id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8875 XMAS: crash in ~QGridLayout() chew0357@… Richard Scheltema "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Opening and closing of ""Visualize"" in XMAS UI Fatal Python error: Segmentation fault Thread 0x000000031bb06000 (most recent call first): File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 316 in wait File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 574 in wait File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 1297 in run File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031ab03000 (most recent call first): File 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""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703439982592, ""CFBundleShortVersionString"" : ""2.1.1"", ""CFBundleIdentifier"" : ""com.apple.HIToolbox"", ""size"" : 3112958, ""uuid"" : ""7bf47984-29cb-319e-a6da-0884d158f96a"", ""path"" : ""\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox"", ""name"" : ""HIToolbox"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703324549120, ""CFBundleShortVersionString"" : ""6.9"", ""CFBundleIdentifier"" : ""com.apple.AppKit"", ""size"" : 16814067, ""uuid"" : ""540cedfd-5a35-3f35-8953-dcb7c4834eb5"", ""path"" : ""\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit"", ""name"" : ""AppKit"", ""CFBundleVersion"" : ""2299.40.118"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4513710080, ""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-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python"", ""name"" : ""Python"", ""CFBundleVersion"" : ""3.9.11"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4369608704, ""CFBundleShortVersionString"" : ""1.5.0"", ""CFBundleIdentifier"" : ""edu.ucsf.cgl.ChimeraX"", ""size"" : 4096, ""uuid"" : ""5df621ee-554e-36a8-b448-93b2334e5480"", ""path"" : ""\/Applications\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX"", ""name"" : ""ChimeraX"", ""CFBundleVersion"" : ""1.5.0.0"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 8664707072, ""size"" : 622592, ""uuid"" : ""bba77709-6cad-3592-ab03-09d0f7b8610e"", ""path"" : ""\/usr\/lib\/dyld"", ""name"" : ""dyld"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 140703127437312, ""size"" : 196608, ""uuid"" : ""f066db2c-ed38-3f37-8d21-81d15fa908fe"", ""path"" : ""\/usr\/libexec\/rosetta\/runtime"", ""name"" : ""runtime"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4608962560, ""size"" : 64028672, ""uuid"" : ""24c9d5c5-4854-3af4-9550-cb0204044dfa"", ""path"" : ""\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib"", ""name"" : ""libopenblas64_.0.dylib"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 5234360320, ""size"" : 165052416, ""uuid"" : ""4aa1de3e-464c-340c-ab61-bcd39bfc7658"", ""path"" : ""\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore"", ""name"" : ""QtWebEngineCore"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 5222494208, ""size"" : 147456, ""uuid"" : ""9a744198-7fb3-3c4f-b935-3646fa131615"", ""path"" : ""\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numexpr\/interpreter.cpython-39-darwin.so"", ""name"" : ""interpreter.cpython-39-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 6109786112, ""size"" : 63373312, ""uuid"" : ""ccf8b470-9ccf-3558-9748-04374e88d1ea"", ""path"" : ""\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/scipy\/.dylibs\/libopenblas.0.dylib"", ""name"" : ""libopenblas.0.dylib"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 5032435712, ""size"" : 6979584, ""uuid"" : ""49d915f7-1c6d-3bbd-b96f-064260e7d998"", ""path"" : ""\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtGui.framework\/Versions\/A\/QtGui"", ""name"" : ""QtGui"" } ], ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)\nWritable regions: Total=3.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.3G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 512K 4 \nActivity Tracing 256K 1 \nCG backing stores 2944K 8 \nCG image 960K 67 \nColorSync 248K 29 \nCoreAnimation 808K 92 \nCoreGraphics 24K 4 \nCoreServices 624K 2 \nCoreUI image data 1556K 22 \nFoundation 36K 2 \nKernel Alloc Once 8K 1 \nMALLOC 1.8G 163 \nMALLOC guard page 192K 9 \nMALLOC_MEDIUM (reserved) 584.0M 8 reserved VM address space (unallocated)\nMach message 16K 4 \nOpenGL GLSL 384K 4 \nRosetta Arena 4096K 2 \nRosetta Generic 1740K 432 \nRosetta JIT 128.0M 1 \nRosetta Return Stack 1140K 114 \nRosetta Thread Context 1140K 114 \nSTACK GUARD 44K 11 \nStack 225.8M 58 \nStack Guard 56.2M 47 \nVM_ALLOCATE 164.4M 432 \nVM_ALLOCATE (reserved) 384.1M 16 reserved VM address space (unallocated)\n__CTF 756 1 \n__DATA 52.3M 919 \n__DATA_CONST 40.2M 395 \n__DATA_DIRTY 1845K 231 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 219.7M 288 \n__OBJC_RO 65.4M 1 \n__OBJC_RW 1987K 2 \n__TEXT 1.0G 901 \ndyld private memory 768K 4 \nmapped file 4.7G 2134 \nshared memory 1004K 32 \nunshared pmap 14.4M 9 \n=========== ======= ======= \nTOTAL 9.4G 6566 \nTOTAL, minus reserved VM space 8.5G 6566 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""60da5e84ab0ca017dace9abf"", ""factorPackIds"" : { }, ""deploymentId"" : 240000008 }, { ""rolloutId"" : ""5fb4245a1bbfe8005e33a1e1"", ""factorPackIds"" : { }, ""deploymentId"" : 240000021 } ], ""experiments"" : [ { ""treatmentId"" : ""c28e4ee6-1b08-4f90-8e05-2809e78310a3"", ""experimentId"" : ""6317d2003d24842ff850182a"", ""deploymentId"" : 400000013 } ] }, ""reportNotes"" : [ ""dyld_process_snapshot_create_for_process failed with 5"" ] } ===== Log before crash start ===== UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. > open /Users/alvinchew/Library/CloudStorage/OneDrive- > NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1-fab562_hdxms10minLXL- > MS_recolored.cxs Opened sNS1wt-Fab562.mrc as #9, grid size 416,416,416, pixel 