id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8745 Crash getting text input from Save dialog? chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-12.6.3-arm64-arm-64bit ChimeraX Version: 1.5rc202211160223 (2022-11-16 02:23:03 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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All rights reserved. How to cite UCSF ChimeraX > open /Users/lenz/Desktop/Nprotein_haddock.pdb format pdb Summary of feedback from opening /Users/lenz/Desktop/Nprotein_haddock.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK FILENAME=""complex_86w.pdb0"" Ignored bad PDB record found on line 2 REMARK =============================================================== Ignored bad PDB record found on line 3 REMARK HADDOCK run for complex Ignored bad PDB record found on line 4 REMARK initial structure: complex_86.pdb Ignored bad PDB record found on line 5 REMARK =============================================================== 29 messages similar to the above omitted Chain information for Nprotein_haddock.pdb #1 --- Chain | Description A B | No description available C D | No description available > rainbow > select add /B:178 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel bychain > select clear > color bychain > select add /A:115 12 atoms, 12 bonds, 1 residue, 1 model selected > select up 87 atoms, 92 bonds, 6 residues, 1 model selected > select up 1190 atoms, 1218 bonds, 124 residues, 1 model selected > hide sel cartoons > select clear > show cartoons > coulombic The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics: /A ALA 178 OXT /B ALA 178 OXT /C PHE 368 OXT /D PHE 368 OXT Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for Nprotein_haddock.pdb_A SES surface #1.1: minimum, -9.85, mean 1.54, maximum 12.78 Coulombic values for Nprotein_haddock.pdb_B SES surface #1.2: minimum, -9.72, mean 1.62, maximum 14.35 Coulombic values for Nprotein_haddock.pdb_C SES surface #1.3: minimum, -10.83, mean 0.56, maximum 12.96 Coulombic values for Nprotein_haddock.pdb_D SES surface #1.4: minimum, -11.37, mean 0.59, maximum 12.77 To also show corresponding color key, enter the above coulombic command and add key true > hide surfaces > rainbow > close #1 > open /Volumes/vonAppen-lab/vonAppen- > Swantje/alphapulldown_lem2/phd_course/predictions/N_protein_235-427_and_N_protein_235-427/ranked_0.pdb Chain information for ranked_0.pdb #1 --- Chain | Description B C | No description available > ui tool show AlphaFold > ui tool show ""AlphaFold Error Plot"" > alphafold pae #1 file /Volumes/vonAppen-lab/vonAppen- > Swantje/alphapulldown_lem2/phd_course/predictions/N_protein_235-427_and_N_protein_235-427/result_model_2_multimer_v3_pred_0.pkl > alphafold pae #1 colorDomains true > color #1/C:255-371 lime > color #1/B:263-363 magenta > color #1/B:372-427 lime > color #1/B:260-369 lime > color #1/C:255-370 lime > color #1/B:264-363 magenta > color #1/C:274-328 lime > color #1/B:281-327 magenta > color #1/C:295-307 lime > color #1/B:288-302 magenta > color bfactor #1 palette alphafold 3010 atoms, 386 residues, atom bfactor range 21.8 to 98.5 > color bychain > ui tool show ""AlphaFold Error Plot"" > alphafold pae #1 file /Volumes/vonAppen-lab/vonAppen- > Swantje/alphapulldown_lem2/phd_course/predictions/N_protein_235-427_and_N_protein_235-427/result_model_2_multimer_v3_pred_0.pkl > alphafold pae #1 colorDomains true > select add /B:371 7 atoms, 6 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel Drag select of 3 residues Drag select of 17 residues Drag select of 2 residues > select up 443 atoms, 448 bonds, 57 residues, 1 model selected > delete atoms sel > delete bonds sel Drag select of 2 residues > select up 1055 atoms, 1076 bonds, 135 residues, 1 model selected > select down 12 atoms, 2 residues, 1 model selected > select down 12 atoms, 2 residues, 1 model selected > select down 12 atoms, 2 residues, 1 model selected > show sel atoms > select clear Drag select of 7 atoms, 2 residues, 6 bonds > delete atoms sel > delete bonds sel > color bfactor #1 palette alphafold 2548 atoms, 326 residues, atom bfactor range 21.8 to 98.5 Drag select of 5 residues Drag select of 13 residues > select up 176 atoms, 175 bonds, 24 residues, 1 model selected > select up 1043 atoms, 1064 bonds, 133 residues, 1 model selected > select down 176 atoms, 175 bonds, 24 residues, 1 model selected > delete atoms sel > delete bonds sel > select add /B:260 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 20 atoms, 19 bonds, 3 residues, 1 model selected > select up 867 atoms, 888 bonds, 109 residues, 1 model selected > select down 20 atoms, 19 bonds, 3 residues, 1 model selected > delete atoms sel > delete bonds sel > rainbow > save N_dimer_disorder.pdb #1 > open /Users/lenz/Desktop/Nprotein_haddock.pdb format pdb Summary of feedback from opening /Users/lenz/Desktop/Nprotein_haddock.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK FILENAME=""complex_86w.pdb0"" Ignored bad PDB record found on line 2 REMARK =============================================================== Ignored bad PDB record found on line 3 REMARK HADDOCK run for complex Ignored bad PDB record found on line 4 REMARK initial structure: complex_86.pdb Ignored bad PDB record found on line 5 REMARK =============================================================== 29 messages similar to the above omitted Chain information for Nprotein_haddock.pdb #2 --- Chain | Description A B | No description available C D | No description available > 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 ranked_0.pdb, chain B (#1) with Nprotein_haddock.pdb, chain C (#2), sequence alignment score = 594.7 RMSD between 106 pruned atom pairs is 0.149 angstroms; (across all 106 pairs: 0.149) > hide #!1 models > color #2 bychain > color #2 #55bef0ff > show #!1 models > close #2 > close #1 > open /Users/lenz/Desktop/N_dimer_disorder.pdb format pdb Chain information for N_dimer_disorder.pdb #1 --- Chain | Description B C | No description available > open /Users/lenz/Documents/phd_course/presentation/c_term_disordered.pb Opened Pseudobonds c_term_disordered.pb, 15 bonds > color #2 #ffcc00ff models Drag select of 10 residues > select up 133 atoms, 132 bonds, 18 residues, 1 model selected > delete atoms sel > delete bonds sel Drag select of 2 residues > select up 49 atoms, 49 bonds, 6 residues, 1 model selected > delete atoms sel > delete bonds sel > hide #2 models Drag select of 34 residues > select up 692 atoms, 706 bonds, 90 residues, 1 model selected > select up 2170 atoms, 2219 bonds, 275 residues, 1 model selected > select down 692 atoms, 706 bonds, 90 residues, 1 model selected > select clear > color bychain > select add /B:278 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 39 atoms, 39 bonds, 5 residues, 1 model selected > select up 798 atoms, 818 bonds, 100 residues, 1 model selected > color sel #E6ABB7 > select clear > select add /C:332 6 atoms, 5 bonds, 1 residue, 1 model selected Drag select of 29 residues > select up 471 atoms, 479 bonds, 62 residues, 1 model selected > select up 2170 atoms, 2219 bonds, 275 residues, 1 model selected > select down 471 atoms, 479 bonds, 62 residues, 1 model selected > color sel #E6ABB7 > select clear Drag select of 6 residues > select up 166 atoms, 168 bonds, 21 residues, 1 model selected > select add /C:355 173 atoms, 174 bonds, 22 residues, 1 model selected > select up 261 atoms, 265 bonds, 32 residues, 1 model selected > color sel #E6ABB7 > select clear Drag select of 49 residues > select up 514 atoms, 520 bonds, 68 residues, 1 model selected > select up 2170 atoms, 2219 bonds, 275 residues, 1 model selected > select down 514 atoms, 520 bonds, 68 residues, 1 model selected > color sel #E6ABB7 > select clear Drag select of 19 residues > select up 301 atoms, 306 bonds, 35 residues, 1 model selected > color sel #E6ABB7 > select clear > select :370-392 188 atoms, 190 bonds, 23 residues, 1 model selected > show #2 models > select clear > style #2 dashes 0 Changed 1 pseudobond dash > lighting soft > set bgColor white > graphics silhouettes true > lighting gentle > select :370-392 188 atoms, 190 bonds, 23 residues, 1 model selected > color sel #E6C943 > select clear Drag select of 7 residues > select add /C:367 56 atoms, 6 bonds, 8 residues, 1 model selected Drag select of 10 residues > select up 495 atoms, 503 bonds, 64 residues, 1 model selected > select up 1372 atoms, 1401 bonds, 175 residues, 1 model selected > select down 495 atoms, 503 bonds, 64 residues, 1 model selected > color sel #AC3A00 > select clear > select add /C:263 7 atoms, 7 bonds, 1 residue, 1 model selected > select add /C:362 15 atoms, 14 bonds, 2 residues, 1 model selected > select add /C:363 23 atoms, 21 bonds, 3 residues, 1 model selected > select subtract /C:263 16 atoms, 14 bonds, 2 residues, 1 model selected > color sel #AC3A00 > select clear > select add /C:262 9 atoms, 8 bonds, 1 residue, 1 model selected > select add /C:263 16 atoms, 15 bonds, 2 residues, 1 model selected > color sel #E6ABB7 > select clear > ui tool show ""Side View"" > save /Users/lenz/Desktop/image35.png supersample 3 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.5rc202211160223 (2022-11-16) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 Pro 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: MacBookPro18,3 Chip: Apple M1 Pro Total Number of Cores: 8 (6 performance and 2 efficiency) Memory: 32 GB System Firmware Version: 8419.80.7 OS Loader Version: 7459.141.1 Software: System Software Overview: System Version: macOS 12.6.3 (21G419) Kernel Version: Darwin 21.6.0 Time since boot: 3 days 1:51 Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: PN-70TH5: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: On Mirror Status: Master Mirror Online: Yes Rotation: Supported Television: Yes Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Mirror: On Mirror Status: Hardware Mirror 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: 1.5rc202211160223 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: 1.6.3 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: 5.0.0 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: 5.0.0 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: 3.0.32 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: 0.6.1 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 closed normal Platform can't reproduce Tom Goddard all ChimeraX