id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14415 Crash using menus chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.2.1-arm64-arm-64bit ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description Last time you used ChimeraX it crashed. 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""com.apple.main-thread"" } }, ""logWritingSignature"" : ""3bab254f791129baaedb8ba77284bef7cc51f958"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""632e3df958740028737bffc0"", ""factorPackIds"" : { ""SIRI_UNDERSTANDING_NL_OVERRIDES"" : ""659c01d6f750153af8282e91"" }, ""deploymentId"" : 240000596 }, { ""rolloutId"" : ""62745b8e85854550ad70b6e4"", ""factorPackIds"" : { ""SIRI_TTS_DEVICE_TRAINING"" : ""6539d7f333b9b7499c6f1b63"" }, ""deploymentId"" : 240000073 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/syed.zawar/Desktop/PC_Data/Vannini > Lab/Manuscript/Figures/colorcoded_model.cxs"" Log from Tue Jan 16 18:11:27 2024UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/syed.zawar/Downloads/FL_OC1_Final_Isolde_Run2_real_space_refined_006_clean_trimmed.pdb Chain information for FL_OC1_Final_Isolde_Run2_real_space_refined_006_clean_trimmed.pdb #1 --- Chain | Description A | No description available C | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available > color /T medium purple > color /X salmon > color /Z pale goldenrod > color /b medium orchid > color /d dark khaki > color /e cyan > color /f lavender > color /g snow > color /h sky blue > color /i medium spring green > color /K medium aquamarine > color /L papaya whip > color /M olive > color /N cornflower blue > color /O light steel blue > color /P gold > color /Q light pink > color /S orange > color /U teal > color /Y plum > color /V royal blue > color /W deep sky blue > color /A pink > color /C burly wood > color /a coral > save ""/Users/syed.zawar/Desktop/PC_Data/Vannini > Lab/Manuscript/Figures/colorcoded_model.cxs"" ——— End of log from Tue Jan 16 18:11:27 2024 ——— opened ChimeraX session > open 7AEA 7aea title: Cryo-EM structure of human RNA Polymerase III elongation complex 2 [more info...] Chain information for 7aea #2 --- Chain | Description | UniProt A | DNA-directed RNA polymerase III subunit RPC1 | RPC1_HUMAN 1-1390 B | DNA-directed RNA polymerase III subunit RPC2 | RPC2_HUMAN 1-1133 C | DNA-directed RNA polymerases I and III subunit RPAC1 | RPAC1_HUMAN 1-346 D | DNA-directed RNA polymerase III subunit RPC9 | RPC9_HUMAN 1-148 E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | RPAB1_HUMAN 1-210 F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | RPAB2_HUMAN 1-127 G | DNA-directed RNA polymerase III subunit RPC8 | RPC8_HUMAN 1-204 H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | RPAB3_HUMAN 1-150 I | DNA-directed RNA polymerase III subunit RPC10 | RPC10_HUMAN 1-108 J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | RPAB5_HUMAN 1-67 K | DNA-directed RNA polymerases I and III subunit RPAC2 | RPAC2_HUMAN 1-133 L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | RPAB4_HUMAN 1-58 M | DNA-directed RNA polymerase III subunit RPC5 | RPC5_HUMAN 1-708 N | DNA-directed RNA polymerase III subunit RPC4 | RPC4_HUMAN 1-398 O | DNA-directed RNA polymerase III subunit RPC3 | RPC3_HUMAN 1-534 P | DNA-directed RNA polymerase III subunit RPC6 | RPC6_HUMAN 1-316 Q | DNA-directed RNA polymerase III subunit RPC7 | RPC7_HUMAN 1-223 R | RNA | S | Non-template DNA | T | Template DNA | Non-standard residues in 7aea #2 --- MG — magnesium ion SF4 — iron/sulfur cluster ZN — zinc ion > open 7AE1 7ae1 title: Cryo-EM structure of human RNA Polymerase III elongation complex 1 [more info...] Chain information for 7ae1 #3 --- Chain | Description | UniProt A | DNA-directed RNA polymerase III subunit RPC1 | RPC1_HUMAN 1-1390 B | DNA-directed RNA polymerase III subunit RPC2 | RPC2_HUMAN 1-1133 C | DNA-directed RNA polymerases I and III subunit RPAC1 | RPAC1_HUMAN 1-346 D | DNA-directed RNA polymerase III subunit RPC9 | RPC9_HUMAN 1-148 