id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16342 Crash moving window between screens chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.1-arm64-arm-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x00000001f7807840 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, 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} ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/gzl289/Desktop/Tom_Lab/Phenix/Xenopus_MCM/RealSpaceRefine_15/MCM_DH_combined_real_space_refined_015.cif Summary of feedback from opening /Users/gzl289/Desktop/Tom_Lab/Phenix/Xenopus_MCM/RealSpaceRefine_15/MCM_DH_combined_real_space_refined_015.cif --- warnings | Skipping chem_comp category: Missing column 'type' on line 2782 Missing entity information. Treating each chain as a separate entity. Bad residue range for struct_conf ""8"" on line 160 Bad residue range for struct_conf ""9"" on line 161 Bad residue range for struct_conf ""10"" on line 162 Bad residue range for struct_conf ""11"" on line 163 Bad residue range for struct_conf ""12"" on line 164 203 messages similar to the above omitted Invalid sheet range for struct_sheet_range ""2 1"" on line 2547 Invalid sheet range for struct_sheet_range ""3 1"" on line 2548 Invalid sheet range for struct_sheet_range ""4 1"" on line 2549 Invalid sheet range for struct_sheet_range ""5 1"" on line 2550 Invalid sheet range for struct_sheet_range ""6 1"" on line 2551 141 messages similar to the above omitted Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for MCM_DH_combined_real_space_refined_015.cif #1 --- Chain | Description A M | No description available B N | No description available C O | No description available D P | No description available E Q | No description available F R | No description available G S | No description available H T | No description available I U | No description available J V | No description available K W | No description available L X | No description available > hide atoms > show cartoons > open > /Users/gzl289/Desktop/Tom_Lab/Phenix/Xenopus_MCM/RealSpaceRefine_15/MCM_DH_combined_real_space_refined_015.pdb Chain information for MCM_DH_combined_real_space_refined_015.pdb #2 --- Chain | Description A M | No description available B N | No description available C O | No description available D P | No description available E Q | No description available F R | No description available G S | No description available H T | No description available I U | No description available J V | No description available K W | No description available L X | No description available > hide atoms > show cartoons > hide #!1 models > set bgColor white > open > /Users/gzl289/Desktop/Tom_Lab/Phenix/Xenopus_MCM/cryosparc_P49_J1555_005_volume_map_C1.mrc Opened cryosparc_P49_J1555_005_volume_map_C1.mrc as #3, grid size 512,512,512, pixel 0.928, shown at level 0.0752, step 2, values float32 > surface dust #3 size 9.28 > volume #3 level 0.2212 > transparency 50 > color zone #3 near #2 distance 5.57 > transparency 0 > transparency 50 > volume #3 level 0.1628 > color zone #3 near #2 distance 5.57 > transparency 0 > transparency 50 > ui tool show ""Color Zone"" Need to color zone map before it can be split > color zone #3 near #2 distance 5.04 > volume splitbyzone #3 Opened cryosparc_P49_J1555_005_volume_map_C1.mrc 0 as #4.1, grid size 512,512,512, pixel 0.928, shown at level 0.163, step 1, values float32 Opened cryosparc_P49_J1555_005_volume_map_C1.mrc 1 as #4.2, grid size 512,512,512, pixel 0.928, shown at level 0.163, step 1, values float32 Opened cryosparc_P49_J1555_005_volume_map_C1.mrc 2 as #4.3, grid size 512,512,512, pixel 0.928, shown at level 0.163, step 1, values float32 Opened cryosparc_P49_J1555_005_volume_map_C1.mrc 3 as #4.4, grid size 512,512,512, pixel 0.928, shown at level 0.163, step 1, values float32 Opened cryosparc_P49_J1555_005_volume_map_C1.mrc 4 as #4.5, grid size 512,512,512, pixel 0.928, shown at level 0.163, step 1, values