id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17480 Crash on Mac waking from sleep sphulera@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.4-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. 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""sharedCache"" : { ""base"" : 6512590848, ""size"" : 5020090368, ""uuid"" : ""32a9f5fd-14a8-3423-8952-1464a6903997"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=2.0G resident=0K(0%) swapped_out_or_unallocated=2.0G(100%)\nWritable regions: Total=8.7G written=317.2M(4%) resident=5317K(0%) swapped_out=312.0M(4%) unallocated=8.4G(96%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 3584K 28 \nActivity Tracing 256K 1 \nCG backing stores 576K 1 \nCG image 4208K 79 \nCG raster data 384K 8 \nColorSync 736K 38 \nCoreAnimation 8528K 387 \nCoreGraphics 64K 4 \nCoreImage 192K 6 \nCoreServices 624K 2 \nCoreUI image data 3920K 29 \nFoundation 32K 2 \nKernel Alloc Once 32K 1 \nMALLOC 7.8G 166 \nMALLOC guard page 288K 18 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.6M 36 \nStack 191.2M 36 \nVM_ALLOCATE 548.5M 355 \nVM_ALLOCATE (reserved) 128.0M 3 reserved VM address space (unallocated)\n__AUTH 5995K 721 \n__AUTH_CONST 79.9M 974 \n__CTF 824 1 \n__DATA 36.8M 1118 \n__DATA_CONST 37.5M 1136 \n__DATA_DIRTY 2786K 347 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 652.5M 158 \n__OBJC_RO 61.3M 1 \n__OBJC_RW 2391K 1 \n__TEXT 1.4G 1155 \n__TEXT (graphics) 384K 2 \n__TPRO_CONST 128K 2 \ndyld private memory 3488K 30 \nmapped file 337.9M 97 \npage table in kernel 5317K 1 \nshared memory 3264K 29 \n=========== ======= ======= \nTOTAL 11.3G 6983 \nTOTAL, minus reserved VM space 11.2G 6983 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""4e6cbfe45bf98dd0119f46c5031b2fdc5873cb15"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""67181b10c68c361a728c7cfa"", ""factorPackIds"" : { }, ""deploymentId"" : 240000005 }, { ""rolloutId"" : ""5f72dc58705eff005a46b3a9"", ""factorPackIds"" : { }, ""deploymentId"" : 240000015 } ], ""experiments"" : [ { ""treatmentId"" : ""d7ff00dd-1c5a-4dbb-85d6-7a936d671384"", ""experimentId"" : ""67f46bbc84eaf455d73c6098"", ""deploymentId"" : 400000001 } ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/sphulera/Desktop/HVTN301/Map_session.cxs Opened 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc as #1, grid size 400,400,400, pixel 1.03, shown at level 0.16, step 1, values float32 Opened 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc as #2, grid size 400,400,400, pixel 1.03, shown at level 0.23, step 1, values float32 Opened 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc as #3, grid size 400,400,400, pixel 1.03, shown at level 0.24, step 1, values float32 Opened 301_48FAB_GT1-1_RM20A3_J336_C3_map_sharp_2.98A.mrc as #4, grid size 400,400,400, pixel 1.03, shown at level 0.21, step 1, values float32 Opened 301_56Fab_426cSM_SOSIP_RM20A3_J1469_map_sharp_2.88A.mrc as #5, grid size 400,400,400, pixel 1.03, shown at level 0.215, step 1, values float32 Opened 301_61FAB_426cSM_SOSIP_RM20A3_J1468_map_sharp_2.87A.mrc as #6, grid size 400,400,400, pixel 1.03, shown at level 0.23, step 1, values float32 Log from Tue Apr 22 15:50:50 2025 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/sphulera/Desktop/HVTN301/maps/301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc Opened 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc as #1, grid size 400,400,400, pixel 1.03, shown at level 0.0574, step 2, values float32 > open > /Users/sphulera/Desktop/HVTN301/maps/301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc Opened 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc as #2, grid size 400,400,400, pixel 1.03, shown at level 0.0637, step 2, values float32 > open > /Users/sphulera/Desktop/HVTN301/maps/301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc Opened 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc as #3, grid size 400,400,400, pixel 1.03, shown at level 0.067, step 2, values float32 > open > /Users/sphulera/Desktop/HVTN301/maps/301_48FAB_GT1-1_RM20A3_J336_C3_map_sharp_2.98A.mrc