id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8944 Crash using color panel chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.6.dev202302010904 (2023-02-01 09:04:26 UTC) Description Last time you used ChimeraX it crashed. 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""rolloutId"" : ""5fb4245a1bbfe8005e33a1e1"", ""factorPackIds"" : { }, ""deploymentId"" : 240000021 } ], ""experiments"" : [ { ""treatmentId"" : ""c28e4ee6-1b08-4f90-8e05-2809e78310a3"", ""experimentId"" : ""6317d2003d24842ff850182a"", ""deploymentId"" : 400000013 }, { ""treatmentId"" : ""6dd670af-0633-45e4-ae5f-122ae4df02be"", ""experimentId"" : ""64406ba83deb637ac8a04419"", ""deploymentId"" : 900000005 } ] } } Log: UCSF ChimeraX version: 1.6.dev202302010904 (2023-02-01) © 2016-2023 Regents of the University of California. All rights reserved. > open /Users/michael/Library/CloudStorage/OneDrive- > Personal/Documents/PhD/Structures/Proteins/1774_closed/chimeraX_docked.cxs Log from Mon May 23 10:33:57 2022UCSF ChimeraX version: 1.4rc202205060510 (2022-05-06) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/michael/Library/CloudStorage/OneDrive- > Personal/Documents/PhD/Structures/Proteins/1774_closed/1774_closed_conf.pdb Summary of feedback from opening /Users/michael/Library/CloudStorage/OneDrive- Personal/Documents/PhD/Structures/Proteins/1774_closed/1774_closed_conf.pdb --- warnings | Ignored bad PDB record found on line 9237 score -10823.2 Ignored bad PDB record found on line 9238 silent_score -10823.2 Ignored bad PDB record found on line 9239 time 4253 Ignored bad PDB record found on line 9240 Chain information for 1774_closed_conf.pdb #1 --- Chain | Description A | No description available > open /Users/michael/Library/CloudStorage/OneDrive- > Personal/Documents/PhD/Structures/Proteins/1774_closed/swissdockd_GWKCW__BAMY45PRCRKMC78AI2AE/1ligand.pdb Summary of feedback from opening /Users/michael/Library/CloudStorage/OneDrive- Personal/Documents/PhD/Structures/Proteins/1774_closed/swissdockd_GWKCW__BAMY45PRCRKMC78AI2AE/1ligand.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Energy: 36.4917 Ignored bad PDB record found on line 2 REMARK SimpleFitness: 36.4917 Ignored bad PDB record found on line 3 REMARK FullFitness: -2550.789 Ignored bad PDB record found on line 4 REMARK InterFull: -104.365 Ignored bad PDB record found on line 5 REMARK IntraFull: 247.171 14 messages similar to the above omitted > open /Users/michael/Library/CloudStorage/OneDrive- > Personal/Documents/PhD/Structures/Proteins/1774_closed/swissdockd_GWKCW__BAMY45PRCRKMC78AI2AE/2ligand.pdb Summary of feedback from opening /Users/michael/Library/CloudStorage/OneDrive- Personal/Documents/PhD/Structures/Proteins/1774_closed/swissdockd_GWKCW__BAMY45PRCRKMC78AI2AE/2ligand.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Energy: 35.7693 Ignored bad PDB record found on line 2 REMARK SimpleFitness: 35.7693 Ignored bad PDB record found on line 3 REMARK FullFitness: -2550.738 Ignored bad PDB record found on line 4 REMARK InterFull: -92.8689 Ignored bad PDB record found on line 5 REMARK IntraFull: 248.262 14 messages similar to the above omitted > open /Users/michael/Library/CloudStorage/OneDrive- > Personal/Documents/PhD/Structures/Proteins/1774_closed/swissdockd_GWKCW__BAMY45PRCRKMC78AI2AE/3ligand.pdb Summary of feedback from opening /Users/michael/Library/CloudStorage/OneDrive- Personal/Documents/PhD/Structures/Proteins/1774_closed/swissdockd_GWKCW__BAMY45PRCRKMC78AI2AE/3ligand.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Energy: 29.7272 Ignored bad PDB record found on line 2 REMARK SimpleFitness: 29.7272 Ignored bad PDB record found on line 3 REMARK FullFitness: -2549.7031 Ignored bad PDB record found on line 4 REMARK InterFull: -122.725 Ignored bad PDB record found on line 5 REMARK IntraFull: 254.779 14 messages similar to the above omitted > open /Users/michael/Library/CloudStorage/OneDrive- > Personal/Documents/PhD/Structures/Proteins/1774_closed/swissdockd_GWKCW__BAMY45PRCRKMC78AI2AE/4ligand.pdb Summary of feedback from opening /Users/michael/Library/CloudStorage/OneDrive- Personal/Documents/PhD/Structures/Proteins/1774_closed/swissdockd_GWKCW__BAMY45PRCRKMC78AI2AE/4ligand.