id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6755 Unknown crash chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description Last time you used ChimeraX it crashed. 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(unallocated)\nMach message 24K 5 \nOpenGL GLSL 384K 5 \nSTACK GUARD 100K 25 \nStack 241.7M 26 \nStack Guard 56.0M 1 \nVM_ALLOCATE 87.8M 148 \nVM_ALLOCATE (reserved) 12K 2 reserved VM address space (unallocated)\n__DATA 16K 1 \n__DATA_CONST 80K 1 \n__LINKEDIT 208K 2 \n__TEXT 432K 1 \ndyld private memory 1024K 1 \nmapped file 827.8M 461 \nshared memory 5828K 37 \n=========== ======= ======= \nTOTAL 1.9G 1564 \nTOTAL, minus reserved VM space 1.7G 1564 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""60da5e84ab0ca017dace9abf"", ""factorPackIds"" : { }, ""deploymentId"" : 240000008 }, { ""rolloutId"" : ""5fc94383418129005b4e9ae0"", ""factorPackIds"" : { }, ""deploymentId"" : 240000359 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet 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/inouechuumu/書類管理/実験データ管理/分子微生物科学研究室/I-TASSER/42-F6-hm502/S682207_results/model1.pdb Chain information for model1.pdb #1 --- Chain | Description A | No description available > rainbow > open /Users/inouechuumu/Downloads/threading1.pdb Summary of feedback from opening /Users/inouechuumu/Downloads/threading1.pdb --- warnings | Ignored bad PDB record found on line 1 Rank :1 Template name:7abw_B Ignored bad PDB record found on line 2 REMARK :Column 1 - 30 present Atom & Residue records of query sequence. Ignored bad PDB record found on line 3 REMARK :Column 31 - 54 present XYZ coordinates of query sequence obtained after threading alignment. Ignored bad PDB record found on line 4 REMARK :Column 55 - 59 present residue number in Template Ignored bad PDB record found on line 5 REMARK :Column 60 - 59 present residue name of Template 355 messages similar to the above omitted > open /Users/inouechuumu/Downloads/threading1.pdb Summary of feedback from opening /Users/inouechuumu/Downloads/threading1.pdb --- warnings | Ignored bad PDB record found on line 1 Rank :1 Template name:7abw_B Ignored bad PDB record found on line 2 REMARK :Column 1 - 30 present Atom & Residue records of query sequence. Ignored bad PDB record found on line 3 REMARK :Column 31 - 54 present XYZ coordinates of query sequence obtained after threading alignment. Ignored bad PDB record found on line 4 REMARK :Column 55 - 59 present residue number in Template Ignored bad PDB record found on line 5 REMARK :Column 60 - 59 present residue name of Template 355 messages similar to the above omitted > open /Users/inouechuumu/Downloads/threading1.pdb Summary of feedback from opening /Users/inouechuumu/Downloads/threading1.pdb --- warnings | Ignored bad PDB record found on line 1 Rank :1 Template name:7abw_B Ignored bad PDB record found on line 2 REMARK :Column 1 - 30 present Atom & Residue records of query sequence. Ignored bad PDB record found on line 3 REMARK :Column 31 - 54 present XYZ coordinates of query sequence obtained after threading alignment. Ignored bad PDB record found on line 4 REMARK :Column 55 - 59 present residue number in Template Ignored bad PDB record found on line 5 REMARK :Column 60 - 59 present residue name of Template 355 messages similar to the above omitted > open /Users/inouechuumu/Downloads/threading1.pdb Summary of feedback from opening /Users/inouechuumu/Downloads/threading1.pdb --- warnings | Ignored bad PDB record found on line 1 Rank :1 Template name:7abw_B Ignored bad PDB record found on line 2 REMARK :Column 1 - 30 present Atom & Residue records of query sequence. Ignored bad PDB record found on line 3 REMARK :Column 31 - 54 present XYZ coordinates of query sequence obtained after threading alignment. Ignored bad PDB record found on line 4 REMARK :Column 55 - 59 present residue number in Template Ignored bad PDB record found on line 5 REMARK :Column 60 - 59 present residue name of Template 355 messages similar to the above omitted > open /Users/inouechuumu/Downloads/threading1.pdb Summary of feedback from opening /Users/inouechuumu/Downloads/threading1.pdb --- warnings | Ignored bad PDB record found on line 1 Rank :1 Template name:7abw_B Ignored bad PDB record found on line 2 REMARK :Column 1 - 30 present Atom & Residue records of query sequence. Ignored bad PDB record found on line 3 REMARK :Column 31 - 54 present XYZ coordinates of query sequence obtained after threading alignment. Ignored bad PDB record found on line 4 REMARK :Column 55 - 59 present residue number in Template Ignored bad PDB record found on line 5 REMARK :Column 60 - 59 present residue name of Template 355 messages similar to the above omitted > open /Users/inouechuumu/Downloads/threading1.pdb Summary of feedback from opening /Users/inouechuumu/Downloads/threading1.pdb --- warnings | Ignored bad PDB record found on line 1 Rank :1 Template name:7abw_B Ignored bad PDB record found on line 2 REMARK :Column 1 - 30 present Atom & Residue records of query sequence. Ignored bad PDB record found on line 3 REMARK :Column 31 - 54 present XYZ coordinates of query sequence obtained after threading alignment. Ignored bad PDB record found on line 4 REMARK :Column 55 - 59 present residue number in Template