E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | RPAB1_HUMAN 1-210 F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | RPAB2_HUMAN 1-127 G | DNA-directed RNA polymerase III subunit RPC8 | RPC8_HUMAN 1-204 H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | RPAB3_HUMAN 1-150 I | DNA-directed RNA polymerase III subunit RPC10 | RPC10_HUMAN 1-108 J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | RPAB5_HUMAN 1-67 K | DNA-directed RNA polymerases I and III subunit RPAC2 | RPAC2_HUMAN 1-133 L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | RPAB4_HUMAN 1-58 M | DNA-directed RNA polymerase III subunit RPC5 | RPC5_HUMAN 1-708 N | DNA-directed RNA polymerase III subunit RPC4 | RPC4_HUMAN 1-398 O | DNA-directed RNA polymerase III subunit RPC3 | RPC3_HUMAN 1-534 P | DNA-directed RNA polymerase III subunit RPC6 | RPC6_HUMAN 1-316 Q | DNA-directed RNA polymerase III subunit RPC7 | RPC7_HUMAN 1-223 R | RNA | S | Non-template DNA | T | Template-DNA | Non-standard residues in 7ae1 #3 --- MG — magnesium ion SF4 — iron/sulfur cluster ZN — zinc ion > hide atoms > show cartoons > set bgColor white > lighting soft > graphics silhouettes true > ui tool show Matchmaker > matchmaker #1/T to #3/A pairing ss Parameters --- Chain pairing | ss 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 7ae1, chain A (#3) with FL_OC1_Final_Isolde_Run2_real_space_refined_006_clean_trimmed.pdb, chain T (#1), sequence alignment score = 6737.7 RMSD between 1200 pruned atom pairs is 1.028 angstroms; (across all 1381 pairs: 1.459) > color #1 #929000ff > color #2 #008f00ff > color #3 #009193ff > select #3/M:6-433 3211 atoms, 3282 bonds, 1 pseudobond, 400 residues, 2 models selected > select #2/M:6-422 3025 atoms, 3089 bonds, 2 pseudobonds, 375 residues, 2 models selected > select clear > select add #2 42422 atoms, 43304 bonds, 86 pseudobonds, 5271 residues, 4 models selected > select subtract #2 Nothing selected > select add #3 42608 atoms, 43497 bonds, 83 pseudobonds, 5296 residues, 4 models selected > select subtract #3 Nothing selected > ui tool show ""Side View"" > open ""/Users/syed.zawar/Desktop/PC_Data/Vannini > Lab/ModelBuilding/Model_building_into_states/OC1/OC1_Class0_P66_J325__localfilter.mrc"" Opened OC1_Class0_P66_J325__localfilter.mrc as #4, grid size 280,280,280, pixel 1.43, shown at level 0.365, step 2, values float32 > volume #4 step 1 > volume #4 level 1.048 > hide #!4 models > select #1/a 1184 atoms, 1216 bonds, 141 residues, 1 model selected > color/ a coral Unknown command: color/ a coral > color / a coral > color / C burly wood > color / #1 C burly wood Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #1/ C burly wood > color #1/ a coral > color #1/ A pink > select clear > save /Users/syed.zawar/Desktop/image78.png supersample 3 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,7 Model Number: Z16R000RDT/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 10151.61.4 OS Loader Version: 10151.61.4 Software: System Software Overview: System Version: macOS 14.2.1 (23C71) Kernel Version: Darwin 23.2.0 Time since boot: 14 days, 41 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal HP Z27k G3: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 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: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.21.0 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 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: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.6.0 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: 1.1.4 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: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 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-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 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: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 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: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Window Toolkit can't reproduce Tom Goddard all ChimeraX