id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15982 Crash disconnecting hdmi projector, Mac, Qt 6.7.2 goddard@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.6.1-arm64-arm-64bit ChimeraX Version: 1.9.dev202407250342 (2024-07-25 03:42:42 UTC) Description Last time you used ChimeraX it crashed. I unplugged the hdmi connection to a projector while the laptop display was open and ChimeraX immediately crashed. Sadly this was in Qt 6.7.2 so apparently the problem is not fixed in latest Qt. Fatal Python error: Segmentation fault Thread 0x000000034fe6b000 (most recent call first): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Users/goddard/Library/Application Support/ChimeraX/1.9/lib/python/site-packages/tqdm/_monitor.py"", line 60 in run File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001ec5c0f40 (most recent call first): File 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""base"" : 0, ""uuid"" : ""00000000-0000-0000-0000-000000000000"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6535938048, ""CFBundleShortVersionString"" : ""6.9"", ""CFBundleIdentifier"" : ""com.apple.Foundation"", ""size"" : 12967936, ""uuid"" : ""c6949f67-60f6-3735-b583-bf1e069a8a0b"", ""path"" : ""\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation"", ""name"" : ""Foundation"", ""CFBundleVersion"" : ""2602"" } ], ""sharedCache"" : { ""base"" : 6512869376, ""size"" : 4214358016, ""uuid"" : ""bb3df3d3-38bd-304c-9233-e43de95f1903"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.8G resident=0K(0%) swapped_out_or_unallocated=1.8G(100%)\nWritable regions: Total=3.7G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.7G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 768K 41 \nColorSync 656K 31 \nCoreAnimation 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""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""644114de41e7236e6177f9bd"", ""factorPackIds"" : { }, ""deploymentId"" : 240000013 }, { ""rolloutId"" : ""64b21a7351cbb02ce3442e4e"", ""factorPackIds"" : { ""REMINDERS_GROCERY"" : ""659475af5595a45664475f23"" }, ""deploymentId"" : 240000037 } ], ""experiments"" : [ { ""treatmentId"" : ""c47ab4cc-c9c3-4b5d-a87c-e2433ce02597"", ""experimentId"" : ""6639bc6ba73d460582162323"", ""deploymentId"" : 400000006 }, { ""treatmentId"" : ""45f4e2a5-551b-4bc2-a2dc-19c244dda8f8"", ""experimentId"" : ""6643969b3099cf28e049862f"", ""deploymentId"" : 400000007 } ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.9.dev202407250342 (2024-07-25) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 8xps format mmcif fromDatabase pdb 8xps title: Structure of Nipah virus Bangladesh string G protein ectodomain monomer bound to single-domain antibody n425 at 3.22 Angstroms overall resolution [more info...] Chain information for 8xps #1 --- Chain | Description A | Nipah virus Bangladesh string G protein B | single-domain antibody n425 Non-standard residues in 8xps #1 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > color bychain > ui tool show ""Similar Structures"" > foldseek /A Found 194 similar structures to 8xps #1/A in pdb database using foldseek, name fs1 > similarstructures traces 194 traces showing 39457 residues with 25376 far or short segment residues hidden > lighting soft > similarstructures cluster /A:579,220,506,360,348 clusterDistance 1.5 Clustered 148 of 194 hits that have the specified 5 residues into 6 groups > similarstructures cluster /A:579,220,506,360,348 clusterDistance 1.5 > ofStructures > 1inh_A,6lxk_C,5nwe_C,8g3r_E,2ht5_A,8g3m_L,8g3o_H,4mc7_D,2cml_A,4b7j_A,2hu4_C,1iny_A,1nma_N,4k3y_C,2htv_A,2b8h_D,1l7g_A,4k3y_D,8g30_M,1nmb_N,5hug_A,7u4e_A,6lxi_B,7e6q_B,4mjv_A,4ks1_A,4mju_A,4d8s_A,6pzy_A,5hun_A,4wa3_A,4wa4_A,6q20_A,4gdj_A,4gdj_C,4gdj_B,4gdj_D,4gez_C,2aep_A,7s0i_A,6n6b_A,8dwb_AAA,5huk_D,6br5_A,4h52_A,4h53_D,4k1j_A,7u4g_A,6pzf_B,6pzd_A,4hzv_A,4hzy_A,6nn9_A,6g01_A,2bat_A,3cl2_E,3ckz_A,6v4n_I,6v4o_I,8g3z_C,1inf_A,4cpo_A,4cpl_A,1b9t_A,3k37_B,3k38_A,1a4g_A Clustered 66 of 67 hits that have the specified 5 residues into 2 groups > similarstructures ligands ofStructures > 1inh_A,6lxk_C,5nwe_C,8g3r_E,2ht5_A,8g3m_L,8g3o_H,4mc7_D,2cml_A,4b7j_A,2hu4_C,1iny_A,1nma_N,4k3y_C,2htv_A,2b8h_D,1l7g_A,4k3y_D,8g30_M,1nmb_N,5hug_A,7u4e_A,6lxi_B,7e6q_B,4mjv_A,4ks1_A,4mju_A,4d8s_A,6pzy_A,5hun_A,4wa3_A,4wa4_A,6q20_A,4gdj_A,4gdj_C,4gdj_B,4gdj_D,4gez_C,2aep_A,7s0i_A,6n6b_A,8dwb_AAA,5huk_D,6br5_A,4h52_A,4h53_D,4k1j_A,7u4g_A,6pzf_B,6pzd_A,4hzv_A,4hzy_A,6nn9_A,6g01_A,2bat_A,3cl2_E,3ckz_A,6v4n_I,6v4o_I,8g3z_C,1inf_A,4cpo_A,4cpl_A,1b9t_A,3k37_B,3k38_A,1a4g_A Found 4680 ligands in 57 hits: CA, EDO, EPE, GLC, GOL, HOH, NAG, SO4, YT3, ZMR > hide #2 models > show #2 models > hide #2 models > hide solvent > hide #1 