id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8236 Graphics hardware encountered an error and was reset chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.6.dev202211300249 (2022-11-30 02:49:47 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.6.dev202211300249 (2022-11-30) © 2016-2022 Regents of the University of California. All rights reserved. > open /Users/yizhang/Desktop/Fig2x_interface.cxs Opened cryosparc_P75_J279_006_volume_map.mrc gaussian as #6, grid size 180,180,180, pixel 1.34, shown at step 1, values float32 Log from Tue Dec 27 15:02:11 2022UCSF ChimeraX version: 1.6.dev202211300249 (2022-11-30) © 2016-2022 Regents of the University of California. All rights reserved. > open /Users/yizhang/Desktop/Fig2x_comp_AF2.cxs Opened cryosparc_P75_J279_006_volume_map.mrc gaussian as #6, grid size 180,180,180, pixel 1.34, shown at step 1, values float32 Log from Tue Dec 27 14:48:09 2022UCSF ChimeraX version: 1.6.dev202211300249 (2022-11-30) © 2016-2022 Regents of the University of California. All rights reserved. > open /Users/yizhang/Library/CloudStorage/Box- > Box/Manuscripts/hsATE1_2023/str_panels/Fig2x_comp_AF2.cxs Opened cryosparc_P75_J279_006_volume_map.mrc gaussian as #6, grid size 180,180,180, pixel 1.34, shown at step 1, values float32 Log from Tue Dec 27 14:31:10 2022UCSF ChimeraX version: 1.6.dev202211300249 (2022-11-30) © 2016-2022 Regents of the University of California. All rights reserved. > open /Users/yizhang/Library/CloudStorage/Box- > Box/Manuscripts/hsATE1_2023/str_panels/Fig2x_compare.cxs Opened cryosparc_P75_J279_006_volume_map.mrc gaussian as #6, grid size 180,180,180, pixel 1.34, shown at step 1, values float32 Log from Sun Dec 25 13:56:17 2022UCSF ChimeraX version: 1.6.dev202211300249 (2022-11-30) © 2016-2022 Regents of the University of California. All rights reserved. > open /Users/yizhang/Library/CloudStorage/Box- > Box/Manuscripts/hsATE1_2023/str_panels/Fig1f.cxs restore_snapshot for ""Volume"" returned None restore_snapshot for ""VolumeSurface"" returned None Opened cryosparc_P75_J279_006_volume_map.mrc gaussian as #6, grid size 180,180,180, pixel 1.34, shown at level 0.19, step 1, values float32 Log from Thu Dec 22 16:39:58 2022UCSF ChimeraX version: 1.6.dev202211300249 (2022-11-30) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/yizhang/Library/CloudStorage/Box- > Box/Manuscripts/hsATE1_2022/_data_structure/_hsATE1_20220701_dataset/cryosparc_P75_J279_006_volume_map.mrc Opened cryosparc_P75_J279_006_volume_map.mrc as #1, grid size 180,180,180, pixel 1.34, shown at level 0.143, step 1, values float32 > open /Users/yizhang/Library/CloudStorage/Box- > Box/Manuscripts/hsATE1_2022/_data_structure/_hsATE1_20220701_dataset/hATE1_dimer_real_space_refined_002_renumber.pdb Chain information for hATE1_dimer_real_space_refined_002_renumber.pdb #2 --- Chain | Description A B | No description available > open /Users/yizhang/Desktop/Preset_yz.cxc > open annotated_ate1_real_space_refined_017.pdb Failed opening file /Users/yizhang/Desktop/Preset_yz.cxc: No such file/path: annotated_ate1_real_space_refined_017.pdb > open /Users/yizhang/Desktop/Preset_yz.cxc > open annotated_ate1_real_space_refined_017.pdb Failed opening file /Users/yizhang/Desktop/Preset_yz.cxc: No such file/path: annotated_ate1_real_space_refined_017.pdb > set bgColor white > transparency 50 > color bychain > preset cylinders 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 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 ribbons 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 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 cylinders 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 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 > volume #1 step 1 > transparency 50 > volume #1 level 1.5 > volume #1 level 1.1 > volume #1 level 0.8 > volume #1 level 0.2 > volume #1 level 0.25 > volume #1 level 0.3 > preset ribbon 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 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 > volume #1 level 0.1 [had to delete a bunch to fit within ticket limits] > matchmaker #3 to #2/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 hATE1_dimer_real_space_refined_002_renumber.pdb, chain A (#2) with