id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16836 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.2-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. Fatal Python error: Segmentation fault Thread 0x000000030c08b000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030b07f000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030a073000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000309067000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030805b000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030704f000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000306043000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000305037000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030402b000 (most 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""6.9"", ""CFBundleIdentifier"" : ""com.apple.CoreFoundation"", ""size"" : 5197824, ""uuid"" : ""41fdd393-3acc-328d-8108-e59a3a947ec5"", ""path"" : ""\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation"", ""name"" : ""CoreFoundation"", ""CFBundleVersion"" : ""3208"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6912552960, ""CFBundleShortVersionString"" : ""2.1.1"", ""CFBundleIdentifier"" : ""com.apple.HIToolbox"", ""size"" : 3178496, ""uuid"" : ""83159ee1-0ca4-3a91-887a-db80b7029337"", ""path"" : ""\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox"", ""name"" : ""HIToolbox"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6718857216, ""size"" : 532288, ""uuid"" : ""4ce86d18-f3fa-3d2a-a1b8-e7cd8a52fb0d"", ""path"" : ""\/usr\/lib\/dyld"", ""name"" : ""dyld"" }, { ""size"" : 0, ""source"" : ""A"", ""base"" : 0, ""uuid"" : ""00000000-0000-0000-0000-000000000000"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6741803008, ""CFBundleShortVersionString"" : ""6.9"", ""CFBundleIdentifier"" : ""com.apple.Foundation"", ""size"" : 14979072, ""uuid"" : ""b39c1e42-f15f-3671-b63e-6be7bdad0fcd"", ""path"" : ""\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation"", ""name"" : ""Foundation"", ""CFBundleVersion"" : ""3208"" } ], ""sharedCache"" : { ""base"" : 6718046208, ""size"" : 4861722624, ""uuid"" : ""e36100c7-89e7-3970-8938-8483ccd7019a"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=5.1G written=3020K(0%) resident=3020K(0%) swapped_out=0K(0%) unallocated=5.1G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 640K 5 \nActivity Tracing 256K 1 \nCG image 320K 16 \nColorSync 672K 32 \nCoreAnimation 3232K 184 \nCoreGraphics 112K 7 \nCoreUI image data 5040K 42 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 4.2G 141 \nMALLOC guard page 288K 18 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 736K 46 \nStack 382.5M 47 \nStack Guard 56.0M 1 \nVM_ALLOCATE 345.7M 283 \nVM_ALLOCATE (reserved) 96.0M 1 reserved VM address space (unallocated)\n__AUTH 5280K 670 \n__AUTH_CONST 70.7M 918 \n__CTF 824 1 \n__DATA 33.1M 1052 \n__DATA_CONST 33.9M 1071 \n__DATA_DIRTY 2763K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 635.5M 147 \n__OBJC_RW 2373K 1 \n__TEXT 1.3G 1091 \n__TPRO_CONST 272K 2 \ndyld private memory 32K 1 \nmapped file 276.5M 62 \nowned unmapped memory 119.1M 1 \npage table in kernel 3020K 1 \nshared memory 3680K 22 \n=========== ======= ======= \nTOTAL 7.5G 6219 \nTOTAL, minus reserved VM space 7.4G 6219 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""cd65fd207913385e1cdd6858a10d44ada73ddc9b"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""5ffde50ce2aacd000d47a95f"", ""factorPackIds"" : { }, ""deploymentId"" : 240000457 }, { ""rolloutId"" : ""64c025b28b7f0e739e4fbe58"", ""factorPackIds"" : { ""SIRI_UNDERSTANDING_CLASSIC_DEPRECATION"" : ""657ba0a39ec5da283662e9d2"" }, ""deploymentId"" : 240000032 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/colinmuir/Downloads/cryosparc_P36_J571_014_volume_map.mrc Opened cryosparc_P36_J571_014_volume_map.mrc as #1, grid size 320,320,320, pixel 0.86, shown at level 0.0488, step 2, values float32 > open > /Users/colinmuir/Desktop/MCU_Alone_Map/WTDataProcessing/WT_models/J500Coot/3DVApreMaskJML_focus250117.mrc Opened 3DVApreMaskJML_focus250117.mrc as #2, grid size 160,160,160, pixel 1.72, shown at level 5.98e-05, step 1, values float32 > volume #1 step 1 > volume #1 level 0.09128 > hide #!1 models > transparency #2.1 50 > show #!1 models > volume #2 level 0.003637 > volume #2 level 0.003 > open /Users/colinmuir/Downloads/Relion5WT_Blush_it20/run_it020_class001.mrc