0.85, shown at level 0.11, step 1, values float32 Opened map 8 as #11, grid size 416,416,416, pixel 0.85, shown at level 0.0375, step 1, values float32 Log from Wed Apr 19 14:11:57 2023UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. > open ""/Users/alvinchew/Library/CloudStorage/OneDrive- > NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Data_MS_Wint/XMAS > files/NS1-apoAI_models-forwint_forAlvin.cxs"" Log from Mon Apr 3 16:43:31 2023UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. > open /Users/wintwintphoo/Downloads/NS1-apoAI_models-forwint_forAlvin.cxs Log from Mon Apr 3 15:19:20 2023UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. > open /Users/wintwintphoo/Downloads/NS1-apoAI_models-forwint.cxs Log from Sat Apr 1 16:55:32 2023UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. > set bgColor #ffffff00 Log from Thu Mar 30 23:52:24 2023UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. > open ""/Users/alvinchew/Library/CloudStorage/OneDrive- > NanyangTechnologicalUniversity/202112_FlaviNS1/Writing/202211_LATEST_NS1manuscript/EM > Maps_docked structures/EDEN2 sNS1wt-Fab562/sNS1wt-Fab- > ApoAI_Ab562_compare.cxs"" Opened sNS1wt-Ab562.mrc as #2, grid size 352,352,352, pixel 0.85, shown at level 0.17, step 1, values float32 Opened sNS1wt-Fab562.mrc as #8, grid size 416,416,416, pixel 0.85, shown at level 0.0754, step 1, values float32 Log from Sat Nov 19 10:30:44 2022UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. > open ""/Users/alvinchew/Library/CloudStorage/OneDrive- > NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Writing/202211_LATEST_NS1manuscript/EM > Maps_docked structures/EDEN2 sNS1wt-Fab562/20220323_NS1wt-Ab-Fab- > ApoAI_hdl.cxs"" Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size 416,416,416, pixel 0.858, shown at level 0.09, step 1, values float32 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size 352,352,352, pixel 0.85, shown at level 0.17, step 1, values float32 Opened cryosparc_P35_J130_004_volume_map_sharp.mrc as #7, grid size 416,416,416, pixel 0.858, shown at level 0.09, step 2, values float32 Opened cryosparc_P39_J166_002_volume_map_sharp (1).mrc as #6, grid size 416,416,416, pixel 0.85, shown at level 0.0687, step 1, values float32 Opened cryosparc_P36_J32_002_volume_map_sharp.mrc as #8, grid size 416,416,416, pixel 0.85, shown at level 0.0754, step 1, values float32 Log from Thu Mar 24 12:02:48 2022UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. > open /Users/alvinchew/Library/CloudStorage/OneDrive- > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt- > Fab-ApoAI_hdl.cxs Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size 416,416,416, pixel 0.858, shown at level 0.09, step 1, values float32 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size 352,352,352, pixel 0.85, shown at level 0.169, step 1, values float32 Opened cryosparc_P35_J130_004_volume_map_sharp.mrc as #7, grid size 416,416,416, pixel 0.858, shown at level 0.09, step 2, values float32 Log from Sat Mar 12 14:58:51 2022UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. > open /Users/alvinchew/Library/CloudStorage/OneDrive- > NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-10_NS1wt- > Fab-ApoAI_hdl_Compare-NS1ts.cxs Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size 416,416,416, pixel 0.858, shown at level 0.09, step 1, values float32 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size 352,352,352, pixel 0.85, shown at level 0.169, step 1, values float32 Opened cryosparc_P35_J90_005_volume_map_sharp.mrc as #6, grid size 416,416,416, pixel 0.858, shown at level 0.135, step 1, values float32 Opened cryosparc_P35_J141_class_00_final_volume.mrc as #8, grid size 128,128,128, pixel 2.79, shown at level 0.318, step 1, values float32 Opened cryosparc_P35_J130_004_volume_map_sharp.mrc as #7, grid size 416,416,416, pixel 0.858, shown at level 0.09, step 2, values float32 Log from Fri Mar 11 18:14:28 2022UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. > open /Users/alvinchew/Library/CloudStorage/OneDrive- > NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt- > Fab-ApoAI_hdl.cxs Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size 416,416,416, pixel 0.858, shown at level 0.127, step 1, values float32 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size 352,352,352, pixel 0.85, shown at level 0.191, step 1, values float32 Log from Thu Mar 3 21:24:07 2022UCSF ChimeraX version: 1.2.2 (2021-05-08) © 2016-2021 Regents of the University of California. All rights reserved. > open ""/Users/alvinchew/OneDrive - Nanyang Technological > University/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"" Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size 416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size 352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32 Opened cryosparc_P47_J128_002_volume_map_sharp.mrc resampled as #7, grid size 352,352,352, pixel 0.85, shown at level 0.0969, step 1, values float32 Log from Thu Mar 3 19:50:19 2022UCSF ChimeraX version: 1.2.2 (2021-05-08) © 2016-2021 Regents of the University of California. All rights reserved. > open ""/Users/alvinchew/OneDrive - Nanyang Technological > University/202112_FlaviNS1/Data_EM_Alvin/20220303_D2NS1ts-Fab5-DL.cxs"" > format session Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size 416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size 352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size 352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32 Opened cryosparc_P35_J100_005_volume_map_sharp (1).mrc as #11, grid size 416,416,416, pixel 0.858, shown at level 0.05, step 1, values float32 Log from Thu Mar 3 12:01:46 2022UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. > open ""C:\\\Users\\\dahailuo\\\OneDrive - Nanyang Technological > University\\\Temporal\\\202112_FlaviNS1\\\Data_EM_Alvin\\\20220302_D2NS1ts- > Ab56-apoa1.cxs"" Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size 416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size 352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size 352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32 Log from Wed Mar 2 00:18:18 2022UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. > open ""D:\OneDrive - Nanyang Technological > University\Temporal\202112_FlaviNS1\Data_EM_Alvin\20220302_D2NS1ts- > Ab56-apoa1.cxs"" format session Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size 416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size 352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size 352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32 Log from Wed Mar 2 00:08:07 2022UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. > open ""D:/OneDrive - Nanyang Technological > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56-AA1.cxs"" Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size 416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size 352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size 352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32 Log from Tue Feb 22 22:03:06 2022UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. > open ""D:\OneDrive - Nanyang Technological > University\Temporal\202112_FlaviNS1\Data_EM_Alvin\20220222_D2NS1-Ab56-AA1.cxs"" > format session Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size 416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size 352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size 352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32 Log from Tue Feb 22 21:54:19 2022UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. > open ""D:\OneDrive - Nanyang Technological > University\Temporal\202112_FlaviNS1\Data_EM_Alvin\20220222_D2NS1-Ab56.cxs"" > format session Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size 416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size 352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32 Opened cryosparc_P47_J59_004_volume_map_sharp (3).mrc as #8, grid size 352,352,352, pixel 0.85, shown at level 0.421, step 2, values float32 Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size 352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32 Opened cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy as #11, grid size 352,352,352, pixel 0.85, shown at level 0.471, step 1, values float32 Log from Tue Feb 22 21:05:12 2022UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""D:/OneDrive - Nanyang Technological > University/Temporal/202109_zvNS1/3_Structures/20220211_NUS-K3_gAU- > sNS1-Fab56-2/cryosparc_P35_J91_006_volume_map_sharp.mrc"" Opened cryosparc_P35_J91_006_volume_map_sharp.mrc as #1, grid size 416,416,416, pixel 0.858, shown at level 0.0468, step 2, values float32 > surface dust #1 size 8.58 > open ""D:/OneDrive - Nanyang Technological > University/Temporal/202109_zvNS1/3_Structures/20220211_NUS-K3_gAU- > sNS1-Fab56-2/cryosparc_P35_J96_006_volume_map_sharp.mrc"" Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #2, grid size 416,416,416, pixel 0.858, shown at level 0.0481, step 2, values float32 > surface dust #1 size 8.58 > surface dust #2 size 8.58 > close #2 > close #1 > open ""D:/OneDrive - Nanyang Technological > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220211_NUS-K3_gAU- > sNS1-Fab56-2/cryosparc_P35_J96_006_volume_map_sharp.mrc"" Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size 416,416,416, pixel 0.858, shown at level 0.0481, step 2, values float32 > open ""D:/OneDrive - Nanyang Technological > University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/cryosparc_P47_J20_004_volume_map_sharp.mrc"" Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size 352,352,352, pixel 0.85, shown at level 0.142, step 2, values float32 > surface dust #1 size 8.58 > surface dust #2 size 8.5 > open ""D:/OneDrive - Nanyang Technological > University/Temporal/202109_zvNS1/3_Structures/20220211_NUS-K3_gAU- > sNS1-Fab56-2/D2NS1.pdb"" Summary of feedback from opening D:/OneDrive - Nanyang Technological University/Temporal/202109_zvNS1/3_Structures/20220211_NUS-K3_gAU- sNS1-Fab56-2/D2NS1.pdb --- warning | Ignored bad PDB record found on line 5732 END Chain information for D2NS1.pdb #3 --- Chain | Description B C | No description available > hide #!2 models > volume #1 level 0.07524 > volume #1 level 0.07 > volume #1 level 0.072 > select #3 5602 atoms, 5744 bonds, 704 residues, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.89628,-0.44038,-0.052381,101.61,0.096778,0.078954,0.99217,-38.919,-0.43279,-0.89433,0.11338,384.44 > view matrix models > #3,0.99109,-0.12056,-0.056551,31.91,0.0080432,0.4781,-0.87827,242.8,0.13292,0.86999,0.47482,-76.088 > view matrix models > #3,0.79841,-0.57175,0.18879,97.95,-0.1953,0.050686,0.97943,19.471,-0.56956,-0.81886,-0.071196,428.68 > view matrix models > #3,0.82022,-0.53629,0.19907,86.322,-0.4792,-0.8342,-0.2729,441.29,0.31242,0.12845,-0.94122,269.29 > view matrix models > #3,0.33094,0.34033,0.88014,-96.351,-0.87516,0.45954,0.15137,217.82,-0.35295,-0.82036,0.44993,298 > view matrix models > #3,0.12486,-0.10929,0.98614,-3.3941,-0.98525,0.10355,0.13622,299.73,-0.117,-0.9886,-0.094748,381.83 > view matrix models > #3,-0.013734,0.34293,0.93926,-46.701,0.87722,0.45496,-0.15328,-35.332,-0.47989,0.82183,-0.30707,179.08 > view matrix models > #3,-0.024741,-0.048477,0.99852,10.486,0.22627,0.97263,0.052827,-44.605,-0.97375,0.22725,-0.013095,313.53 > view matrix models > #3,0.22803,-0.14862,0.96224,-10.67,-0.86757,-0.4796,0.13152,377.92,0.44195,-0.86481,-0.23831,288.28 > view matrix models > #3,-0.090598,0.23885,0.96682,-20.594,-0.90644,0.38234,-0.1794,295.23,-0.4125,-0.89262,0.18187,368.38 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.090598,0.23885,0.96682,-20.895,-0.90644,0.38234,-0.1794,305.2,-0.4125,-0.89262,0.18187,368.62 > view matrix models > #3,-0.090598,0.23885,0.96682,-18.453,-0.90644,0.38234,-0.1794,307.34,-0.4125,-0.89262,0.18187,380.09 > ui tool show ""Fit in Map"" Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 5602 atoms average map value = 0.09223, steps = 72 shifted from previous position = 2.04 rotated from previous position = 4.6 degrees atoms outside contour = 3319, contour level = 0.072 Position of D2NS1.pdb (#3) relative to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation -0.06802577 0.24460859 0.96723274 -24.08767794 -0.87342564 0.45395004 -0.17623011 287.61942533 -0.48218273 -0.85679405 0.18276711 387.90605974 Axis -0.34848182 0.74217118 -0.57248788 Axis point 265.32854097 -0.00000000 317.95880744 Rotation angle (degrees) 102.45391693 Shift along axis -0.21455122 Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 5602 atoms average map value = 0.09223, steps = 40 shifted from previous position = 0.0168 rotated from previous position = 0.017 degrees atoms outside contour = 3323, contour level = 0.072 Position of D2NS1.pdb (#3) relative to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation -0.06800908 0.24437415 0.96729317 -24.07786550 -0.87335170 0.45412951 -0.17613415 287.55836847 -0.48231900 -0.85676584 0.18253965 387.96533381 Axis -0.34851775 0.74227452 -0.57233199 Axis point 265.31869899 0.00000000 317.91033718 Rotation angle (degrees) 102.45483514 Shift along axis -0.20615891 Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 5602 atoms average map value = 0.09224, steps = 44 shifted from previous position = 0.00415 rotated from previous position = 0.0128 degrees atoms outside contour = 3322, contour level = 0.072 Position of D2NS1.pdb (#3) relative to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation -0.06778785 0.24439903 0.96730241 -24.12733834 -0.87337367 0.45415748 -0.17595301 287.52563608 -0.48231036 -0.85674392 0.18266531 387.93712068 Axis -0.34858450 0.74224338 -0.57233173 Axis point 265.33740374 0.00000000 317.91776063 Rotation angle (degrees) 102.44383763 Shift along axis -0.20430725 Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 5602 atoms average map value = 0.09223, steps = 44 shifted from previous position = 0.0152 rotated from previous position = 0.013 degrees atoms outside contour = 3321, contour level = 0.072 Position of D2NS1.pdb (#3) relative to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation -0.06797653 0.24451862 0.96725895 -24.09141306 -0.87335854 0.45410159 -0.17617224 287.57257739 -0.48231121 -0.85673942 0.18268417 387.93432608 Axis -0.34847884 0.74224049 -0.57239982 Axis point 265.31882258 -0.00000000 317.92823841 Rotation angle (degrees) 102.45045928 Shift along axis -0.21017795 > transparency #1.1 50 > open ""D:/OneDrive - Nanyang Technological > University/Temporal/202109_zvNS1/3_Structures/20220211_NUS-K3_gAU- > sNS1-Fab56-2/F562a.pdb"" Chain information for F562a.pdb #4 --- Chain | Description B | No description available C | No description available > ui tool show ""Color Actions"" > color sel bychain > color sel bychain > select #4 3401 atoms, 3493 bonds, 442 residues, 1 model selected > color sel bychain > color sel bychain > color sel bychain > open ""D:/OneDrive - Nanyang Technological > University/Temporal/202109_zvNS1/3_Structures/7bsc_DEN2 NS1c.pdb"" 7bsc_DEN2 NS1c.pdb title: Complex structure of 1G5.3 fab bound to DENV2 NS1C [more info...] Chain information for 7bsc_DEN2 NS1c.pdb #5 --- Chain | Description A | non-structural protein 1 H | 1G5.3 fab heavy chain L | 1G5.3 fab light chain > mmaker #5 to #3 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 D2NS1.pdb, chain B (#3) with 7bsc_DEN2 NS1c.pdb, chain A (#5), sequence alignment score = 896.9 RMSD between 162 pruned atom pairs is 0.535 angstroms; (across all 177 pairs: 2.714) > mmaker #4 to #5 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 7bsc_DEN2 NS1c.pdb, chain H (#5) with F562a.pdb, chain B (#4), sequence alignment score = 1028.9 RMSD between 105 pruned atom pairs is 0.627 angstroms; (across all 215 pairs: 11.308) > ~select #4 Nothing selected > hide #!5 models > select #4 3401 atoms, 3493 bonds, 442 residues, 1 model selected > view matrix models > #4,0.59089,-0.15644,-0.79144,253.32,0.26071,0.96541,0.0038114,-36.876,0.76347,-0.20859,0.61123,8.3612 > view matrix models > #4,0.59089,-0.15644,-0.79144,249.54,0.26071,0.96541,0.0038114,-38.171,0.76347,-0.20859,0.61123,-6.5674 > view matrix models > #4,0.59089,-0.15644,-0.79144,250.18,0.26071,0.96541,0.0038114,-52.258,0.76347,-0.20859,0.61123,-8.7931 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 3401 atoms average map value = 0.08302, steps = 284 shifted from previous position = 3.86 rotated from previous position = 9.32 degrees atoms outside contour = 2026, contour level = 0.072 Position of F562a.pdb (#4) relative to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.70756240 -0.18104725 -0.68306467 216.74116501 0.24257753 0.97011437 -0.00585274 -48.06381473 0.66371047 -0.16155497 0.73033445 -11.10097449 Axis -0.10961944 -0.94817357 0.29824565 Axis point 132.17662306 0.00000000 263.68811665 Rotation angle (degrees) 45.25073566 Shift along axis 18.50297639 > transparency #1.1 0 > view matrix models > #4,0.70756,-0.18105,-0.68306,218.9,0.24258,0.97011,-0.0058527,-47.556,0.66371,-0.16155,0.73033,-11.137 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.60929,0.056492,-0.79093,206.86,0.79214,-0.088481,0.60389,-30.096,-0.035867,-0.99447,-0.09866,369.53 > view matrix models > #4,0.13536,-0.077461,-0.98776,343.37,0.97999,0.15727,0.12197,-53.095,0.1459,-0.98451,0.097201,310.49 