ScAte1_real_space_refined_038.pdb, chain A (#3), sequence alignment score = 466.7 RMSD between 167 pruned atom pairs is 1.238 angstroms; (across all 325 pairs: 12.594) > hide #!2 models > color #3 sky blue > color #3 deep sky blue > show #!2 models > hide #!2 models > color #3:25-53,126-151,198-219,337-448 spring green > show #!2 models > color #3 byatom > hide #!1 models > 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 > save /Users/yizhang/Library/CloudStorage/Box- > Box/Manuscripts/hsATE1_2023/str_panels/Fig2x_compare.cxs > view [Repeated 1 time(s)] > show #!1 models > view > zoom Pixel size at center of rotation is 0.268 > view [Repeated 4 time(s)] > view orient [Repeated 1 time(s)] > hide #!1 models > show #!1 models > hide #!3 models > lighting simple > lighting soft > lighting full > lighting simple > lighting soft > lighting shadows true intensity 0.5 > lighting soft > lighting simple > lighting soft > lighting simple [Repeated 1 time(s)] > save /Users/yizhang/Desktop/image1.png supersample 3 > show #!3 models > hide #!1 models > save /Users/yizhang/Desktop/image2.png supersample 3 > save /Users/yizhang/Library/CloudStorage/Box- > Box/Manuscripts/hsATE1_2023/str_panels/Fig2x_compare.cxs ——— End of log from Sun Dec 25 13:56:17 2022 ——— opened ChimeraX session > open /Users/yizhang/Downloads/AF-O95260-F1-model_v4.pdb AF-O95260-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for arginyl-TRNA--protein transferase 1 (O95260) [more info...] Chain information for AF-O95260-F1-model_v4.pdb #4 --- Chain | Description | UniProt A | arginyl-TRNA--protein transferase 1 | ATE1_HUMAN > matchmaker #4 to #2 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 hATE1_dimer_real_space_refined_002_renumber.pdb, chain A (#2) with AF-O95260-F1-model_v4.pdb, chain A (#4), sequence alignment score = 1458.6 RMSD between 315 pruned atom pairs is 1.012 angstroms; (across all 349 pairs: 1.272) > color #4 slate gray > save /Users/yizhang/Desktop/Fig2x_comp_AF2.cxs > view > hide #!3 models > open /Users/yizhang/Library/CloudStorage/Box- > Box/Manuscripts/hsATE1_2023/_data_structure/_hsATE1_20220701_dataset/hATE1_dimer_real_space_refined_002_renumber.pdb Chain information for hATE1_dimer_real_space_refined_002_renumber.pdb #5 --- Chain | Description A B | No description available > matchmaker #5/A to #2 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 hATE1_dimer_real_space_refined_002_renumber.pdb, chain A (#2) with hATE1_dimer_real_space_refined_002_renumber.pdb, chain A (#5), sequence alignment score = 1858.4 RMSD between 349 pruned atom pairs is 0.000 angstroms; (across all 349 pairs: 0.000) > select add #5 11214 atoms, 11380 bonds, 2 pseudobonds, 698 residues, 2 models selected > select subtract #5 Nothing selected > close #5 > open /Users/yizhang/Library/CloudStorage/Box- > Box/Manuscripts/hsATE1_2023/_data_structure/_hsATE1_20220701_dataset/hATE1_dimer_real_space_refined_002_renumber.pdb Chain information for hATE1_dimer_real_space_refined_002_renumber.pdb #5 --- Chain | Description A B | No description available > select #5 11214 atoms, 11380 bonds, 2 pseudobonds, 698 residues, 2 models selected > select add #2 22428 atoms, 22760 bonds, 4 pseudobonds, 1396 residues, 4 models selected > select subtract #2 11214 atoms, 11380 bonds, 2 pseudobonds, 698 residues, 2 models selected > select subtract #5 Nothing selected > color #4:103-264 spring green > color #4:102-264 spring green > undo [Repeated 1 time(s)] > color #4:101-265 spring green > undo > color #4:104-265 spring green > hide #5/A > color #5/B yellow > color #5/B dark khaki > 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 > preset ""overall look"" interactive Using preset: Overall Look / Interactive Preset expands to these ChimeraX commands: ~set bg 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 > 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 > view > orient Unknown command: orient > orient Unknown command: orient > view orient > lighting simple > lighting soft > lighting full > 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 > lighting simple > lighting soft > lighting simple > lighting shadows true > lighting shadows false > open /Users/yizhang/Downloads/AF-O95260-F1-model_v4.pdb