id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17045 Crash on Mac waking from sleep sphulera@… 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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portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=4.1G written=2506K(0%) resident=2506K(0%) swapped_out=0K(0%) unallocated=4.1G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG image 3376K 55 \nColorSync 736K 38 \nCoreAnimation 6160K 324 \nCoreGraphics 48K 3 \nCoreGraphics (reserved) 16K 1 reserved VM address space (unallocated)\nCoreImage 192K 6 \nCoreServices 80K 1 \nCoreUI image data 5344K 40 \nFoundation 32K 2 \nKernel Alloc Once 32K 1 \nMALLOC 3.4G 106 \nMALLOC guard page 288K 18 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.6M 36 \nStack 191.2M 36 \nVM_ALLOCATE 294.4M 401 \nVM_ALLOCATE (reserved) 160.0M 2 reserved VM address space (unallocated)\n__AUTH 5288K 672 \n__AUTH_CONST 70.9M 920 \n__CTF 824 1 \n__DATA 33.4M 1064 \n__DATA_CONST 34.2M 1082 \n__DATA_DIRTY 2763K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 637.6M 156 \n__OBJC_RW 2374K 1 \n__TEXT 1.3G 1102 \n__TPRO_CONST 272K 2 \ndyld private memory 32K 2 \nmapped file 587.4M 96 \nowned unmapped memory 90.5M 1 \npage table in kernel 2506K 1 \nshared memory 3200K 26 \n=========== ======= ======= \nTOTAL 6.8G 6552 \nTOTAL, minus reserved VM space 6.6G 6552 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""f465458cb810aa99eb40bd8302cb48a9e0ac260b"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""642da32dea3b2418c750f848"", ""factorPackIds"" : { ""VISUAL_INTELLIGENCE_VICTORIA"" : ""66d8b2f77cd4b62688efd2cf"" }, ""deploymentId"" : 240000004 }, { ""rolloutId"" : ""5ffde50ce2aacd000d47a95f"", ""factorPackIds"" : { }, ""deploymentId"" : 240000460 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== 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 > open /Users/sphulera/Library/CloudStorage/OneDrive- > TheScrippsResearchInstitute/EM/Briney/PC94-A15_BG505_RM20A3/RealSpaceRefine_3/PC94A15_BG505_RM20A3_J1466_real_space_refined_003.pdb Chain information for PC94A15_BG505_RM20A3_J1466_real_space_refined_003.pdb #1 --- Chain | Description A C E | No description available B D F | No description available H | No description available I K Q | No description available L | No description available M O S | No description available > open /Users/sphulera/Library/CloudStorage/OneDrive- > TheScrippsResearchInstitute/EM/Briney/PC94-A30_BG505_RM20A3/RealSpaceRefine_2/PC94-A30_BG505_RM20A3_P2661_real_space_refined_002.pdb Chain information for PC94-A30_BG505_RM20A3_P2661_real_space_refined_002.pdb #2 --- Chain | Description A C E | No description available B D F | No description available H J P | No description available I K Q | No description available L N R | No description available M O S | No description available > open /Users/sphulera/Library/CloudStorage/OneDrive- > TheScrippsResearchInstitute/EM/Briney/PC94-A31/RealSpaceRefine_4/PC94A31_BG505SOSIP_RM20A3_J1526_real_space_refined_052_updated.pdb Chain information for PC94A31_BG505SOSIP_RM20A3_J1526_real_space_refined_052_updated.pdb #3 --- Chain | Description A | No description available B D F | No description available C | No description available E | No description available H | No description available I | No description available K Q | No description available L | No description available M O S | No description available > mmaker #3/A to #1/A 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 PC94A15_BG505_RM20A3_J1466_real_space_refined_003.pdb, chain A (#1) with PC94A31_BG505SOSIP_RM20A3_J1526_real_space_refined_052_updated.pdb, chain A (#3), sequence alignment score = 2182.6 RMSD between 430 pruned atom pairs is 0.526 angstroms; (across all 435 pairs: 0.634) > mmaker #2/A to #1/A 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 PC94A15_BG505_RM20A3_J1466_real_space_refined_003.pdb, chain A (#1) with PC94-A30_BG505_RM20A3_P2661_real_space_refined_002.pdb, chain A (#2), sequence alignment score = 2187.6 RMSD between 430 pruned atom pairs is 0.406 angstroms; (across all 437 pairs: 0.521) > hide atoms > show cartoons > select ~/A,H,L 70464 atoms, 71771 bonds, 36 pseudobonds, 6482 residues, 6 models selected > hide sel cartoons > 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 > lighting soft > dssp Computing secondary structure > select clear > select /A:332 29 atoms, 26 bonds, 3 residues, 3 models selected > show sel atoms > select clear > select #1/H,L 1805 atoms, 1854 bonds, 232 residues, 1 model selected > ui tool show Axes/Planes/Centroids > define centroid sel Centroid 'centroid' placed at [261.75550803 228.82803546 133.81233518] > select #2/H,L 3531 atoms, 3577 bonds, 232 residues, 1 model selected > define centroid sel Centroid 'centroid' placed at [210.96783093 141.31256075 152.24647267] > select clear > select #3/H,L 1832 atoms, 1883 bonds, 233 residues, 1 model selected > define centroid sel Centroid 'centroid' placed at [165.63171397 252.88298144 272.36567303] > select clear > hide #!1 models > hide #!2 models > show #!2 models > show #!1 models > hide #!2 models > hide #!3 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > show #!3 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!3 models > show #!3 models > hide #!3 models > ui tool show Distances > ui mousemode right select > select #1.2 1 atom, 1 residue, 1 model selected > select #!1/A:332@CA 1 atom, 1 residue, 1 model selected > select #1.2 1 atom, 1 residue, 1 model selected > select add #!1/A:332@CA 2 atoms, 2 residues, 2 models selected > distance #1.2 #!1/A:332@CA Distance between PC94A15_BG505_RM20A3_J1466_real_space_refined_003.pdb #!1/A ASN 332 CA and centroid #1.2: 36.124Å > distance style color black > distance style dashes 0 > hide #4.1 models > select clear > show #!2 models > hide #!1 models > hide #!4 models > select #2.2 1 atom, 1 residue, 1 model selected > select #!2/A:332@CA 1 atom, 1 residue, 1 model selected > select add #2.2 2 atoms, 2 residues, 2 models selected > distance #!2/A:332@CA #2.2 Distance between PC94-A30_BG505_RM20A3_P2661_real_space_refined_002.pdb #!2/A ASN 332 CA and centroid #2.2: 35.510Å > distance #!2/A:332@CA #2.2 Distance already exists; modify distance properties with 'distance style' > show #!4 models > show #4.1 models > hide #4.1 models > show #!3 models > distance style color #ff2600 > distance style color black > hide #!2 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!2 models > select clear > show #!3 models > hide #!2 models > hide #!1 models > select add #3.2 1 atom, 1 residue, 1 model selected > select add #!3/A:332@CA 2 atoms, 2 residues, 2 models selected > distance #3.2 #!3/A:332@CA Distance between PC94A31_BG505SOSIP_RM20A3_J1526_real_space_refined_052_updated.pdb #!3/A ASN 332 CA and centroid #3.2: 35.480Å > hide #!4 models > show #!4 models > distance style color #0433ff > distance style color black > show #!2 models > show #!1 models > select clear > angle #1.2 #1/A:332@ca #2.2 Angle between centroid #1.2, PC94A15_BG505_RM20A3_J1466_real_space_refined_003.pdb #!1/A ASN 332 CA, and centroid #2.2: 4.438 > angle #1.2 #1/A:332@ca #2.2 Angle between centroid #1.2, PC94A15_BG505_RM20A3_J1466_real_space_refined_003.pdb #!1/A ASN 332 CA, and centroid #2.2: 4.438 > angle #1.2 #1/A:332@ca #3.2 Angle between centroid #1.2, PC94A15_BG505_RM20A3_J1466_real_space_refined_003.pdb #!1/A ASN 332 CA, and centroid #3.2: 4.741 > angle #2.2 #1/A:332@ca #3.2 Angle between centroid #2.2, PC94A15_BG505_RM20A3_J1466_real_space_refined_003.pdb #!1/A ASN 332 CA, and centroid #3.2: 2.366 > hide #!1 models > show #!1 models > save /Users/sphulera/Desktop/image56.png supersample 3 > open /Users/sphulera/Library/CloudStorage/OneDrive- > TheScrippsResearchInstitute/EM/Clinical_trial_samples/C101/1D07_GT1-1_RM20A3/RealSpaceRefine_1/1D07_GT1-1_RM20A3_J1753_real_space_refined_001.pdb Chain information for 1D07_GT1-1_RM20A3_J1753_real_space_refined_001.pdb #5 --- Chain | Description A C E | No description available B D F | No description available H I P | No description available J K Q | No description available L N R | No description available M O S | No description available > open /Users/sphulera/Library/CloudStorage/OneDrive- > TheScrippsResearchInstitute/EM/Clinical_trial_samples/C101/1D07_GT1-1_RM20A3/1D07_GT1-1_RM20A3_P455_J1753_C3_3.02.mrc Opened 1D07_GT1-1_RM20A3_P455_J1753_C3_3.02.mrc as #6, grid size 400,400,400, pixel 1.03, shown at level 0.0606, step 2, values float32 > close #5 > close #6 > open /Users/sphulera/Library/CloudStorage/OneDrive- > TheScrippsResearchInstitute/EM/Clinical_trial_samples/C101/1D07_GT1-1_RM20A3/J1692_40A_sphere_1D07.mrc Opened J1692_40A_sphere_1D07.mrc as #5, grid size 400,400,400, pixel 1.03, shown at level 0.000431, step 2, values float32 > close #5 > ui tool show ""Side View"" > distance style radius 0.2 > save /Users/sphulera/Desktop/image57.png supersample 3 > transparentBackground true Unknown command: transparentBackground true > save /Users/sphulera/Desktop/image57.png width 709 height 757 supersample 3 > transparentBackground true > hide #!1 models > hide #!2 models > hide #!3 models > show #!1 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > hide #!2 models > show #!1 models > select /A 15387 atoms, 15726 bonds, 13 pseudobonds, 1409 residues, 6 models selected > ui tool show ""Color Actions"" > color (#!1 & sel) #00f900ff > select clear > select #1 /H 985 atoms, 1010 bonds, 126 residues, 1 model selected > color sel byelement > color sel byhetero > color sel byelement > color sel byhetero > color sel orchid > color sel dark orchid > select #1 /L 820 atoms, 844 bonds, 106 residues, 1 model selected > color sel orchid > select clear > select #2 /L 1611 atoms, 1635 bonds, 106 residues, 1 model selected > show #!2 models > hide #!1 models > color sel lime > color sel wheat > select #2 /H 1920 atoms, 1942 bonds, 126 residues, 1 model selected > color sel tan > select clear > show #!3 models > hide #!2 models > select #3 /H 1007 atoms, 1034 bonds, 127 residues, 1 model selected > color sel light cyan > select #3 /L 825 atoms, 849 bonds, 106 residues, 1 model selected > color sel light cyan > select #3 /H 1007 atoms, 1034 bonds, 127 residues, 1 model selected > color sel cyan > lighting soft > select clear > select #3 /L 825 atoms, 849 bonds, 106 residues, 1 model selected > select #3 /H 1007 atoms, 1034 bonds, 127 residues, 1 model selected > color sel royal blue > select #3 /L 825 atoms, 849 bonds, 106 residues, 1 model selected > color sel dark turquoise > color sel medium aquamarine > select clear > show #!2 models > show #!1 models > select /A 15387 atoms, 15726 bonds, 13 pseudobonds, 1409 residues, 6 models selected > color sel green > color sel chartreuse > select clear > select /A 15387 atoms, 15726 bonds, 13 pseudobonds, 1409 residues, 6 models selected > color sel green > select clear > select /A:332 29 atoms, 26 bonds, 3 residues, 3 models selected > style sel stick Changed 29 atom styles > color sel byelement > ui tool show ""Color Actions"" > color sel forest green > select clear > select /A:332 29 atoms, 26 bonds, 3 residues, 3 models selected > color sel byhetero > select H 24423 atoms, 3174 residues, 1 model selected > select clear > select H 24423 atoms, 3174 residues, 1 model selected > delete atoms sel > delete bonds sel > hide #!3 models > hide #!2 models > hide #!1 models > show #!1 models > show #!2 models > show #!3 models > hide #!2 models > hide #!1 models > show #!1 models > show #!2 models > save /Users/sphulera/Desktop/image57.png width 709 height 757 supersample 3 > transparentBackground true > hide #!2 models > hide #!3 models > show #!2 models > hide #!1 models > select #2 /L 822 atoms, 846 bonds, 106 residues, 1 model selected > ui tool show ""Color Actions"" > color sel wheat > select clear > select #2 /H 977 atoms, 999 bonds, 126 residues, 1 model selected > color sel dark goldenrod > show #!1 models > show #!3 models > hide #!3 models > hide #!2 models > show #!2 models > show #!3 models > select clear > save /Users/sphulera/Desktop/image57.png