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 3401 atoms average map value = 0.1078, steps = 96 shifted from previous position = 8.35 rotated from previous position = 5.73 degrees atoms outside contour = 1603, contour level = 0.072 Position of F562a.pdb (#4) relative to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.18515527 -0.12030538 -0.97531746 334.84540290 0.98054878 0.08839233 0.17524520 -44.47549541 0.06512764 -0.98879392 0.13433160 327.48525231 Axis -0.60933659 -0.54463915 0.57626133 Axis point 0.00000000 23.05515362 346.04002443 Rotation angle (degrees) 107.22113422 Shift along axis 8.90662490 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 3401 atoms average map value = 0.1078, steps = 28 shifted from previous position = 0.017 rotated from previous position = 0.0169 degrees atoms outside contour = 1608, contour level = 0.072 Position of F562a.pdb (#4) relative to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.18543237 -0.12023134 -0.97527394 334.76776945 0.98049261 0.08847529 0.17551742 -44.49851310 0.06518495 -0.98879550 0.13429212 327.47372226 Axis -0.60944823 -0.54461805 0.57616320 Axis point 0.00000000 23.10963968 345.96113737 Rotation angle (degrees) 107.21151966 Shift along axis 8.88937821 Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 3401 atoms average map value = 0.1078, steps = 44 shifted from previous position = 0.0205 rotated from previous position = 0.0218 degrees atoms outside contour = 1604, contour level = 0.072 Position of F562a.pdb (#4) relative to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.18554107 -0.12011878 -0.97526714 334.73699226 0.98049338 0.08814571 0.17567888 -44.47566373 0.06486328 -0.98883862 0.13413032 327.56427605 Axis -0.60959315 -0.54447990 0.57614045 Axis point 0.00000000 23.17721063 345.92539580 Rotation angle (degrees) 107.22299700 Shift along axis 8.88575635 > transparency #1.1 50 > view matrix models > #4,0.95986,-0.22484,0.16768,73.526,0.27579,0.64758,-0.71034,90.606,0.051126,0.72807,0.68359,-47.104 [deleted to fit within ticket limits] > select #3/B:212-217 #4/A:212-217 #10/D,A:212-217 192 atoms, 192 bonds, 24 residues, 3 models selected > color sel #f7f5ffff > select #3/B:218 #4/A:218 #10/D,A:218 32 atoms, 28 bonds, 4 residues, 3 models selected > select #3/B:218-220 #4/A:218-220 #10/D,A:218-220 96 atoms, 92 bonds, 12 residues, 3 models selected > select #3/B:218-219 #4/A:218-219 #10/D,A:218-219 68 atoms, 64 bonds, 8 residues, 3 models selected > select #3/B:218-219 #4/A:218-219 #10/D,A:218-219 68 atoms, 64 bonds, 8 residues, 3 models selected > color sel #c9d5ffff > color sel #cad4ffff [Repeated 1 time(s)] > color sel #cbd4ffff > color sel #ccd4ffff [Repeated 1 time(s)] > color sel #cdd3ffff > color sel #ced3ffff [Repeated 2 time(s)] > color sel #cfd3ffff > color sel #cfd2ffff [Repeated 1 time(s)] > color sel #d0d2ffff [Repeated 2 time(s)] > color sel #d1d2ffff > color sel #d1d1ffff [Repeated 2 time(s)] > select #3/B:220 #4/A:220 #10/D,A:220 28 atoms, 24 bonds, 4 residues, 3 models selected > select #3/B:220-231 #4/A:220-231 #10/D,A:220-231 396 atoms, 412 bonds, 48 residues, 3 models selected > color sel #c8c9ffff > select #3/B:232-233 #4/A:232-233 #10/D,A:232-233 80 atoms, 84 bonds, 8 residues, 3 models selected > select #3/B:232-240 #4/A:232-240 #10/D,A:232-240 284 atoms, 288 bonds, 36 residues, 3 models selected > color sel #d4d6ffff > select #3/B:241 #4/A:241 #10/D,A:241 32 atoms, 28 bonds, 4 residues, 3 models selected > select #3/B:241-242 #4/A:241-242 #10/D,A:241-242 64 atoms, 60 bonds, 8 residues, 3 models selected > select #3/B:242 #4/A:242 #10/D,A:242 32 atoms, 28 bonds, 4 residues, 3 models selected > select #3/B:241-242 #4/A:241-242 #10/D,A:241-242 64 atoms, 60 bonds, 8 residues, 3 models selected > select #3/B:241 #4/A:241 #10/D,A:241 32 atoms, 28 bonds, 4 residues, 3 models selected > select #3/B:241-242 #4/A:241-242 #10/D,A:241-242 64 atoms, 60 bonds, 8 residues, 3 models selected > select #3/B:241 #4/A:241 #10/D,A:241 32 atoms, 28 bonds, 4 residues, 3 models selected > select #3/B:241 #4/A:241 #10/D,A:241 32 atoms, 28 bonds, 4 residues, 3 models selected > color sel #dddfffff > select #3/B:242 #4/A:242 #10/D,A:242 32 atoms, 28 bonds, 4 residues, 3 models selected > select #3/B:242-247 #4/A:242-247 #10/D,A:242-247 204 atoms, 208 bonds, 24 residues, 3 models selected > color sel #d3d6ffff > select #3/B:248 #4/A:248 #10/D,A:248 20 atoms, 16 bonds, 4 residues, 3 models selected > select #3/B:248-254 #4/A:248-254 #10/D,A:248-254 192 atoms, 196 bonds, 28 residues, 3 models selected > select #3/B:254 #4/A:254 #10/D,A:254 40 atoms, 40 bonds, 4 residues, 3 models selected > select #3/B:254 #4/A:254 #10/D,A:254 40 atoms, 40 bonds, 4 residues, 3 models selected > select #3/B:253 #4/A:253 #10/D,A:253 36 atoms, 32 bonds, 4 residues, 3 models selected > select #3/B:248-253 #4/A:248-253 #10/D,A:248-253 152 atoms, 152 bonds, 24 residues, 3 models selected > color sel #dedfffff > color sel #e1e1ffff > select #3/B:254-255 #4/A:254-255 #10/D,A:254-255 72 atoms, 72 bonds, 8 residues, 3 models selected > select #3/B:254-262 #4/A:254-262 #10/D,A:254-262 324 atoms, 340 bonds, 36 residues, 3 models selected > color sel #d6d6ffff > select #3/B:263 #4/A:263 #10/D,A:263 36 atoms, 32 bonds, 4 residues, 3 models selected > select #3/B:263-265 #4/A:263-265 #10/D,A:263-265 84 atoms, 80 bonds, 12 residues, 3 models selected > color sel #dad9ffff > select #3/B:266 #4/A:266 #10/D,A:266 16 atoms, 12 bonds, 4 residues, 3 models selected > select #3/B:266-267 #4/A:266-267 #10/D,A:266-267 44 atoms, 44 bonds, 8 residues, 3 models selected > color sel #cfcfffff > color sel #d0cfffff > color sel #d0d0ffff > color sel #cecbffff > select #3/B:268-269 #4/A:268-269 #10/D,A:268-269 96 atoms, 104 bonds, 8 residues, 3 