Opened 301_48FAB_GT1-1_RM20A3_J336_C3_map_sharp_2.98A.mrc as #4, grid size 400,400,400, pixel 1.03, shown at level 0.0606, step 2, values float32 > open > /Users/sphulera/Desktop/HVTN301/maps/301_56Fab_426cSM_SOSIP_RM20A3_J1469_map_sharp_2.88A.mrc Opened 301_56Fab_426cSM_SOSIP_RM20A3_J1469_map_sharp_2.88A.mrc as #5, grid size 400,400,400, pixel 1.03, shown at level 0.0655, step 2, values float32 > open > /Users/sphulera/Desktop/HVTN301/maps/301_61FAB_426cSM_SOSIP_RM20A3_J1468_map_sharp_2.87A.mrc Opened 301_61FAB_426cSM_SOSIP_RM20A3_J1468_map_sharp_2.87A.mrc as #6, grid size 400,400,400, pixel 1.03, shown at level 0.0718, step 2, values float32 > surface dust #1 size 10.3 > surface dust #2 size 10.3 > surface dust #3 size 10.3 > surface dust #4 size 10.3 > surface dust #5 size 10.3 > surface dust #6 size 10.3 > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > hide #!6 models > show #!2 models > hide #!2 models > show #!2 models > select add #2 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.68055,0.73228,-0.02489,-71.656,-0.73235,0.68088,0.0076984,213.17,0.022585,0.012989,0.99966,-7.1686 > fitmap #2 inMap #1 Fit map 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc in map 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc using 79679 points correlation = 0.8247, correlation about mean = 0.7973, overlap = 1739 steps = 120, shift = 8.87, angle = 3.49 degrees Position of 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) relative to 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc (#1) coordinates: Matrix rotation and translation 0.72068270 0.69325818 -0.00309118 -85.16213772 -0.69326501 0.72067722 -0.00282255 201.53581721 0.00027098 0.00417717 0.99999124 -0.24291772 Axis 0.00504832 -0.00242485 -0.99998432 Axis point 207.52227718 206.45020110 0.00000000 Rotation angle (degrees) 43.88971452 Shift along axis -0.67570642 > select clear > volume #2 step 1 > volume #1 step 1 > hide #!2 models > volume #1 level 0.08067 > volume #1 level 0.2202 > show #!2 models > fitmap #1 inMap #2 Fit map 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc in map 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 81884 points correlation = 0.9559, correlation about mean = 0.7508, overlap = 1.157e+04 steps = 40, shift = 0.00539, angle = 0.0285 degrees Position of 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc (#1) relative to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates: Matrix rotation and translation 0.72098069 -0.69295515 0.00005930 201.01210114 0.69294854 0.72097417 0.00430886 -86.23281590 -0.00302860 -0.00306551 0.99999071 0.58334473 Axis -0.00532089 0.00222804 0.99998336 Axis point 207.58699714 206.48913474 0.00000000 Rotation angle (degrees) 43.86514598 Shift along axis -0.67835847 > fitmap #1 inMap #2 Fit map 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc in map 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 81884 points correlation = 0.9558, correlation about mean = 0.7506, overlap = 1.158e+04 steps = 48, shift = 0.0118, angle = 0.00601 degrees Position of 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc (#1) relative to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates: Matrix rotation and translation 0.72103666 -0.69289691 0.00005690 200.98869703 0.69289010 0.72102993 0.00437570 -86.24757234 -0.00307294 -0.00311561 0.99999042 0.59133203 Axis -0.00540573 0.00225849 0.99998284 Axis point 207.60609202 206.48162074 0.00000000 Rotation angle (degrees) 43.86053881 Shift along axis -0.68995794 > volume #2 level 0.1202 > lighting soft > set bgColor white > volume #2 level 0.2083 > fitmap #1 inMap #2 Fit map 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc in map 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 81884 points correlation = 0.9558, correlation about mean = 0.7505, overlap = 1.159e+04 steps = 40, shift = 0.00345, angle = 0.00653 degrees Position of 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc (#1) relative to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates: Matrix rotation and translation 0.72108006 -0.69285173 