id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18241 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.5-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 Current thread 0x000000020b8c5f00 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, 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""arch"" : ""arm64"", ""base"" : 6136758272, ""size"" : 131072, ""uuid"" : ""c8b24269-c8a2-3244-b044-b85c3449800d"", ""path"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/_elementpath.cpython-311-darwin.so"", ""name"" : ""_elementpath.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 13121142784, ""size"" : 32768, ""uuid"" : ""8abbdcef-1901-3d4b-9e6b-a38214b79214"", ""path"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/_imagingmath.cpython-311-darwin.so"", ""name"" : ""_imagingmath.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6936805376, ""size"" : 243284, ""uuid"" : ""60485b6f-67e5-38c1-aec9-efd6031ff166"", ""path"" : ""\/usr\/lib\/system\/libsystem_kernel.dylib"", ""name"" : ""libsystem_kernel.dylib"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6937051136, ""size"" : 51784, ""uuid"" : ""647b91fc-96d3-3bbb-af08-970df45257c8"", ""path"" : ""\/usr\/lib\/system\/libsystem_pthread.dylib"", ""name"" : ""libsystem_pthread.dylib"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6935572480, ""size"" : 529520, ""uuid"" : ""f4529d5e-24f3-3bbb-bd3c-984856875fc8"", ""path"" : ""\/usr\/lib\/system\/libsystem_c.dylib"", ""name"" : ""libsystem_c.dylib"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6937300992, ""size"" : 31568, ""uuid"" : ""519f3220-7499-334a-96d6-ccf3dc28f986"", ""path"" : ""\/usr\/lib\/system\/libsystem_platform.dylib"", ""name"" : ""libsystem_platform.dylib"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 7004016640, ""CFBundleShortVersionString"" : ""6.9"", ""CFBundleIdentifier"" : ""com.apple.AppKit"", ""size"" : 21568640, ""uuid"" : ""5d0da1bd-412c-3ed8-84e9-40ca62fe7b42"", ""path"" : ""\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit"", ""name"" : ""AppKit"", ""CFBundleVersion"" : ""2575.60.5"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 7038005248, ""CFBundleShortVersionString"" : ""1.600.0"", ""CFBundleIdentifier"" : ""com.apple.SkyLight"", ""size"" : 5395200, ""uuid"" : ""3a386772-a7fe-3359-aac4-1ae9c903cb49"", ""path"" : ""\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight"", ""name"" : ""SkyLight"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6935269376, ""size"" : 288576, ""uuid"" : ""8bf83cda-8db1-3d46-94b0-d811bd77e078"", ""path"" : ""\/usr\/lib\/system\/libdispatch.dylib"", ""name"" : ""libdispatch.dylib"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6937530368, ""CFBundleShortVersionString"" : ""6.9"", ""CFBundleIdentifier"" : ""com.apple.CoreFoundation"", ""size"" : 5500928, ""uuid"" : ""df489a59-b4f6-32b8-9bb4-9b832960aa52"", ""path"" : ""\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation"", ""name"" : ""CoreFoundation"", ""CFBundleVersion"" : ""3502.1.401"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 7132876800, ""CFBundleShortVersionString"" : ""2.1.1"", ""CFBundleIdentifier"" : ""com.apple.HIToolbox"", ""size"" : 3174368, ""uuid"" : ""9286e29f-fcee-31d0-acea-2842ea23bedf"", ""path"" : ""\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox"", ""name"" : ""HIToolbox"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6933250048, ""size"" : 636112, ""uuid"" : ""9cf0401a-a938-389e-a77d-9e9608076ccf"", ""path"" : ""\/usr\/lib\/dyld"", ""name"" : ""dyld"" }, { ""size"" : 0, ""source"" : ""A"", ""base"" : 0, ""uuid"" : ""00000000-0000-0000-0000-000000000000"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6960533504, ""CFBundleShortVersionString"" : ""6.9"", ""CFBundleIdentifier"" : ""com.apple.Foundation"", ""size"" : 14586624, ""uuid"" : ""e8f6a451-0acc-3e05-b18f-fec6618ce44a"", ""path"" : ""\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation"", ""name"" : ""Foundation"", ""CFBundleVersion"" : ""3502.1.401"" } ], ""sharedCache"" : { ""base"" : 6932414464, ""size"" : 