id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8904 ChimeraX bug report submission chimerax-bug-report@… "{{{ The following bug report has been submitted: Platform: macOS-12.2.1-arm64-arm-64bit ChimeraX Version: 1.5rc202210270150 (2022-10-27 01:50:44 UTC) Description Last time you used ChimeraX it crashed. 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All rights reserved. How to cite UCSF ChimeraX > open > /Volumes/chand/Alphafold/AF2-Pred/Output/MTR4_PAPOLG_660_690/MTR4_PAPOLG_660_696.cxc > open > /Volumes/chand/Alphafold/AF2-Pred/Output/MTR4_PAPOLG_660_690/ranked_*.pdb Chain information for ranked_0.pdb #1 --- Chain | Description A | No description available B | No description available Chain information for ranked_1.pdb #2 --- Chain | Description A | No description available B | No description available Chain information for ranked_10.pdb #3 --- Chain | Description A | No description available B | No description available Chain information for ranked_11.pdb #4 --- Chain | Description A | No description available B | No description available Chain information for ranked_12.pdb #5 --- Chain | Description A | No description available B | No description available Chain information for ranked_13.pdb #6 --- Chain | Description A | No description available B | No description available Chain information for ranked_14.pdb #7 --- Chain | Description A | No description available B | No description available Chain information for ranked_15.pdb #8 --- Chain | Description A | No description available B | No description available Chain information for ranked_16.pdb #9 --- Chain | Description A | No description available B | No description available Chain information for ranked_17.pdb #10 --- Chain | Description A | No description available B | No description available Chain information for ranked_18.pdb #11 --- Chain | Description A | No description available B | No description available Chain information for ranked_19.pdb #12 --- Chain | Description A | No description available B | No description available Chain information for ranked_2.pdb #13 --- Chain | Description A | No description available B | No description available Chain information for ranked_20.pdb #14 --- Chain | Description A | No description available B | No description available Chain information for ranked_21.pdb #15 --- Chain | Description A | No description available B | No description available Chain information for ranked_22.pdb #16 --- Chain | Description A | No description available B | No description available Chain information for ranked_23.pdb #17 --- Chain | Description A | No description available B | No description available Chain information for ranked_24.pdb #18 --- Chain | Description A | No description available B | No description available Chain information for ranked_3.pdb #19 --- Chain | Description A | No description available B | No description available Chain information for ranked_4.pdb #20 --- Chain | Description A | No description available B | No description available Chain information for ranked_5.pdb #21 --- Chain | Description A | No description available B | No description available Chain information for ranked_6.pdb #22 --- Chain | Description A | No description available B | No description available Chain information for ranked_7.pdb #23 --- Chain | Description A | No description available B | No description available Chain information for ranked_8.pdb #24 --- Chain | Description A | No description available B | No description available Chain information for ranked_9.pdb #25 --- Chain | Description A | No description available B | No description available > name PAPOLG_660_690 /B > name MTR4 /A > color PAPOLG_660_690 dark magenta > color MTR4 cadet blue > set bgColor white > graphics silhouettes true > lighting depthCue false > mmaker all & ~#1 to #1/A 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 ranked_0.pdb, chain A (#1) with ranked_12.pdb, chain A (#5), sequence alignment score = 5316.8 RMSD between 719 pruned atom pairs is 0.271 angstroms; (across all 1042 pairs: 13.167) Matchmaker ranked_0.pdb, chain A (#1) with ranked_1.pdb, chain A (#2), sequence alignment score = 5372.6 RMSD between 982 pruned atom pairs is 0.445 angstroms; (across all 1042 pairs: 1.305) Matchmaker ranked_0.pdb, chain A (#1) with ranked_10.pdb, chain A (#3), sequence alignment score = 5340.2 RMSD between 920 pruned atom pairs is 0.595 angstroms; (across all 1042 pairs: 7.737) Matchmaker ranked_0.pdb, chain A (#1) with ranked_11.pdb, chain A (#4), sequence alignment score = 5351 RMSD between 694 pruned atom pairs is 0.289 angstroms; (across all 1042 pairs: 15.949) Matchmaker ranked_0.pdb, chain A (#1) with ranked_13.pdb, chain A (#6), sequence alignment score = 5337.2 RMSD between 701 pruned atom pairs is 0.301 angstroms; (across all 1042 pairs: 15.218) Matchmaker ranked_0.pdb, chain A (#1) with ranked_6.pdb, chain A (#22), sequence alignment score = 5352.2 RMSD between 883 pruned