0.00014459 200.95025525 0.69284476 0.72107372 0.00433882 -86.23782963 -0.00311042 -0.00302846 0.99999058 0.57786141 Axis -0.00531658 0.00234896 0.99998311 Axis point 207.58433723 206.46143216 0.00000000 Rotation angle (degrees) 43.85692728 Shift along axis -0.69308527 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 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 > hide #!2 models > show #!2 models > hide #!2 models > volume #2 level 0.22 > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > surface dust #2 size 10.3 [Repeated 1 time(s)] > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > volume #3 level 0.22 > volume #3 step 1 > hide #!1 models > show #!2 models > hide #!3 models > volume #2 level 0.1847 > surface dust #2 size 10.3 [Repeated 1 time(s)] > ui tool show ""Hide Dust"" > surface dust #2 size 1.03 > surface dust #2 size 1.09 > surface dust #2 size 1.6 [Repeated 1 time(s)] > surface dust #2 size 1.5 > surface dust #2 size 5.28 [Repeated 1 time(s)] > surface dust #2 size 5.46 > surface dust #2 size 13.76 > surface dust #2 size 10 [Repeated 1 time(s)] > volume #2 level 0.2 > volume #2 level 0.201 > volume #2 level 0.2 > volume #2 level 0.205 > volume #2 level 0.209 > volume #2 level 0.22 > volume #2 level 0.2 > volume #2 level 0.18 > volume #2 level 0.19 > volume #2 level 0.1 > volume #2 level 0.15 > volume #2 level 0.16 > volume #2 level 0.17 > volume #2 level 0.19 > volume #2 level 0.2 > show #!3 models > select add #3 2 models selected > view matrix models > #3,0.67263,0.70376,0.22866,-129.08,0.72859,-0.68387,-0.038439,212.71,0.12933,0.19246,-0.97275,349.38 > view matrix models > #3,0.090582,0.90746,0.41025,-86.538,0.99416,-0.10667,0.016445,20.574,0.058685,0.40636,-0.91182,305.78 > view matrix models > #3,0.0053953,0.99627,0.086076,-18.574,0.99998,-0.0056737,0.0029901,0.55108,0.0034673,0.086058,-0.99628,404.11 > view matrix models > #3,0.12784,0.98971,0.064272,-38.772,0.99172,-0.12837,0.0041183,28.357,0.012326,0.063213,-0.99792,407.45 > fitmap #3 inMap #2 Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 105956 points correlation = 0.4032, correlation about mean = 0.05819, overlap = 4262 steps = 164, shift = 2.58, angle = 10.1 degrees Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates: Matrix rotation and translation -0.46454226 0.88503527 -0.03021685 124.58564296 0.88539497 0.46483037 0.00290874 -75.39081319 0.01662005 -0.02540261 -0.99953913 424.06340972 Axis -0.51729269 -0.85578331 0.00657234 Axis point 81.68795033 0.00000000 212.75016737 Rotation angle (degrees) 178.43190949 Shift along axis 2.85804462 > show #!1 models > hide #!2 models > select clear > select subtract #3 Nothing selected > select add #3 2 models selected > view matrix models > #3,0.10598,0.9943,-0.011975,-20.206,0.99432,-0.10608,-0.0081687,22.594,-0.0093924,-0.011041,-0.99989,427.34 > fitmap #3 inMap #1 Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc using 105956 points correlation = 0.395, correlation about mean = 0.08193, overlap = 4058 steps = 180, shift = 2.14, angle = 10.6 degrees Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative to 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc (#1) coordinates: Matrix rotation and translation 0.28424491 0.95867659 -0.01200103 -50.89752473 0.95853292 -0.28389039 0.02491736 61.68796215 0.02048071 -0.01858601 -0.99961747 422.50869425 Axis -0.80128428 -0.59827795 -0.00264617 Axis point 0.00000000 53.42444368 210.80184256 Rotation angle (degrees) 178.44445594 Shift along axis 2.75881144 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.28479,0.95851,-0.012008,-45.119,0.95837,-0.28444,0.02472,59.144,0.020279,-0.018548,-0.99962,423.37 > fitmap #3 inMap #1 Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc using 105956 points correlation = 0.3936, correlation about mean = 0.09039, overlap = 4063 steps = 116, shift = 2.17, angle = 2.59 degrees Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative to 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc (#1) coordinates: Matrix rotation and translation 0.29774158 0.95454612 0.01384345 -53.74675777 0.95463380 -0.29763152 -0.00947480 70.54085059 -0.00492389 0.01603647 -0.99985928 420.08974848 Axis 0.80551150 0.59257367 0.00276843 Axis point 0.00000000 52.97504125 210.48490537 Rotation angle (degrees) 179.09265783 Shift along axis -0.32999286 > view matrix models > #3,0.29829,0.95438,0.013817,-54.211,0.95446,-0.29818,-0.0096868,73.551,-0.005125,0.016077,-0.99986,424.15 > view matrix models > #3,0.29829,0.95438,0.013817,-55.606,0.95446,-0.29818,-0.0096868,74.218,-0.005125,0.016077,-0.99986,424.22 > fitmap #3 inMap #1 Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc using 105956 points correlation = 0.7444, correlation about mean = 0.4384, overlap = 1.063e+04 steps = 56, shift = 1.35, angle = 1.67 degrees Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative to 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc (#1) coordinates: Matrix rotation and translation 0.32035097 0.94729415 0.00300724 -56.17053089 0.94728987 -0.32036018 0.00335510 76.28573060 0.00414167 0.00177391 -0.99998985 425.49648100 Axis -0.81251176 -0.58294065 -0.00220026 Axis point 0.00000000 58.42016887 212.80141511 Rotation angle (degrees) 179.94424980 Shift along axis 0.23295894 > hide #!3 models > show #!2 models > show #!3 models > select subtract #3 Nothing selected > select add #2 2 models selected > select subtract #2 Nothing selected > hide #!1 models > fitmap #2 inMap #3 Fit map 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc in map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc using 102847 points correlation = 0.7803, correlation about mean = 0.4458, overlap = 1.145e+04 steps = 48, shift = 0.173, angle = 0.039 degrees Position of 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) relative to 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) coordinates: Matrix rotation and translation -0.42483714 0.90526980 -0.00001636 107.44748660 0.90526980 0.42483714 0.00007650 -68.27029075 0.00007620 0.00001770 -1.00000000 426.17304121 Axis -0.53626559 -0.84404930 -0.00004244 Axis point 75.40454102 0.00000000 213.08998179 Rotation angle (degrees) 179.99685841 Shift along axis -0.01498541 > show #!1 models > hide #!2 models > fitmap #1 inMap #3 Fit map 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc in map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc using 81884 points correlation = 0.7811, correlation about mean = 0.4261, overlap = 1.012e+04 steps = 40, shift = 0.0259, angle = 0.0171 degrees Position of 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc (#1) relative to 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) coordinates: Matrix rotation and translation 0.32028343 0.94731170 0.00436808 -56.06305096 0.94731730 -0.32029267 0.00159397 76.90062542 0.00290905 0.00362744 -0.99998919 425.34770344 Axis 0.81249099 0.58296944 0.00223865 Axis point -0.00000000 58.39940114 212.78064492 Rotation angle (degrees) 179.92830103 Shift along axis 0.23219609 > hide #!3 models > show #!3 models > fitmap #1 inMap #3 Fit map 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc in map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc using 81884 points correlation = 0.7811, correlation about mean = 0.4259, overlap = 1.012e+04 steps = 44, shift = 0.0153, angle = 0.00548 degrees Position of 301_02Fab_GT11_RM20A3_J329_map_sharp_3.2A.mrc (#1) relative to 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) coordinates: Matrix rotation and translation 0.32026654 0.94731754 0.00433953 -56.05470088 0.94732278 -0.32027602 0.00168360 76.89189165 0.00298475 0.00357173 -0.99998917 425.34487757 Axis 0.81248581 0.58297661 0.00225313 Axis point 0.00000000 58.40411956 212.77760327 Rotation angle (degrees) 179.93342543 Shift along axis 0.24088441 > hide #!1 models > show #!2 models > surface dust #2 size 10.3 > surface dust #3 size 10.3 > ui tool show ""Fit in Map"" > fitmap #3 inMap #2 Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 105956 points correlation = 0.7771, correlation about mean = 0.4363, overlap = 1.159e+04 steps = 40, shift = 0.0225, angle = 0.0453 