id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5796 Stack overflow, possibly due to screen locking nxb318@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19043 ChimeraX Version: 1.3.dev202109080319 (2021-09-08 03:19:35 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Windows fatal exception: stack overflow Thread 0x000024ac (most recent call first): File ""C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-packages\ChimeraX_main.py"", line 880 in init File ""C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-packages\ChimeraX_main.py"", line 1029 in File ""C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\runpy.py"", line 197 in _run_module_as_main Windows fatal exception: stack overflow Thread 0x000106c4 (most recent call first): File ""C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-packages\ChimeraX_main.py"", line 880 in init File ""C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\site-packages\ChimeraX_main.py"", line 1029 in File ""C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.3.dev202109080319\bin\lib\runpy.py"", line 197 in _run_module_as_main ===== Log before crash start ===== UCSF ChimeraX version: 1.3.dev202109080319 (2021-09-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > C:\\\Users\\\nxb318\\\Documents\\\EM_related\\\rGluK2-3m-domoic_acid_processing\\\FROM_EXX\\\cls5_relion\\\run_class001-zflip.mrc Opened run_class001-zflip.mrc as #1, grid size 420,420,420, pixel 1.06, shown at level 0.00715, step 2, values float32 > lighting soft > volume #1 step 1 > volume #1 level 0.01312 > ui tool show ""Hide Dust"" > surface dust #1 size 6.36 > open > C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls5_relion/Swissprot/swissmodel/cls5_LBDmonomer/models/02/model.pdb model.pdb title: SWISS-MODEL SERVER (https://swissmodel.expasy.org) cls5_LBD-monomer [more info...] Chain information for model.pdb #2 --- Chain | Description A B C D | No description available > material transparentCastShadows true > transparency 50 > open > C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls5_relion/model02_real_space_refined_007.pdb Chain information for model02_real_space_refined_007.pdb #3 --- Chain | Description A B C D | No description available > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > open 5kuf 5kuf title: GluK2EM with 2S,4R-4-methylglutamate [more info...] Chain information for 5kuf #4 --- Chain | Description | UniProt A hide #3 models hide #3 models > show #!2 models > hide #!2 models > show #3 models > open > C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls2_relion/model02_real_space_refined_008.pdb | Chain information for model02_real_space_refined_008.pdb #4 --- Chain | Description A B C D | No description available > hide #3 models > show #!2 models > hide #!2 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #!2 models > hide #!2 models > hide #4 models > show #3 models > hide #3 models > show #!2 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > hide #!2 models > show #3 models > hide #3 models > show #4 models > select #4/D:552 7 atoms, 6 bonds, 1 residue, 1 model selected > select #4/C:594 7 atoms, 7 bonds, 1 residue, 1 model selected > hide #4 models > open > C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_relion/run_class001-zflip.mrc Opened run_class001-zflip.mrc as #5, grid size 420,420,420, pixel 1.06, shown at level 0.00802, step 2, values float32 > open > C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls2_relion/run_class001-zflip.mrc Opened run_class001-zflip.mrc as #6, grid size 420,420,420, pixel 1.06, shown at level 0.00731, step 2, values float32 > open > C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls4_relion/run_class001-zflip.mrc Opened run_class001-zflip.mrc as #7, grid size 420,420,420, pixel 1.06, shown at level 0.00747, step 2, values float32 > open > C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls5_relion/run_class001-zflip.mrc Opened run_class001-zflip.mrc as #8, grid size 420,420,420, pixel 1.06, shown at level 0.00715, step 2, values float32 > volume #5 step 1 > volume #6 step 1 > volume #7 step 1 > volume #8 step 1 > volume #8 level 0.01312 > volume #7 level 0.01291 > volume #7 level 0.01447 > volume #6 level 0.01285 > volume #5 level 0.01196 > volume #5 level 0.01352 > volume #5 level 0.01609 > volume #5 level 0.01371 > volume #5 level 0.01573 > volume #6 level 0.01491 > volume #7 level 0.01563 > volume #8 level 0.0139 > ui tool show ""Hide Dust"" > surface dust #5 size 6.36 > surface dust #6 size 6.36 > surface dust #7 size 6.36 > surface dust #8 size 6.36 > volume #5 level 0.0149 div> > show #3 models > hide #3 models > show #3 models > hide #3 models > show #!4 models > hide #!4 models > show #3 models > select #3/B 6380 atoms, 6528 bonds, 806 residues, 1 model selected > color sel orange > select clear > hide #3 models > show #!4 models > hide #!4 models > show #!4 models > select #4/D:423@O 1 atom, 1 residue, 1 model selected > select clear > select #4/D 5932 atoms, 6062 bonds, 2 pseudobonds, 751 residues, 2 models selected > color (#!4 & sel) orange > select clear > select #4/B 5932 atoms, 6062 bonds, 2 pseudobonds, 751 residues, 2 models selected > color (#!4 & sel) #b1ff7dff > color (#!4 & sel) #aeff7cff > color (#!4 & sel) #92ff74ff > color (#!4 & sel) #88ff73ff > color (#!4 & sel) #85ff72ff > color (#!4 & sel) #80ff72ff > color (#!4 & sel) #6eff6eff > color (#!4 & sel) #6aff74ff > select clear > hide #!4 models > show #3 models > show #!4 models > hide #!4 models > show #!4 models > color #3 #ff0f0f > color #3 #ff8f06 > color #4 #fda000 > morph #3,4 Computed 51 frame morph #6 > coordset #6 1,51 > hide #!6 models > close #6 > show #3 models > hide #3 models > show #3 models > open > C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls1_init_model_real_space_refined_004_loops.pdb Chain information for cls1_init_model_real_space_refined_004_loops.pdb #6 --- Chain | Description A B C D | No description available > hide #3 models > cartoon hide #6 > show #6 target ab > style #6 sphere Changed 23744 atom styles > ui tool show ""Color Actions"" > color bychain > show #3 models > hide #6 models > show #6 models > hide #6 models > show #6 models > hide #6 models > show #6 models > hide #6 models > show #6 models > morph #4,6 Computed 51 frame morph #7 > coordset #7 1,51 > close #7 > close #4 > morph #3,6 Computed 51 frame morph #4 > coordset #4 1,51 > hide #!4 models > show #!4 models > hide #!4 models > show #3 models > hide #3 models > show #3 models > show #6 models > hide #3 models > hide #6 models > show #!4 models > surface dust #1 size 6.35 > surface dust #1 size 6.34 > surface dust #1 size 6.31 > show #!1 models > hide #!4 models > show #3 models > show #!4 models > hide #3 models > hide #!1 models > close #4 > close > open > C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls2_relion/run_class001-zflip.mrc Opened run_class001-zflip.mrc as #1, grid size 420,420,420, pixel 1.06, shown at level 0.00731, step 2, values float32 > volume #1 step 1 > volume #1 level 0.01222 > volume #1 level 0.01304 > open > C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls5_relion/cls5_monomer- > model02_real_space_refined_007.pdb Chain information for cls5_monomer-model02_real_space_refined_007.pdb #2 --- Chain | Description A B C D | No description available > material transparentCastShadows true > transparency 50 > hide #2 models > show #2 models > hide #!1 models > open > C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls4_relion/run_class001-zflip.mrc Opened run_class001-zflip.mrc as #3, grid size 420,420,420, pixel 1.06, shown at level 0.00747, step 2, values float32 > volume #3 step 1 > volume #3 level 0.01341 > select #2/C:585-625 331 atoms, 344 bonds, 41 residues, 1 model selected > show (sel-residues & sidechain) target ab > hide #2 models > show #!3 models > close #3 > open > C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls2_relion/model02_real_space_refined_008.pdb > C:/Users/nxb318/Documents/EM_related/rGluK2-3m-domoic_acid_processing/FROM_EXX/cls2_relion/run_class001-zflip.mrc Chain information for model02_real_space_refined_008.pdb #3 --- Chain | Description A B C D | No description available Opened run_class001-zflip.mrc as #4, grid size 420,420,420, pixel 1.06, shown at level 0.00731, step 2, values float32 > volume #4 step 1 > volume #4 level 0.01404 > volume #4 level 0.01614 > select #3:777-789 404 atoms, 400 bonds, 52 residues, 1 model selected > show (sel-residues & sidechain) target ab > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #!4 models ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.3.dev202109080319 (2021-09-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 3.3.0 NVIDIA 471.41 OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Dell Inc. Model: OptiPlex 7071 OS: Microsoft Windows 10 Pro (Build 19043) Memory: 34,140,291,072 MaxProcessMemory: 137,438,953,344 CPU: 8 Intel(R) Core(TM) i7-9700 CPU @ 3.00GHz 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: 2021.5.30 cftime: 1.5.0 chardet: 4.0.0 ChimeraX-AddCharge: 1.1.4 ChimeraX-AddH: 2.1.10 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.29.1 ChimeraX-AtomicLibrary: 4.1.4 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: 2.5.3 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: 2.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.4.1 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3.dev202109080319 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.4 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: 2.1.1 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: 2.0.1 ChimeraX-MDcrds: 2.5 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.1.1 ChimeraX-ModelPanel: 1.1 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: 2.6.1 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.1 ChimeraX-PDBMatrices: 1.0 ChimeraX-Phenix: 0.3 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 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: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.3 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 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: 1.12 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 comtypes: 1.1.10 cxservices: 1.1 cycler: 0.10.0 Cython: 0.29.23 decorator: 5.0.9 distlib: 0.3.1 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.4.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.20 imagecodecs: 2021.4.28 imagesize: 1.2.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 2.11.3 jupyter-client: 6.1.12 jupyter-core: 4.7.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 1.1.1 matplotlib: 3.4.2 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.6 networkx: 2.6.2 numexpr: 2.7.3 numpy: 1.21.0 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.2 pickleshare: 0.7.5 Pillow: 8.2.0 pip: 21.1.1 pkginfo: 1.7.0 prompt-toolkit: 3.0.20 psutil: 5.8.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.9.0 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: 22.2.1 qtconsole: 5.1.0 QtPy: 1.11.0 RandomWords: 0.3.0 requests: 2.25.1 scipy: 1.6.3 setuptools: 57.0.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.1.0 sortedcontainers: 2.4.0 Sphinx: 4.0.1 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 tables: 3.6.1 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.0 urllib3: 1.26.6 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.2 wheel-filename: 1.3.0 WMI: 1.5.1 }}} " defect closed normal Core can't reproduce Tom Goddard all ChimeraX