5047205888, ""uuid"" : ""d7397d7f-8df9-3920-81a7-c0a144be9c51"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=6.4G written=91.0M(1%) resident=3550K(0%) swapped_out=87.6M(1%) unallocated=6.3G(99%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 1952K 85 \nCG raster data 384K 8 \nColorSync 656K 33 \nCoreAnimation 2944K 174 \nCoreGraphics 48K 3 \nCoreUI image data 5664K 62 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 5.8G 171 \nMALLOC guard page 288K 18 \nMach message 128K 7 \nOpenGL GLSL 384K 4 \nSTACK GUARD 608K 38 \nStack 215.3M 39 \nStack Guard 56.0M 1 \nVM_ALLOCATE 321.2M 255 \nVM_ALLOCATE (reserved) 96.0M 2 reserved VM address space (unallocated)\n__AUTH 5521K 697 \n__AUTH_CONST 77.4M 944 \n__CTF 824 1 \n__DATA 34.3M 1088 \n__DATA_CONST 37.0M 1106 \n__DATA_DIRTY 2778K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 647.4M 156 \n__OBJC_RO 61.4M 1 \n__OBJC_RW 2396K 1 \n__TEXT 1.3G 1123 \n__TEXT (graphics) 4976K 3 \n__TPRO_CONST 128K 2 \ndyld private memory 3360K 28 \nmapped file 304.0M 87 \npage table in kernel 3550K 1 \nshared memory 3824K 25 \n=========== ======= ======= \nTOTAL 8.9G 6514 \nTOTAL, minus reserved VM space 8.8G 6514 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""2274fae58bf627dc917e5243709f5c1fba85b3bd"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""64628732bf2f5257dedc8988"", ""factorPackIds"" : { }, ""deploymentId"" : 240000001 }, { ""rolloutId"" : ""645eb1d0417dab722a215927"", ""factorPackIds"" : { }, ""deploymentId"" : 240000005 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- warning | Registration file '/Users/u0159610/Library/Application Support/ChimeraX/registration' has expired 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 > ui tool show Registration > open ""/Users/u0159610/SwitchLab Dropbox/brajabandhu > pradhan/Heterotypic_Abeta_medin_manuscript/Data/Morphology_2_Models/morph2_foldxmodel.cxs"" > format session Opened cryosparc_P7_J438_map_sharp.mrc z flip as #5, grid size 256,256,256, pixel 1.39, shown at level 0.129, step 1, values float32 Opened cryosparc_P7_J418_009_volume_map_sharp (1).mrc z flip as #2, grid size 256,256,256, pixel 1.39, shown at level 0.359, step 1, values float32 Opened cryosparc_P7_J438_map_sharp.mrc z flip zone as #1, grid size 256,256,256, pixel 1.39, shown at level 0.041, step 1, values float32 Opened cryosparc_P7_J438_map_sharp.mrc z flip zone as #6, grid size 256,256,256, pixel 1.39, shown at level 0.0509, step 1, values float32 Opened cryosparc_P7_J418_009_volume_map_sharp (1).mrc z flip zone as #7, grid size 256,256,256, pixel 1.39, shown at level 0.384, step 1, values float32 Opened cryosparc_P7_J418_009_volume_map_sharp (1).mrc z flip zone as #8, grid size 256,256,256, pixel 1.39, shown at level 0.368, step 1, values float32 opened ChimeraX session > hide #!9 models > show #!9 models > hide #!8 models > show #!8 models > hide #!8 models > hide #!7 models > hide #!6 models > show #!6 models > show #!2 models > hide #!2 models > hide #!1 models > show #!1 models > hide #!6 models > hide #!9 models > hide #!1 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!5 models > volume #5 style surface > view name p1 > view name p2 > show #!1 models > hide #!1 models > volume #5 style mesh > show #!8 models > hide #!8 models > show #!1 models > hide #!1 models > show #!2 models > hide #!2 models > show #!2 models > show #!9 models > hide #!9 models > hide #!2 models > hide #!5 models > show #!5 models > hide #!5 models > show #!6 models > hide #!6 models > show #!7 models > ui tool show ""Side View"" > show #!8 models > show #!2 models > lighting soft > volume #2 color #d783ff > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > view name p3 > hide #!8 models > show #!8 models > show #!1 models > hide #!1 models > hide #!8 models > show #!1 models > hide #!7 models > hide #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!5 models > hide #!5 models > show #!6 models > hide #!6 models > show #!6 models > show #!7 models > hide #!7 models > hide #!6 models > show #!8 models > hide #!8 models > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > show #!8 models > show #!7 models > view name p4 > show #!9 models > view name p5 > view p1 > show #!1 models > show #!2 models > hide #!9 models > view p2 > view p3 > view p5 > view p4 > fly p1 p2 p3 p4 > hide #!8 models > hide #!7 models > hide #!2 models > show #!2 models > hide #!1 models > movie record > volume #2 level 0.469 > volume #2 level 0.4941 > volume #2 level 0.7098 > movie record Already recording a movie > movie stop > roll y 10 36 #2 Expected a keyword > roll y 10 36 center #2 > roll y 20 18 center #2 > roll y 4 90 center #2 > roll y 2 180 center #2 > turn y 90 > turn z 90 > turn x 90 > turn y 90 > turn x 90 > volume #2 level 0.3537 > show #!9 models > volume #2 style mesh > hide #!2 models > show #!2 models > hide #!9 models > show #!9 models > hide #!2 models > show #!1 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!9 models > show #!9 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!9 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!3 models > show #!4 models > hide #!4 models > show #!4 models > show #!9 models > hide #!4 models > hide #!3 models > show #!8 models > show #!7 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > show #!1 models > show #!2 models > hide #!2 models > show #!5 models > hide #!5 models > show #!4 models > hide #!4 models > show #!6 models > hide #!7 models > hide #!8 models > hide #!6 models > show #!6 models > show #!7 models > show #!8 models > hide #!8 models > show #!8 models > hide #!7 models > hide #!6 models > show #!6 models > hide #!9 models > hide #!1 models > show #!1 models > show #!7 models > hide #!8 models > show #!8 models > show #!5 models > hide #!5 models > show #!2 models > hide #!2 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > hide #!1 models > show #!1 models > show #!2 models > hide #!2 models > show #!5 models > hide #!5 models > hide #!6 models > show #!6 models > show #!2 models > hide #!2 models > show #!9 models > hide #!9 models > hide #!8 models > show #!8 models > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > volume #2 style surface > volume #2 level 0.6195 > hide #!8 models > hide #!7 models > hide #!6 models > hide #!2 models > show #!2 models > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > graphics silhouettes true > volume #2 level 0.6345 > roll y 4 90 center #2 > turn x 90 > zoom 0.75 moved plane near -336.7457502740981 [ 0.00715726 0.03333838 -0.9994185 ] moved plane far -336.7457502740981 [ 0.00715726 0.03333838 -0.9994185 ] > zoom 1.5 moved plane near 448.9943346236103 [ 0.00715726 0.03333838 -0.9994185 ] moved plane far 448.9943346236103 [ 0.00715726 0.03333838 -0.9994185 ] > zoom 5 moved plane near 718.3909324383754 [ 0.00715726 0.03333838 -0.9994185 ] moved plane far 718.3909324383754 [ 0.00715726 0.03333838 -0.9994185 ] > zoom 3 moved plane near 119.73181812719434 [ 0.00715726 0.03333838 -0.9994185 ] moved plane far 119.73181812719434 [ 0.00715726 0.03333838 -0.9994185 ] > zoom 0.2 moved plane near -239.46363230852052 [ 0.00715726 0.03333838 -0.9994185 ] moved plane far -239.46363230852052 [ 0.00715726 0.03333838 -0.9994185 ] > zoom 0.2 moved plane near -1197.3181697663215 [0.99051076 0.10057255 0.09366753] moved plane far -1197.3181697663215 [0.99051076 0.10057255 0.09366753] > zoom 0.4 moved plane near -2244.971583606832 [0.99051076 0.10057255 0.09366753] moved plane far -2244.971583606832 [0.99051076 0.10057255 0.09366753] > zoom 1 moved plane near -0.0 [0.99051076 0.10057255 0.09366753] moved plane far -0.0 [0.99051076 0.10057255 0.09366753] > zoom 1.5 moved plane near 1247.2064417100366 [0.99051076 0.10057255 0.09366753] moved plane far 1247.2064417100366 [0.99051076 0.10057255 0.09366753] > zoom 1.5 moved plane near 831.4709575995204 [0.99051076 0.10057255 0.09366753] moved plane far 831.4709575995204 [0.99051076 0.10057255 0.09366753] > zoom 1.5 moved plane near 554.3139693726773 [0.99051076 0.10057255 0.09366753] moved plane far 554.3139693726773 [0.99051076 0.10057255 0.09366753] > zoom 1.5 moved plane near 369.5426446748941 [0.99051076 0.10057255 0.09366753] moved plane far 369.5426446748941 [0.99051076 0.10057255 0.09366753] > zoom 1.5 moved plane near 246.36176206755792 [0.99051076 0.10057255 