id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8589 Unknown crash after selection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC) Description Last time you used ChimeraX it crashed. 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""usedImages"" : [ { ""size"" : 0, ""source"" : ""A"", ""base"" : 0, ""uuid"" : ""00000000-0000-0000-0000-000000000000"" } ], ""vmSummary"" : ""ReadOnly portion of Libraries: Total=182.4M resident=0K(0%) swapped_out_or_unallocated=182.4M(100%)\nWritable regions: Total=743.8M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=743.8M(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nKernel Alloc Once 8K 1 \nMALLOC 221.9M 111 \nMALLOC guard page 16K 4 \nMALLOC_LARGE (reserved) 128K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nSTACK GUARD 12K 3 \nStack 9752K 4 \nStack Guard 56.0M 1 \nVM_ALLOCATE 96.3M 8 \nVM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)\n__DATA 11K 1 \n__DATA_CONST 20K 1 \n__DATA_DIRTY 7K 1 \n__LINKEDIT 181.8M 1 \n__TEXT 596K 1 \ndyld private memory 256K 1 \nmapped file 81.6M 141 \nshared memory 20K 3 \n=========== ======= ======= \nTOTAL 1.0G 285 \nTOTAL, minus reserved VM space 648.0M 285 \n"", ""legacyInfo"" : { ""threadTriggered"" : { } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""6112e3d2fc54bc3389840661"", ""factorPackIds"" : { ""SIRI_TEXT_TO_SPEECH"" : ""63e590a947bae55eb0b06441"" }, ""deploymentId"" : 240000333 }, { ""rolloutId"" : ""63582c5f8a53461413999550"", ""factorPackIds"" : { }, ""deploymentId"" : 240000002 } ], ""experiments"" : [ ] }, ""reportNotes"" : [ ""dyld_process_snapshot_create_for_process failed with 5"" ] } ===== Log before crash start ===== Startup Errors --- error | Bundle 'ChimeraX-ISOLDE' custom initialization failed warning | Traceback (most recent call last): File ""/private/var/folders/vv/hpmpr_655t5ch8t1fncstg_m0000gp/T/AppTranslocation/DE38C9D8-A3E5-4EF7-952E-06884CC21B2A/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 484, in get_module m = importlib.import_module(self.package_name) File ""/private/var/folders/vv/hpmpr_655t5ch8t1fncstg_m0000gp/T/AppTranslocation/DE38C9D8-A3E5-4EF7-952E-06884CC21B2A/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/importlib/__init__.py"", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File """", line 1030, in _gcd_import File """", line 1007, in _find_and_load File """", line 986, in _find_and_load_unlocked File """", line 680, in _load_unlocked File """", line 850, in exec_module File """", line 228, in _call_with_frames_removed File ""/Users/andreaswisniewski/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/isolde/__init__.py"", line 51, in __version__ = _version() File ""/Users/andreaswisniewski/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/isolde/__init__.py"", line 49, in _version return pkg_resources.require('ChimeraX-ISOLDE')[0].version File ""/private/var/folders/vv/hpmpr_655t5ch8t1fncstg_m0000gp/T/AppTranslocation/DE38C9D8-A3E5-4EF7-952E-06884CC21B2A/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/pkg_resources/__init__.py"", line 886, in require needed = self.resolve(parse_requirements(requirements)) File ""/private/var/folders/vv/hpmpr_655t5ch8t1fncstg_m0000gp/T/AppTranslocation/DE38C9D8-A3E5-4EF7-952E-06884CC21B2A/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/pkg_resources/__init__.py"", line 772, in resolve raise DistributionNotFound(req, requirers) pkg_resources.DistributionNotFound: The 'ChimeraX-Clipper~=0.17.0' distribution was not found and is required by ChimeraX-ISOLDE During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/private/var/folders/vv/hpmpr_655t5ch8t1fncstg_m0000gp/T/AppTranslocation/DE38C9D8-A3E5-4EF7-952E-06884CC21B2A/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 359, in initialize api = self._get_api(session.logger) File ""/private/var/folders/vv/hpmpr_655t5ch8t1fncstg_m0000gp/T/AppTranslocation/DE38C9D8-A3E5-4EF7-952E-06884CC21B2A/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 503, in _get_api m = self.get_module() File ""/private/var/folders/vv/hpmpr_655t5ch8t1fncstg_m0000gp/T/AppTranslocation/DE38C9D8-A3E5-4EF7-952E-06884CC21B2A/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 486, in get_module raise ToolshedError(""Error importing bundle %s's module: %s"" % (self.name, str(e))) chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's module: The 'ChimeraX-Clipper~=0.17.0' distribution was not found and is required by ChimeraX-ISOLDE UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/andreaswisniewski/Desktop/ADAPT_IL17/IL17c/Structure_ChimeraX/ADAPT_IL17c_7.pdb > format pdb ADAPT_IL17c_7.pdb title: SWISS-MODEL SERVER (https://swissmodel.expasy.org) Template Alignment: 1gjt.1 [more info...] Chain information for ADAPT_IL17c_7.pdb #1 --- Chain | Description A | No description available > coulombic Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for ADAPT_IL17c_7.pdb_A SES