atom pairs is 0.824 angstroms; (across all 1042 pairs: 11.234) Matchmaker ranked_0.pdb, chain A (#1) with ranked_14.pdb, chain A (#7), sequence alignment score = 5346.8 RMSD between 925 pruned atom pairs is 0.618 angstroms; (across all 1042 pairs: 5.489) Matchmaker ranked_0.pdb, chain A (#1) with ranked_15.pdb, chain A (#8), sequence alignment score = 5324 RMSD between 714 pruned atom pairs is 0.307 angstroms; (across all 1042 pairs: 10.747) Matchmaker ranked_0.pdb, chain A (#1) with ranked_16.pdb, chain A (#9), sequence alignment score = 5348.6 RMSD between 714 pruned atom pairs is 0.326 angstroms; (across all 1042 pairs: 9.752) Matchmaker ranked_0.pdb, chain A (#1) with ranked_17.pdb, chain A (#10), sequence alignment score = 5339.6 RMSD between 729 pruned atom pairs is 0.319 angstroms; (across all 1042 pairs: 8.718) Matchmaker ranked_0.pdb, chain A (#1) with ranked_18.pdb, chain A (#11), sequence alignment score = 5320.4 RMSD between 721 pruned atom pairs is 0.304 angstroms; (across all 1042 pairs: 11.114) Matchmaker ranked_0.pdb, chain A (#1) with ranked_19.pdb, chain A (#12), sequence alignment score = 5319.2 RMSD between 726 pruned atom pairs is 0.286 angstroms; (across all 1042 pairs: 11.676) Matchmaker ranked_0.pdb, chain A (#1) with ranked_2.pdb, chain A (#13), sequence alignment score = 5375.6 RMSD between 996 pruned atom pairs is 0.283 angstroms; (across all 1042 pairs: 1.084) Matchmaker ranked_0.pdb, chain A (#1) with ranked_20.pdb, chain A (#14), sequence alignment score = 5339.6 RMSD between 803 pruned atom pairs is 0.550 angstroms; (across all 1042 pairs: 7.600) Matchmaker ranked_0.pdb, chain A (#1) with ranked_21.pdb, chain A (#15), sequence alignment score = 5325.2 RMSD between 731 pruned atom pairs is 0.305 angstroms; (across all 1042 pairs: 8.407) Matchmaker ranked_0.pdb, chain A (#1) with ranked_22.pdb, chain A (#16), sequence alignment score = 5346.2 RMSD between 731 pruned atom pairs is 0.321 angstroms; (across all 1042 pairs: 8.684) Matchmaker ranked_0.pdb, chain A (#1) with ranked_23.pdb, chain A (#17), sequence alignment score = 5357 RMSD between 932 pruned atom pairs is 0.673 angstroms; (across all 1042 pairs: 7.666) Matchmaker ranked_0.pdb, chain A (#1) with ranked_24.pdb, chain A (#18), sequence alignment score = 5334.2 RMSD between 725 pruned atom pairs is 0.322 angstroms; (across all 1042 pairs: 6.130) Matchmaker ranked_0.pdb, chain A (#1) with ranked_3.pdb, chain A (#19), sequence alignment score = 5366 RMSD between 982 pruned atom pairs is 0.675 angstroms; (across all 1042 pairs: 1.678) Matchmaker ranked_0.pdb, chain A (#1) with ranked_4.pdb, chain A (#20), sequence alignment score = 5368.4 RMSD between 981 pruned atom pairs is 0.510 angstroms; (across all 1042 pairs: 1.467) Matchmaker ranked_0.pdb, chain A (#1) with ranked_5.pdb, chain A (#21), sequence alignment score = 5336.6 RMSD between 926 pruned atom pairs is 0.593 angstroms; (across all 1042 pairs: 9.312) Matchmaker ranked_0.pdb, chain A (#1) with ranked_7.pdb, chain A (#23), sequence alignment score = 5352.2 RMSD between 701 pruned atom pairs is 0.310 angstroms; (across all 1042 pairs: 13.219) Matchmaker ranked_0.pdb, chain A (#1) with ranked_8.pdb, chain A (#24), sequence alignment score = 5352.2 RMSD between 930 pruned atom pairs is 0.553 angstroms; (across all 1042 pairs: 6.249) Matchmaker ranked_0.pdb, chain A (#1) with ranked_9.pdb, chain A (#25), sequence alignment score = 5359.4 RMSD between 973 pruned atom pairs is 0.774 angstroms; (across all 1042 pairs: 5.328) > color byelement > hide /A :1-80 cartoons executed MTR4_PAPOLG_660_696.cxc OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 OpenGL vendor: Apple 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: MacBookPro17,1 Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 7429.81.3 OS Loader Version: 7429.81.3 Software: System Software Overview: System Version: macOS 12.2.1 (21D62) Kernel Version: Darwin 21.3.0 Time since boot: 6 days 12:59 Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.0.8 Babel: 2.10.3 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: 1.41.4 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: 1.5rc202210270150 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: 1.24.2 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: 1.6.3 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.1.1 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.0 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: 5.0.0 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: 4.11.2 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 prompt-toolkit: 3.0.31 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: 2022.5 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.2.1 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: 0.5.1 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: 1.26.12 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 zipp: 3.10.0 }}} " defect new normal Unassigned