0.09366753] moved plane far 246.36176206755792 [0.99051076 0.10057255 0.09366753] > zoom 1.5 moved plane near 164.24117401234642 [0.99051076 0.10057255 0.09366753] moved plane far 164.24117401234642 [0.99051076 0.10057255 0.09366753] > zoom 1.5 moved plane near 109.49411554199169 [0.99051076 0.10057255 0.09366753] moved plane far 109.49411554199169 [0.99051076 0.10057255 0.09366753] > turn x 90 > rotate z 90 Unknown command: rotate z 90 > turn z 90 > turn x 90 > turn y > roll y 4 90 center #2 > turn x 90 > zoom 3 moved plane near 757.8687109848526 [ 0.04187114 -0.01361814 -0.99903029] moved plane far 757.8687109848526 [ 0.04187114 -0.01361814 -0.99903029] > turn z50 Expected an axis vector or a keyword > turn z 50 > volume #2 level 0.3587 > show #!8 models > hide #!8 models > hide #!2 models > show #!8 models > hide #!8 models > graphics silhouettes false > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!8 models > hide #!8 models > show #!8 models > show #!7 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!9 models > hide #!8 models > hide #!7 models > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > orient #2 Unknown command: orient #2 > select add #2 4 models selected > hide #!2 models > show #!2 models > select add #2 4 models selected > select subtract #2 Nothing selected > volume #2 level 0.6997 > volume #2 level 0.6897 > graphics silhouettes false > graphics silhouettes true > view name p1 > roll y 4 90 #2 Expected a keyword > roll y 4 90 center #2 > turn x 90 > show #!9 models > roll y 4 90 center #2 > turn x 90 > zoom 4 moved plane near 956.2278958008205 [ 0.06741475 0.06378036 -0.99568445] moved plane far 956.2278958008205 [ 0.06741475 0.06378036 -0.99568445] > volume #2 level 0.3587 > hide #!2 models > show #!8 models > hide #!8 models > graphics silhouettes false > show #!8 models > show #!7 models > show #7,8 > hide #7,8 > show #7,8 > view p1 > show #!2 models > hide #!8 models > hide #!7 models > hide #!9 models > show #!9 models > hide #!9 models > show #9 > show #!9 models > hide #!9 models > roll y 4 90 center #2 > turn x 90 > view name p2 > zoom 4 moved plane near 774.4056942753766 [ 0.03176016 0.02803891 -0.99910224] moved plane far 774.4056942753766 [ 0.03176016 0.02803891 -0.99910224] > zoom 0.75 moved plane near -86.04503129289363 [ 0.03176016 0.02803891 -0.99910224] moved plane far -86.04503129289363 [ 0.03176016 0.02803891 -0.99910224] > turn z 50 > turn z 32 > turn z 20 > turn z 5 > view name p3 > volume #2 level 0.3587 > volume #2 level 0.2835 > volume #2 level 0.2835 > volume #2 level 0.283 > volume #2 level 0.27 > hide #2 > graphics silhouettes false > show #7,8 > show #!9 models > hide #!9 models > show #!3 models > show #!4 models > show #!3,4 models > hide #!3,4 models > show #!3,4 models > zoom 1.5 moved plane near 113.76157937209423 [ 0.03382792 0.02426317 -0.99913313] moved plane far 113.76157937209423 [ 0.03382792 0.02426317 -0.99913313] > turn z 5 > turn z -5 > turn z 5 > view p1 > view p2 > view p4 > view p5 > view p1 > view p2 > view p3 > view pp4 Expected an objects specifier or a view name or a keyword > view p4 > view p1 > hide #!7 models > show #!7 models > hide #!3 models > show #!3 models > hide #!7 models > hide #!8 models > hide #!4 models > hide #!3 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > color #2 #ff85ffff models > show #!1 models > hide #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!9 models > hide #!9 models > show #!9 models > select #9/p 66 atoms, 65 bonds, 9 residues, 1 model selected > select #9/p,F 372 atoms, 377 bonds, 49 residues, 1 model selected > select #9/p,F,H 678 atoms, 689 bonds, 89 residues, 1 model selected > select ~sel & ##selected 4374 atoms, 4446 bonds, 574 residues, 1 model selected > delete atoms sel > delete bonds sel > color #2 #d783ffff models > hide #!9 models > hide #!2 models > show #!2 models > volume #2 level 0.6812 > graphics silhouettes true > view name p1 > roll y 4 90 center #2 > turn x 90 > view name p2 > zoom 3 moved plane near 702.6577642138668 [ 0.00539731 -0.00371411 0.99997855] moved plane far 702.6577642138668 [ 0.00539731 -0.00371411 