state directory: C:\Users\goddard\AppData\Local\UCSF\ChimeraX > open ""C:/Users/goddard/Desktop/laptop manual.pdf"" Unrecognized file suffix '.pdf' > open D:/vrdemos/opioids-vr-2018/pdbs/carfentanil-muor.pdb Summary of feedback from opening D:/vrdemos/opioids-vr-2018/pdbs/carfentanil- muor.pdb --- warnings | Ignored bad PDB record found on line 4 HELIX 1 1 MET A 65 ARG A 95 1 Generated by MOE 31 Ignored bad PDB record found on line 5 HELIX 2 2 ALA A 102 THR A 118 1 Generated by MOE 17 Ignored bad PDB record found on line 6 HELIX 3 3 LEU A 121 LEU A 129 1 Generated by MOE 9 Ignored bad PDB record found on line 7 HELIX 4 4 GLY A 136 CYS A 170 1 Generated by MOE 35 Ignored bad PDB record found on line 8 HELIX 5 5 PRO A 172 PHE A 178 1 Generated by MOE 7 22 messages similar to the above omitted Chain information for carfentanil-muor.pdb #2 --- Chain | Description A | No description available B | No description available > open C:/Users/goddard/Desktop/test2/emd_1080.map Opened emd_1080.map as #3, grid size 100,100,100, pixel 2.7, shown at level 1.68, step 1, values float32 > open C:/Users/goddard/Desktop/test3/emd_1080.map Opened emd_1080.map as #4, grid size 100,100,100, pixel 2.7, shown at level 1.68, step 1, values float32 > open E:/ForTom/r12c09f01p01-ch1sk1fk1fl1.tiff Opened r12c09f01p01-ch1sk1fk1fl1.tiff as #5, grid size 1080,1080,1, pixel 1, shown at step 1, values uint16 > open E:/ForTom/r12c09f01p01-ch1sk3fk1fl1.tiff Opened r12c09f01p01-ch1sk3fk1fl1.tiff as #6, grid size 1080,1080,1, pixel 1, shown at step 1, values uint16 > open C:/Users/goddard/Desktop/vrdemos/milk-oct2019/casein-beta.pdb Chain information for casein-beta.pdb #7 --- Chain | Description A | No description available QWindowsNativeFileDialogBase::shellItem : Unhandled scheme: ""data"" > open C:/Users/goddard/Desktop/vrdemos/milk-oct2019/casein-beta3.pdb Chain information for casein-beta3.pdb #8 --- Chain | Description A | No description available > open C:/Users/goddard/Desktop/vrdemos/milk-oct2019/pdbtojson.py~ Unrecognized file suffix '.py~' OpenGL version: 3.3.0 NVIDIA 398.35 OpenGL renderer: GeForce GTX 1070 with Max-Q Design/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Micro-Star International Co., Ltd. Model: GS65 Stealth Thin 8RF OS: Microsoft Windows 10 Pro (Build 19041) Memory: 34,195,668,992 MaxProcessMemory: 137,438,953,344 CPU: 12 Intel(R) Core(TM) i7-8750H CPU @ 2.20GHz OSLanguage: en-US Locale: ('en_US', 'cp1252') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.12.5 cftime: 1.5.0 chardet: 3.0.4 ChimeraX-AddCharge: 1.0.1 ChimeraX-AddH: 2.1.6 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.13.2 ChimeraX-AtomicLibrary: 3.1.3 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.5.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-Clipper: 0.16.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.2.1 ChimeraX-CommandLine: 1.1.4 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.5 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.1.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.3 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: 1.0 ChimeraX-Hbonds: 2.1 ChimeraX-Help: 1.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.0.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.2.1 ChimeraX-MDcrds: 2.2 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.3 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.0.1 ChimeraX-ModelPanel: 1.0.1 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: 2.0.1 ChimeraX-OpenCommand: 1.5 ChimeraX-PDB: 2.4.1 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.1 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.0.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.4 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.3.1 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: 1.0.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.7.6 ChimeraX-uniprot: 2.1 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 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: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.21 decorator: 5.0.9 distlib: 0.3.1 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.17 imagecodecs: 2020.5.30 imagesize: 1.2.0 ipykernel: 5.3.4 ipython: 7.18.1 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.7 jupyter-core: 4.7.1 kiwisolver: 1.3.1 line-profiler: 2.1.2 lxml: 4.6.2 lz4: 3.1.0 MarkupSafe: 2.0.1 matplotlib: 3.3.2 msgpack: 1.0.0 netCDF4: 1.5.4 networkx: 2.5 numexpr: 2.7.3 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.9 ParmEd: 3.2.0 parso: 0.7.1 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 21.0.1 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.18 psutil: 5.7.2 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.7.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 pywin32: 228 pyzmq: 22.0.3 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 setuptools: 50.3.2 sfftk-rw: 0.6.7.dev1 six: 1.15.0 snowballstemmer: 2.1.0 sortedcontainers: 2.2.2 Sphinx: 3.2.1 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 tables: 3.6.1 tifffile: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.0 wheel-filename: 1.3.0 WMI: 1.5.1 File attachment: crash_traceback.txt }}} [attachment:""crash_traceback.txt""] " defect closed normal Platform not a bug Eric Pettersen Greg Couch all ChimeraX