surface #1.1: minimum, -16.86, mean -4.14, maximum 7.11 To also show corresponding color key, enter the above coulombic command and add key true > show surfaces > hide atoms > hide cartoons > hide surfaces > show surfaces > color byhetero > color bychain > hide surfaces > show atoms > show cartoons > hide atoms Alignment identifier is 1/A > select /A:5-23,27-34,39-52 330 atoms, 335 bonds, 41 residues, 1 model selected > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > color sel bynucleotide > color sel bypolymer > rainbow sel > mlp sel Map values for surface ""ADAPT_IL17c_7.pdb_A SES surface"": minimum -23.61, mean -1.771, maximum 23.02 To also show corresponding color key, enter the above mlp command and add key true > mlp sel Map values for surface ""ADAPT_IL17c_7.pdb_A SES surface"": minimum -23.61, mean -1.771, maximum 23.02 To also show corresponding color key, enter the above mlp command and add key true > hide sel surfaces > mlp sel Map values for surface ""ADAPT_IL17c_7.pdb_A SES surface"": minimum -23.61, mean -1.771, maximum 23.02 To also show corresponding color key, enter the above mlp command and add key true > hide sel cartoons > hide sel surfaces > hide sel cartoons > hide sel atoms > show sel cartoons > hide sel atoms > hide sel cartoons > style sel stick Changed 330 atom styles > style sel sphere Changed 330 atom styles > style sel ball Changed 330 atom styles > show sel cartoons > coulombic sel Coulombic values for ADAPT_IL17c_7.pdb_A SES surface #1.1: minimum, -16.86, mean -4.14, maximum 7.11 To also show corresponding color key, enter the above coulombic command and add key true > hide sel surfaces > coulombic sel Coulombic values for ADAPT_IL17c_7.pdb_A SES surface #1.1: minimum, -16.86, mean -4.14, maximum 7.11 To also show corresponding color key, enter the above coulombic command and add key true > ui tool show ""Show Sequence Viewer"" > sequence chain /A Destroying pre-existing alignment with identifier 1/A Alignment identifier is 1/A ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/andreaswisniewski/Desktop/ADAPT_IL17/IL17c/Structure_ChimeraX/ADAPT_IL17c_7.pdb > format pdb ADAPT_IL17c_7.pdb title: SWISS-MODEL SERVER (https://swissmodel.expasy.org) Template Alignment: 1gjt.1 [more info...] Chain information for ADAPT_IL17c_7.pdb #1 --- Chain | Description A | No description available Alignment identifier is 1/A > select /A:5-23,27-34,39-52 330 atoms, 335 bonds, 41 residues, 1 model selected OpenGL version: 4.1 INTEL-20.2.50 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655 OpenGL vendor: Intel Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro15,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2,4 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1916.80.2.0.0 (iBridge: 20.16.3045.0.0,0) OS Loader Version: 564.40.4~66 Software: System Software Overview: System Version: macOS 13.2.1 (22D68) Kernel Version: Darwin 22.3.0 Time since boot: 2 days, 13 hours, 41 minutes Graphics/Displays: Intel Iris Plus Graphics 655: Chipset Model: Intel Iris Plus Graphics 655 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3ea5 Revision ID: 0x0001 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.1.0 Babel: 2.11.0 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.4 ChimeraX-AddH: 2.2.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.6 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.41.5 ChimeraX-AtomicLibrary: 8.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.4 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.5 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 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-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.8 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.8 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 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 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.7.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.24.3 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.4 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.2.0 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.7.31 imagesize: 1.4.1 importlib-metadata: 5.1.0 ipykernel: 6.15.3 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 5.1.0 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.4 numpy: 1.23.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.2.0 pip: 22.2.2 pkginfo: 1.8.3 platformdirs: 2.5.4 prompt-toolkit: 3.0.33 psutil: 5.9.1 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2022.6 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.3.0 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.0 setuptools: 65.1.1 setuptools-scm: 7.0.5 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 typing-extensions: 4.4.0 urllib3: 1.26.13 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 zipp: 3.11.0 }}} " defect closed normal Core can't reproduce Tom Goddard all ChimeraX