id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16251 Crash on Mac waking from sleep, Qt 6.7 chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-12.7.6-x86_64-i386-64bit ChimeraX Version: 1.9rc202411012347 (2024-11-01 23:47:45 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x000070001c2ad000 (most recent call first): File ""/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001b2aa000 (most recent call first): File ""/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File 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""/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001729e000 (most recent call first): File ""/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9-rc2024.11.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File 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\nMALLOC_LARGE (reserved) 256K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nMach message 16K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 140K 35 \nStack 314.3M 36 \nStack Guard 56.0M 1 \nVM_ALLOCATE 165.3M 213 \n__CTF 756 1 \n__DATA 39.7M 727 \n__DATA_CONST 42.0M 446 \n__DATA_DIRTY 1805K 238 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 676.7M 161 \n__OBJC_RO 82.9M 1 \n__OBJC_RW 3200K 2 \n__TEXT 857.0M 730 \n__UNICODE 592K 1 \ndyld private memory 1064K 3 \nmapped file 202.5M 47 \nshared memory 2972K 26 \n=========== ======= ======= \nTOTAL 3.2G 3564 \nTOTAL, minus reserved VM space 2.8G 3564 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""5fb4245a1bbfe8005e33a1e1"", ""factorPackIds"" : { }, ""deploymentId"" : 240000021 }, { ""rolloutId"" : ""5fc94383418129005b4e9ae0"", ""factorPackIds"" : { }, ""deploymentId"" : 240000614 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- warning | QCoreApplication::postEvent: Unexpected null receiver note | available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.9rc202411012347 (2024-11-01) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/fredrikleo/Library/CloudStorage/OneDrive-GenovisAB(2)/PhD/Paper > 3 - MdpS2/Figures for manuscript/Structural comparison/MdpS - > AF-A0A1X1FWK3-F1-model_v4.pdb"" > ""/Users/fredrikleo/Library/CloudStorage/OneDrive-GenovisAB(2)/PhD/Paper 3 - > MdpS2/Figures for manuscript/Structural comparison/MdpS2 - > AF-A0A1X1FVD9-F1-model_v4.pdb"" Summary of feedback from opening /Users/fredrikleo/Library/CloudStorage/OneDrive-GenovisAB(2)/PhD/Paper 3 - MdpS2/Figures for manuscript/Structural comparison/MdpS - AF-A0A1X1FWK3-F1-model_v4.pdb --- warning | Ignored bad PDB record found on line 38 DBREF XXXX A 1 336 UNP A0A1X1FWK3 A0A1X1FWK3_STROR 1 336 Summary of feedback from opening /Users/fredrikleo/Library/CloudStorage/OneDrive-GenovisAB(2)/PhD/Paper 3 - MdpS2/Figures for manuscript/Structural comparison/MdpS2 - AF-A0A1X1FVD9-F1-model_v4.pdb --- warning | Ignored bad PDB record found on line 40 DBREF XXXX A 1 227 UNP A0A1X1FVD9 A0A1X1FVD9_STROR 1 227 MdpS - AF-A0A1X1FWK3-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for TRNA N6-adenosine threonylcarbamoyltransferase (A0A1X1FWK3) [more info...] Chain information for MdpS - AF-A0A1X1FWK3-F1-model_v4.pdb #1 --- Chain | Description A | TRNA N6-adenosine threonylcarbamoyltransferase MdpS2 - AF-A0A1X1FVD9-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for TRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex dimerization subunit type 1 tsab (A0A1X1FVD9) [more info...] Chain information for MdpS2 - AF-A0A1X1FVD9-F1-model_v4.pdb #2 --- Chain | Description A | TRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex dimerization subunit type 1 tsab Computing secondary structure > matchmaker #1 to #2 Computing secondary structure 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 MdpS2 - AF-A0A1X1FVD9-F1-model_v4.pdb, chain A (#2) with MdpS - AF-A0A1X1FWK3-F1-model_v4.pdb, chain A (#1), sequence alignment score = 203.3 RMSD between 79 pruned atom pairs is 0.924 angstroms; (across all 197 pairs: 22.814) > color #2 #b1c1dfff > color #2 #ffec83ff > color #2 #ffe000ff > color #2 #fff7d0ff > color #1 #1e4589ff > color #1 #9197c2ff > color #1 #1e4589ff > color #1 #ef7748ff > color #1 #a9115fff > color #1 #e96aa4ff > color #2 #b1c1dfff > color #2 #e1f1efff > color #2 #deecd5ff > color #2 #b6d6a7ff > color #2 #deecd5ff > color #2 #c8c3dcff > color #1 #453777ff > color #1 #968eb8ff > color #1 #453777ff > color #1 #ffe000ff > color #1 #ffec83ff > color #1 #ef7748ff > color #1 black > color #1 silver > color #2 #929000ff > color #2 #4f8f00ff > color #1 #ff9300ff > color #1 #fffb00ff > color #1 #0096ffff > color #1 #ff2f92ff > color #1 #ff7e79ff > color #1 #ffd479ff > color #1 #fffc79ff > color #1 #d4fb79ff > color #1 #76d6ffff > color #1 #7a81ffff > color #1 #d783ffff > color #1 #ff85ffff > color #1 #d783ffff > color #2 #941100ff > color #2 #008f00ff > color #2 #009193ff > color #2 #005493ff > color #2 #531b93ff > color #2 #ff2600ff > color #2 #941751ff > color #2 #0096ffff > color #2 #ffd479ff > set bgColor white > set bgColor #ffffff00 > set bgColor black > set bgColor transparent > set bgColor white > set bgColor #ffffff00 > color #2 #4f8f00ff > color #1 silver > color #1 #929292ff > color #1 darkgrey > color #1 #424242ff > color #1 black > set bgColor black > set bgColor transparent > set bgColor white > set bgColor #ffffff00 > color #1 white > set bgColor black > set bgColor transparent > color #1 #e1f1efff > color #1 #ecececff > color #1 white > color #1 #ff40ffff > movie record > turn y 2 180 > wait 180 > movie encode /Users/fredrikleo/Desktop/movie1.mp4 Movie saved to /Users/fredrikleo/Desktop/movie1.mp4 > style stick Changed 4310 atom styles > style sphere Changed 4310 atom styles > style ball Changed 4310 atom styles > color byhetero > color bychain > color byhetero > undo > ui tool show ""Side View"" > lighting simple > view > ui mousemode right ""color key"" > ui mousemode right translate > hide #3 models > select add #1 2527 atoms, 2572 bonds, 336 residues, 1 model selected > select subtract #1 Nothing selected > select add #2 1783 atoms, 1819 bonds, 227 residues, 1 model selected > select subtract #2 Nothing selected > ui mousemode right ""clip rotate"" > undo > select subtract #1 Nothing selected > hide #1 models > show #1 models > rainbow > color bfactor 4310 atoms, 563 residues, atom bfactor range 38.5 to 98.9 > mlp Map values for surface ""MdpS - AF-A0A1X1FWK3-F1-model_v4.pdb_A SES surface"": minimum -32.48, mean -5.429, maximum 21.22 Map values for surface ""MdpS2 - AF-A0A1X1FVD9-F1-model_v4.pdb_A SES surface"": minimum -25.18, mean -4.859, maximum 22.47 To also show corresponding color key, enter the above mlp command and add key true > color bynucleotide > color bfactor 4310 atoms, 563 residues, 2 surfaces, atom bfactor range 38.5 to 98.9 > color byhetero > color bychain > style stick Changed 4310 atom styles > style sphere Changed 4310 atom styles > undo > show #!2 cartoons > show #!2 surfaces > hide #!2 models > show #!2 models > show #!1 models > color bynucleotide > style stick Changed 4310 atom styles > style sphere Changed 4310 atom styles > style ball Changed 4310 atom styles > show cartoons > show atoms > color bynucleotide > style ball Changed 4310 atom styles > show target m > hide target m > show #!1 models > show #!2 models > nucleotides atoms > style nucleic stick Changed 0 atom styles > style ball Changed 4310 atom styles > style sphere Changed 4310 atom styles > style stick Changed 4310 atom styles > nucleotides fill > style nucleic stick Changed 0 atom styles > style stick Changed 4310 atom styles > style sphere Changed 4310 atom styles > style ball Changed 4310 atom styles > color bychain > style sphere Changed 4310 atom styles > style stick Changed 4310 atom styles > style ball Changed 4310 atom styles > show cartoons > hide atoms > color #1 #00f900ff > color #2 #ff40ffff > undo > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > undo > show cartoons > hide atoms > label #1/A text MdpS color green > undo > hide atoms > color #1 #00f900ff > color #2 #ff40ffff > label #1/A > undo > unlabel #1/A Unknown command: unlabel #1/A > label #1.2#!1-2 text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > undo > show cartoons > hide atoms > ~label #1/A > ~label #1/A text MdpS color green > label delete #1/A text MdpS color green Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a keyword > hide atoms > ~label #1.2#!1-2 text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > label delete #1.2#!1-2 text ""/{0.chain_id} {0.name} > {0.number}{0.insertion_code}"" Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a keyword > ~label #2.2#!1-2 residues > label #1/A models text MdpS color white > label #2/A models text MdpS2 color white > label #1/B models text MdpS color white > color #1 #00f900ff > color #2 #ff40ffff > ~label #1/B models text ""MdpS"" color white > label delete #1/B models text ""MdpS"" color white Expected a keyword > ~label #1/A models text ""MdpS"" color white > label delete #1/A models text ""MdpS"" color white Expected a keyword > show atoms > show cartoons > hide atoms > ~label #1/A models text ""MdpS"" color white > label delete #1/A models text ""MdpS"" color white Expected a keyword > ~label #2/A models text ""MdpS2"" color white > label delete #2/A models text ""MdpS2"" color white Expected a keyword > ~label #2/A > ~label #1/A > ~label #1/B > color bynucleotide > set bgColor gray > set bgColor #80808000 > set bgColor black > set bgColor transparent > set bgColor white > set bgColor #ffffff00 > set bgColor gray > set bgColor #80808000 > set bgColor black > set bgColor transparent > set bgColor gray > set bgColor #80808000 Color zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic models, 0 maps. > show #3 models > hide #3 models > select add #3 1 model selected > show #3 models > hide #3 models > select subtract #3 Nothing selected > ui mousemode right distance > ui mousemode right ""color key"" > ui mousemode right distance > color byhetero #1/A Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color byhetero #1 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color byhetero models #1 Expected ',' or a keyword > color byhetero models #1 Expected ',' or a keyword > color byhet, models #1 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color byhet, models #1 green Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color byhetero green, models #1 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color byhetero green, 'models' #1 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color byhetero models #1 green Expected ',' or a keyword > color byhet, 'models' #1 green Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color byhetero models #1, green Expected ',' or a keyword > color byattribute seq_conservation #1 No known/registered numeric attribute seq_conservation > color byhetero seq_conservation #1 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > select #1: 1-100 736 atoms, 744 bonds, 100 residues, 1 model selected > select #1: 1-100 736 atoms, 744 bonds, 100 residues, 1 model selected > color green sel Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color green sel Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9rc202411012347 (2024-11-01) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-18.8.16 OpenGL renderer: Intel(R) HD Graphics 6000 OpenGL vendor: Intel Inc. 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 Air Model Identifier: MacBookAir7,2 Processor Name: Dual-Core Intel Core i5 Processor Speed: 1,8 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 3 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 489.0.0.0.0 OS Loader Version: 540.120.3~37 SMC Version (system): 2.27f2 Software: System Software Overview: System Version: macOS 12.7.6 (21H1320) Kernel Version: Darwin 21.6.0 Time since boot: 5 days 20:30 Graphics/Displays: Intel HD Graphics 6000: Chipset Model: Intel HD Graphics 6000 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x1626 Revision ID: 0x0009 Metal Family: Supported, Metal GPUFamily macOS 1 Displays: Color LCD: Display Type: LCD Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 Framebuffer Depth: 24-Bit Color (ARGB8888) Mirror: On Mirror Status: Hardware Mirror Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal HP E273: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: CNK9130CWH Main Display: Yes Mirror: On Mirror Status: Master Mirror Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.7.1 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.17 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: 1.58.7 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: 2.4.7 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13 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: 1.9rc202411012347 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: 1.2.5 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 ChimeraX-Label: 1.1.11 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: 2.7.1 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: 1.5.17 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: 1.6.1 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: 3.2.4 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: 1.3.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.7 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.54.1 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.12.1 html2text: 2024.2.26 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: 2.10.1 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: 2.4.1 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 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: 6.4.1 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 can't reproduce all ChimeraX