id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9497 Crash querying cursor position chimerax-bug-report@… Tom Goddard "W{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Bus error Current thread 0x000000010db77600 (most recent call first): File ""/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/mouse_modes/mousemodes.py"", line 514 in _cursor_position File ""/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/mouse_modes/mousemodes.py"", line 472 in mouse_pause_tracking File ""/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py"", line 140 in _redraw_timer_callback File ""/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File 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All rights reserved. How to cite UCSF ChimeraX > open /Users/emilieleroy/Desktop/complex_clean_map1.mrc format mrc No such file/path: /Users/emilieleroy/Desktop/complex_clean_map1.mrc > open /Users/emilieleroy/Desktop/JAK2-LNK_MAPs_Models/complex_clean_map1.mrc Opened complex_clean_map1.mrc as #1, grid size 78,99,87, pixel 1.67, shown at level 0.577, step 1, values float32 > open /Volumes/eleroy/MAP.mrc Opened MAP.mrc as #2, grid size 78,99,87, pixel 0.822,0.822,0.822, shown at level 0.577, step 1, values float32 > close #2 > close #1 > open > /Users/emilieleroy/Desktop/JAK2-LNK_MAPs_Models/complex_clean_072823.mrc Opened complex_clean_072823.mrc as #1, grid size 78,99,87, pixel 1.67, shown at level 0.577, step 1, values float32 > molmap #0 15 No atoms specified > vop add #0 > resample #1 onGrid #0 Unknown command: resample #1 onGrid #0 > resample #1 onGrid #1 Unknown command: resample #1 onGrid #1 > vop resample #1 ongrid #1 Opened complex_clean_072823.mrc resampled as #2, grid size 78,99,87, pixel 1.67, shown at step 1, values float32 > ui tool show ""Volume Viewer"" No map chosen to save > close #1 > save /Users/emilieleroy/test1.mrc models #2 > vop resample #1 ongrid #0 > open > /Users/emilieleroy/Downloads/cryosparc_P205_J215_class_02_final_volume.mrc > format mrc Opened cryosparc_P205_J215_class_02_final_volume.mrc as #1, grid size 128,128,128, pixel 1.64, shown at level 0.11, step 1, values float32 > vop resample #1 ongrid #2 Opened cryosparc_P205_J215_class_02_final_volume.mrc resampled as #3, grid size 78,99,87, pixel 1.67, shown at step 1, values float32 > volume #3 level 0.003298 > volume #3 level 0.0006552 > ui tool show ""Volume Viewer"" > close #3 > ui tool show ""Map Coordinates"" > ui tool show ""Model Panel"" > select add #1 2 models selected > ui mousemode right ""move picked models"" > ui mousemode right ""translate selected atoms"" > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.97538,-0.20965,0.068355,17.722,0.18494,0.94657,0.26421,-40.09,-0.12009,-0.24507,0.96204,42.019 > view matrix models > #1,0.78216,0.56827,-0.25553,-11.529,-0.55355,0.82202,0.13366,62.548,0.28601,0.036908,0.95752,-29.2 > ui mousemode right ""move picked models"" > view matrix models > #1,0.78216,0.56827,-0.25553,-105.9,-0.55355,0.82202,0.13366,-43.846,0.28601,0.036908,0.95752,-105.43 > view matrix models > #1,0.78216,0.56827,-0.25553,-104.22,-0.55355,0.82202,0.13366,-51.588,0.28601,0.036908,0.95752,-113.11 > view matrix models #2,1,0,0,4.7536,0,1,0,0.87004,0,0,1,-0.14601 > view matrix models #2,1,0,0,39.498,0,1,0,49.796,0,0,1,85.848 > view matrix models > #1,0.78216,0.56827,-0.25553,-83.091,-0.55355,0.82202,0.13366,13.544,0.28601,0.036908,0.95752,-40.455 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.081929,0.16436,-0.98299,121.96,0.6948,0.71654,0.061898,-97.302,0.71453,-0.67791,-0.1729,104.09 > ui mousemode right ""move picked models"" > view matrix models > #1,-0.081929,0.16436,-0.98299,129.67,0.6948,0.71654,0.061898,-103.18,0.71453,-0.67791,-0.1729,108.01 > view matrix models > #1,-0.081929,0.16436,-0.98299,136.55,0.6948,0.71654,0.061898,-104.78,0.71453,-0.67791,-0.1729,102.18 > view matrix models > #1,-0.081929,0.16436,-0.98299,134.85,0.6948,0.71654,0.061898,-102.95,0.71453,-0.67791,-0.1729,105.11 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.35635,0.097549,-0.92925,164.86,0.018333,0.99507,0.097429,-65.832,0.93417,0.017683,-0.35639,27.681 > ui mousemode right ""move picked models"" > view matrix models > #1,-0.35635,0.097549,-0.92925,168.11,0.018333,0.99507,0.097429,-66.732,0.93417,0.017683,-0.35639,28.314 > view matrix models > #1,-0.35635,0.097549,-0.92925,166.65,0.018333,0.99507,0.097429,-63.09,0.93417,0.017683,-0.35639,31.272 > volume #1 level 0.07359 > select subtract #1 Nothing selected > open /Volumes/eleroy/test1newbox.mrc Opened test1newbox.mrc as #3, grid size 40,40,40, pixel 1.67, shown at level 0.742, step 1, values float32 > volume #3 level 0.2567 > open /Volumes/eleroy/test1newbox1.mrc Opened test1newbox1.mrc as #4, grid size 80,80,80, pixel 1.67, shown at level 0.618, step 1, values float32 > open /Volumes/eleroy/test1newbox2.mrc Opened test1newbox2.mrc as #5, grid size 160,160,160, pixel 1.67, shown at level 0.116, step 1, values float32 > view matrix models #5,1,0,0,-10.863,0,1,0,-36.66,0,0,1,-62.418 > volume #5 level 0.5508 > hide #2.1 models > hide #1.1 models > open /Volumes/eleroy/MAP.mrc Opened MAP.mrc as #6, grid size 78,99,87, pixel 0.822,0.822,0.822, shown at level 0.577, step 1, values float32 > view matrix models #6,1,0,0,67.833,0,1,0,-17.689,0,0,1,97.988 > open /Volumes/eleroy/MAPnewbox.mrc Opened MAPnewbox.mrc as #7, grid size 160,160,160, pixel 0.822,0.822,0.822, shown at level 0.116, step 1, values float32 > view matrix models #7,1,0,0,17.55,0,1,0,-9.9591,0,0,1,10.784 > view matrix models #7,1,0,0,39.528,0,1,0,-27.269,0,0,1,28.318 > view matrix models #7,1,0,0,29.076,0,1,0,-58.9,0,0,1,-8.7401 > volume #7 level 0.5218 > view matrix models #7,1,0,0,30.909,0,1,0,-78.329,0,0,1,-7.3066 > view matrix models #7,1,0,0,-1.6388,0,1,0,-93.294,0,0,1,22.536 > view matrix models #7,1,0,0,3.358,0,1,0,-93.499,0,0,1,23.384 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/emilieleroy/Downloads/cryosparc_P205_J282_class_02_final_volume.mrc Opened cryosparc_P205_J282_class_02_final_volume.mrc as #1, grid size 128,128,128, pixel 2.31, shown at level 0.0613, step 1, values float32 OpenGL version: 4.1 ATI-4.8.101 OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac19,2 Processor Name: 6-Core Intel Core i7 Processor Speed: 3.2 GHz Number of Processors: 1 Total Number of Cores: 6 L2 Cache (per Core): 256 KB L3 Cache: 12 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1968.120.12.0.0 OS Loader Version: 540.120.3~22 SMC Version (system): 2.47f3 Software: System Software Overview: System Version: macOS 12.6.6 (21G646) Kernel Version: Darwin 21.6.0 Time since boot: 49 days 4:57 Graphics/Displays: Radeon Pro 560X: Chipset Model: Radeon Pro 560X Type: GPU Bus: PCIe PCIe Lane Width: x8 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x67ef Revision ID: 0x00c2 ROM Revision: 113-C981AA-042 VBIOS Version: 113-C9819A1X-009 EFI Driver Version: 01.B1.042 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: iMac: Display Type: Built-In Retina LCD Resolution: 4096 x 2304 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal ASUS VG236: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: B4LMTF077013 Mirror: Off Online: Yes Rotation: Supported Connection Type: DVI or HDMI Adapter Firmware Version: 0.00 Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 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: 1.2.1 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-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 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: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal General Controls can't reproduce all ChimeraX