models selected > select #3/B:268-273 #4/A:268-273 #10/D,A:268-273 220 atoms, 228 bonds, 24 residues, 3 models selected > color sel #d3d1ffff > select #3/B:274 #4/A:274 #10/D,A:274 36 atoms, 32 bonds, 4 residues, 3 models selected > select #3/B:274-275 #4/A:274-275 #10/D,A:274-275 68 atoms, 64 bonds, 8 residues, 3 models selected > color sel #c3c6ffff > select #3/B:276 #4/A:276 #10/D,A:276 32 atoms, 28 bonds, 4 residues, 3 models selected > select #3/B:276-277 #4/A:276-277 #10/D,A:276-277 76 atoms, 76 bonds, 8 residues, 3 models selected > color sel #d1d4ffff > select #3/B:278-279 #4/A:278-279 #10/D,A:278-279 76 atoms, 76 bonds, 8 residues, 3 models selected > select #3/B:278-279 #4/A:278-279 #10/D,A:278-279 76 atoms, 76 bonds, 8 residues, 3 models selected > color sel #dddcffff > select #3/B:287-288 #4/A:287-288 #10/D,A:287-288 56 atoms, 52 bonds, 8 residues, 3 models selected > select #3/B:287-298 #4/A:287-298 #10/D,A:287-298 340 atoms, 340 bonds, 48 residues, 3 models selected > select #3/B:287-298 #4/A:287-298 #10/D,A:287-298 340 atoms, 340 bonds, 48 residues, 3 models selected > select #3/B:287-300 #4/A:287-300 #10/D,A:287-300 412 atoms, 412 bonds, 56 residues, 3 models selected > select #3/B:287-288 #4/A:287-288 #10/D,A:287-288 56 atoms, 52 bonds, 8 residues, 3 models selected > select #3/B:287-299 #4/A:287-299 #10/D,A:287-299 384 atoms, 384 bonds, 52 residues, 3 models selected > color sel #d3d2ffff > color sel #cbccffff > select #3/B:300 #4/A:300 #10/D,A:300 28 atoms, 24 bonds, 4 residues, 3 models selected > select #3/B:300-309 #4/A:300-309 #10/D,A:300-309 272 atoms, 268 bonds, 40 residues, 3 models selected > color sel #bfc3ffff > select #3/B:310 #4/A:310 #10/D,A:310 36 atoms, 32 bonds, 4 residues, 3 models selected > select #3/B:310 #4/A:310 #10/D,A:310 36 atoms, 32 bonds, 4 residues, 3 models selected > color sel #c8ceffff > select #3/B:311-312 #4/A:311-312 #10/D,A:311-312 80 atoms, 84 bonds, 8 residues, 3 models selected > select #3/B:311-333 #4/A:311-333 #10/D,A:311-333 756 atoms, 784 bonds, 1 pseudobond, 92 residues, 4 models selected > color (#3-4,10 & sel) #d2d3ffff > select #3/B:334 #4/A:334 #10/D,A:334 36 atoms, 32 bonds, 4 residues, 3 models selected > select #3/B:334 #4/A:334 #10/D,A:334 36 atoms, 32 bonds, 4 residues, 3 models selected > color sel #cbd5ffff > color sel #cbceffff > select #3/B:335 #4/A:335 #10/D,A:335 32 atoms, 28 bonds, 4 residues, 3 models selected > select #3/B:335-340 #4/A:335-340 #10/D,A:335-340 208 atoms, 208 bonds, 24 residues, 3 models selected > color sel #ceceffff > color sel #cfd1ffff > select #3/B:341 #4/A:341 #10/D,A:341 36 atoms, 32 bonds, 4 residues, 3 models selected > select #3/B:341-349 #4/A:341-349 #10/D,A:341-349 288 atoms, 284 bonds, 36 residues, 3 models selected > color sel #caceffff > color sel #c8ccffff > color sel #c3caffff > color sel #bdcbffff > select #3/B:350 #4/A:350 #10/D,A:350 28 atoms, 24 bonds, 4 residues, 3 models selected > select #3/B:350-352 #4/A:350-352 #10/D,A:350-352 76 atoms, 72 bonds, 12 residues, 3 models selected > color sel #ffebf3ff > color sel #ffe8efff > select #3/B:301-302 #4/A:301-302 #10/D,A:301-302 56 atoms, 52 bonds, 8 residues, 3 models selected > select #3/B:301-310 #4/A:301-310 #10/D,A:301-310 280 atoms, 276 bonds, 40 residues, 3 models selected > color sel #8c8cf7ff > color sel #8587ffff > color sel #8282ffff > color sel #7c83ffff > select add #3 3011 atoms, 3079 bonds, 45 pseudobonds, 382 residues, 5 models selected > select add #4 5742 atoms, 5882 bonds, 90 pseudobonds, 724 residues, 5 models selected > select subtract #3 2941 atoms, 3010 bonds, 45 pseudobonds, 372 residues, 4 models selected > select subtract #4 140 atoms, 138 bonds, 20 residues, 1 model selected > select add #12 3541 atoms, 3631 bonds, 462 residues, 2 models selected > select add #10 12337 atoms, 12617 bonds, 1560 residues, 2 models selected > select subtract #10 3401 atoms, 3493 bonds, 442 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models > #12,0.82562,-0.34186,-0.44887,168.94,-0.52138,-0.76634,-0.37535,482.82,-0.21567,0.54392,-0.81094,284.87 > view matrix models > #12,0.82562,-0.34186,-0.44887,169.91,-0.52138,-0.76634,-0.37535,479.02,-0.21567,0.54392,-0.81094,283.58 > view matrix models > #12,0.82562,-0.34186,-0.44887,170.32,-0.52138,-0.76634,-0.37535,480.41,-0.21567,0.54392,-0.81094,282.28 > view matrix models > #12,0.82562,-0.34186,-0.44887,171.18,-0.52138,-0.76634,-0.37535,479.61,-0.21567,0.54392,-0.81094,282.22 > ui mousemode right zoom > ui mousemode right ""rotate selected models"" > view matrix models > #12,0.94747,-0.06803,0.31253,-40.388,-0.27852,-0.65592,0.70156,212.57,0.15727,-0.75175,-0.64041,392.6 > view matrix models > #12,0.65713,0.16685,-0.73508,171.79,0.09209,-0.98566,-0.1414,332.31,-0.74813,0.025227,-0.66307,473.05 > view matrix models > #12,0.95731,-0.18789,-0.21965,72.476,-0.15301,-0.97411,0.16641,333.66,-0.24523,-0.1257,-0.96128,433.82 > view matrix models > #12,0.96798,-0.24602,-0.049963,50.221,-0.17279,-0.7973,0.57833,234.35,-0.18211,-0.55117,-0.81427,467.97 > ui mousemode right ""translate selected models"" > ui mousemode right zoom > show #!9 models > fitmap #12 inMap #9 Fit molecule F562a.pdb (#12) to map sNS1wt-Fab562.mrc (#9) using 3401 atoms average map value = 0.09851, steps = 252 shifted from previous position = 4.87 rotated from previous position = 66.7 degrees atoms outside contour = 1988, contour level = 0.11015 Position of F562a.pdb (#12) relative to sNS1wt-Fab562.mrc (#9) coordinates: Matrix rotation and translation -0.10506635 -0.15760122 0.98189762 53.59780496 -0.09254653 -0.98152811 -0.16744470 397.44466486 0.99014960 -0.10846402 0.08854013 -3.70228919 Axis 0.66872859 -0.09356170 0.73759629 Axis point 22.53945284 199.32977295 0.00000000 Rotation angle (degrees) 177.47248714 Shift