id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8581 Crash in QMainWindow::removeDockWidget chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-13.2.1-arm64-arm-64bit ChimeraX Version: 1.6.dev202302220544 (2023-02-22 05:44:49 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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\nActivity Tracing 256K 1 \nCG backing stores 3392K 4 \nCG image 560K 30 \nColorSync 592K 29 \nCoreAnimation 256K 16 \nCoreGraphics 48K 3 \nCoreUI image data 5392K 39 \nFoundation 32K 2 \nKernel Alloc Once 32K 1 \nMALLOC 14.0G 305 \nMALLOC guard page 192K 11 \nMALLOC_MEDIUM (reserved) 744.0M 8 reserved VM address space (unallocated)\nMach message 64K 2 \nOpenCL 25.3M 81 \nOpenCL (reserved) 240K 7 reserved VM address space (unallocated)\nOpenGL GLSL 384K 4 \nSTACK GUARD 976K 61 \nStack 182.6M 63 \nStack Guard 56.0M 1 \nVM_ALLOCATE 410.9M 975 \nVM_ALLOCATE (reserved) 384.0M 4 reserved VM address space (unallocated)\n__AUTH 1938K 361 \n__AUTH_CONST 24.9M 589 \n__CTF 756 1 \n__DATA 24.3M 891 \n__DATA_CONST 40.3M 878 \n__DATA_DIRTY 1984K 229 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 815.2M 289 \n__OBJC_CONST 4758K 325 \n__OBJC_RO 65.5M 1 \n__OBJC_RW 1988K 1 \n__TEXT 892.5M 900 \ndyld private memory 560K 4 \nmapped file 238.9M 70 \nshared memory 3200K 27 \n=========== ======= ======= \nTOTAL 17.8G 6217 \nTOTAL, minus reserved VM space 16.7G 6217 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""62cdf63ddb3b7109d6d765cc"", ""factorPackIds"" : { ""SIRI_UNDERSTANDING_TMDC"" : ""62cdf6dddb3b7109d6d765cd"" }, ""deploymentId"" : 240000007 }, { ""rolloutId"" : ""5ffde50ce2aacd000d47a95f"", ""factorPackIds"" : { }, ""deploymentId"" : 240000251 } ], ""experiments"" : [ ] }, ""reportNotes"" : [ ""dyld_process_snapshot_create_for_process failed with 5"" ] } ===== Log before crash start ===== UCSF ChimeraX version: 1.6.dev202302220544 (2023-02-22) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/rashmi/research/em/s8/monomer/halfwrap/mrc/cryosparc_P12_J1836_map_sharp.mrc Opened cryosparc_P12_J1836_map_sharp.mrc as #1, grid size 336,336,336, pixel 0.86, shown at level 0.000112, step 2, values float32 > volume #1 level 0.006041 > volume #1 step 1 > volume #1 level 0.01235 > lighting soft > open > /Users/rashmi/research/em/s8/monomer/halfwrap/models/Halfwrap_J1836map_canonicalJ1823model_resideleted.pdb Chain information for Halfwrap_J1836map_canonicalJ1823model_resideleted.pdb #2 --- Chain | Description A | No description available B F | No description available C | No description available D | No description available E | No description available G | No description available H | No description available I | No description available J | No description available > volume #1 style mesh > hide atoms > style stick Changed 20125 atom styles > show atoms > ui tool show ""Fit in Map"" > fitmap #2 inMap #1 Fit molecule Halfwrap_J1836map_canonicalJ1823model_resideleted.pdb (#2) to map cryosparc_P12_J1836_map_sharp.mrc (#1) using 20125 atoms average map value = 0.2675, steps = 40 shifted from previous position = 0.00613 rotated from previous position = 0.0143 degrees atoms outside contour = 2439, contour level = 0.012349 Position of Halfwrap_J1836map_canonicalJ1823model_resideleted.pdb (#2) relative to cryosparc_P12_J1836_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 1.00000000 -0.00001023 0.00000095 0.00174527 0.00001023 0.99999997 -0.00024984 0.02908510 -0.00000094 0.00024984 0.99999997 -0.03911981 Axis 0.99915572 0.00377882 0.04090914 Axis point 0.00000000 156.63314106 116.38976479 Rotation angle (degrees) 0.01432708 Shift along axis 0.00025334 > clipper associate #1 toModel #2 Opened cryosparc_P12_J1836_map_sharp.mrc as #1.1.1.1, grid size 336,336,336, pixel 0.86, shown at level 0.33, step 1, values float32 Chain information for Halfwrap_J1836map_canonicalJ1823model_resideleted.pdb --- Chain | Description 1.2/A | No description available 1.2/B 1.2/F | No description available 1.2/C | No description available 1.2/D | No description available 1.2/E | No description available 1.2/G | No description available 1.2/H | No description available 1.2/I | No description available 1.2/J | No description available > clipper spotlight radius 99 > volume #1.1.1.1 level 0.02389 > isolde start > set selectionWidth 4 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 92 residues in model #1.2 to IUPAC-IUB standards. Populating font family aliases took 167 ms. Replace uses of missing font family ""Carlito"" with one that exists to avoid this cost. > isolde sim start sel ISOLDE: started sim ""Adjust for PAE"" is checked in the distance restraint options, but