Opened run_it020_class001.mrc as #3, grid size 320,320,320, pixel 0.86, shown at level 3.87e-06, step 2, values float32 > open /Users/colinmuir/Downloads/Relion5WT_Blush_it20/run_it020_class002.mrc Opened run_it020_class002.mrc as #4, grid size 320,320,320, pixel 0.86, shown at level 2.78e-06, step 2, values float32 > open /Users/colinmuir/Downloads/Relion5WT_Blush_it20/run_it020_class003.mrc Opened run_it020_class003.mrc as #5, grid size 320,320,320, pixel 0.86, shown at level 3.5e-06, step 2, values float32 > open /Users/colinmuir/Downloads/Relion5WT_Blush_it20/run_it020_class004.mrc Opened run_it020_class004.mrc as #6, grid size 320,320,320, pixel 0.86, shown at level 3.61e-06, step 2, values float32 > open /Users/colinmuir/Downloads/Relion5WT_Blush_it20/run_it020_class005.mrc Opened run_it020_class005.mrc as #7, grid size 320,320,320, pixel 0.86, shown at level 2e-06, step 2, values float32 > open /Users/colinmuir/Downloads/Relion5WT_Blush_it20/run_it020_class006.mrc Opened run_it020_class006.mrc as #8, grid size 320,320,320, pixel 0.86, shown at level 3.5e-06, step 2, values float32 > hide #!1 models > hide #!2 models > volume #4 step 1 > volume #5 step 1 > volume #6 step 1 > volume #7 step 1 > volume #8 step 1 > volume #7 level 0.0007845 > volume #6 level 0.0004282 > volume level 0.003 > hide #!8 models > hide #!7 models > hide #!6 models > hide #!5 models > hide #!4 models > show #!4 models > hide #!3 models > show #!5 models > hide #!4 models > show #!6 models > hide #!5 models > show #!7 models > hide #!6 models > show #!8 models > hide #!7 models > show #!3 models > hide #!8 models > volume #3 step 1 > hide #!3 models > show #!1 models > volume #1 level 0.1036 > show #!8 models > hide #!8 models > open /Users/colinmuir/Downloads/cryosparc_P12_J492_mask.mrc Opened cryosparc_P12_J492_mask.mrc as #9, grid size 180,180,180, pixel 1.72, shown at level 0.823, step 1, values float32 > open /Users/colinmuir/Downloads/cryosparc_P12_J507_mask.mrc Opened cryosparc_P12_J507_mask.mrc as #10, grid size 320,320,320, pixel 0.86, shown at level 1, step 2, values float32 > hide #!9 models > hide #!10 models > show #!10 models > volume #10 level 0.9834 > hide #!1 models > transparency #10.1 50 > show #!1 models > open /Users/colinmuir/Downloads/cryosparc_P12_J524_mask.mrc Opened cryosparc_P12_J524_mask.mrc as #11, grid size 160,160,160, pixel 1.72, shown at level 0.59, step 1, values float32 > open /Users/colinmuir/Downloads/mask.mrc Opened mask.mrc as #12, grid size 360,360,360, pixel 0.86, shown at level 1, step 2, values float32 > volume #12 step 1 > volume #12 level 1 > hide #!11 models > hide #!10 models > hide #!1 models > show #!1 models > hide #!12 models > show #!12 models > hide #!12 models > open /Users/colinmuir/Downloads/mask.mrc Opened mask.mrc as #13, grid size 360,360,360, pixel 0.86, shown at level 1, step 2, values float32 > volume #13 level 1 > volume #13 step 1 > volume #13 level 1 > show #!3 models > show #!4 models > show #!5 models > show #!6 models > show #!7 models > show #!8 models > open /Users/colinmuir/Downloads/mask.mrc Opened mask.mrc as #14, grid size 360,360,360, pixel 0.86, shown at level 1, step 2, values float32 > volume #14 level 1 > open /Users/colinmuir/Downloads/job019mask.mrc Opened job019mask.mrc as #15, grid size 160,160,160, pixel 1.72, shown at level 0.5, step 1, values float32 > open /Users/colinmuir/Downloads/job004mask_Relion5.mrc Opened job004mask_Relion5.mrc as #16, grid size 160,160,160, pixel 1.72, shown at level 0.516, step 1, values float32 > hide #!14 models > hide #!13 models > hide #!15 models > volume #16 level 1 > volume #15 level 0.5204 > volume #15 level 1 > volume #15 level 0.5416 > volume #15 level 1 > hide #!8 models > hide #!7 models > hide #!6 models > hide #!5 models > hide #!4 models > hide #!3 models > volume #15 level 0.8725 > hide #!1 models > transparency #15.1 50 > show #!1 models > set bgColor white > volume #15 level 0.5102 > volume #15 level 0.5065 > save /Users/colinmuir/Desktop/image1.png supersample 3 > hide #!1 models > hide #!15 models > open > /Users/colinmuir/Desktop/MCU_Alone_Map/WTDataProcessing/WTRelion/Relion3D_J21/run_it040_class001.mrc Opened run_it040_class001.mrc as #17, grid size 320,320,320, pixel 0.86, shown at level 2.61e-05, step 2, values float32 > open > /Users/colinmuir/Desktop/MCU_Alone_Map/WTDataProcessing/WTRelion/Relion3D_J21/run_it040_class002.mrc Opened run_it040_class002.mrc as #18, grid size 320,320,320, pixel 0.86, shown at level 3.67e-05, step 2, values float32 > open > /Users/colinmuir/Desktop/MCU_Alone_Map/WTDataProcessing/WTRelion/Relion3D_J21/run_it040_class003.mrc Opened run_it040_class003.mrc as #19, grid size 320,320,320, pixel 0.86, shown at level 2.6e-05, step 2, values float32 > open > /Users/colinmuir/Desktop/MCU_Alone_Map/WTDataProcessing/WTRelion/Relion3D_J21/run_it040_class004.mrc Opened run_it040_class004.mrc as #20, grid size 320,320,320, pixel 0.86, shown at level 1.82e-05, step 2, values float32 > open > /Users/colinmuir/Desktop/MCU_Alone_Map/WTDataProcessing/WTRelion/Relion3D_J21/run_it040_class005.mrc Opened run_it040_class005.mrc as #21, grid size 320,320,320, pixel 0.86, shown at level 2.91e-05, step 2, values float32 > open > /Users/colinmuir/Desktop/MCU_Alone_Map/WTDataProcessing/WTRelion/Relion3D_J21/run_it040_class006.mrc Opened run_it040_class006.mrc as #22, grid size 320,320,320, pixel 0.86, shown at level 2.57e-05, step 2, values float32 > volume #17 step 1 > volume #18 step 1 > volume #19 step 1 > volume #20 step 1 > volume #21 step 1 > volume #22 step 1 > volume level 0.003 > tile 6 models tiled > ui tool show ""Side View"" > show #!1 models > hide #!22 models > hide #!21 models > hide #!20 models > hide #!19 models > hide #!18 models > hide #!17 models > volume #1 level 0.09055 > volume #1 level 0.05033 > hide #!1 models > show #!22 models > show #!21 models > show #!20 models > show #!19 models > show #!18 models > show #!17 models > open /Users/colinmuir/Downloads/cryosparc_P36_J557_007_volume_map.mrc Opened cryosparc_P36_J557_007_volume_map.mrc as #23, grid size 320,320,320, pixel 0.86, shown at level 0.0476, step 2, values float32 > hide #!23 models > hide #!22 models > hide #!21 models > hide #!20 models > show #!20 models > hide #!20 models > show #!20 models > hide #!19 models > hide #!18 models > tile 2 models tiled > color #20 #ff2f92ff models > color #20 #00f900ff models > color #20 #929000ff models > color #20 #4f8f00ff models > color #20 #005493ff models > color #20 #009193ff models > color #20 #009051ff models > color #20 #009193ff models > color #17 #ff9300ff models > color #17 #00fdffff models > color #17 #00fa92ff models > color #17 #73fcd6ff models > color #17 #73fdffff models > lighting soft > graphics silhouettes true > color #17 #929000ff models > color #17 #ffd479ff models > show #!18 models > show #!19 models > show #!21 models > show #!22 models > tile 6 models tiled > lighting soft > hide #!22 models > hide #!21 models > hide #!20 models > hide #!19 models > hide #!18 models > show #!16 models > hide #!17 models > hide #!16 models > show #!23 models > volume #23 step 1 > volume #23 level 0.1133 > volume #23 level 0.08675 > volume #23 level 0.1021 > show #!1 models > tile 2 models tiled > lighting soft > volume 0.1 Expected a density maps specifier or a keyword > volume level 0.1 > open /Users/colinmuir/Downloads/cryosparc_P12_J561_map_sharp.mrc Opened cryosparc_P12_J561_map_sharp.mrc as #24, grid size 320,320,320, pixel 0.86, shown at level 1.8e-05, step 2, values float32 > volume #24 step 1 > volume #24 level 0.1102 > hide #!1 models > volume #24 level 0.0315 > open /Users/colinmuir/Downloads/cryosparc_P12_J484_map_sharp.mrc Opened cryosparc_P12_J484_map_sharp.mrc as #25, grid size 320,320,320, pixel 0.86, shown at level 0.000263, step 2, values float32 > volume #25 step 1 > volume #25 level 0.06784 > hide #!24 models > hide #!23 models > volume #25 level 0.04081 > volume #24 level 0.03465 > volume #25 level 0.03067 > volume #24 level 0.06299 > ui tool show ""Side View"" ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/colinmuir/Downloads/cryosparc_P12_J484_map_sharp.mrc Opened cryosparc_P12_J484_map_sharp.mrc as #1, grid size 320,320,320, pixel 0.86, shown at level 0.000263, step 2, values float32 OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: MacBookAir10,1 Model Number: Z124000FLLL/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 11881.61.3 OS Loader Version: 11881.61.3 Software: System Software Overview: System Version: macOS 15.2 (24C101) Kernel Version: Darwin 24.2.0 Time since boot: 10 days, 9 hours, 15 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 SMS27A550H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX