id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15495 Crash changing Mac display configuration, Intel/AMD graphics chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.5-x86_64-i386-64bit 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. 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""logWritingSignature"" : ""9b32d37eed40f7db94dcf0c0e7f64901f98a5d9d"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""62699e1ec1ff2978b47f6c3b"", ""factorPackIds"" : { ""SIRI_FIND_MY_CONFIGURATION_FILES"" : ""652805151bce5442b8d752e1"" }, ""deploymentId"" : 240000031 }, { ""rolloutId"" : ""63508950b3714d3622fc77f7"", ""factorPackIds"" : { ""SIRI_MEMORY_SYNC_CONFIG"" : ""6526e111d0c9ce2f459b54a8"" }, ""deploymentId"" : 240000015 } ], ""experiments"" : [ { ""treatmentId"" : ""3dff9c91-a8fb-424e-a656-c8d6e6037574"", ""experimentId"" : ""662152ede2d11d1408c4db33"", ""deploymentId"" : 400000014 }, { ""treatmentId"" : ""c47ab4cc-c9c3-4b5d-a87c-e2433ce02597"", ""experimentId"" : ""6639bc6ba73d460582162323"", ""deploymentId"" : 400000006 } ] } } ===== 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/kirk/Downloads/022124_VW-DNA-Cryo-EM.cxs format session Opened run_class001.mrc as #1, grid size 80,80,80, pixel 3.74, shown at level 0.0612, step 1, values float32 opened ChimeraX session > open /Users/kirk/Downloads/HD_DNA_trimmed_to40.pdb format pdb Chain information for HD_DNA_trimmed_to40.pdb #4 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > hide #3 models Drag select of 1 run_class001.mrc , 11 residues, 15 shapes > select subtract #1 264 atoms, 12 residues, 1 model selected > ui tool show ""Fit in Map"" > select add #4 3666 atoms, 4072 bonds, 164 residues, 1 model selected > ui mousemode right ""translate selected models"" > ui mousemode right ""move picked models"" > view matrix models #4,1,0,0,-17.779,0,1,0,-47.527,0,0,1,-27.89 > fitmap #4 inMap #1 Fit molecule HD_DNA_trimmed_to40.pdb (#4) to map run_class001.mrc (#1) using 3666 atoms average map value = 0.06768, steps = 88 shifted from previous position = 31.3 rotated from previous position = 13.2 degrees atoms outside contour = 1500, contour level = 0.061193 Position of HD_DNA_trimmed_to40.pdb (#4) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation 0.99241543 -0.07652344 0.09620691 -32.98968350 0.05641488 0.97885149 0.19663956 -60.67025953 -0.10921982 -0.18972063 0.97574439 25.69343570 Axis -0.84482473 0.44919116 0.29068622 Axis point 0.00000000 80.12802268 335.62582877 Rotation angle (degrees) 13.21836536 Shift along axis 8.08668357 > view matrix models > #4,0.99242,-0.076523,0.096207,-31.072,0.056415,0.97885,0.19664,-60.047,-0.10922,-0.18972,0.97574,24.227 > undo > select subtract #4 Nothing selected > select add #4 3666 atoms, 4072 bonds, 164 residues, 1 model selected > view matrix models > #4,0.99242,-0.076523,0.096207,-28.177,0.056415,0.97885,0.19664,-135.27,-0.10922,-0.18972,0.97574,53.12 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.93972,-0.31904,0.12307,22.871,0.28831,0.93273,0.21654,-171.78,-0.18388,-0.168,0.96849,63.711 > view matrix models > #4,0.94499,-0.31904,0.072101,30.617,0.29787,0.93048,0.21324,-172.52,-0.13512,-0.18004,0.97434,56.196 > view matrix models > #4,0.96238,-0.26793,-0.045122,37.763,0.27139,0.93987,0.20737,-168.51,-0.013153,-0.21181,0.97722,39.719 > view matrix models > #4,-0.98086,-0.19103,-0.037677,372.82,0.14892,-0.86068,0.48688,148.27,-0.12544,0.47195,0.87265,-52.175 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.98086,-0.19103,-0.037677,391.07,0.14892,-0.86068,0.48688,202.61,-0.12544,0.47195,0.87265,-64.07 > fitmap #4 inMap #1 Fit molecule HD_DNA_trimmed_to40.pdb (#4) to map run_class001.mrc (#1) using 3666 atoms average map value = 0.0687, steps = 92 shifted from previous position = 27 rotated from previous position = 18.5 degrees atoms outside contour = 1461, contour level = 0.061193 Position of HD_DNA_trimmed_to40.pdb (#4) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.99231953 0.10326630 -0.06810310 320.74791749 -0.12087175 -0.92652162 0.35629722 293.65221966 -0.02630550 0.36179243 0.93188747 -83.70333927 Axis 0.02409459 -0.18326799 -0.98276767 Axis point 168.08706751 145.32120457 0.00000000 Rotation angle (degrees) 173.45208356 Shift along axis 36.17217313 > view matrix models > #4,-0.99232,0.10327,-0.068103,320.9,-0.12087,-0.92652,0.3563,294,-0.026305,0.36179,0.93189,-81.444 > undo > select subtract #4 Nothing selected > vop gaussian #1 sdev 11.2 Opened run_class001.mrc gaussian as #5, grid size 80,80,80, pixel 3.74, shown at step 1, values float32 > undo > volume #1 level 0.1396 > volume #5 level 0.0302 > hide #!5 models > close session > open /Users/kirk/Downloads/022124_VW-DNA-Cryo-EM.cxs format