id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15841 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.6.1-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. 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All rights reserved. How to cite UCSF ChimeraX > open /Users/naito/Downloads/cryosparc_P106_J266_class_02_final_volume.mrc Opened cryosparc_P106_J266_class_02_final_volume.mrc as #1, grid size 180,180,180, pixel 1.38, shown at level 0.0506, step 1, values float32 > open /Users/naito/Downloads/cryosparc_P106_J115_009_volume_map_sharp.mrc Opened cryosparc_P106_J115_009_volume_map_sharp.mrc as #2, grid size 180,180,180, pixel 1.38, shown at level 0.0602, step 1, values float32 > set bgColor white > lighting soft > graphics silhouettes true > hide #!1 models > volume #2 level 0.2386 > show #!1 models > hide #!2 models > volume #1 level 0.1449 > open /Users/naito/Library/CloudStorage/OneDrive- > ImperialCollegeLondon/rMRP2/04_Cisplatine- > glutathione/cryosparc_P29_J24_005_volume_map_sharp.mrc Opened cryosparc_P29_J24_005_volume_map_sharp.mrc as #3, grid size 180,180,180, pixel 2.38, shown at level 0.115, step 1, values float32 > hide #!1 models > open /Users/naito/Library/CloudStorage/OneDrive- > ImperialCollegeLondon/rMRP2/03_Vinblastin- > glutathione/cryosparc_P28_J27_006_volume_map_sharp.mrc Opened cryosparc_P28_J27_006_volume_map_sharp.mrc as #4, grid size 256,256,256, pixel 1.68, shown at level 0.048, step 1, values float32 > hide #!4 models > open /Users/naito/Library/CloudStorage/OneDrive- > ImperialCollegeLondon/rMRP2/05_Sulindac/cryosparc_P30_J32_005_volume_map_sharp.mrc Opened cryosparc_P30_J32_005_volume_map_sharp.mrc as #5, grid size 256,256,256, pixel 1.68, shown at level 0.0417, step 1, values float32 > hide #!5 models > show #!4 models > hide #!3 models > volume #4 level 0.1545 > show #!5 models > hide #!4 models > volume #5 level 0.1379 > show #!3 models > hide #!5 models > volume #3 level 0.3585 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > open > /Users/naito/Library/CloudStorage/Dropbox/UK_Project/MRP2/Phenix/rMRP2-MK517/rMRP2_MK_J22-coot-1.pdb > format pdb Summary of feedback from opening /Users/naito/Library/CloudStorage/Dropbox/UK_Project/MRP2/Phenix/rMRP2-MK517/rMRP2_MK_J22-coot-1.pdb --- warning | Start residue of secondary structure not found: HELIX 34 34 ARG A 900 SER A 912 1 13 Chain information for rMRP2_MK_J22-coot-1.pdb #6 --- Chain | Description A | No description available > select add #6 11137 atoms, 11374 bonds, 2 pseudobonds, 1402 residues, 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.96347,-0.20551,-0.17175,68.71,-0.187,-0.97526,0.11793,326.11,-0.19174,-0.081502,-0.97806,388.24 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.96347,-0.20551,-0.17175,130.76,-0.187,-0.97526,0.11793,384.15,-0.19174,-0.081502,-0.97806,404.06 > view matrix models > #6,0.96347,-0.20551,-0.17175,112.76,-0.187,-0.97526,0.11793,394.55,-0.19174,-0.081502,-0.97806,418.08 > show #!4 models > hide #!3 models > ui mousemode right ""rotate selected models"" > view matrix models > #6,-0.99014,0.13896,-0.017573,362.41,0.13379,0.97543,0.17504,19.335,0.041464,0.17096,-0.9844,339.4 > ui mousemode right ""translate selected models"" > view matrix models > #6,-0.99014,0.13896,-0.017573,361.77,0.13379,0.97543,0.17504,0.059394,0.041464,0.17096,-0.9844,338.73 > fitmap #6 inMap #4 Fit molecule rMRP2_MK_J22-coot-1.pdb (#6) to map cryosparc_P28_J27_006_volume_map_sharp.mrc (#4) using 11137 atoms average map value = 0.3362, steps = 64 shifted from previous position = 4.91 rotated from previous position = 5.85 degrees atoms outside contour = 2629, contour level = 0.15454 Position of rMRP2_MK_J22-coot-1.pdb (#6) relative to cryosparc_P28_J27_006_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.99788207 0.05938548 0.02654723 366.12256504 0.06378206 0.97341231 0.22000078 4.97978977 -0.01277655 0.22122807 -0.97513841 342.40108694 Axis 0.03100166 0.99333018 0.11105876 Axis point 184.65942373 0.00000000 169.10645919 Rotation angle (degrees) 178.86581819 Shift along axis 54.32362029 > save /Users/naito/desktop/240829_rMRP2_Vinblastine-Glu.pdb #6 > select subtract #6 Nothing selected > hide #!6 models > open /Users/naito/Desktop/240829_rMRP2_Vinblastine-Glu-coot-0.pdb Chain information for 240829_rMRP2_Vinblastine-Glu-coot-0.pdb #7 --- Chain | Description A | No description available > volume #4 level 0.3061 > volume #4 level 0.1955 > volume zone #7/A:1601 range 5 Missing required ""near_atoms"" argument > volume zone #4 nearAtoms #7/A:1601 range 5 newMap map true Invalid ""newMap"" argument: Expected true or false (or 1 or 0) > volume zone #4 nearAtoms #7/A:1601 range 5 newMap true Opened cryosparc_P28_J27_006_volume_map_sharp.mrc zone as #8, grid size 256,256,256, pixel 1.68, shown at step 1, values float32 > transparency #7-8 50 > volume #8 level 0.2351 > ui tool show ""Side View"" > color #7 #0019cdff > color #7/A:1601 orange > select #7/A:1601 59 atoms, 70 bonds, 1 residue, 1 model selected > color sel byhetero > select add #7 11196 atoms, 11444 bonds, 2 pseudobonds, 1403 residues, 2 models selected > select subtract #7 Nothing selected > color #8 #929292ff models > transparency #7-8 50 > color #!7 byhetero > save /Users/naito/Desktop/image13.png supersample 3 > save /Users/naito/Desktop/image14.png supersample 3 > open /Users/naito/Library/CloudStorage/OneDrive- > ImperialCollegeLondon/rMRP2/01_MK-571/Model_Map_080824/PDB_file/rMRP2_MK_local_J056-coot-1.pdb Chain information for rMRP2_MK_local_J056-coot-1.pdb #9 --- Chain | Description A | No description available > hide #!8 models > ui tool show Matchmaker The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > matchmaker #!7 to #9/A pairing bs Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker rMRP2_MK_local_J056-coot-1.pdb, chain A (#9) with 240829_rMRP2_Vinblastine-Glu-coot-0.pdb, chain A (#7), sequence alignment score = 7288.3 RMSD between 1402 pruned atom pairs is 0.018 angstroms; (across all 1402 pairs: 0.018) > undo > hide #!9 models > show #!9 models > hide #!8 models > color #9/A:1600-1603 magenta > color #!7,9 byhetero > ui tool show ""Side View"" > save /Users/naito/Desktop/image15.png supersample 3 > lighting simple > lighting full > lighting soft > save /Users/naito/Desktop/image16.png supersample 3 > movie record > turn y 2 180 > wait 180 > movie encode /Users/naito/Desktop/movie1.mp4 Movie saved to /Users/naito/Desktop/movie1.mp4 > hide #!7 models > hide #!9 models > show #!7 models > show #!4 models > ui mousemode right ""rotate selected models"" > select add #7 11196 atoms, 11444 bonds, 2 pseudobonds, 1403 residues, 2 models selected > view matrix models > #7,0.88025,-0.36556,0.30254,-2.2953,0.25214,0.90046,0.35441,-154.81,-0.40198,-0.23569,0.8848,124.24 > ui mousemode right ""translate selected models"" > view matrix models > #7,0.88025,-0.36556,0.30254,2.7605,0.25214,0.90046,0.35441,-93.807,-0.40198,-0.23569,0.8848,163.38 > view matrix models > #7,0.88025,-0.36556,0.30254,10.486,0.25214,0.90046,0.35441,-94.83,-0.40198,-0.23569,0.8848,141.93 > view matrix models > #7,0.88025,-0.36556,0.30254,44.476,0.25214,0.90046,0.35441,-96.317,-0.40198,-0.23569,0.8848,151.08 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.96806,-0.12476,0.21745,-6.9629,0.091171,0.98319,0.15822,-39.122,-0.23354,-0.13335,0.96316,77.861 > view matrix models > #7,0.96822,-0.13721,0.20908,-2.6577,0.1236,0.98935,0.076914,-30.463,-0.21741,-0.048629,0.97487,54.278 > ui mousemode right ""translate selected models"" > view matrix models > #7,0.96822,-0.13721,0.20908,-4.2342,0.1236,0.98935,0.076914,-37.289,-0.21741,-0.048629,0.97487,60.976 > fitmap #7 inMap #4 Fit molecule 240829_rMRP2_Vinblastine-Glu-coot-0.pdb (#7) to map cryosparc_P28_J27_006_volume_map_sharp.mrc (#4) using 11196 atoms average map value = 0.3363, steps = 96 shifted from previous position = 3.09 rotated from previous position = 14.9 degrees atoms outside contour = 3239, contour level = 0.1955 Position of 240829_rMRP2_Vinblastine-Glu-coot-0.pdb (#7) relative to cryosparc_P28_J27_006_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation 0.99999996 -0.00017468 -0.00021665 0.09518558 0.00017474 0.99999995 0.00026926 -0.12121246 0.00021661 -0.00026930 0.99999994 0.02611168 Axis -0.69535836 -0.55940720 0.45115445 Axis point 0.00000000 74.42087296 422.34775449 Rotation angle (degrees) 0.02218775 Shift along axis 0.01339944 > select subtract #7 Nothing selected > transparency #4,7 50 > volume #4 level 0.3184 > transparency #4,7 0 > save /Users/naito/Desktop/image17.png supersample 3 > transparency #4,7 30 > volume #4 level 0.3225 > save /Users/naito/Desktop/image18.png supersample 3 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M1 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: MacBookPro18,3 Model Number: Z15H000XGJ/A Chip: Apple M1 Pro Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 32 GB System Firmware Version: 10151.140.19 OS Loader Version: 10151.140.19 Software: System Software Overview: System Version: macOS 14.6.1 (23G93) Kernel Version: Darwin 23.6.0 Time since boot: 1日 4時間 9分 Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 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 P2422HE: 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 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