Ignored bad PDB record found on line 5 REMARK :Column 60 - 59 present residue name of Template 355 messages similar to the above omitted > open /Users/inouechuumu/Downloads/threading1.pdb Summary of feedback from opening /Users/inouechuumu/Downloads/threading1.pdb --- warnings | Ignored bad PDB record found on line 1 Rank :1 Template name:7abw_B Ignored bad PDB record found on line 2 REMARK :Column 1 - 30 present Atom & Residue records of query sequence. Ignored bad PDB record found on line 3 REMARK :Column 31 - 54 present XYZ coordinates of query sequence obtained after threading alignment. Ignored bad PDB record found on line 4 REMARK :Column 55 - 59 present residue number in Template Ignored bad PDB record found on line 5 REMARK :Column 60 - 59 present residue name of Template 355 messages similar to the above omitted > select #1 8456 atoms, 8552 bonds, 529 residues, 1 model selected > ~select #1 Nothing selected > hide #1 models > open /Users/inouechuumu/Downloads/threading1.pdb Summary of feedback from opening /Users/inouechuumu/Downloads/threading1.pdb --- warnings | Ignored bad PDB record found on line 1 Rank :1 Template name:7abw_B Ignored bad PDB record found on line 2 REMARK :Column 1 - 30 present Atom & Residue records of query sequence. Ignored bad PDB record found on line 3 REMARK :Column 31 - 54 present XYZ coordinates of query sequence obtained after threading alignment. Ignored bad PDB record found on line 4 REMARK :Column 55 - 59 present residue number in Template Ignored bad PDB record found on line 5 REMARK :Column 60 - 59 present residue name of Template 355 messages similar to the above omitted > open /Users/inouechuumu/Downloads/7abw.pdb 7abw.pdb title: Crystal structure of siderophore reductase foxb [more info...] Chain information for 7abw.pdb #2 --- Chain | Description A | peptidase B | peptidase Non-standard residues in 7abw.pdb #2 --- DMU — decyl-β-D-maltopyranoside (decylmaltoside) HEM — protoporphyrin IX containing Fe (HEME) PE5 — 3,6,9,12,15,18,21,24-octaoxahexacosan-1-ol (2-(2-{2-[2-(2-{2-[2-(2-ethoxy- ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethanol; polyethyleneglycol PEG400) ZN — zinc ion > show #1 models > ui tool show Matchmaker > matchmaker #!2 to #1 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 model1.pdb, chain A (#1) with 7abw.pdb, chain B (#2), sequence alignment score = 169.6 RMSD between 6 pruned atom pairs is 1.301 angstroms; (across all 320 pairs: 47.160) > color #1 #fffb00 transparency 0 > color bynucleotide Alignment identifier is 1/A Alignment identifier is 2/A Alignment identifier is 2/B Destroying pre-existing alignment with identifier 1/A Alignment identifier is 1/A Destroying pre-existing alignment with identifier 2/A Alignment identifier is 2/A Destroying pre-existing alignment with identifier 2/B Alignment identifier is 2/B > select #1/A:54-55 34 atoms, 35 bonds, 2 residues, 1 model selected > select #1/A:54-65 185 atoms, 189 bonds, 12 residues, 1 model selected > select > #1/A:10-15,35-51,100-106,108-115,134-145,158-171,193-214,218-224,247-249,256-266,268-274,327-339,348-351,358-378,385-415,422-445,453-484,488-511,523-527 4266 atoms, 4288 bonds, 268 residues, 1 model selected > select #2/A:92 11 atoms, 10 bonds, 1 residue, 1 model selected > select #2/A:92-101 77 atoms, 77 bonds, 10 residues, 1 model selected > select #2/A:141 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:141-219 486 atoms, 505 bonds, 1 pseudobond, 61 residues, 2 models selected > select #2/A:161-226 381 atoms, 394 bonds, 1 pseudobond, 48 residues, 2 models selected > select #2/A:161-234 443 atoms, 458 bonds, 1 pseudobond, 56 residues, 2 models selected ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-18.5.8 OpenGL renderer: Intel(R) UHD Graphics 617 OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: MacBookAir8,1 Processor Name: Dual-Core Intel Core i5 Processor Speed: 1.6 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 4 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1731.100.130.0.0 (iBridge: 19.16.14243.0.0,0) OS Loader Version: 540.100.7~23 Software: System Software Overview: System Version: macOS 12.3.1 (21E258) Kernel Version: Darwin 21.4.0 Time since boot: 5 days 12:21 Graphics/Displays: Intel UHD Graphics 617: Chipset Model: Intel UHD Graphics 617 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x87c0 Revision ID: 0x0002 Metal Family: Supported, Metal GPUFamily macOS 2 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: No Connection Type: Internal Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.5.30 cftime: 1.5.1.1 charset-normalizer: 2.0.9 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 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 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 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 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.7 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.8.0 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.3 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 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 suds-jurko: 0.6 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 }}} " defect closed normal Depiction can't reproduce Tom Goddard all ChimeraX