0.99997855] > volume #2 level 0.28 > view name p4 > hide #2 > graphics silhouettes false > show #7,8 > view name p5 > show #!9 models > turn z 5 > fly p1 > fly p1 p2 > fly p1 p2 p3 p4 > show #!1 models > show #!2 models > fly p1 p2 p3 p4 > volume #2 level 0.2599 > fly p1 p2 p3 p4 > fly p2 p3 p4 > fly p1 p2 > fly p2 p3 > fly p3 p4 > fly p3 p5 > hide #!1 models > show #!1 models > close #1 > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > close #3 > close #4 > show #!5 models > hide #!5 models > hide #!7 models > show #!7 models > hide #!2 models > hide #!7 models > show #!7 models > hide #!8 models > show #!8 models > show #!6 models > hide #!6 models > close #6 > close #5 > hide #!7 models > show #!7 models > hide #!9 models > show #!9 models > show #!2 models > select add #2 3 models selected > view sel > select subtract #2 Nothing selected > select add #7 2 models selected > select subtract #7 Nothing selected > select add #8 2 models selected > select subtract #8 Nothing selected > select add #9 678 atoms, 689 bonds, 89 residues, 2 models selected > select subtract #9 Nothing selected > hide #!9 models > hide #!8 models > hide #!7 models > hide #!2 models > show #!2 models > volume #2 level 0.621 > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > scene side_view Unknown command: scene side_view > show #!9 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > hide #!9 models > show #!9 models > show #!7 models > show #!8 models > show #!2 models > movie record > hide #!9 models > hide #!8 models > hide #!7 models > hide #!2 models > show #!2 models > volume #2 level 0.3352 > show #!7 models > show #!8 models > show #!9 models > movie stop > save /Users/u0159610/Desktop/image34.png supersample 3 > movie encode /Users/u0159610/Desktop/itieam.mp4 Movie saved to /Users/u0159610/Desktop/itieam.mp4 > hide #!9 models > hide #!8 models > hide #!7 models > show #!2 models > volume #2 level 0.6511 > movie record > roll y 4 90 center #2 > turn x 90 > volume #2 level 0.3903 > show #!7 models > show #!8 models > hide #!2 models > show #!9 models > movie stop > movie encode /Users/u0159610/Desktop/itieam.mp4 Movie saved to /Users/u0159610/Desktop/itieam.mp4 > hide #!9 models > hide #!8 models > hide #!7 models > show #!2 models > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > volume #2 level 0.7163 > movie record > roll y 4 90 center #2 > turn x 90 > volume #2 level 0.3753 > graphics silhouettes false > show #!7 models > show #!8 models > hide #!2 models > show #!9 models > movie stop > movie encode /Users/u0159610/Desktop/itieam.mp4 Movie saved to /Users/u0159610/Desktop/itieam.mp4 > view name p5 > hide #!9 models > hide #!8 models > hide #!7 models > show #!2 models > volume #2 level 0.6762 > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > view name p1 > turn x 90 > view name p2 > view name p3 > show #!7 models > show #!8 models > hide #!8 models > hide #!7 models > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > show #!8 models > show #!7 models > show #!9 models > hide #!9 models > hide #!2 models > hide #!7 models > hide #!8 models > view p1 > show #!2 models > graphics silhouettes true > movie record > roll y 4 90 center #2 > flyby p1 p2 Unknown command: flyby p1 p2 > fly p1 p2 > fly p2 p3 > show #!8 models > hide #!8 models > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > hide #!2 models > show #!7 models > show #!8 models > fly p3 p5 > show #!9 models > movie stop > movie encode /Users/u0159610/Desktop/itieam.mp4 Movie saved to /Users/u0159610/Desktop/itieam.mp4 > view p1 > show #!2 models > hide #!7 models > hide #!8 models > hide #!9 models > view p2 > view p3 > fly p2 p3 > fly p1 p2 p3 > view p1 > view p2 > view name p2 > view p3 > fly p1 p2 p3 > hide #!2 models > show #!2 models > select add #2 2 models selected > view sel > select add #2 3 models selected > select subtract #2 Nothing selected > view #2 clip false > view clip false > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > fly p1 > fly p1 p2 > fly p1 p2 p3 > fly p1 p2 > volume #2 level 0.6685 > view name p2 > fly p1 p2 > ui tool show ""Side View"" > view name p3 > fly p1 p2 p3 > fly p2 p3 > view p2 > view p3 > fly p2 p3 > fly p1 p3 > view p3 > view name p3 > fly p1 p2 p3 > view p1 > view name p1 > turn x 90 > view p2 > view p1 > turn x 90 > zoom 3 moved plane near 588.9770379832257 [-0.01605782 0.05060235 -0.99858977] moved plane far 588.9770379832257 [-0.01605782 0.05060235 -0.99858977] > zoom 0.3 moved plane near -369.46825134938763 [-0.01605782 0.05060235 -0.99858977] moved plane far -369.46825134938763 [-0.01605782 0.05060235 -0.99858977] > view p§ Expected an objects specifier or a view name or a keyword > view name p1 > turn x 90 > view p2 > fly p1 p2 > view name p3 > fly p1 p2 p3 > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > graphics silhouettes false > volume #2 level 0.5066 > graphics silhouettes true > graphics silhouettes false > show #!7 models > show #!8 models > show #!8,9 models > hide #!2 models > view name o4 > view name p4 > hide #!9 models > hide #!8 models > hide #!7 models > show #!2 models > view p1 > video record Unknown command: video record > movie record > turn y 2 180 > wait 180 > movie encode /Users/u0159610/Desktop/movie8.mp4 Movie saved to /Users/u0159610/Desktop/movie8.mp4 > volume #2 level 0.4835 > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > movie encode No frames have been recorded > movie record > roll y 4 90 center #2 > fly p1 p2 > fly p2 p3 > volume #2 level 0.3679 > fly p3 p4 > hide #!2 models > show #!7 models > show #!8 models > show #!9 models > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > movie stop > view p1 > hide #!9 models > hide #!8 models > hide #!7 models > show #!2 models > view p2 > view p3 > fly p2 p3 > fly p1 p3 > volume #2 level 0.2985 > view name p4 > fly p1 p4 > graphics silhouettes false > show #!8,9 models > hide #!9 models > show #!7 models > show #!7,8 models > hide #!2 models > view name p4 > show #!9 models > view name p5 > fly p1 p5 > show #!2 models > hide #!7 models > hide #!8 models > hide #!9 models > View p1 Unknown command: View p1 > view p1 > roll y 4 90 center #2 > roll y 5 72 center #2 > roll y 3 120 center #2 > fly p1 p3 > view name p3 > fly p1 p3 > fly p1 p2 p3 > view p2 > fly p1 p2 > fly p1 p2 p3 > view p2 > view name p3 > fly p1 p2 p3 > view p1 > turn y 90 > view p1 > turn x 90 > view name p2 > fly p1 p2 > view name p3 > fly p1 p2 p3 > view p1 > view p2 > view p3 > fly p1 p3 > view p1 > turn y 90 > view p1 > turn x 90 > view name p2 > fly p1 p2 > view name p2 > fly p1 p2 > view p1 > view name p1 > fly p1 p2 > fly p1 p2 p3 > view name p4 > fly p1 p4 > fly p1 p2 p3 p4 > fly p1 p2 p4 > show #!8 models > show #!7 models > graphics silhouettes false > show #!7,8 models > hide #!2 models > view name p4 > fly p1 p4 > hide #!8 models > hide #!7 models > show #!2 models > show #!9 models > hide #!9 models > view p1 > view p2 > view p3 > view p1 > view p2 > view p3 > view p2 > view name p3 > fly p1 p2 p3 > view p1 > fly p1 p3 > fly p1 p2 > view name p3 > fly p1 p2 p3 > fly p1 p2 > view name p3 > fly p1 p2 p3 > fly p1 p2 > fly p2 p3 > show #!7,8 models > hide #!2 models > show #!9 models > view name p4 > fly p3 p4 > view p1 > hide #!7 models > hide #!8 models > hide #!9 models > show #!2 models > movie record > roll y 3 120 center #2 > fly p1 p2 > fly p2 p3 > graphics silhouettes false > show #!7,8 models > hide #!2 models > show #!9 models > fly p3 p4 > movie stop > movie encode /Users/u0159610/Desktop/itieam.mp4 Movie saved to /Users/u0159610/Desktop/itieam.mp4 > view p1 > hide #!7 models > hide #!8 models > hide #!9 models > view p1 > show #!2 models > graphics silhouettes true > fly p1 p2 > fly p2 p3 > view p2 > view name p3 > fly p2 > fly p2 p3 > fly p1 p2 p3 > fly p1 p2 > view p1 > view p2 > view p3 > view p1 > view p2 > fly p1 p2 > view name p2 > fly p1 p2 > view p1 > view name p1 > view name p2 > view name p1 > view p2 > turn x 90 > view p2 > turn x 90 > view name p2 > view name p3 > view p2 > view p3 > fly p1 p3 > fly p1 p2 > fly p1 p23 fly: Unknown position name ""p23"" > fly p1 p2 p3 > view name p3 > view p1 p3 Expected an integer >= 1 or a keyword > fly p1 p3 > fly p1 p2 > fly p1 p2 p3 > show #!7 models > show #!8 models > graphics silhouettes false > hide #!2 models > view name p4 > fly p3 p4 > show #!9 models > hide #!7 models > hide #!8 models > hide #!9 models > show #!2 models > view p1 > fly p1 p2 p3 > fly p1 p3 > fly p2 p3 > View p1 Unknown command: View p1 > view p1 > movie record > roll y 3 120 center #2 > fly p1 p2 p3 > graphics silhouettes false > show #!7,8 models > hide #!2 models > fly p3 p4 > show #!9 models > movie stop > view p1 > show #!2 models > hide #!7 models > hide #!8 models > hide #!9 models > graphics silhouettes true > fly p1 p3 > view name p5 > fly p1 p2 p3 > view p1 > fly p1 p2 p3 > view p5 > fly p3 p5 > view p1 > view p2 > view p3 > view p1 p2 Expected an integer >= 1 or a keyword > fly p1 p2 > fly p2 p3 > view p1 > fly p1 p2 > fly p2 p3 > fly p3 p5 > view name p4 > fly p3 p4 > view p5 > view p4 > show #!7 models > show #!8 models > show #!9 models > hide #!9 models > hide #!2 models > graphics silhouettes false > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!7 models > hide #!8 models > show #!2 models > View p1 Unknown command: View p1 > View p1 Unknown command: View p1 > view p1 > movie record > roll y 3 120 center #2 > fly p1 p2 p3 > fly p3 p4 > show #!7,8 models > hide #!2 models > fly p3 p4 > show #!9 models > movie stop > movie encode /Users/u0159610/Desktop/itieam.mp4 Movie saved to /Users/u0159610/Desktop/itieam.mp4 > movie reset No movie being recorded. > hide #!7 models > hide #!9 models > hide #!8 models > show #!2 models > view p1 > fly p1 p3 > view p4 > fly p3 p4 > view p1 > fly p1 p4 > view p4 > fly p3 p4 > view p1 > fly p3 p4 > view p4 > show #!8 models > show #!7 models > hide #!2 models > view name p5 > show #!9 models > hide #!9 models > fly p4 p5 > hide #!7 models > hide #!8 models > show #!2 models > hide #!2 models > show #!2 models > view p1 > fly p1 p2 p3 > view p4 > view p3 p4 Expected an integer >= 1 or a keyword > fly p3 p4 > view p3 > view p2 > view p4 > view name p3 > fly p1 p3 > view p1 > fly p1 p3 > view p3 > graphics silhouettes false > show #!7,8 models > hide #!2 models > show #!2 models > view name p3 > fly p2 p3 > view p1 > fly p1 p2 > fly p2 p3 > view p3 > fly p2 p3 > view pe Expected an objects specifier or a view name or a keyword > view p1 > view p3 > fly p1 p3 > view p1 > view p3 > view p1 > view p2 > view p3 > fly p1 p3 > view p1 > view p3 > view p1 > fly p1 p3 > view p3 > view p1 > view name p1 > view p3 > fly p1 p3 > view p1 > view p2 > fly p1 p3 > view p3 > view name p2 > fly p1 p2 > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > view p4 > hide #!2 models > view name p3 > fly p2 p3 > show #!9 models > view p1 > show #!2 models > hide #!7 models > hide #!8 models > hide #!9 models > movie record > roll y 3 120 center #2 > fly p1 p2 > show #!7,8 models > hide #!2 models > fly p3 p4 > fly p2 p3 > movie stop > movie reset > view p1 > hide #!7 models > hide #!8 models > show #!2 models > view p2 > view p1 > view p2 > view p3 > view p2 > hide #!2 models > show #!7 models > show #!8 models > view name p3 > view name p4 > show #!9 models > hide #!9 models > view p1 > hide #!7 models > hide #!8 models > show #!2 models > view p2 > fly p1 p2 > view p1 > fly p1 p2 > view p1 > view p2 > show #!7 models > show #!8 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > view p2 > view p1 > view p2 > view p3 > fly p1 p2 > view p1 > fly p1 p2 > view p2 > graphics silhouettes true > view p1 > movie record > movie stop > movie reset > view p1 > fly p1 p2 > view p1 > view name p1 > fly p1 p2 > view p2 > view p1 > view p3 > fly p2 p3 > view p1 p3 Expected an integer >= 1 or a keyword > fly p1 p3 > hide #!2 models > show #!2 models > graphics silhouettes false > hide #!2 models > fly p4 p5 > fly p2 p3 > view p3 > view p4 > view p1 > show #!2 models > graphics silhouettes true > movie record > roll y 3 120 center #2 > fly p1 p2 > graphics silhouettes false > hide #!2 models > fly p3 p4 > show #!9 models > movie stop > movie reset > view p1 > hide #!7 models > hide #!8 models > hide #!9 models > show #!2 models > fly p1 p2 > hide #!2 models > show #!7 models > show #!8 models > fly p3 p4 > view p3 > view name p4 > view