atoms > hide #!3 models > show #!3 models > open 2cml 2cml title: Structure of Neuraminidase from English Duck Subtype N6 Complexed with 30 MM ZANAMIVIR, Crystal Soaked for 3 Hours at 291 K. [more info...] Chain information for 2cml #4 --- Chain | Description | UniProt A B C D | NEURAMINIDASE | Q6XV27_9INFA 88-476 1088-1476 2088-2476 3088-3476 Non-standard residues in 2cml #4 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) CA — calcium ion MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) ZMR — zanamivir (4-GUANIDINO-2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID; 4-guanidino-Neu5Ac2en; MODIFIED SIALIC ACID) Deleted 3 extra chains, 15 C-terminal residues, 1 N-terminal residues. Alignment of 2cml chain A to query has RMSD 1.33 using 71 of 329 paired residues within cutoff distance 2.0 > ui tool show ""Side View"" > sequence search #1/A Found 158 similar structures to 8xps #1/A in pdb database using mmseqs2, name mm1 > open /Users/goddard/Downloads/ChimeraX/Foldseek/8xps_foldseek_pdb_1.sms > format sms Summary of feedback from opening /Users/goddard/Downloads/ChimeraX/Foldseek/8xps_foldseek_pdb_1.sms --- note | Found 194 similar structures to 8xps #1/A in pdb database using foldseek, name fs1 Read 194 similar structures to 8xps #1/A in pdb database using foldseek, name fs1 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.9.dev202407250342 (2024-07-25) © 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 Max OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.0, Qt 6.7.1 Qt runtime version: 6.7.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,2 Model Number: MK1H3LL/A Chip: Apple M1 Max 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: 16 days, 19 hours, 3 minutes Graphics/Displays: Apple M1 Max: Chipset Model: Apple M1 Max Type: GPU Bus: Built-In Total Number of Cores: 32 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No 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: 2.14 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.7 ChimeraX-AtomicLibrary: 14.1.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.7 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13 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: 1.9.dev202407250342 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-DeepMutationalScan: 1.0 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: 1.3 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.3 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: 1.1.7 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 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: 2.1.5 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-NIHPresets: 1.1.18 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 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: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3 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: 3.1.5 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.13 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.3 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18 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: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.40.1 ChimeraX-Ummbas-Anaglyph: 0.1 ChimeraX-uniprot: 2.3.1 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: 1.8.2 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.1 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: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.3 jedi: 0.19.1 Jinja2: 3.1.4 joblib: 1.4.2 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 llvmlite: 0.43.0 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 numba: 0.60.0 numexpr: 2.10.1 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: 24.1.2 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt_toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 Pygments: 2.17.2 pynmrstar: 3.3.4 pynndescent: 0.5.13 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: 6.7.0 PyQt6-Qt6: 6.7.2 PyQt6-sip: 13.6.0 PyQt6-WebEngine: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.2 PyQt6-WebEngineSubwheel-Qt6: 6.7.2 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.2 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.32.3 scikit-learn: 1.5.1 scipy: 1.13.0 setuptools: 70.3.0 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: 2.0.6 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.8 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia_utils: 1.5.1 threadpoolctl: 3.5.0 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 tqdm: 4.66.4 traitlets: 5.14.2 typing_extensions: 4.12.2 tzdata: 2024.1 umap-learn: 0.5.6 urllib3: 2.2.2 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 can't reproduce all ChimeraX