AF-O95260-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for arginyl-TRNA--protein transferase 1 (O95260) [more info...] Chain information for AF-O95260-F1-model_v4.pdb #7 --- Chain | Description | UniProt A | arginyl-TRNA--protein transferase 1 | ATE1_HUMAN > matchmaker #7 to #5/B 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 hATE1_dimer_real_space_refined_002_renumber.pdb, chain B (#5) with AF-O95260-F1-model_v4.pdb, chain A (#7), sequence alignment score = 1413.6 RMSD between 320 pruned atom pairs is 1.063 angstroms; (across all 349 pairs: 1.404) > close #7 > view > lighting simple > save /Users/yizhang/Desktop/Fig2x_comp_AF2.cxs ——— End of log from Tue Dec 27 14:31:10 2022 ——— opened ChimeraX session > open /Users/yizhang/Library/CloudStorage/Box- > Box/Manuscripts/hsATE1_2023/str_panels/Fig2x_comp_AF2.cxc > open O95260 'O95260' has no suffix > open /Users/yizhang/Library/CloudStorage/Box- > Box/Manuscripts/hsATE1_2023/str_panels/Fig2x_comp_AF2.cxc > matchmaker #4 to #2 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 hATE1_dimer_real_space_refined_002_renumber.pdb, chain A (#2) with AF-O95260-F1-model_v4.pdb, chain A (#4), sequence alignment score = 1458.6 RMSD between 315 pruned atom pairs is 1.012 angstroms; (across all 349 pairs: 1.272) > hide #5/A > color #5/B dark khaki > color #4 light gray > color #4:104-265 blue executed Fig2x_comp_AF2.cxc > view [Repeated 1 time(s)] > save /Users/yizhang/Desktop/Fig2x_comp_AF2.cxs ——— End of log from Tue Dec 27 14:48:09 2022 ——— opened ChimeraX session > save /Users/yizhang/Desktop/Fig2x_interface.cxs ——— End of log from Tue Dec 27 15:02:11 2022 ——— opened ChimeraX session OpenGL version: 4.1 INTEL-20.2.44 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine OpenGL vendor: Intel Inc. 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: MacBookPro16,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 512 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1916.40.8.0.0 (iBridge: 20.16.420.0.0,0) OS Loader Version: 564.40.4~27 Software: System Software Overview: System Version: macOS 13.0.1 (22A400) Kernel Version: Darwin 22.1.0 Time since boot: 6 days, 6 hours, 39 minutes Graphics/Displays: Intel Iris Plus Graphics: Chipset Model: Intel Iris Plus Graphics Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x8a53 Revision ID: 0x0007 Metal Support: Metal 3 Displays: U32R59x: Resolution: 4608 x 2592 UI Looks like: 2304 x 1296 @ 30.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: HNAT600173 Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Connection Type: Thunderbolt/DisplayPort Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.0 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: 1.5.7 ChimeraX-AddH: 2.2.3 ChimeraX-AlignmentAlgorithms: 2.0 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: 1.0 ChimeraX-Atomic: 1.43.4 ChimeraX-AtomicLibrary: 8.0.4 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: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.dev202211300249 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.1 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: 1.0.1 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: 1.2 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: 2.9 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.7 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: 1.9.3 ChimeraX-PDB: 2.6.9 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: 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: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8 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 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-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.25.2 ChimeraX-uniprot: 2.2.1 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: 1.0.1 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: 1.6.4 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: 5.1.0 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: 5.1.0 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: 3.0.33 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: 0.6.2 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: 1.26.13 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 zipp: 3.11.0 }}} " defect accepted normal Graphics all ChimeraX