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Energy: 21.2218 Ignored bad PDB record found on line 2 REMARK SimpleFitness: 21.2218 Ignored bad PDB record found on line 3 REMARK FullFitness: -2543.667 Ignored bad PDB record found on line 4 REMARK InterFull: -106.868 Ignored bad PDB record found on line 5 REMARK IntraFull: 245.779 14 messages similar to the above omitted > select add #1 9235 atoms, 9356 bonds, 589 residues, 1 model selected > hide sel cartoons > show sel surfaces > transparency sel 90 Alignment identifier is 1/A > select #1/A:8 17 atoms, 16 bonds, 1 residue, 1 model selected > select #1/A:8 17 atoms, 16 bonds, 1 residue, 1 model selected > save > /Users/michael/OneDrive/Documents/PhD/Structures/Proteins/1774_closed/chimeraX_docked.cxs > show sel atoms > hide sel surfaces > color (#!1 & sel) orange > select #1/A:14 19 atoms, 18 bonds, 1 residue, 1 model selected > select #1/A:14 19 atoms, 18 bonds, 1 residue, 1 model selected > hide sel surfaces > show sel atoms > color (#!1 & sel) orange > select #1/A:22 14 atoms, 14 bonds, 1 residue, 1 model selected > select #1/A:22 14 atoms, 14 bonds, 1 residue, 1 model selected > hide sel surfaces > show sel atoms > color (#!1 & sel) orange > select #1/A:37 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/A:37 7 atoms, 6 bonds, 1 residue, 1 model selected > hide sel surfaces > show sel atoms > color (#!1 & sel) orange > style sel stick Changed 7 atom styles > select #1/A:82 20 atoms, 20 bonds, 1 residue, 1 model selected > select #1/A:82 20 atoms, 20 bonds, 1 residue, 1 model selected > hide sel surfaces [Repeated 1 time(s)] > show sel atoms > color (#!1 & sel) orange > select #1/A:84 19 atoms, 18 bonds, 1 residue, 1 model selected > select #1/A:84 19 atoms, 18 bonds, 1 residue, 1 model selected > hide sel surfaces > show sel atoms > color (#!1 & sel) orange > select #1/A:169 19 atoms, 18 bonds, 1 residue, 1 model selected > select #1/A:169 19 atoms, 18 bonds, 1 residue, 1 model selected > hide sel surfaces > show sel atoms > style sel stick Changed 19 atom styles > color (#!1 & sel) yellow > color (#!1 & sel) orange > select #1/A:182 10 atoms, 9 bonds, 1 residue, 1 model selected > select #1/A:182 10 atoms, 9 bonds, 1 residue, 1 model selected > hide sel surfaces [Repeated 1 time(s)] > show sel atoms > color (#!1 & sel) orange > select #1/A:278 17 atoms, 16 bonds, 1 residue, 1 model selected > select #1/A:278 17 atoms, 16 bonds, 1 residue, 1 model selected > style sel stick Changed 17 atom styles > hide sel surfaces > show sel atoms > style sel stick Changed 17 atom styles > color (#!1 & sel) orange > select #1/A:300 14 atoms, 14 bonds, 1 residue, 1 model selected > select #1/A:300 14 atoms, 14 bonds, 1 residue, 1 model selected > hide sel surfaces > show sel atoms > color (#!1 & sel) orange > select #1/A:368 19 atoms, 18 bonds, 1 residue, 1 model selected > select #1/A:368 19 atoms, 18 bonds, 1 residue, 1 model selected > hide sel surfaces > show sel atoms > color (#!1 & sel) orange > select #1/A:383 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/A:383 7 atoms, 6 bonds, 1 residue, 1 model selected > hide sel surfaces > show sel atoms > color (#!1 & sel) orange > select #1/A:393 14 atoms, 13 bonds, 1 residue, 1 model selected > select #1/A:393 14 atoms, 13 bonds, 1 residue, 1 model selected > hide sel surfaces [Repeated 1 time(s)] > show sel atoms > color (#!1 & sel) orange > select #1/A:471 14 atoms, 13 bonds, 1 residue, 1 model selected > select #1/A:471 14 atoms, 13 bonds, 1 residue, 1 model selected > show sel atoms > hide sel surfaces > color (#!1 & sel) orange > select #1/A:532 12 atoms, 11 bonds, 1 residue, 1 model selected > select #1/A:532 12 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > hide sel surfaces > color (#!1 & sel) orange > select #1/A:545 16 atoms, 15 bonds, 1 residue, 1 model selected > select #1/A:545 16 atoms, 15 bonds, 1 residue, 1 model selected > color (#!1 & sel) orange > hide sel surfaces [Repeated 1 time(s)] > show sel atoms > select #1/A:584 24 atoms, 25 bonds, 1 residue, 1 model selected > select #1/A:583-584 48 atoms, 51 bonds, 2 residues, 1 model selected > show sel atoms > hide sel atoms > show sel surfaces > select add #1 9235 atoms, 9356 bonds, 589 residues, 2 models selected > select subtract #1 1 model selected > select add #1 9235 atoms, 9356 bonds, 589 residues, 1 model selected > color (#!1 & sel) white > undo > transparency sel 70 > transparency sel 95 > transparency sel 90 > color sel bychain > undo > select subtract #1 1 model selected > select add #2 123 atoms, 125 bonds, 1 residue, 1 model selected > hide sel atoms > show sel surfaces > select add #3 246 atoms, 250 bonds, 2 residues, 3 models selected > select subtract #2 123 atoms, 125 bonds, 1 residue, 2 models selected > color sel bychain > hide sel atoms > show sel surfaces > select add #2 246 atoms, 250 bonds, 2 residues, 3 models selected > select subtract #3 123 atoms, 125 bonds, 1 residue, 3 models selected > select subtract #2 1 model selected > select add #4 123 atoms, 125 bonds, 1 residue, 1 model selected > hide sel atoms > show sel surfaces > select subtract #4 1 model selected > select add #5 123 atoms, 125 bonds, 1 residue, 1 model selected > hide sel atoms > show sel surfaces > select subtract #5 1 model selected > save /Users/Michael/Desktop/test2.png format png width 5000 supersample 9 > transparentBackground true > lighting soft > save /Users/Michael/Desktop/test2.png format png width 5000 supersample 9 > transparentBackground true > save /Users/Michael/Desktop/test3.png format png width 5000 supersample 9 > transparentBackground true > save > /Users/michael/OneDrive/Documents/PhD/Structures/Proteins/1774_closed/chimeraX_docked.cxs ——— End of log from Mon May 23 10:33:57 2022 ——— opened ChimeraX session OpenGL version: 4.1 INTEL-18.8.5 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645 OpenGL vendor: Intel Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.1, Qt 6.4.2 Qt runtime version: 6.4.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro15,4 Processor Name: Quad-Core Intel Core i5 Processor Speed: 1.4 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: 8 GB System Firmware Version: 1731.140.2.0.0 (iBridge: 19.16.16067.0.0,0) OS Loader Version: 540.120.3~22 Software: System Software Overview: System Version: macOS 12.6 (21G115) Kernel Version: Darwin 21.6.0 Time since boot: 23 days 5:32 Graphics/Displays: Intel Iris Plus Graphics 645: Chipset Model: Intel Iris Plus Graphics 645 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3ea6 Revision ID: 0x0001 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: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.11.0 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.0.1 ChimeraX-AddCharge: 1.5.8 ChimeraX-AddH: 2.2.3 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.8 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.7 ChimeraX-AtomicLibrary: 10.0.3 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: 2.7.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.1 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-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.dev202302010904 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: 1.1 ChimeraX-DistMonitor: 1.3.3 ChimeraX-DockPrep: 1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-ExperimentalCommands: 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-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: 2.0.11 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.11 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.8 ChimeraX-ModelPanel: 1.3.6 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-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10 ChimeraX-PDB: 2.6.13 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: 1.0 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: 2.8.1 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: 1.10.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.1 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: 1.26 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.6 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: 0.1.2 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.6 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.38.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.9.26 imagesize: 1.4.1 importlib-metadata: 6.0.0 ipykernel: 6.19.2 ipython: 8.7.0 ipython-genutils: 0.2.0 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 7.4.8 jupyter-core: 5.2.0 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 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: 2.6.2 prompt-toolkit: 3.0.36 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 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.1 PyQt6-Qt6: 6.4.2 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.2 python-dateutil: 2.8.2 pytz: 2022.7.1 pyzmq: 25.0.0 qtconsole: 5.4.0 QtPy: 2.3.0 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 65.1.1 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 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 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.9.0 typing-extensions: 4.4.0 urllib3: 1.26.14 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 zipp: 3.12.0 }}} " defect closed normal Window Toolkit can't reproduce Tom Goddard all ChimeraX