id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17110 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.3.1-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. 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All rights reserved. How to cite UCSF ChimeraX > open > /Users/dsimberg/Downloads/fold_2025_03_10_16_50_b3col1/fold_2025_03_10_16_50_b3col1_model_0.cif > format mmcif Chain information for fold_2025_03_10_16_50_b3col1_model_0.cif #1 --- Chain | Description A | . Computing secondary structure > style sphere Changed 1052 atom styles > select add #1 1052 atoms, 1079 bonds, 137 residues, 1 model selected > style sel sphere Changed 1052 atom styles > preset ""molecular surfaces"" ""ghostly white"" Using preset: Molecular Surfaces / Ghostly White Changed 1052 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color white targ s trans 80 > preset ""molecular surfaces"" ""atomic coloring (transparent)"" Using preset: Molecular Surfaces / Atomic Coloring (Transparent) Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color fromatoms targ s trans 70 > preset ""initial styles"" ""original look"" Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. > view sel > show (#!1 & sel) target ab > ui tool show Toolbar > set bgColor white > style sel sphere Changed 1052 atom styles > show sel cartoons > hide sel cartoons > show sel cartoons > hide sel cartoons > style sel sphere Changed 1052 atom styles > style sel stick Changed 1052 atom styles > hide sel atoms > show sel atoms > lighting simple > lighting soft > lighting full > cartoon (#!1 & sel) > hide (#!1 & sel-residues & (protein|nucleic)) target a > cartoon hide (#!1 & sel-residues) > show (#!1 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab > cartoon (#!1 & sel) > select hydroxyl 35 atoms, 35 residues, 1 model selected > show (#!1 & sel-residues & sidechain) target ab > style sel sphere Changed 35 atom styles > style sel ball Changed 35 atom styles > style sel sphere Changed 35 atom styles > style sel sphere Changed 35 atom styles > style sel stick Changed 35 atom styles > surface (#!1 & sel) > surface hidePatches (#!1 & sel) > style (#!1 & sel) sphere Changed 35 atom styles > style (#!1 & sel) ball Changed 35 atom styles > style (#!1 & sel) stick Changed 35 atom styles > select add #1 1052 atoms, 1079 bonds, 137 residues, 2 models selected > style sel sphere Changed 1052 atom styles > select 1052 atoms, 1079 bonds, 137 residues, 1 model selected > style sel sphere Changed 1052 atom styles > style sel sphere Changed 1052 atom styles > style sel sphere Changed 1052 atom styles > style sel ball Changed 1052 atom styles > style sel sphere Changed 1052 atom styles > show (#!1 & sel-residues & sidechain) target ab > select subtract #1 1 model selected > movie record > turn y 2 180 > wait 180 > movie encode /Users/dsimberg/Desktop/movie1.mp4 Movie saved to /Users/dsimberg/Desktop/movie1.mp4 > movie record > turn y 2 180 > wait 180 > movie encode /Users/dsimberg/Desktop/movie2.mp4 Movie saved to /Users/dsimberg/Desktop/movie2.mp4 > movie record > turn y 2 180 > wait 180 > movie encode /Users/dsimberg/Desktop/movie3.mp4 Movie saved to /Users/dsimberg/Desktop/movie3.mp4 > movie record > turn y 2 180 > wait 180 > movie encode /Users/dsimberg/Desktop/movie4.mp4 Movie saved to /Users/dsimberg/Desktop/movie4.mp4 > movie record > turn y 2 180 > wait 180 > movie encode /Users/dsimberg/Desktop/movie5.mp4 Movie saved to /Users/dsimberg/Desktop/movie5.mp4 > save /Users/dsimberg/Desktop/rotatte.gif width 882 height 739 supersample 3 > show target ab > style stick Changed 1052 atom styles > save /Users/dsimberg/Desktop/image9.png supersample 3 > save /Users/dsimberg/Desktop/image10.png supersample 3 > color byhetero > color bychain > color byhetero > color bypolymer > rainbow > coulombic Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for fold_2025_03_10_16_50_b3col1_model_0.cif_A SES surface #1.1: minimum, -16.85, mean -0.59, maximum 12.94 To also show corresponding color key, enter the above coulombic command and add key true > coulombic Coulombic values for fold_2025_03_10_16_50_b3col1_model_0.cif_A SES surface #1.1: minimum, -16.85, mean -0.59, maximum 12.94 To also show corresponding color key, enter the above coulombic command and add key true > mlp Map values for surface ""fold_2025_03_10_16_50_b3col1_model_0.cif_A SES surface"": minimum -27.02, mean -5.279, maximum 22.97 To also show corresponding color key, enter the above mlp command and add key true > color bfactor 1052 atoms, 137 residues, 1 surfaces, atom bfactor range 26.3 to 98.9 > hbonds reveal true 109 hydrogen bonds found > hbonds reveal true 109 hydrogen bonds found > ~hbonds > hbonds reveal true 109 hydrogen bonds found > interfaces ~solvent 0 buried areas: > interfaces ~solvent 0 buried areas: > color byhetero > color bychain > color bypolymer > rainbow > style stick Changed 1052 atom styles > style stick Changed 1052 atom styles > nucleotides atoms > style nucleic stick Changed 0 atom styles > nucleotides atoms > style nucleic stick Changed 0 atom styles > nucleotides atoms > style nucleic stick Changed 0 atom styles > nucleotides atoms > style nucleic stick Changed 0 atom styles > hide #1.2 models > hide #1.1 models > style stick Changed 1052 atom styles > style sphere Changed 1052 atom styles > color bychain > color byhetero > coulombic Coulombic values for fold_2025_03_10_16_50_b3col1_model_0.cif_A SES surface #1.1: minimum, -16.85, mean -0.59, maximum 12.94 To also show corresponding color key, enter the above coulombic command and add key true > hide #!1 models > show #!1 models > hide #1.1 models > show #1.1 models > hide #1.1 models > show #1.1 models > style stick Changed 1052 atom styles > hide surfaces > color #1 #e4e5ebff > color #1 #bdbec4ff > color #1 #737478ff > color #1 #828286ff > show cartoons > show atoms > select add #1.1 1052 atoms, 137 residues, 1 model selected > select subtract #1.1 1 model selected > hide atoms > hide cartoons > show cartoons > show surfaces > style stick Changed 1052 atom styles > style stick Changed 1052 atom styles > hide surfaces > preset ""molecular surfaces"" ""ghostly white"" Using preset: Molecular Surfaces / Ghostly White Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color white targ s trans 80 > preset ""molecular surfaces"" ""atomic coloring (transparent)"" Using preset: Molecular Surfaces / Atomic Coloring (Transparent) Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color fromatoms targ s trans 70 > color byhetero > show atoms > hide atoms > show cartoons > hide cartoons > show cartoons > transparency 0 > volume showOutlineBox true No volumes specified > transparency 50 > transparency 0 > transparency 50 > volume style mesh No volumes specified > volume style mesh No volumes specified > volume style surface No volumes specified > volume style surface No volumes specified > volume hide No volumes specified > volume hide No volumes specified > lighting shadows false > lighting simple > lighting full > lighting soft > set bgColor gray > set bgColor white > preset ""initial styles"" cartoon Using preset: Initial Styles / Cartoon Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""molecular surfaces"" ""atomic coloring (transparent)"" Using preset: Molecular Surfaces / Atomic Coloring (Transparent) Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color fromatoms targ s trans 70 > preset ""initial styles"" cartoon Using preset: Initial Styles / Cartoon Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > preset cartoons/nucleotides cylinders/stubs Using preset: Cartoons/Nucleotides / Cylinders/Stubs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > preset cartoons/nucleotides licorice/ovals Using preset: Cartoons/Nucleotides / Licorice/Ovals Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh default arrows f x round width 1 thick 1 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides tube/slab shape ellipsoid > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > select /A:99 5 atoms, 4 bonds, 1 residue, 1 model selected > select /A:99-118 154 atoms, 159 bonds, 7 pseudobonds, 20 residues, 2 models selected > color (#!1 & sel) purple > select /A:48 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:48-62 108 atoms, 109 bonds, 6 pseudobonds, 15 residues, 2 models selected > color (#!1 & sel) red > select /A:28 4 atoms, 3 bonds, 1 residue, 1 model selected > select /A:28-36 71 atoms, 73 bonds, 2 pseudobonds, 9 residues, 2 models selected > color (#!1 & sel) blue > select add #1 1052 atoms, 1079 bonds, 109 pseudobonds, 137 residues, 3 models selected > select subtract #1 1 model selected > hide #!1 models > show #!1 models > select add #1 1052 atoms, 1079 bonds, 109 pseudobonds, 137 residues, 2 models selected > select /A:28 4 atoms, 3 bonds, 1 residue, 1 model selected > select /A:28-36 71 atoms, 73 bonds, 2 pseudobonds, 9 residues, 2 models selected > select add #1 1052 atoms, 1079 bonds, 109 pseudobonds, 137 residues, 3 models selected > select subtract #1.1 1 model selected > ui tool show ""Side View"" > graphics silhouettes false > graphics silhouettes true > view > view orient > view > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > select add #1 1052 atoms, 1079 bonds, 109 pseudobonds, 137 residues, 2 models selected > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > preset ""initial styles"" ""original look"" Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. > graphics silhouettes false > graphics silhouettes true > select hydroxyl 35 atoms, 35 residues, 1 model selected > show sel atoms > show (#!1 & sel-residues & sidechain) target ab > color sel byhetero > select add #1 1052 atoms, 1079 bonds, 109 pseudobonds, 137 residues, 3 models selected > color sel byhetero > coulombic sel Coulombic values for fold_2025_03_10_16_50_b3col1_model_0.cif_A SES surface #1.1: minimum, -16.85, mean -0.59, maximum 12.94 To also show corresponding color key, enter the above coulombic command and add key true > color sel byhetero > style sel sphere Changed 1052 atom styles > style sel ball Changed 1052 atom styles > style sel stick Changed 1052 atom styles > hide sel surfaces > show sel cartoons > preset ""molecular surfaces"" ""ghostly white"" Using preset: Molecular Surfaces / Ghostly White Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color white targ s trans 80 > preset ""initial styles"" ""space-filling (chain colors)"" Using preset: Initial Styles / Space-Filling (Chain Colors) Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""initial styles"" ""space-filling (single color)"" Using preset: Initial Styles / Space-Filling (Single Color) Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""initial styles"" ""original look"" Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. > show sel atoms > color sel byhetero > show sel surfaces > hide sel surfaces > hide sel atoms > select hydroxyl 35 atoms, 35 residues, 1 model selected > show sel atoms > show (#!1 & sel-residues & sidechain) target ab > preset ""molecular surfaces"" ""atomic coloring (transparent)"" Using preset: Molecular Surfaces / Atomic Coloring (Transparent) Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color fromatoms targ s trans 70 > select subtract #1.1 1 model selected > select add #1.1 1052 atoms, 137 residues, 1 model selected > select subtract #1.1 1 model selected > select add #1 1052 atoms, 1079 bonds, 109 pseudobonds, 137 residues, 2 models selected > select subtract #1 1 model selected > select add #1 1052 atoms, 1079 bonds, 109 pseudobonds, 137 residues, 2 models selected > color sel byhetero > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > select subtract #1 1 model selected > select add #1.1 1052 atoms, 137 residues, 1 model selected > select subtract #1.1 1 model selected > select add #1 1052 atoms, 1079 bonds, 109 pseudobonds, 137 residues, 2 models selected > select subtract #1 1 model selected > hide cartoons > hide atoms > color byhetero > coulombic Coulombic values for fold_2025_03_10_16_50_b3col1_model_0.cif_A SES surface #1.1: minimum, -16.85, mean -0.59, maximum 12.94 To also show corresponding color key, enter the above coulombic command and add key true > hide surfaces > show cartoons > show atoms ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Model Number: MKGQ3LL/A Chip: Apple M1 Pro Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 11881.81.4 OS Loader Version: 11881.81.4 Software: System Software Overview: System Version: macOS 15.3.1 (24D70) Kernel Version: Darwin 24.3.0 Time since boot: 5 days, 23 hours, 41 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Thunderbolt Display: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: Yes Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 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: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 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: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX