id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 10336 Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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""x86_64"", ""base"" : 4449808384, ""CFBundleShortVersionString"" : ""3.9.11, (c) 2001-2021 Python Software Foundation."", ""CFBundleIdentifier"" : ""org.python.python"", ""size"" : 2527232, ""uuid"" : ""ef9cc1f4-5991-3213-9a9e-e68c578b6c1b"", ""path"" : ""\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python"", ""name"" : ""Python"", ""CFBundleVersion"" : ""3.9.11"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4441182208, ""CFBundleShortVersionString"" : ""1.6.1"", ""CFBundleIdentifier"" : ""edu.ucsf.cgl.ChimeraX"", ""size"" : 4096, ""uuid"" : ""5df621ee-554e-36a8-b448-93b2334e5480"", ""path"" : ""\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX"", ""name"" : ""ChimeraX"", ""CFBundleVersion"" : ""1.6.1.0"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4706205696, ""size"" : 442368, ""uuid"" : ""7de33963-bbc5-3996-ba6e-f1d562c17c95"", ""path"" : ""\/usr\/lib\/dyld"", ""name"" : ""dyld"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 5093015552, ""size"" : 174571520, ""uuid"" : ""473ca65c-6149-3bfa-a88b-95ac735bcd3b"", ""path"" : ""\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore"", ""name"" : ""QtWebEngineCore"" } ], ""sharedCache"" : { ""base"" : 140703629950976, ""size"" : 15216836608, ""uuid"" : ""0939015d-8308-3e69-b095-bd928f835202"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.4G resident=0K(0%) swapped_out_or_unallocated=1.4G(100%)\nWritable regions: Total=1.0G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.0G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 512K 4 \nActivity Tracing 256K 1 \nCG backing stores 6240K 16 \nCG image 72K 5 \nColorSync 232K 26 \nCoreAnimation 144K 11 \nCoreGraphics 16K 3 \nCoreUI image data 2292K 16 \nFoundation 16K 1 \nIOKit 15.5M 2 \nKernel Alloc Once 8K 1 \nMALLOC 377.4M 498 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 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 88K 22 \nStack 154.2M 23 \nStack Guard 56.0M 1 \nVM_ALLOCATE 98.1M 72 \nVM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)\n__DATA 44.0M 652 \n__DATA_CONST 31.4M 335 \n__DATA_DIRTY 1621K 213 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 670.4M 142 \n__OBJC_RO 81.8M 1 \n__OBJC_RW 3136K 2 \n__TEXT 796.2M 656 \n__UNICODE 588K 1 \ndyld private memory 1056K 3 \nmapped file 107.2M 42 \nshared memory 3028K 37 \n=========== ======= ======= \nTOTAL 2.8G 2805 \nTOTAL, minus reserved VM space 2.4G 2805 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""602ad4dac86151000cf27e46"", ""factorPackIds"" : { ""SIRI_DICTATION_ASSETS"" : ""6193d03f2171a2330e561dfc"" }, ""deploymentId"" : 240000305 }, { ""rolloutId"" : ""60da5e84ab0ca017dace9abf"", ""factorPackIds"" : { }, ""deploymentId"" : 240000008 }, { ""rolloutId"" : ""607844aa04477260f58a8077"", ""factorPackIds"" : { ""SIRI_MORPHUN_ASSETS"" : ""6103050cbfe6dc472e1c982a"" }, ""deploymentId"" : 240000066 }, { ""rolloutId"" : ""601d9415f79519000ccd4b69"", ""factorPackIds"" : { }, ""deploymentId"" : 240000414 }, { ""rolloutId"" : ""63582c5f8a53461413999550"", ""factorPackIds"" : { }, ""deploymentId"" : 240000002 }, { ""rolloutId"" : ""5fb4245a1bbfe8005e33a1e1"", ""factorPackIds"" : { }, ""deploymentId"" : 240000021 }, { ""rolloutId"" : ""5f72dc58705eff005a46b3a9"", ""factorPackIds"" : { }, ""deploymentId"" : 240000015 }, { ""rolloutId"" : ""60f8ddccefea4203d95cbeef"", ""factorPackIds"" : { }, ""deploymentId"" : 240000025 }, { ""rolloutId"" : ""5fc94383418129005b4e9ae0"", ""factorPackIds"" : { }, ""deploymentId"" : 240000614 }, { ""rolloutId"" : ""60186475825c62000ccf5450"", ""factorPackIds"" : { }, ""deploymentId"" : 240000068 }, { ""rolloutId"" : ""5ffde50ce2aacd000d47a95f"", ""factorPackIds"" : { }, ""deploymentId"" : 240000352 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX QPainter::begin: Paint device returned engine == 0, type: 3 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/fli05@amgen.com/Library/CloudStorage/OneDrive-Amgen/General - > HGSNAT_Data_Share/Paper/Fig2_Mechanism/BindingSite.cxs"" Opened cryosparc_P130_J67_008_volume_map_sharp.mrc as #3, grid size 432,432,432, pixel 0.813, shown at level 0.242, step 1, values float32 Opened cryosparc_P130_J67_008_volume_map.mrc as #4, grid size 432,432,432, pixel 0.813, shown at level 0.103, step 1, values float32 Opened cryosparc_P129_J167_008_volume_map_sharp.mrc as #6, grid size 432,432,432, pixel 0.813, shown at level 0.169, step 1, values float32 Opened cryosparc_P129_J167_008_volume_map.mrc as #2, grid size 432,432,432, pixel 0.813, shown at level 0.0795, step 1, values float32 Opened cryosparc_P130_J67_008_volume_map_sharp.mrc 0 as #7.1, grid size 432,432,432, pixel 0.813, shown at level 0.242, step 1, values float32 Opened cryosparc_P130_J67_008_volume_map_sharp.mrc 1 as #7.2, grid size 432,432,432, pixel 0.813, shown at level 0.242, step 1, values float32 Opened cryosparc_P130_J67_008_volume_map_sharp.mrc 2 as #7.3, grid size 432,432,432, pixel 0.813, shown at level 0.242, step 1, values float32 Opened cryosparc_P130_J67_008_volume_map_sharp.mrc 3 as #7.4, grid size 432,432,432, pixel 0.813, shown at level 0.242, step 1, values float32 Opened cryosparc_P130_J67_008_volume_map_sharp.mrc 4 as #7.5, grid size 432,432,432, pixel 0.813, shown at level 0.242, step 1, values float32 Opened cryosparc_P129_J167_008_volume_map_sharp.mrc 0 as #8.1, grid size 432,432,432, pixel 0.813, shown at level 0.169, step 1, values float32 Opened cryosparc_P129_J167_008_volume_map_sharp.mrc 1 as #8.2, grid size 432,432,432, pixel 0.813, shown at level 0.169, step 1, values float32 Opened cryosparc_P129_J167_008_volume_map_sharp.mrc 2 as #8.3, grid size 432,432,432, pixel 0.813, shown at level 0.169, step 1, values float32 Opened cryosparc_P129_J167_008_volume_map_sharp.mrc 3 as #8.4, grid size 432,432,432, pixel 0.813, shown at level 0.169, step 1, values float32 Opened cryosparc_P129_J167_008_volume_map_sharp.mrc 4 as #8.5, grid size 432,432,432, pixel 0.813, shown at level 0.169, step 1, values float32 Log from Tue Dec 12 10:07:44 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/fli05@amgen.com/Library/CloudStorage/OneDrive-Amgen/General - > HGSNAT_Data_Share/Paper/Fig1/Overall_CoAProduct_Map.cxs"" Opened cryosparc_P130_J87_map_lp7.mrc as #2, grid size 432,432,432, pixel 0.813, shown at level 0.0461, step 1, values float32 Opened cryosparc_P130_J67_008_volume_map_sharp.mrc as #3, grid size 432,432,432, pixel 0.813, shown at level 0.708, step 1, values float32 Opened cryosparc_P130_J67_008_volume_map.mrc as #4, grid size 432,432,432, pixel 0.813, shown at level 0.0908, step 1, values float32 Log from Sun Nov 12 13:03:29 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/fli05@amgen.com/Documents/Phenix/HGSNAT_CoAProduct/RealSpaceRefine_11/CoA_Product_Boyang_real_space_refined_001-coot_CH3Up_real_space_refined_002-coot-7_real_space_refined_011.pdb Summary of feedback from opening /Users/fli05@amgen.com/Documents/Phenix/HGSNAT_CoAProduct/RealSpaceRefine_11/CoA_Product_Boyang_real_space_refined_001-coot_CH3Up_real_space_refined_002-coot-7_real_space_refined_011.pdb --- warnings | Cannot find consistent set of bond orders for ring system containing atom C07 in residue MUG /A:789 Cannot find consistent set of bond orders for ring system containing atom C07 in residue MUG /B:785 Chain information for CoA_Product_Boyang_real_space_refined_001-coot_CH3Up_real_space_refined_002-coot-7_real_space_refined_011.pdb #1 --- Chain | Description A | No description available B | No description available > set bgColor white > open ""/Users/fli05@amgen.com/Library/CloudStorage/OneDrive-Amgen/General - > HGSNAT_Data_Share/StructureData/CoAandProduct/Map/cryosparc_P130_J87_map_lp7.mrc"" Cannot open files: [Errno 60] Operation timed out > open ""/Users/fli05@amgen.com/Library/CloudStorage/OneDrive-Amgen/General - > HGSNAT_Data_Share/StructureData/CoAandProduct/Map/cryosparc_P130_J87_map_lp7.mrc"" Opened cryosparc_P130_J87_map_lp7.mrc as #2, grid size 432,432,432, pixel 0.813, shown at level 0.0254, step 2, values float32 > volume #2 step 1 > volume #2 level 0.07837 > hide #!2 models > show #!2 models > volume #2 level 0.08585 > hide #!2 models > select /B:198 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 125 atoms, 124 bonds, 25 residues, 1 model selected > select up 1021 atoms, 1040 bonds, 151 residues, 1 model selected > select up 4179 atoms, 4301 bonds, 548 residues, 1 model selected > ui tool show ""Color Actions"" > color sel dark orange > select clear > select /A:505 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 170 atoms, 171 bonds, 23 residues, 1 model selected > select up 3127 atoms, 3229 bonds, 399 residues, 1 model selected > select up 4256 atoms, 4382 bonds, 556 residues, 1 model selected > select up 8435 atoms, 8683 bonds, 1104 residues, 1 model selected > select down 4256 atoms, 4382 bonds, 556 residues, 1 model selected > ui tool show ""Color Actions"" > color sel royal blue > select clear > select ::name=""COA"" 96 atoms, 100 bonds, 2 residues, 1 model selected > ui tool show ""Color Actions"" > open ""/Users/fli05@amgen.com/Library/CloudStorage/OneDrive-Amgen/General - > HGSNAT_Data_Share/StructureData/CoAandProduct/Map/cryosparc_P130_J67_008_volume_map_sharp.mrc"" Opened cryosparc_P130_J67_008_volume_map_sharp.mrc as #3, grid size 432,432,432, pixel 0.813, shown at level 0.0404, step 2, values float32 > color sel lime green [Repeated 1 time(s)] > hide #!1 models > volume #3 step 1 > volume #3 level 0.2106 > hide #!3 models > open ""/Users/fli05@amgen.com/Library/CloudStorage/OneDrive-Amgen/General - > HGSNAT_Data_Share/StructureData/CoAandProduct/Map/cryosparc_P130_J67_008_volume_map.mrc"" Opened cryosparc_P130_J67_008_volume_map.mrc as #4, grid size 432,432,432, pixel 0.813, shown at level 0.0226, step 2, values float32 > volume #4 step 1 > volume #4 level 0.08856 > volume #4 color #ffff99 > hide #!4 models > show #!1 models > select ::name=""MUG"" 54 atoms, 58 bonds, 2 residues, 1 model selected > ui tool show ""Color Actions"" > color sel deep pink > ui tool show ""Color Zone"" > color zone #4 near #1 distance 4.88 > ui tool show ""Hide Dust"" > surface dust #4 size 4.88 > volume #3 level 0.7083 > volume #4 level 0.1048 > color zone #4 near #1 distance 4.98 > color zone #4 near #1 distance 5.08 > color zone #4 near #1 distance 5.18 > color zone #4 near #1 distance 5.28 > color zone #4 near #1 distance 5.38 > color zone #4 near #1 distance 5.48 > color zone #4 near #1 distance 5.58 > color zone #4 near #1 distance 5.68 > color zone #4 near #1 distance 5.78 > color zone #4 near #1 distance 5.88 > color zone #4 near #1 distance 5.98 > color zone #4 near #1 distance 6.08 > color zone #4 near #1 distance 6.18 > color zone #4 near #1 distance 6.28 > color zone #4 near #1 distance 6.38 > color zone #4 near #1 distance 6.48 > color zone #4 near #1 distance 6.58 > color zone #4 near #1 distance 6.68 > color zone #4 near #1 distance 6.78 > color zone #4 near #1 distance 6.88 > color zone #4 near #1 distance 6.98 > color zone #4 near #1 distance 7.08 > color zone #4 near #1 distance 7.18 > color zone #4 near #1 distance 7.28 > color zone #4 near #1 distance 7.38 > color zone #4 near #1 distance 7.48 > color zone #4 near #1 distance 7.58 > color zone #4 near #1 distance 7.68 > color zone #4 near #1 distance 7.78 > color zone #4 near #1 distance 7.88 > color zone #4 near #1 distance 7.98 > color zone #4 near #1 distance 8.08 > color zone #4 near #1 distance 8.18 > color zone #4 near #1 distance 8.28 > color zone #4 near #1 distance 8.38 > color zone #4 near #1 distance 8.48 > color zone #4 near #1 distance 8.58 > color zone #4 near #1 distance 8.68 > color zone #4 near #1 distance 8.78 > color zone #4 near #1 distance 8.88 > color zone #4 near #1 distance 8.98 > color zone #4 near #1 distance 9.08 > color zone #4 near #1 distance 9.18 > color zone #4 near #1 distance 9.28 > color zone #4 near #1 distance 9.38 > color zone #4 near #1 distance 9.48 > color zone #4 near #1 distance 9.58 > color zone #4 near #1 distance 9.68 > color zone #4 near #1 distance 9.78 > color zone #4 near #1 distance 9.88 > color zone #4 near #1 distance 9.98 > color zone #4 near #1 distance 10.08 > color zone #4 near #1 distance 9.98 > color zone #4 near #1 distance 9.88 > color zone #4 near #1 distance 9.78 > color zone #4 near #1 distance 9.68 > color zone #4 near #1 distance 9.58 > color zone #4 near #1 distance 9.48 > color zone #4 near #1 distance 9.38 > color zone #4 near #1 distance 9.28 > color zone #4 near #1 distance 9.18 > color zone #4 near #1 distance 9.08 > color zone #4 near #1 distance 8.98 > color zone #4 near #1 distance 8.88 > color zone #4 near #1 distance 8.78 > color zone #4 near #1 distance 8.68 > color zone #4 near #1 distance 8.58 > color zone #4 near #1 distance 8.48 > color zone #4 near #1 distance 8.38 > color zone #4 near #1 distance 8.48 > volume #4 level 0.09191 > volume #4 level 0.088 > surface dust #4 size 4.84 > surface dust #4 size 65.33 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > volume #4 level 0.08409 > volume #4 level 0.102 > surface dust #4 size 64.92 > surface dust #4 size 3.09 > volume #4 level 0.0908 > volume #4 color white > color zone #4 near #1 distance 8.48 > volume #2 level 0.04615 > volume #4 color #cccccc > volume #4 color #cccccc2a > volume #4 color #cccccc > volume #2 color #b2b2b21e > color zone #4 near #1 distance 8.48 > volume #4 color white > volume #4 color #ffffff00 > color zone #4 near #1 distance 8.48 > surface dust #4 size 3.11 > surface dust #4 size 4.97 > surface dust #4 size 4.94 > surface dust #4 size 6.26 > color zone #4 near #1 distance 8.47 > color zone #4 near #1 distance 7.64 > color zone #4 near #1 distance 7.74 > color zone #4 near #1 distance 1.83 > color zone #4 near #1 distance 5 [Repeated 1 time(s)] > color zone #4 near #1 distance 7 [Repeated 1 time(s)] > color zone #4 near #1 distance 8 [Repeated 1 time(s)] > color zone #4 near #1 distance 1 > color zone #4 near #1 distance 10 [Repeated 1 time(s)] > surface dust #4 size 6.22 > surface dust #4 size 4.61 > surface dust #4 size 4.52 > surface dust #4 size 4.61 > hide #!1 models > show #!2 models > save ""/Users/fli05@amgen.com/OneDrive - Amgen/General - > HGSNAT_Data_Share/Paper/Fig1/Overall_CoAProduct_Map.cxs"" ——— End of log from Sun Nov 12 13:03:29 2023 ——— opened ChimeraX session > open ""/Users/fli05@amgen.com/Library/CloudStorage/OneDrive-Amgen/General - > HGSNAT_Data_Share/StructureData/ActylCoAandSubstrate/Model/RealSpaceRefine_10/ACO_MGN_Dock_J167-coot-24_Hflip_real_space_refined_010.pdb"" Summary of feedback from opening /Users/fli05@amgen.com/Library/CloudStorage/OneDrive-Amgen/General - HGSNAT_Data_Share/StructureData/ActylCoAandSubstrate/Model/RealSpaceRefine_10/ACO_MGN_Dock_J167-coot-24_Hflip_real_space_refined_010.pdb --- warnings | Cannot find consistent set of bond orders for ring system containing atom C07 in residue MGN /A:788 Cannot find consistent set of bond orders for ring system containing atom C07 in residue MGN /B:784 Chain