id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15666 Deleting chain B of 3h7s leads to a crash goddard@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.5-arm64-arm-64bit ChimeraX Version: 1.9.dev202407240247 (2024-07-24 02:47:28 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. The following sequence causes a crash. The PDB 3h7s has something weird about it as evidenced by two chain Bs listed in the log when it is opened. open 3h7s delete /B # In Python shell m = session.models[0] m.chains[1].existing_residues.ribbon_displays = True Fatal Python error: Segmentation fault Thread 0x000000035de13000 (most recent call first): File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 561 in select File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/asyncio/base_events.py"", line 1884 in _run_once File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/asyncio/base_events.py"", line 607 in run_forever File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tornado/platform/asyncio.py"", line 205 in start File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ipykernel/iostream.py"", line 92 in _thread_main File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000035ce07000 (most recent call first): File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 320 in wait File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/IPython/core/history.py"", line 903 in run File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/IPython/core/history.py"", line 61 in only_when_enabled File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/decorator.py"", line 232 in fun File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001fa614c00 (most recent call first): File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py"", line 234 in set_prop File ""/var/folders/jb/f14hkn9s19l691b68w_lvm0w0000gn/T/ipykernel_75239/3694637564.py"", line 1 in File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/IPython/core/interactiveshell.py"", line 3577 in run_code File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/IPython/core/interactiveshell.py"", line 3517 in run_ast_nodes File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/IPython/core/interactiveshell.py"", line 3334 in run_cell_async File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/IPython/core/async_helpers.py"", line 128 in _pseudo_sync_runner File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/IPython/core/interactiveshell.py"", line 3130 in _run_cell File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/IPython/core/interactiveshell.py"", line 3075 in run_cell File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ipykernel/zmqshell.py"", line 549 in run_cell File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ipykernel/ipkernel.py"", line 449 in do_execute File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ipykernel/kernelbase.py"", line 778 in execute_request File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ipykernel/ipkernel.py"", line 362 in execute_request File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ipykernel/inprocess/ipkernel.py"", line 81 in execute_request File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ipykernel/kernelbase.py"", line 437 in dispatch_shell File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/asyncio/events.py"", line 80 in _run File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/asyncio/base_events.py"", line 1922 in _run_once File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/asyncio/base_events.py"", line 607 in run_forever File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/asyncio/base_events.py"", line 640 in run_until_complete File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/jupyter_core/utils/__init__.py"", line 165 in wrapped File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ipykernel/inprocess/client.py"", line 195 in _dispatch_to_kernel File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ipykernel/inprocess/client.py"", line 119 in execute File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/qtconsole/frontend_widget.py"", line 288 in _execute File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/qtconsole/console_widget.py"", line 680 in do_execute File ""/Users/goddard/Desktop/ChimeraX July 24 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/qtconsole/history_console_widget.py"", line 42 in do_execute File ""/Users/goddard/Desktop/ChimeraX 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""66873a7bac50a445f5985ee3"" }, ""deploymentId"" : 240000215 } ], ""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.dev202407240247 (2024-07-24) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 3h7s Summary of feedback from opening 3h7s fetched from pdb --- warnings | Ignoring microheterogeneity for label_seq_id 63 in chain A Ignoring microheterogeneity for label_seq_id 63 in chain B 3h7s title: Crystal structures of K63-linked di- and tri-ubiquitin reveal a highly extended chain architecture [more info...] Chain information for 3h7s #1 --- Chain | Description | UniProt A B | Ubiquitin | UBIQ_HUMAN 1-76 B | Ubiquitin | UBIQ_HUMAN 1-76 Non-standard residues in 3h7s #1 --- ZN — zinc ion 3h7s mmCIF Assemblies --- 1| author_defined_assembly 2| software_defined_assembly 3| software_defined_assembly 19 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > ui tool show Shell > delete /B ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.9.dev202407240247 (2024-07-24) © 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 M2 Ultra 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: Mac Studio Model Identifier: Mac14,14 Model Number: Z1800003VLL/A Chip: Apple M2 Ultra Total Number of Cores: 24 (16 performance and 8 efficiency) Memory: 64 GB System Firmware Version: 10151.121.1 OS Loader Version: 10151.121.1 Software: System Software Overview: System Version: macOS 14.5 (23F79) Kernel Version: Darwin 23.5.0 Time since boot: 36 days, 19 hours, 13 minutes Graphics/Displays: Apple M2 Ultra: Chipset Model: Apple M2 Ultra Type: GPU Bus: Built-In Total Number of Cores: 60 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: PHL 278B1: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes 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 biopython: 1.83 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: 1.58.3 ChimeraX-AtomicLibrary: 14.1.1 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: 2.13 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: 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ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.7 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-maskChains: 1.1 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: 1.1.19 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-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: 1.39.8 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 fsspec: 2024.3.1 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: 0.42.0 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 mpmath: 1.3.0 mrcfile: 1.5.0 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: 0.59.1 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: 0.5.12 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: 6.7.0 PyQt6-Qt6: 6.7.2 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 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: 1.4.2 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 sympy: 1.12 tables: 3.8.0 tcia_utils: 1.5.1 threadpoolctl: 3.5.0 tifffile: 2024.1.30 tinyarray: 1.2.4 torch: 2.3.0 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 Core fixed Greg Couch all ChimeraX