session Opened run_class001.mrc as #1, grid size 80,80,80, pixel 3.74, shown at level 0.0612, step 1, values float32 opened ChimeraX session > open /Users/kirk/Downloads/HD_DNA_trimmed_to40.pdb format pdb Chain information for HD_DNA_trimmed_to40.pdb #4 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > fitmap #2 inMap #1 Fit molecule 6yhr (#2) to map run_class001.mrc (#1) using 4499 atoms average map value = 0.06708, steps = 60 shifted from previous position = 0.0092 rotated from previous position = 0.0436 degrees atoms outside contour = 2090, contour level = 0.061193 Position of 6yhr (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation 0.78650093 -0.59455935 -0.16707922 156.44741680 0.61197227 0.78668976 0.08129678 176.37889701 0.08310375 -0.16618784 0.98258606 105.49593164 Axis -0.19691570 -0.19906268 0.95999909 Axis point -181.23197224 339.92053988 0.00000000 Rotation angle (degrees) 38.93235843 Shift along axis 35.35858987 > select add #4 8165 atoms, 8467 bonds, 7 pseudobonds, 903 residues, 4 models selected > select subtract #2 3666 atoms, 4072 bonds, 164 residues, 1 model selected > fitmap #4 inMap #1 Fit molecule HD_DNA_trimmed_to40.pdb (#4) to map run_class001.mrc (#1) using 3666 atoms average map value = 0.06768, steps = 120 shifted from previous position = 50.3 rotated from previous position = 13.2 degrees atoms outside contour = 1497, contour level = 0.061193 Position of HD_DNA_trimmed_to40.pdb (#4) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation 0.99243498 -0.07661208 0.09593430 -32.95071053 0.05660644 0.97893360 0.19617523 -60.65555053 -0.10894270 -0.18926066 0.97586469 25.54670639 Axis -0.84455059 0.44891771 0.29190271 Axis point 0.00000000 79.68453251 336.18339009 Rotation angle (degrees) 13.19052887 Shift along axis 8.05634397 > hide #3 models ===== 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 > open /Users/kirk/Library/CloudStorage/Box-Box/Tyra- > Research/Discovery/Crystallography/Tyra_Solved_Structures/%First_Look_Structure_Data/TARDIS/ForKirk/PDB_Dep_Prep/FGFR1_TYRX-0347_structurefiles/pdb_extract_coord_24523.cif Summary of feedback from opening /Users/kirk/Library/CloudStorage/Box- Box/Tyra- Research/Discovery/Crystallography/Tyra_Solved_Structures/%First_Look_Structure_Data/TARDIS/ForKirk/PDB_Dep_Prep/FGFR1_TYRX-0347_structurefiles/pdb_extract_coord_24523.cif --- warnings | Unknown polymer entity '1' on line 33 Unknown polymer entity '4' on line 314 Atom CL1 is not in the residue template for 300 /A:1002 Atom CL1 is not in the residue template for 300 /B:902 Skipping chem_comp category: Missing column 'type' on line 10269 notes | Fetching CCD EDO from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/EDO/EDO.cif Fetching CCD 300 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/0/300/300.cif pdb_extract_coord_24523.cif title: FGFR1 with TYRA-300 [more info...] Non-standard residues in pdb_extract_coord_24523.cif #1 --- 300 — (300) ALA — (ALA) ARG — (ARG) ASN — (ASN) ASP — (ASP) CYS — (CYS) EDO — (EDO) GLN — (GLN) GLU — (GLU) GLY — (GLY) HIS — (HIS) ILE — (ILE) LEU — (LEU) LYS — (LYS) MET — (MET) PHE — (PHE) PRO — (PRO) SER — (SER) SO4 — (SO4) THR — (THR) TRP — (TRP) TYR — (TYR) VAL — (VAL) 12 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. OpenGL version: 4.1 ATI-5.5.17 OpenGL renderer: AMD Radeon Pro 5600M OpenGL Engine OpenGL vendor: ATI Technologies Inc. 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: MacBookPro16,4 Processor Name: 8-Core Intel Core i9 Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 64 GB System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.5077.0.0,0) OS Loader Version: 580~2215 Software: System Software Overview: System Version: macOS 14.5 (23F79) Kernel Version: Darwin 23.5.0 Time since boot: 15 days, 12 hours, 57 minutes Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 AMD Radeon Pro 5600M: Chipset Model: AMD Radeon Pro 5600M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 8 GB Vendor: AMD (0x1002) Device ID: 0x7360 Revision ID: 0x0041 ROM Revision: 113-D3000E-192 VBIOS Version: 113-D3000A0U-015 Option ROM Version: 113-D3000A0U-015 EFI Driver Version: 01.A1.192 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal 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 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-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 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 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 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 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 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 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 duplicate all ChimeraX