the reference model has no PAE matrix assigned. This option has been ignored. > isolde restrain distances > ""#1.2/A"",""#1.2/B"",""#1.2/C"",""#1.2/D"",""#1.2/E"",""#1.2/F"",""#1.2/G"",""#1.2/H"" > templateAtoms > ""#1.2/A"",""#1.2/B"",""#1.2/C"",""#1.2/D"",""#1.2/E"",""#1.2/F"",""#1.2/G"",""#1.2/H"" > perChain false adjustForConfidence false useCoordinateAlignment false kappa > 4.40 fallOff 2.50 groupName ""Reference Distance Restraints"" ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 11 residues in model #1.2 to IUPAC-IUB standards. > isolde restrain torsions #1.2/A templateResidues #1.2/A adjustForConfidence > false sidechains true springConstant 250.00 alpha 0.20 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... > isolde restrain torsions #1.2/B templateResidues #1.2/B adjustForConfidence > false sidechains true springConstant 250.00 alpha 0.20 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... > isolde restrain torsions #1.2/C templateResidues #1.2/C adjustForConfidence > false sidechains true springConstant 250.00 alpha 0.20 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... > isolde restrain torsions #1.2/D templateResidues #1.2/D adjustForConfidence > false sidechains true springConstant 250.00 alpha 0.20 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... > isolde restrain torsions #1.2/E templateResidues #1.2/E adjustForConfidence > false sidechains true springConstant 250.00 alpha 0.20 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... > isolde restrain torsions #1.2/F templateResidues #1.2/F adjustForConfidence > false sidechains true springConstant 250.00 alpha 0.20 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... > isolde restrain torsions #1.2/G templateResidues #1.2/G adjustForConfidence > false sidechains true springConstant 250.00 alpha 0.20 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... > isolde restrain torsions #1.2/H templateResidues #1.2/H adjustForConfidence > false sidechains true springConstant 250.00 alpha 0.20 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... > select clear > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > clipper associate #1 toModel #2 Invalid ""toModel"" argument: Must specify 1 model, got 0 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.6.dev202302220544 (2023-02-22) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 83 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac21,1 Model Number: Z12V000LXLL/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 8419.80.7 OS Loader Version: 8419.80.7 Software: System Software Overview: System Version: macOS 13.2.1 (22D68) Kernel Version: Darwin 22.3.0 Time since boot: 7 hours, 29 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: iMac: Display Type: Built-In Retina LCD Resolution: Retina 4.5K (4480 x 2520) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 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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: 2.0.11 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: 1.5.8 ChimeraX-ModelPanel: 1.3.6 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-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.6.13 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: 1.0 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: 1.10.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.1 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: 1.27.1 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: 0.1.2 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.6 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.38.0 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: 6.0.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.4 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.2.0 jupyterlab-widgets: 3.0.5 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 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 pandas: 1.5.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pkginfo: 1.9.6 platformdirs: 3.0.0 prompt-toolkit: 3.0.37 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 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: 6.4.2 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.2 python-dateutil: 2.8.2 pytz: 2022.7.1 pyzmq: 25.0.0 qtconsole: 5.4.0 QtPy: 2.3.0 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 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: 1.0.2 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.9.0 typing-extensions: 4.5.0 urllib3: 1.26.14 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.5 zipp: 3.14.0 }}} " defect closed normal Window Toolkit can't reproduce Tom Goddard all ChimeraX