information for ACO_MGN_Dock_J167-coot-24_Hflip_real_space_refined_010.pdb #5 --- Chain | Description A | No description available B | No description available > open ""/Users/fli05@amgen.com/Library/CloudStorage/OneDrive-Amgen/General - > HGSNAT_Data_Share/StructureData/ActylCoAandSubstrate/Map/cryosparc_P129_J167_008_volume_map_sharp.mrc"" Opened cryosparc_P129_J167_008_volume_map_sharp.mrc as #6, grid size 432,432,432, pixel 0.813, shown at level 0.0397, step 2, values float32 > volume #6 step 1 > volume #6 level 0.15 > hide #!2 models > close #2 > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > save ""/Users/fli05@amgen.com/OneDrive - Amgen/General - > HGSNAT_Data_Share/Paper/Fig2_Mechanism/BindingSite.cxs"" > hide #!6 models > hide #!5 models > hide #!4 models > show #!1 models > select clear > show #!3 models > volume #3 level 0.2914 > volume #3 color #ffffb277 > volume #3 color #ffffb263 > volume #3 level 0.364 > volume #3 level 0.3156 > show #!4 models > color #4 #ffffff62 models > color #4 #ffffff2e models > color #4 #ffffff6a models > volume #4 level 0.1009 > volume #4 level 0.1073 > volume #4 level 0.1035 > hide #!3 models > open ""/Users/fli05@amgen.com/Library/CloudStorage/OneDrive-Amgen/General - > HGSNAT_Data_Share/StructureData/ActylCoAandSubstrate/Map/cryosparc_P129_J167_008_volume_map.mrc"" Opened cryosparc_P129_J167_008_volume_map.mrc as #2, grid size 432,432,432, pixel 0.813, shown at level 0.0235, step 2, values float32 > volume #2 step 1 > volume #2 level 0.1075 > volume #2 color #ffffb289 > hide #!4 models > hide #!2 models > hide #!1 models > show #!5 models > show #!2 models > volume #2 level 0.09946 > volume #2 level 0.07946 [Repeated 1 time(s)] > hide #!5 models > show #!6 models > show #!5 models > hide #!2 models > volume #6 color #b2b2b26a > volume #6 color #b2b2b250 > volume #6 level 0.1913 > volume #6 level 0.2372 > volume #6 level 0.2143 > volume #6 level 0.1821 > volume #6 level 0.2143 > hide #!6 models > hide #!5 models > show #!3 models > show #!1 models > save ""/Users/fli05@amgen.com/OneDrive - Amgen/General - > HGSNAT_Data_Share/Paper/Fig2_Mechanism/BindingSite.cxs"" > hide #!3 models > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 27 atoms, 29 bonds, 1 residue, 1 model selected > select add #1/B:785@C18 28 atoms, 29 bonds, 2 residues, 1 model selected > select up 54 atoms, 58 bonds, 2 residues, 1 model selected > select up 8435 atoms, 8683 bonds, 1104 residues, 1 model selected > select down 54 atoms, 58 bonds, 2 residues, 1 model selected > select add #1/A:788@C2P 55 atoms, 58 bonds, 3 residues, 1 model selected > select up 57 atoms, 59 bonds, 4 residues, 1 model selected > select up 150 atoms, 158 bonds, 4 residues, 1 model selected > select up 8435 atoms, 8683 bonds, 1104 residues, 1 model selected > select down 150 atoms, 158 bonds, 4 residues, 1 model selected > color sel lime > show #!3 models > ui tool show ""Color Zone"" > color zone #3 near #1 distance 4.88 > color zone #3 near #1 distance 4.76 > color zone #3 near #1 distance 3.62 > color zone #3 near #1 distance 3.67 > color zone #3 near #1 distance 2.19 > volume #3 level 0.3309 > volume #3 level 0.3563 > volume #3 level 0.2418 > color zone #3 near #1 distance 2.15 > color zone #3 near #1 distance 2.37 > color zone #3 near #1 distance 2.26 > color zone #3 near #1 distance 2.72 > volume splitbyzone #3 Opened cryosparc_P130_J67_008_volume_map_sharp.mrc 0 as #7.1, grid size 432,432,432, pixel 0.813, shown at level 0.242, step 1, values float32 Opened cryosparc_P130_J67_008_volume_map_sharp.mrc 1 as #7.2, grid size 432,432,432, pixel 0.813, shown at level 0.242, step 1, values float32 Opened cryosparc_P130_J67_008_volume_map_sharp.mrc 2 as #7.3, grid size 432,432,432, pixel 0.813, shown at level 0.242, step 1, values float32 Opened cryosparc_P130_J67_008_volume_map_sharp.mrc 3 as #7.4, grid size 432,432,432, pixel 0.813, shown at level 0.242, step 1, values float32 > hide #!7.2 models > hide #!7.4 models > hide #!7.1 models > save ""/Users/fli05@amgen.com/OneDrive - Amgen/General - > HGSNAT_Data_Share/Paper/Fig2_Mechanism/BindingSite.cxs"" > hide #!7 models > hide #!7.3 models > hide #!1 models > show #!5 models > show #!6 models > hide #!6 models > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 24 atoms, 26 bonds, 1 residue, 1 model selected > select add #5/B:781@P3B 25 atoms, 28 bonds, 2 residues, 1 model selected > select up 29 atoms, 28 bonds, 4 residues, 1 model selected > select up 150 atoms, 158 bonds, 4 residues, 1 model selected > color sel yellow > show #!6 models > color zone #6 near #5 distance 4.88 > color zone #6 near #5 distance 4.93 > color zone #6 near #5 distance 4.75 > color zone #6 near #5 distance 4.9 > color zone #6 near #5 distance 3.89 > color zone #6 near #5 distance 3.92 > color zone #6 near #5 distance 2.11 > color zone #6 near #5 distance 1.43 > color single #6 > select clear > select #5/B:75 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 43 atoms, 42 bonds, 6 residues, 1 model selected > select up 996 atoms, 1014 bonds, 150 residues, 1 model selected > select up 4122 atoms, 4242 bonds, 544 residues, 1 model selected > select up 8312 atoms, 8558 bonds, 1097 residues, 1 model selected > select up 16747 atoms, 17241 bonds, 2201 residues, 11 models selected > select up 16747 atoms, 17241 bonds, 2201 residues, 11 models selected > hide #!6 models > select up 16747 atoms, 17241 bonds, 2201 residues, 11 models selected > color (#!5 & sel) hot pink > select clear > select add #5/A:275 11 atoms, 13 bonds, 1 residue, 1 model selected > select subtract #5/A:275 3 bonds, 1 model selected > select up 8 atoms, 4 bonds, 4 residues, 1 model selected > select up 150 atoms, 158 bonds, 4 residues, 1 model selected > color sel blue > select clear > show #!6 models > color zone #6 near #5 distance 1.43 > color zone #6 near #5 distance 1.44 > color zone #6 near #5 distance 1.67 > color zone #6 near #5 distance 2.08 > color zone #6 near #5 distance 2.07 > color zone #6 near #5 distance 2.24 > hide #!6 models > select #5/B:781@C2B 1 atom, 1 residue, 1 model selected > select #5/A:784@O3B 1 atom, 1 residue, 1 model selected > select add #5/A:788@C04 2 atoms, 1 bond, 2 residues, 1 model selected > select up 6 atoms, 2 bonds, 4 residues, 1 model selected > select up 150 atoms, 158 bonds, 4 residues, 1 model selected > show #!6 models > color zone #6 near #5 distance 2.31 > color zone #6 near #5 distance 2.29 > color zone #6 near #5 distance 2.72 > color zone #6 near #5 distance 2.7 > color zone #6 near #5 distance 3 > volume #6 level 0.1967 > volume #6 level 0.1694 > color zone #6 near #5 distance 2.95 > color zone #6 near #5 distance 2.6 > volume splitbyzone #6 Opened cryosparc_P129_J167_008_volume_map_sharp.mrc 0 as #8.1, grid size 432,432,432, pixel 0.813, shown at level 0.169, step 1, values float32 Opened cryosparc_P129_J167_008_volume_map_sharp.mrc 1 as #8.2, grid size 432,432,432, pixel 0.813, shown at level 0.169, step 1, values float32 Opened cryosparc_P129_J167_008_volume_map_sharp.mrc 2 as #8.3, grid size 432,432,432, pixel 0.813, shown at level 0.169, step 1, values float32 > hide #!5 models > select add #5 8312 atoms, 8558 bonds, 5 pseudobonds, 1097 residues, 2 models selected > select subtract #5 Nothing selected > hide #!8 models > hide #!8.3 models > show #!1 models > select clear > select #1/B:784@P1A 1 atom, 1 residue, 1 model selected > select subtract #1/B:784@P1A Nothing selected > select #1/A:788@N8P 1 atom, 1 residue, 1 model selected > select add #1/B:784@CBP 2 atoms, 2 residues, 1 model selected > select subtract #1/B:784@CBP 1 atom, 1 residue, 1 model selected > select up 48 atoms, 50 bonds, 1 residue, 1 model selected > select up 4256 atoms, 4382 bonds, 556 residues, 1 model selected > select clear > select add #1/B:784@CCP 1 atom, 1 bond, 1 residue, 1 model selected > select up 3 atoms, 1 bond, 2 residues, 1 model selected > select up 96 atoms, 100 bonds, 2 residues, 1 model selected > ui tool show ""Color Actions"" > select clear [Repeated 1 time(s)] > select add #1/A:369 5 atoms, 4 bonds, 1 residue, 1 model selected > select clear > select #1/A:631 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 142 atoms, 148 bonds, 16 residues, 1 model selected > select up 3127 atoms, 3229 bonds, 399 residues, 1 model selected > select up 4256 atoms, 4382 bonds, 556 residues, 1 model selected > select down 3127 atoms, 3229 bonds, 399 residues, 1 model selected > ui tool show ""Color Actions"" > color sel light goldenrod yellow > color sel pale goldenrod > select clear [Repeated 1 time(s)] > select add #1/B:85 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 64 atoms, 64 bonds, 8 residues, 1 model selected > select up 1021 atoms, 1040 bonds, 151 residues, 1 model selected > select up 4179 atoms, 4301 bonds, 548 residues, 1 model selected > select up 8435 atoms, 8683 bonds, 1104 residues, 1 model selected > select down 4179 atoms, 4301 bonds, 548 residues, 1 model selected > ui tool show ""Color Actions"" > color sel orange > select #1/A:157 11 atoms, 11 bonds, 1 residue, 1 model selected > select up 50 atoms, 51 bonds, 6 residues, 1 model selected > select up 1054 atoms, 1074 bonds, 155 residues, 1 model selected > ui tool show ""Color Actions"" > color sel pale goldenrod > select clear [Repeated 1 time(s)] > select up 4 atoms, 2 bonds, 2 residues, 1 model selected > select up 96 atoms, 100 bonds, 2 residues, 1 model selected > select ::name=""NAG"" 182 atoms, 184 bonds, 13 residues, 2 models selected > hide sel & #!1 atoms > select ::name=""COA"" 96 atoms, 100 bonds, 2 residues, 1 model selected > ui tool show ""Color Actions"" > color sel royal blue > select clear > select add #1/A:789@C18 1 atom, 1 bond, 1 residue, 1 model selected > select up 4 atoms, 2 bonds, 2 residues, 1 model selected > select up 54 atoms, 58 bonds, 2 residues, 1 model selected > ui tool show ""Color Actions"" > color sel medium spring green > show #!3 models > close #7 > close #8 > color zone #3 near #5 distance 2.72 > color zone #3 near #1 distance 2.72 > hide #!3 models > show #!3 models > volume splitbyzone #3 Opened cryosparc_P130_J67_008_volume_map_sharp.mrc 0 as #7.1, grid size 432,432,432, pixel 0.813, shown at level 0.242, step 1, values float32 Opened cryosparc_P130_J67_008_volume_map_sharp.mrc 1 as #7.2, grid size 432,432,432, pixel 0.813, shown at level 0.242, step 1, values float32 Opened cryosparc_P130_J67_008_volume_map_sharp.mrc 2 as #7.3, grid size 432,432,432, pixel 0.813, shown at level 0.242, step 1, values float32 Opened cryosparc_P130_J67_008_volume_map_sharp.mrc 3 as #7.4, grid size 432,432,432, pixel 0.813, shown at level 0.242, step 1, values float32 Opened cryosparc_P130_J67_008_volume_map_sharp.mrc 4 as #7.5, grid size 432,432,432, pixel 0.813, shown at level 0.242, step 1, values float32 > hide #!7 models > show #!7 models > hide #!7 models > show #!3 models > hide #!3 models > show #!7 models > hide #!7.1 models > hide #!7.2 models > hide #!7.5 models > save ""/Users/fli05@amgen.com/OneDrive - Amgen/General - > HGSNAT_Data_Share/Paper/Fig2_Mechanism/BindingSite.cxs"" > hide #!1 models > show #!1 models > show #!5 models > hide #!1 models > hide #!7.4 models > hide #!7.3 models > hide #!7 models > show #!7.4 models > show #!7.3 models > hide #!7 models > show #!6 models > hide #!6 models > show #!1 models > hide #!1 models > select #5/A:570 12 atoms, 12 bonds, 1 residue, 1 model selected > select up 192 atoms, 197 bonds, 24 residues, 1 model selected > select up 3079 atoms, 3180 bonds, 399 residues, 1 model selected > select up 4190 atoms, 4316 bonds, 553 residues, 1 model selected > ui tool show ""Color Actions"" > color sel light pink > select clear > select #5/B:430 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 212 atoms, 219 bonds, 26 residues, 1 model selected > select up 2004 atoms, 2070 bonds, 257 residues, 1 model selected > select up 2035 atoms, 2102 bonds, 262 residues, 1 model selected > select up 3051 atoms, 3149 bonds, 392 residues, 1 model selected > select up 4122 atoms, 4242 bonds, 544 residues, 1 model selected > color sel violet > select clear > select ::name=""NAG"" 182 atoms, 184 bonds, 13 residues, 2 models selected > hide sel & #!5 cartoons > hide sel & #!5 atoms > select clear > hide #!5 atoms > select ::name=""ACO"" 102 atoms, 106 bonds, 2 residues, 1 model selected > show sel atoms > select ::name=""MGN"" 48 atoms, 52 bonds, 2 residues, 1 model selected > show sel atoms > ui tool show ""Color Actions"" > color sel pale green > select ::name=""ACO"" 102 atoms, 106 bonds, 2 residues, 1 model selected > color sel cyan > select clear > show #!6 models > color zone #6 near #5 distance 2.6 > volume splitbyzone #6 Opened cryosparc_P129_J167_008_volume_map_sharp.mrc 0 as #8.1, grid size 432,432,432, pixel 0.813, shown at level 0.169, step 1, values float32 Opened cryosparc_P129_J167_008_volume_map_sharp.mrc 1 as #8.2, grid size 432,432,432, pixel 0.813, shown at level 0.169, step 1, values float32 Opened cryosparc_P129_J167_008_volume_map_sharp.mrc 2 as #8.3, grid size 432,432,432, pixel 0.813, shown at level 0.169, step 1, values float32 Opened cryosparc_P129_J167_008_volume_map_sharp.mrc 3 as #8.4, grid size 432,432,432, pixel 0.813, shown at level 0.169, step 1, values float32 Opened cryosparc_P129_J167_008_volume_map_sharp.mrc 4 as #8.5, grid size 432,432,432, pixel 0.813, shown at level 0.169, step 1, values float32 > hide #!8.5 models > hide #!8.2 models > hide #!8.1 models > save ""/Users/fli05@amgen.com/OneDrive - Amgen/General - > HGSNAT_Data_Share/Paper/Fig2_Mechanism/BindingSite.cxs"" > dssp > ui tool show ""Hide Dust"" > surface dust #8.4 size 4.88 > save ""/Users/fli05@amgen.com/OneDrive - Amgen/General - > HGSNAT_Data_Share/Paper/Fig2_Mechanism/BindingSite.cxs"" ——— End of log from Tue Dec 12 10:07:44 2023 ——— opened ChimeraX session OpenGL version: 4.1 INTEL-18.4.6 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine OpenGL vendor: Intel Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,2 Processor Name: Quad-Core Intel Core i7 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 512 KB L3 Cache: 8 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1715.81.2.0.0 (iBridge: 19.16.10744.0.0,0) OS Loader Version: 540.80.2~11 Software: System Software Overview: System Version: macOS 12.2.1 (21D62) Kernel Version: Darwin 21.3.0 Time since boot: 30 days 23:34 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 Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal P27h-20: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 59.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: V908KKL1 Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: Yes Connection Type: Thunderbolt/DisplayPort Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 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: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBImages: 1.2 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: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 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: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Window Toolkit duplicate Tom Goddard all ChimeraX