id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16820 Crash in event loop chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-12.5-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Bus error Thread 0x000000029bafb000 (most recent call first): File ""/Users/nardinabdalla/Desktop/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Users/nardinabdalla/Desktop/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Users/nardinabdalla/Desktop/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Users/nardinabdalla/Desktop/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Users/nardinabdalla/Desktop/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x0000000101098580 (most recent call first): File ""/Users/nardinabdalla/Desktop/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop File ""/Users/nardinabdalla/Desktop/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Users/nardinabdalla/Desktop/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, 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""deploymentId"" : 240000002 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/nardinabdalla/Desktop/Cas9 Structure /Cas9 structure > activity_1.cxs"" opened ChimeraX session > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Alignment identifier is 1/A ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/nardinabdalla/Desktop/Cas9 Structure /Cas9 structure > activity_1.cxs"" Log from Sun Feb 9 13:21:56 2025 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/nardinabdalla/Desktop/Cas9 Structure / 4cmp_apo..pdb"" 4cmp_apo..pdb title: Crystal structure of S. Pyogenes CAS9 [more info...] Chain information for 4cmp_apo..pdb #1 --- Chain | Description | UniProt A B | CAS9 | CAS9_STRP1 1-1368 Non-standard residues in 4cmp_apo..pdb #1 --- MG — magnesium ion SO4 — sulfate ion Cell requested for row 0 is out of bounds for table with 0 rows! Resizing table model. [Repeated 5 time(s)] > select /B:4-1363 19284 atoms, 19436 bonds, 16 pseudobonds, 1166 residues, 2 models selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) Drag select of 15 atoms, 1 pseudobonds, 8 bonds > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) Drag select of 5 atoms, 4 bonds > delete atoms sel > delete bonds sel > open ""/Users/nardinabdalla/Desktop/Cas9 Structure /4zt0_NoRNA.pdb"" 4zt0_NoRNA.pdb title: Crystal structure of catalytically-active streptococcus pyogenes CAS9 In complex with single-guide RNA At 2.9 angstrom resolution [more info...] Chain information for 4zt0_NoRNA.pdb #2 --- Chain | Description A C | crispr-associated endonuclease CAS9 B D | single-guide RNA Cell requested for row 0 is out of bounds for table with 0 rows! Resizing table model. [Repeated 11 time(s)] > select #2/C:4-1366 10046 atoms, 10220 bonds, 9 pseudobonds, 1296 residues, 2 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > select #2/B:11-82 1545 atoms, 1732 bonds, 72 residues, 1 model selected > delete atoms sel > delete bonds sel > select #2/D:11-82 1545 atoms, 1732 bonds, 72 residues, 1 model selected > delete atoms sel > delete bonds sel > open ""/Users/nardinabdalla/Desktop/Cas9 Structure / 4un3_NoNuc..pdb"" 4un3_NoNuc..pdb title: Crystal structure of CAS9 bound to pam-containing DNA target [more info...] Chain information for 4un3_NoNuc..pdb #3 --- Chain | Description | UniProt A | SGRNA | B | CAS9 | CAS9_STRP1 1-1368 C | target DNA strand | D | non-target DNA strand | Non-standard residues in 4un3_NoNuc..pdb #3 --- MG — magnesium ion Cell requested for row 0 is out of bounds for table with 0 rows! Resizing table model. [Repeated 11 time(s)] > select #3/A:1-81 1732 atoms, 1942 bonds, 81 residues, 1 model selected > delete atoms sel > delete bonds sel > select #3/C:1-28 567 atoms, 634 bonds, 28 residues, 1 model selected > delete atoms sel > delete bonds sel > select #3/D:2-12 227 atoms, 255 bonds, 11 residues, 1 model selected > delete atoms sel > delete bonds sel > open ""/Users/nardinabdalla/Desktop/Cas9 Structure /4zt0_RNP.pdb"" 4zt0_RNP.pdb title: Crystal structure of catalytically-active streptococcus pyogenes CAS9 In complex with single-guide RNA At 2.9 angstrom resolution [more info...] Chain information for 4zt0_RNP.pdb #4 --- Chain | Description A C | crispr-associated endonuclease CAS9 B D | single-guide RNA Cell requested for row 0 is out of bounds for table with 0 rows! Resizing table model. [Repeated 11 time(s)] > select #4/C:4-1366 10046 atoms, 10220 bonds, 9 pseudobonds, 1296 residues, 2 models selected > delete atoms (#!4 & sel) > delete bonds (#!4 & sel) > select #4/D:11-82 1545 atoms, 1732 bonds, 72 residues, 1 model selected > delete atoms sel > delete bonds sel > open ""/Users/nardinabdalla/Desktop/Cas9 Structure /4un3_DNA_RNP.pdb"" 4un3_DNA_RNP.pdb title: Crystal structure of CAS9 bound to pam-containing DNA target [more info...] Chain information for 4un3_DNA_RNP.pdb #5 --- Chain | Description | UniProt A | SGRNA | B | CAS9 | CAS9_STRP1 1-1368 C | target DNA strand | D | non-target DNA strand | Non-standard residues in 4un3_DNA_RNP.pdb #5 --- MG — magnesium ion > ui tool show Matchmaker > matchmaker #!1-3,5 to #4 Computing secondary structure [Repeated 4 time(s)] Parameters --- Chain pairing | bb 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 4zt0_RNP.pdb, chain A (#4) with 4cmp_apo..pdb, chain A (#1), sequence alignment score = 6340 RMSD between 461 pruned atom pairs is 0.839 angstroms; (across all 1144 pairs: 34.831) Matchmaker 4zt0_RNP.pdb, chain A (#4) with 4zt0_NoRNA.pdb, chain A (#2), sequence alignment score = 6996.2 RMSD between 1364 pruned atom pairs is 0.000 angstroms; (across all 1364 pairs: 0.000) Matchmaker 4zt0_RNP.pdb, chain A (#4) with 4un3_NoNuc..pdb, chain B (#3), sequence alignment score = 6562.2 RMSD between 358 pruned atom pairs is 0.640 angstroms; (across all 1306 pairs: 11.172) Matchmaker 4zt0_RNP.pdb, chain A (#4) with 4un3_DNA_RNP.pdb, chain B (#5), sequence alignment score = 6562.2 RMSD between 358 pruned atom pairs is 0.640 angstroms; (across all 1306 pairs: 11.172) > save ""/Users/nardinabdalla/Desktop/Cas9 Structure /Cas9 structure > activity_1.cxs"" ——— End of log from Sun Feb 9 13:21:56 2025 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac14,2 Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 7459.141.1 OS Loader Version: 7459.141.1 Software: System Software Overview: System Version: macOS 12.5 (21G72) Kernel Version: Darwin 21.6.0 Time since boot: 59 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 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ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 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: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 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: 1.18.1 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: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 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: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 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0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Core can't reproduce Tom Goddard all ChimeraX