id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8966 Crash using color chooser chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.6rc202304180021 (2023-04-18 00:21:01 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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""60da5e84ab0ca017dace9abf"", ""factorPackIds"" : { }, ""deploymentId"" : 240000008 } ], ""experiments"" : [ { ""treatmentId"" : ""c28e4ee6-1b08-4f90-8e05-2809e78310a3"", ""experimentId"" : ""6317d2003d24842ff850182a"", ""deploymentId"" : 400000013 }, { ""treatmentId"" : ""6dd670af-0633-45e4-ae5f-122ae4df02be"", ""experimentId"" : ""64406ba83deb637ac8a04419"", ""deploymentId"" : 900000005 } ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.6rc202304180021 (2023-04-18) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/yoshi/Downloads/cryosparc_P59_J250_class_00_00162_volume.mrc Opened cryosparc_P59_J250_class_00_00162_volume.mrc as #1, grid size 100,100,100, pixel 2.58, shown at level 0.743, step 1, values float32 > open /Users/yoshi/Downloads/cryosparc_P59_J250_class_03_00162_volume.mrc Opened cryosparc_P59_J250_class_03_00162_volume.mrc as #2, grid size 100,100,100, pixel 2.58, shown at level 0.633, step 1, values float32 > open /Users/yoshi/Downloads/cryosparc_P59_J250_class_02_00162_volume.mrc Opened cryosparc_P59_J250_class_02_00162_volume.mrc as #3, grid size 100,100,100, pixel 2.58, shown at level 0.75, step 1, values float32 > open /Users/yoshi/Downloads/cryosparc_P59_J250_class_01_00162_volume.mrc Opened cryosparc_P59_J250_class_01_00162_volume.mrc as #4, grid size 100,100,100, pixel 2.58, shown at level 0.795, step 1, values float32 > ui tool show Registration > tile 4 models tiled > volume #1 level 0.5786 > volume #4 level 0.758 > volume #4 level 0.8993 > set bgColor black > set bgColor white > lighting soft > close > open /Users/yoshi/Downloads/cryosparc_P59_J246_class_00_00102_volume.mrc Opened cryosparc_P59_J246_class_00_00102_volume.mrc as #1, grid size 100,100,100, pixel 2.58, shown at level 0.781, step 1, values float32 > open /Users/yoshi/Downloads/cryosparc_P59_J246_class_03_00102_volume.mrc Opened cryosparc_P59_J246_class_03_00102_volume.mrc as #2, grid size 100,100,100, pixel 2.58, shown at level 0.754, step 1, values float32 > open /Users/yoshi/Downloads/cryosparc_P59_J246_class_02_00102_volume.mrc Opened cryosparc_P59_J246_class_02_00102_volume.mrc as #3, grid size 100,100,100, pixel 2.58, shown at level 0.62, step 1, values float32 > open /Users/yoshi/Downloads/cryosparc_P59_J246_class_01_00102_volume.mrc Opened cryosparc_P59_J246_class_01_00102_volume.mrc as #4, grid size 100,100,100, pixel 2.58, shown at level 0.793, step 1, values float32 > tile 4 models tiled > lighting soft > open /Users/yoshi/Desktop/cut_J237_004.mrc Opened cut_J237_004.mrc as #5, grid size 500,500,500, pixel 0.515, shown at level 0.0689, step 2, values float32 > hide #!1 models > hide #!2 models > hide #!3 models > hide #!4 models > open /Users/yoshi/Desktop/1_binding_domain_bncg.mrc Opened 1_binding_domain_bncg.mrc as #6, grid size 85,77,104, pixel 1.67,1.67,1.67, shown at level 0.634, step 1, values float32 > hide #!5 models > volume #6 level 0.3145 > open /Users/yoshi/Downloads/cryosparc_P59_J121_008_volume_map.mrc Opened cryosparc_P59_J121_008_volume_map.mrc as #7, grid size 500,500,500, pixel 0.515, shown at level 0.0474, step 2, values float32 > hide #!6 models > volume #7 step 1 > open /Users/yoshi/Downloads/cryosparc_P59_J239_010_volume_map.mrc Opened cryosparc_P59_J239_010_volume_map.mrc as #8, grid size 500,500,500, pixel 0.515, shown at level 0.0629, step 2, values float32 > hide #!7 models > volume #8 step 1 > volume #8 level 0.05705 > open /Users/yoshi/Downloads/cryosparc_P59_J238_011_volume_map.mrc Opened cryosparc_P59_J238_011_volume_map.mrc as #9, grid size 500,500,500, pixel 0.515, shown at level 0.0471, step 2, values float32 > hide #!8 models > open /Users/yoshi/Downloads/cryosparc_P59_J107_class_00_00162_volume.mrc Opened cryosparc_P59_J107_class_00_00162_volume.mrc as #10, grid size 100,100,100, pixel 2.58, shown at level 0.68, step 1, values float32 > open /Users/yoshi/Downloads/cryosparc_P59_J107_class_04_00162_volume.mrc Opened cryosparc_P59_J107_class_04_00162_volume.mrc as #11, grid size 100,100,100, pixel 2.58, shown at level 0.822, step 1, values float32 > open /Users/yoshi/Downloads/cryosparc_P59_J107_class_03_00162_volume.mrc Opened cryosparc_P59_J107_class_03_00162_volume.mrc as #12, grid size 100,100,100, pixel 2.58, shown at level 0.594, step 1, values float32 > open /Users/yoshi/Downloads/cryosparc_P59_J107_class_02_00162_volume.mrc Opened cryosparc_P59_J107_class_02_00162_volume.mrc as #13, grid size 100,100,100, pixel 2.58, shown at level 0.749, step 1, values float32 > open /Users/yoshi/Downloads/cryosparc_P59_J107_class_01_00162_volume.mrc Opened cryosparc_P59_J107_class_01_00162_volume.mrc as #14, grid size 100,100,100, pixel 2.58, shown at level 0.679, step 1, values float32 > hide #!9 models > tile 5 models tiled > open /Users/yoshi/Downloads/cryosparc_P59_J107_class_05_00162_volume.mrc Opened cryosparc_P59_J107_class_05_00162_volume.mrc as #15, grid size 100,100,100, pixel 2.58, shown at level 0.587, step 1, values float32 > tile 6 models tiled > hide #!15 models > hide #!14 models > hide #!13 models > hide #!12 models > hide #!11 models > hide #!10 models > show #!10 models > show #!11 models > show #!13 models > show #!12 models > show #!14 models > show #!15 models > select add #15 2 models selected > hide #!10 models > hide #!11 models > hide #!12 models > hide #!13 models > hide #!15 models > show #!15 models > hide #!14 models > show #!14 models > hide #!14 models > select subtract #15 Nothing selected > show #!14 models > show #!13 models > show #!12 models > show #!11 models > show #!10 models > lighting soft > hide #!10 models > show #!10 models > hide #!15 models > show #!15 models > hide #!14 models > show #!14 models > hide #!13 models > show #!13 models > hide #!12 models > show #!12 models > open /Users/yoshi/Downloads/cryosparc_P59_J121_008_volume_map.mrc Opened cryosparc_P59_J121_008_volume_map.mrc as #16, grid size 500,500,500, pixel 0.515, shown at level 0.0474, step 2, values float32 > hide #!15 models > hide #!14 models > hide #!13 models > hide #!12 models > hide #!11 models > hide #!10 models > color #16 #94aaf7ff models > color #16 #5ccaf7ff models > color #16 #0433ffff models > color #16 #00fdffff models > color #16 #0096ffff models > color #16 #0066ccff models > color #16 #b3d7ffff models > color #16 #0067f47f models > color #16 #b3d7ffff models > color #16 #0096ffff models > color #16 #76d6ffff models > color #16 #0096ffff models > color #16 #00fdffff models > color #16 #73fcd6ff models > color #16 #00f900ff models > color #16 #7a81ffff models > color #16 #74fae6ff models > color #16 #73f8f7ff models > color #13 #f3f3f2ff models > color #13 #82a1c2ff models ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.6rc202304180021 (2023-04-18) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/yoshi/Downloads/cryosparc_P59_J122_010_volume_map.mrc Opened cryosparc_P59_J122_010_volume_map.mrc as #1, grid size 500,500,500, pixel 0.515, shown at level 0.0606, step 2, values float32 > set bgColor white > lighting soft OpenGL version: 4.1 ATI-4.8.101 OpenGL renderer: AMD Radeon R9 M390 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: iMac17,1 Processor Name: Quad-Core Intel Core i5 Processor Speed: 3.2 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Memory: 8 GB System Firmware Version: 509.0.0.0.0 OS Loader Version: 540.120.3~22 SMC Version (system): 2.33f12 Software: System Software Overview: System Version: macOS 12.6.5 (21G531) Kernel Version: Darwin 21.6.0 Time since boot: 1 day 6:02 Graphics/Displays: AMD Radeon R9 M390: Chipset Model: AMD Radeon R9 M390 Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 2 GB Vendor: AMD (0x1002) Device ID: 0x6819 Revision ID: 0x0000 ROM Revision: 113-C408WA-799 VBIOS Version: 113-C408W1-009 EFI Driver Version: 01.00.799 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: iMac: Display Type: Built-In Retina LCD Resolution: Retina 5K (5120 x 2880) Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal 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 ChimeraX-AddH: 2.2.4 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: 1.6rc202304180021 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: 1.10.2 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: 6.4.1 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: 3.2.0 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 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 Window Toolkit can't reproduce Tom Goddard all ChimeraX