float32 Opened cryosparc_P49_J1555_005_volume_map_C1.mrc 5 as #4.6, grid size 512,512,512, pixel 0.928, shown at level 0.163, step 1, values float32 Opened cryosparc_P49_J1555_005_volume_map_C1.mrc 6 as #4.7, grid size 512,512,512, pixel 0.928, shown at level 0.163, step 1, values float32 Opened cryosparc_P49_J1555_005_volume_map_C1.mrc 7 as #4.8, grid size 512,512,512, pixel 0.928, shown at level 0.163, step 1, values float32 Opened cryosparc_P49_J1555_005_volume_map_C1.mrc 8 as #4.9, grid size 512,512,512, pixel 0.928, shown at level 0.163, step 1, values float32 Opened cryosparc_P49_J1555_005_volume_map_C1.mrc 9 as #4.10, grid size 512,512,512, pixel 0.928, shown at level 0.163, step 1, values float32 Opened cryosparc_P49_J1555_005_volume_map_C1.mrc 10 as #4.11, grid size 512,512,512, pixel 0.928, shown at level 0.163, step 1, values float32 Opened cryosparc_P49_J1555_005_volume_map_C1.mrc 11 as #4.12, grid size 512,512,512, pixel 0.928, shown at level 0.163, step 1, values float32 Opened cryosparc_P49_J1555_005_volume_map_C1.mrc 12 as #4.13, grid size 512,512,512, pixel 0.928, shown at level 0.163, step 1, values float32 > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #2 models > hide #!4 models > show #!4 models > hide #!4.1 models > hide #!4.2 models > hide #!4.3 models > hide #!4.4 models > hide #!4.5 models > hide #!4.6 models > hide #!4.8 models > hide #!4.7 models > hide #!4.9 models > hide #!4.10 models > hide #!4.11 models > hide #!4.12 models > show #!4.12 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!4.12 models > show #2 models > hide #2 models > show #2 models > hide #!4 models > show #!4.1 models > hide #!4.1 models > show #!4.1 models > hide #2 models > volume #4.1 level 0.1638 > show #!4.2 models > hide #!4.2 models > show #!4.2 models > show #!4.3 models > hide #!4.3 models > show #!4.3 models > view > ui tool show ""Side View"" > show #!4.4 models > hide #!4.4 models > show #!4.4 models > view > surface dust #4.1 size 9.28 > surface dust #4.2 size 9.28 > surface dust #4.3 size 9.28 > surface dust #4.4 size 9.28 > surface dust #4.13 size 9.28 > show #!4.5 models > hide #!4.5 models > show #!4.5 models > show #!4.6 models > hide #!4.6 models > show #!4.6 models > hide #!4.6 models > show #2 models > hide #2 models > show #2 models > hide #!4.2 models > hide #!4.1 models > show #!4.1 models > hide #!4.3 models > hide #!4.4 models > hide #!4.5 models > hide #!4.13 models > lighting shadows false > graphics silhouettes true > lighting flat > graphics silhouettes false > graphics silhouettes true > lighting soft > graphics silhouettes false > graphics silhouettes true > show #!3 models > transparency #3.1#4.1.1 0 > transparency #3.1#4.1.1 50 ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M3 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac15,6 Model Number: MRX33DK/A Chip: Apple M3 Pro Total Number of Cores: 11 (5 performance and 6 efficiency) Memory: 18 GB System Firmware Version: 11881.41.5 OS Loader Version: 11881.41.5 Software: System Software Overview: System Version: macOS 15.1 (24B83) Kernel Version: Darwin 24.1.0 Time since boot: 17 hours, 35 minutes Graphics/Displays: Apple M3 Pro: Chipset Model: Apple M3 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL E2725H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 biopython: 1.83 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PhenixUI: 1.3.7 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 DiffFit: 0.6.2 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 fsspec: 2024.10.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 mpmath: 1.3.0 mrcfile: 1.5.0 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 Send2Trash: 1.8.3 SEQCROW: 1.8.16 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 sympy: 1.13.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 torch: 2.2.1 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Window Toolkit can't reproduce all ChimeraX