p1 > fly p1 p2 > fly p3 p4 > view p2 > view name p3 > fly p1 p2 > view p1 > fly p1 p2 > fly p2 p3 > view p2 > fly p2 p3 > view p2 > show #!2 models > view name p2 > fly p2 p3 > hide #!2 models > hide #!7 models > show #!7 models > view p3 > fly p2 p3 > fly p1 p2 > fly p2 p3 > view p1 > fly p1 p2 > fly p2 p3 > view p1 > view name p1 > fly p1 p2 > fly p2 p3 > hide #!7 models > hide #!8 models > show #!2 models > view p1 > fly p1 p2 > fly p2 p3 > fly p1 p2 > fly p2 p3 > view p1 > graphics silhouettes false > show #!7 models > show #!8 models > view p3 > hide #!2 models > show #!2 models > hide #!2 models > hide #!7 models > hide #!8 models > fly p1 p3 fly: Nothing displayed to calculate center of rotation > show #!2 models > fly p1 p3 > fly p3 p4 > hide #!2 models > show #!7 models > show #!8 models > fly p3 p4 > view p3 > show #!2 models > hide #!2 models > show #!9 models > hide #!9 models > view p1 > show #!2 models > fly p1 p3 > view p2 > fly p1 p3 > view p3 > fly p1 p3 > view p1 > view p2 > fly p1 p2 > view p1 > view name p1 > view name p1 > view p1 > fly p1 p2 > view p2 > view p3 > fly p2 p3 > fly p1 p3 > view p1 > view p3 > movie record > fly p1 p3 > movie stop > movie encode /Users/u0159610/Desktop/itieam.mp4 Movie saved to /Users/u0159610/Desktop/itieam.mp4 > movie reset No movie being recorded. > movie encode No frames have been recorded > movie record > fly p1 p3 > movie stop > movie encode /Users/u0159610/Desktop/itieam.mp4 Movie saved to /Users/u0159610/Desktop/itieam.mp4 > movie reset No movie being recorded. > view p1 > movie record > roll y 3 120 center #2 > movie stop > view p3 > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > crossfade > show #!2 models > crossfade > hide #2 > crossfade > hide #2 > crossfade > hide #2 > crossfade > hide #2: wait 20 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > movie crossfade > hide #2: wait 20 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > movie crossfade > crossfade > hide #2: wait 20 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > crossfade > hide #2: wait 20 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > crossfade > hide #2: wait 20 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show #!2 models > movie crossfade > hide #2: wait 20 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide #!2 models > show #!2 models > view p1 > hide #!2 models > show #!2 models > select add #2 2 models selected > view sel No displayed objects specified. > color #2 #ff85ffff models > color #2 #d783ffff models > hide #!7 models > hide #!8 models > view p1 > view p2 > view p3 > select add #2 3 models selected > select subtract #2 Nothing selected > show #!7 models > show #!8 models > view p1 > crossfade fade; hide #2 Expected an integer >= 1 or a keyword > hide #!2 models > show #!2 models > crossfade fade;hide #!2 models Expected an integer >= 1 or a keyword > crossfade > hide #!2 models > crossfade > hide #!2 models > crossfade > hide #!2 models > show #!2 models > crossfade > hide #!2 models > crossfade > hide #!2 models > crossfade > hide #!2 models > crossfade > show #!2 models > crossfade > show #!2 models > crossfade > show #!2 models > crossfade > show #!2 models > crossfade > show #!2 models > crossfade > show #!2 models > view p2 > volume morph #2 #3 volume morph requires 2 or more volumes, got 1 > hide #!7 models > hide #!8 models > hide #!2 models ===== Log before crash end ===== Log: Startup Messages --- warning | Registration file '/Users/u0159610/Library/Application Support/ChimeraX/registration' has expired note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.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 Pro Model Identifier: Mac14,7 Model Number: Z16S000UNFN/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 11881.121.1 OS Loader Version: 11881.121.1 Software: System Software Overview: System Version: macOS 15.5 (24F74) Kernel Version: Darwin 24.5.0 Time since boot: 2 days, 22 hours, 51 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 10 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 S24R65x: 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