along axis -4.07401058 > volume #9 level 0.08287 > volume #9 level 0.06241 > hide #10 models > show #10 models > hide #10 models > color #5 #7b137cff models > color #5 #7c0e7cff models > color #5 #fe1effff models > color #5 #ee1cefff models > hide #5 models > show #5 models > hide #6 models > show #6 models > hide #6 models > show #6 models > hide #6 models > show #6 models > show #7 models > hide #7 models > hide #4 models > show #4 models > hide #8 models > show #8 models > select add #2 5068 atoms, 5183 bonds, 29 pseudobonds, 649 residues, 4 models selected > select subtract #2 3401 atoms, 3493 bonds, 442 residues, 1 model selected > select add #2 5068 atoms, 5183 bonds, 29 pseudobonds, 649 residues, 4 models selected > select subtract #2 3401 atoms, 3493 bonds, 442 residues, 1 model selected > select subtract #12 Nothing selected > select add #2 1667 atoms, 1690 bonds, 29 pseudobonds, 207 residues, 3 models selected > select subtract #2 Nothing selected > select add #2 1667 atoms, 1690 bonds, 29 pseudobonds, 207 residues, 3 models selected > select add #1 3334 atoms, 3380 bonds, 58 pseudobonds, 414 residues, 4 models selected > select add #3 6135 atoms, 6252 bonds, 103 pseudobonds, 766 residues, 6 models selected > select add #4 8936 atoms, 9124 bonds, 148 pseudobonds, 1118 residues, 7 models selected > ui mousemode right ""translate selected models"" > view matrix models > #1,1,0,0,-1.2223,0,1,0,1.8538,0,0,1,0.27533,#2,1,0,0,-1.2223,0,1,0,1.8538,0,0,1,0.27533,#3,1,0,0,-1.2223,0,1,0,1.8538,0,0,1,0.27533,#4,1,0,0,-1.2223,0,1,0,1.8538,0,0,1,0.27533,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #1,1,0,0,-0.55596,0,1,0,1.8607,0,0,1,0.33178,#2,1,0,0,-0.55596,0,1,0,1.8607,0,0,1,0.33178,#3,1,0,0,-0.55596,0,1,0,1.8607,0,0,1,0.33178,#4,1,0,0,-0.55596,0,1,0,1.8607,0,0,1,0.33178,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #1,1,0,0,-0.68222,0,1,0,1.9897,0,0,1,0.3731,#2,1,0,0,-0.68222,0,1,0,1.9897,0,0,1,0.3731,#3,1,0,0,-0.68222,0,1,0,1.9897,0,0,1,0.3731,#4,1,0,0,-0.68222,0,1,0,1.9897,0,0,1,0.3731,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0 > ui mousemode right zoom > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.99968,0.01848,-0.017519,-0.75045,-0.018381,0.99981,0.0057709,4.0941,0.017623,-0.005447,0.99983,-1.6124,#2,0.99968,0.01848,-0.017519,-0.75045,-0.018381,0.99981,0.0057709,4.0941,0.017623,-0.005447,0.99983,-1.6124,#3,0.99968,0.01848,-0.017519,-0.75045,-0.018381,0.99981,0.0057709,4.0941,0.017623,-0.005447,0.99983,-1.6124,#4,0.99968,0.01848,-0.017519,-0.75045,-0.018381,0.99981,0.0057709,4.0941,0.017623,-0.005447,0.99983,-1.6124,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #1,0.99895,0.041357,0.019524,-12.294,-0.041363,0.99914,-0.00012487,9.3748,-0.019512,-0.00068282,0.99981,3.9302,#2,0.99895,0.041357,0.019524,-12.294,-0.041363,0.99914,-0.00012487,9.3748,-0.019512,-0.00068282,0.99981,3.9302,#3,0.99895,0.041357,0.019524,-12.294,-0.041363,0.99914,-0.00012487,9.3748,-0.019512,-0.00068282,0.99981,3.9302,#4,0.99895,0.041357,0.019524,-12.294,-0.041363,0.99914,-0.00012487,9.3748,-0.019512,-0.00068282,0.99981,3.9302,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #1,0.99756,0.056365,0.04122,-19.199,-0.056012,0.99838,-0.0096742,13.936,-0.041698,0.0073418,0.9991,6.3748,#2,0.99756,0.056365,0.04122,-19.199,-0.056012,0.99838,-0.0096742,13.936,-0.041698,0.0073418,0.9991,6.3748,#3,0.99756,0.056365,0.04122,-19.199,-0.056012,0.99838,-0.0096742,13.936,-0.041698,0.0073418,0.9991,6.3748,#4,0.99756,0.056365,0.04122,-19.199,-0.056012,0.99838,-0.0096742,13.936,-0.041698,0.0073418,0.9991,6.3748,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #1,0.99732,0.064513,0.034504,-19.405,-0.064796,0.99787,0.0071201,12.257,-0.033971,-0.0093368,0.99938,8.1881,#2,0.99732,0.064513,0.034504,-19.405,-0.064796,0.99787,0.0071201,12.257,-0.033971,-0.0093368,0.99938,8.1881,#3,0.99732,0.064513,0.034504,-19.405,-0.064796,0.99787,0.0071201,12.257,-0.033971,-0.0093368,0.99938,8.1881,#4,0.99732,0.064513,0.034504,-19.405,-0.064796,0.99787,0.0071201,12.257,-0.033971,-0.0093368,0.99938,8.1881,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #1,0.99543,0.089424,0.033513,-23.673,-0.09018,0.99569,0.021758,14.2,-0.031423,-0.02468,0.9992,10.732,#2,0.99543,0.089424,0.033513,-23.673,-0.09018,0.99569,0.021758,14.2,-0.031423,-0.02468,0.9992,10.732,#3,0.99543,0.089424,0.033513,-23.673,-0.09018,0.99569,0.021758,14.2,-0.031423,-0.02468,0.9992,10.732,#4,0.99543,0.089424,0.033513,-23.673,-0.09018,0.99569,0.021758,14.2,-0.031423,-0.02468,0.9992,10.732,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.99543,0.089424,0.033513,-24.695,-0.09018,0.99569,0.021758,12.433,-0.031423,-0.02468,0.9992,10.949,#2,0.99543,0.089424,0.033513,-24.695,-0.09018,0.99569,0.021758,12.433,-0.031423,-0.02468,0.9992,10.949,#3,0.99543,0.089424,0.033513,-24.695,-0.09018,0.99569,0.021758,12.433,-0.031423,-0.02468,0.9992,10.949,#4,0.99543,0.089424,0.033513,-24.695,-0.09018,0.99569,0.021758,12.433,-0.031423,-0.02468,0.9992,10.949,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0 > ui mousemode right zoom > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.99325,0.11577,-0.0074717,-21.346,-0.11546,0.99274,0.033636,15.045,0.011311,-0.032546,0.99941,5.0242,#2,0.99325,0.11577,-0.0074717,-21.346,-0.11546,0.99274,0.033636,15.045,0.011311,-0.032546,0.99941,5.0242,#3,0.99325,0.11577,-0.0074717,-21.346,-0.11546,0.99274,0.033636,15.045,0.011311,-0.032546,0.99941,5.0242,#4,0.99325,0.11577,-0.0074717,-21.346,-0.11546,0.99274,0.033636,15.045,0.011311,-0.032546,0.99941,5.0242,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #1,0.98411,0.17655,-0.018861,-29.201,-0.17622,0.98419,0.018033,30.268,0.021747,-0.014422,0.99966,-0.31268,#2,0.98411,0.17655,-0.018861,-29.201,-0.17622,0.98419,0.018033,30.268,0.021747,-0.014422,0.99966,-0.31268,#3,0.98411,0.17655,-0.018861,-29.201,-0.17622,0.98419,0.018033,30.268,0.021747,-0.014422,0.99966,-0.31268,#4,0.98411,0.17655,-0.018861,-29.201,-0.17622,0.98419,0.018033,30.268,0.021747,-0.014422,0.99966,-0.31268,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0 > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > ui mousemode right zoom > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.98312,0.18157,-0.022504,-29.276,-0.18111,0.98324,0.020831,30.746,0.025909,-0.016403,0.99953,-0.62775,#2,0.98312,0.18157,-0.022504,-29.276,-0.18111,0.98324,0.020831,30.746,0.025909,-0.016403,0.99953,-0.62775,#3,0.98312,0.18157,-0.022504,-29.276,-0.18111,0.98324,0.020831,30.746,0.025909,-0.016403,0.99953,-0.62775,#4,0.98312,0.18157,-0.022504,-29.276,-0.18111,0.98324,0.020831,30.746,0.025909,-0.016403,0.99953,-0.62775,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #1,0.97783,0.20908,-0.011102,-35.867,-0.20922,0.97778,-0.013144,43.339,0.008107,0.015175,0.99985,-3.6449,#2,0.97783,0.20908,-0.011102,-35.867,-0.20922,0.97778,-0.013144,43.339,0.008107,0.015175,0.99985,-3.6449,#3,0.97783,0.20908,-0.011102,-35.867,-0.20922,0.97778,-0.013144,43.339,0.008107,0.015175,0.99985,-3.6449,#4,0.97783,0.20908,-0.011102,-35.867,-0.20922,0.97778,-0.013144,43.339,0.008107,0.015175,0.99985,-3.6449,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #1,0.9833,0.18192,0.0055417,-34.889,-0.18172,0.983,-0.026391,40.159,-0.010249,0.024943,0.99964,-2.2795,#2,0.9833,0.18192,0.0055417,-34.889,-0.18172,0.983,-0.026391,40.159,-0.010249,0.024943,0.99964,-2.2795,#3,0.9833,0.18192,0.0055417,-34.889,-0.18172,0.983,-0.026391,40.159,-0.010249,0.024943,0.99964,-2.2795,#4,0.9833,0.18192,0.0055417,-34.889,-0.18172,0.983,-0.026391,40.159,-0.010249,0.024943,0.99964,-2.2795,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0 [Repeated 1 time(s)] > ui mousemode right ""translate selected models"" > view matrix models > #1,0.9833,0.18192,0.0055417,-35.853,-0.18172,0.983,-0.026391,40.8,-0.010249,0.024943,0.99964,-2.2243,#2,0.9833,0.18192,0.0055417,-35.853,-0.18172,0.983,-0.026391,40.8,-0.010249,0.024943,0.99964,-2.2243,#3,0.9833,0.18192,0.0055417,-35.853,-0.18172,0.983,-0.026391,40.8,-0.010249,0.024943,0.99964,-2.2243,#4,0.9833,0.18192,0.0055417,-35.853,-0.18172,0.983,-0.026391,40.8,-0.010249,0.024943,0.99964,-2.2243,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0 > ui mousemode right zoom > select subtract #1 7269 atoms, 7434 bonds, 119 pseudobonds, 911 residues, 6 models selected > select subtract #2 5602 atoms, 5744 bonds, 90 pseudobonds, 704 residues, 4 models selected > select subtract #3 2801 atoms, 2872 bonds, 45 pseudobonds, 352 residues, 3 models selected > select subtract #4 Nothing selected > select add #12 3401 atoms, 3493 bonds, 442 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #12/C Alignment identifier is 12/C > select subtract #12 Nothing selected > select #12/C:1 5 atoms, 4 bonds, 1 residue, 1 model selected > select #12/C 1769 atoms, 1825 bonds, 228 residues, 1 model selected > hide #!9 models > save ""/Users/alvinchew/OneDrive - Nanyang Technological University > (1)/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1-fab562_hdxms10minLXL- > MS_recolored.cxs"" includeMaps true ——— End of log from Wed Apr 19 17:03:52 2023 ——— opened ChimeraX session > show #!9 models > color #9 #b4e3e61f models > color #9 #b4e3e61c models > color #9 #b4e3e61b models > color #9 #e4ebc51b models > color #9 #e3ebbc1b models > color #9 #ebe98a1b models > color #9 #e9eb971b models > color #9 #e1eba01b models OpenGL version: 4.1 Metal - 83 OpenGL renderer: Apple M1 OpenGL vendor: Apple 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 Air Model Identifier: MacBookAir10,1 Model Number: MGN63ZP/A Chip: Unknown Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 8419.80.7 OS Loader Version: 8419.80.7 Software: System Software Overview: System Version: macOS 13.2.1 (22D68) Kernel Version: Darwin 22.3.0 Time since boot: 13 days, 18 hours, 3 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 7 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal CB242Y: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 75.00Hz Mirror: Off Online: Yes Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.1.0 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: 1.4 ChimeraX-AddH: 2.2.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.6 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.41.5 ChimeraX-AtomicLibrary: 8.0.3 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: 1.2.4 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.5 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 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 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 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: 2.8 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.6 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: 1.9.1 ChimeraX-PDB: 2.6.8 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-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 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.7.2 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 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-Tug: 1.0.1 ChimeraX-UI: 1.24.3 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.4 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-XMAS: 1.1.2 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 et-xmlfile: 1.1.0 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 openpyxl: 3.1.2 openvr: 1.23.701 packaging: 21.3 pandas: 1.5.3 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 QtRangeSlider: 0.1.5 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.0 seaborn: 0.12.2 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 closed normal Third Party fixed Eric Pettersen all ChimeraX