width 709 height 757 supersample 3 > transparentBackground true > hide #!1 models > hide #!3 models > show #!3 models > hide #!2 models > show #!1 models > hide #!3 models > show #!3 models > hide #!1 models > show #!2 models > show #!1 models > hide #!3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > show #!3 models > hide #!2 models > select #1 /H 985 atoms, 1010 bonds, 126 residues, 1 model selected > ui tool show Axes/Planes/Centroids > define centroid sel name centroid_HC_15 Centroid 'centroid_HC_15' placed at [268.73964061 223.60277462 137.52658883] > select clear > select #3 /H 1007 atoms, 1034 bonds, 127 residues, 1 model selected > define centroid sel name centroid_HC_31 Centroid 'centroid_HC_31' placed at [157.8284002 248.42483714 268.66567825] > select clear > angle #1.3 #1/A:332@ca #3.3 Angle between centroid_HC_15 #1.3, PC94A15_BG505_RM20A3_J1466_real_space_refined_003.pdb #!1/A ASN 332 CA, and centroid_HC_31 #3.3: 8.910 > hide #1.1 models > hide #2.1 models > hide #2.2 models > hide #3.2 models > hide #1.2 models > select #2 /H 977 atoms, 999 bonds, 126 residues, 1 model selected > ui tool show Axes/Planes/Centroids > define centroid sel name centroid_HC_30 Centroid 'centroid_HC_30' placed at [205.19048004 135.52411975 157.24736336] > hide #2.3 models > show #2.3 models > hide #2.3 models > show #2.3 models > select clear > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > select #1 /L 820 atoms, 844 bonds, 106 residues, 1 model selected > define centroid sel name centroid_LC_15 Centroid 'centroid_LC_15' placed at [253.36603171 235.10472073 129.35070122] > select #3 /L 825 atoms, 849 bonds, 106 residues, 1 model selected > define centroid sel name centroid_LC_31 Centroid 'centroid_LC_31' placed at [175.15648606 258.32461939 276.88190909] > hide #!3 models > select add #1.3 826 atoms, 849 bonds, 107 residues, 2 models selected > select add #!1/A:332@CA 827 atoms, 849 bonds, 108 residues, 3 models selected Either three or four atoms must be selected! > select #1.3 #1/A:332@ca 2 atoms, 2 residues, 2 models selected Either three or four atoms must be selected! > select clear > select #1.3 1 atom, 1 residue, 1 model selected > select add #!1/A:332@CA 2 atoms, 2 residues, 2 models selected Either three or four atoms must be selected! > select clear > distance #1.3 #1/A:332@ca Distance between PC94A15_BG505_RM20A3_J1466_real_space_refined_003.pdb #!1/A ASN 332 CA and centroid_HC_15 #1.3: 34.665Å > show #!3 models > distance #1/A:332@ca #3.3 Distance between PC94A15_BG505_RM20A3_J1466_real_space_refined_003.pdb #!1/A ASN 332 CA and centroid_HC_31 #3.3: 33.088Å > angle #1.3 #1/A:332@ca #3.3 Angle between centroid_HC_15 #1.3, PC94A15_BG505_RM20A3_J1466_real_space_refined_003.pdb #!1/A ASN 332 CA, and centroid_HC_31 #3.3: 8.910 > show #!2 models > hide #!3 models > show #!3 models > hide #!2 models > ui tool show ""Side View"" > ui tool show Distances > distance style color #929000 > distance style color black > distance style color #0433ff > distance style color #ff2600 > distance style color #941100 > distance style color black > save /Users/sphulera/Desktop/image58.png width 709 height 757 supersample 3 > transparentBackground true > show #!2 models > hide #!3 models > save /Users/sphulera/Desktop/image59.png width 709 height 757 supersample 3 > hide #3.3 models > hide #3.4 models > hide #1.3 models > hide #1.4 models > hide #2.3 models > ui tool show ""Side View"" > show #!3 models > hide #!2 models ===== 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 M3 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 Air Model Identifier: Mac15,12 Model Number: Z1B600163LL/A Chip: Apple M3 Total Number of Cores: 8 (4 performance and 4 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: 2 days, 22 minutes Graphics/Displays: Apple M3: Chipset Model: Apple M3 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal LG HDR 4K: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported 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