degrees Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates: Matrix rotation and translation -0.42413851 0.90559733 -0.00007474 107.24333558 0.90559733 0.42413850 -0.00006687 -68.15706733 -0.00002885 -0.00009605 -0.99999999 426.22092767 Axis -0.53659058 -0.84384273 0.00001895 Axis point 75.28840961 0.00000000 213.11056241 Rotation angle (degrees) 179.99844201 Shift along axis -0.02384081 > fitmap #3 inMap #2 Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 105956 points correlation = 0.7766, correlation about mean = 0.4362, overlap = 1.16e+04 steps = 28, shift = 0.016, angle = 0.0129 degrees Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates: Matrix rotation and translation -0.42419054 0.90557295 -0.00002206 107.24376704 0.90557294 0.42419054 0.00014393 -68.21540991 0.00013969 0.00004108 -0.99999999 426.14533600 Axis -0.53656720 -0.84385759 -0.00006313 Axis point 75.29718197 0.00000000 213.07826444 Rotation angle (degrees) 179.99450876 Shift along axis -0.00629711 > fitmap #3 inMap #2 Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 105956 points correlation = 0.7767, correlation about mean = 0.4363, overlap = 1.16e+04 steps = 44, shift = 0.00763, angle = 0.00962 degrees Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates: Matrix rotation and translation -0.42415723 0.90558856 0.00005023 107.22521538 0.90558856 0.42415723 -0.00000315 -68.18250636 -0.00002416 0.00004415 -1.00000000 426.18239974 Axis 0.53658381 0.84384703 -0.00000594 Axis point 75.29605323 0.00000000 213.08955957 Rotation angle (degrees) 179.99747437 Shift along axis -0.00282250 > fitmap #3 inMap #2 Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 105956 points correlation = 0.7774, correlation about mean = 0.4363, overlap = 1.157e+04 steps = 44, shift = 0.0177, angle = 0.00397 degrees Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates: Matrix rotation and translation -0.42409701 0.90561676 0.00006090 107.20311177 0.90561676 0.42409701 0.00001301 -68.17909308 -0.00001404 0.00006067 -0.99999999 426.19455771 Axis 0.53661186 0.84382920 0.00000388 Axis point 75.28554877 0.00000000 213.09602508 Rotation angle (degrees) 179.99745575 Shift along axis -0.00339605 > fitmap #3 inMap #2 Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 105956 points correlation = 0.7774, correlation about mean = 0.4363, overlap = 1.157e+04 steps = 44, shift = 0.00443, angle = 0.00847 degrees Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates: Matrix rotation and translation -0.42411817 0.90560685 -0.00008466 107.23870306 0.90560685 0.42411817 0.00000227 -68.17491613 0.00003796 -0.00007571 -0.99999999 426.21268790 Axis -0.53660081 -0.84383622 0.00001079 Axis point 75.28660753 0.00000000 213.10821664 Rotation angle (degrees) 179.99583688 Shift along axis -0.01131451 > select add #3 2 models selected > view matrix models > #3,0.32165,0.94686,0.0028615,-56.803,0.94685,-0.32165,0.0032496,77.252,0.0039973,0.0016642,-0.99999,424.24 > view matrix models > #3,0.32165,0.94686,0.0028615,-56.863,0.94685,-0.32165,0.0032496,76.477,0.0039973,0.0016642,-0.99999,425.05 > fitmap #3 inMap #2 Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 105956 points correlation = 0.7772, correlation about mean = 0.4363, overlap = 1.158e+04 steps = 52, shift = 0.764, angle = 0.00805 degrees Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates: Matrix rotation and translation -0.42412997 0.90560133 0.00003263 107.21681880 0.90560132 0.42412996 0.00007863 -68.19754869 0.00005737 0.00006290 -0.99999999 426.17522111 Axis -0.53659352 -0.84384085 -0.00009632 Axis point 75.28977250 0.00000000 213.09196817 Rotation angle (degrees) 179.99916032 Shift along axis -0.02502133 > fitmap #3 inMap #2 Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 105956 points correlation = 0.7768, correlation about mean = 0.4363, overlap = 1.159e+04 steps = 40, shift = 0.0142, angle = 0.00614 degrees Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates: Matrix rotation and translation -0.42414492 0.90559432 -0.00006281 107.24888311 0.90559432 0.42414493 0.00003275 -68.18644325 0.00005630 -0.00004299 -0.99999999 426.18590942 Axis -0.53658833 -0.84384416 -0.00000826 Axis point 75.29491885 0.00000000 213.09553069 Rotation angle (degrees) 179.99595654 Shift along axis -0.01328821 > fitmap #3 inMap #2 Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 105956 points correlation = 0.7767, correlation about mean = 0.4362, overlap = 1.16e+04 steps = 40, shift = 0.00779, angle = 0.00363 degrees Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates: Matrix rotation and translation -0.42417025 0.90558246 -0.00004143 107.24472659 0.90558245 0.42417025 0.00008541 -68.20089090 0.00009492 -0.00000129 -0.99999999 426.16706978 Axis -0.53657659 -0.84385162 -0.00003479 Axis point 75.29547795 0.00000000 213.08750754 Rotation angle (degrees) 179.99537094 Shift along axis -0.00840261 > fitmap #3 inMap #2 Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 105956 points correlation = 0.7773, correlation about mean = 0.4363, overlap = 1.158e+04 steps = 44, shift = 0.016, angle = 0.00412 degrees Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates: Matrix rotation and translation -0.42413018 0.90560122 -0.00006698 107.24002872 0.90560122 0.42413019 0.00003482 -68.18614701 0.00005994 -0.00004589 -0.99999999 426.19939305 Axis -0.53659523 -0.84383977 -0.00000732 Axis point 75.29020325 0.00000000 213.10238152 Rotation angle (degrees) 179.99569100 Shift along axis -0.00942393 > fitmap #3 inMap #2 Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 105956 points correlation = 0.7773, correlation about mean = 0.4363, overlap = 1.157e+04 steps = 44, shift = 0.00344, angle = 0.0033 degrees Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates: Matrix rotation and translation -0.42412314 0.90560452 -0.00006372 107.23622514 0.90560452 0.42412314 -0.00002210 -68.17686328 0.00000701 -0.00006708 -0.99999999 426.21518166 Axis -0.53659816 -0.84383791 0.00000741 Axis point 75.28971970 0.00000000 213.10862322 Rotation angle (degrees) 179.99759853 Shift along axis -0.00938304 > fitmap #3 inMap #2 Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 105956 points correlation = 0.7768, correlation about mean = 0.4362, overlap = 1.159e+04 steps = 40, shift = 0.0182, angle = 0.00179 degrees Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates: Matrix rotation and translation -0.42414966 0.90559210 -0.00006928 107.25092542 0.90559210 0.42414966 -0.00001300 -68.17191484 0.00001762 -0.00006825 -0.99999999 426.19881611 Axis -0.53658595 -0.84384567 0.00000859 Axis point 75.29359494 0.00000000 213.10069686 Rotation angle (degrees) 179.99704981 Shift along axis -0.01910210 > fitmap #3 inMap #2 Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 105956 points correlation = 0.7769, correlation about mean = 0.4363, overlap = 1.159e+04 steps = 40, shift = 0.0101, angle = 0.00298 degrees Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates: Matrix rotation and translation -0.42416360 0.90558557 -0.00008804 107.25194691 0.90558557 0.42416360 0.00003300 -68.19000892 0.00006723 -0.00006573 -0.99999999 426.18961038 Axis -0.53657974 -0.84384962 0.00000103 Axis point 75.29439134 0.00000000 213.09768660 Rotation angle (degrees) 179.99472882 Shift along axis -0.00666800 > fitmap #3 inMap #2 Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 105956 points correlation = 0.777, correlation about mean = 0.4363, overlap = 1.159e+04 steps = 40, shift = 0.0123, angle = 0.0085 degrees Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates: Matrix rotation and translation -0.42413291 0.90559995 0.00004920 107.21522113 0.90559995 0.42413291 0.00007821 -68.20736376 0.00004996 0.00007772 -0.99999999 426.16800583 Axis -0.53652100 -0.84388504 -0.00180371 Axis point 75.28982105 0.00000000 213.15691001 Rotation angle (degrees) 179.99997402 Shift along axis -0.73272608 > fitmap #3 inMap #2 Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 105956 points correlation = 0.7765, correlation about mean = 0.4362, overlap = 1.161e+04 steps = 24, shift = 0.0212, angle = 0.00772 degrees Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates: Matrix rotation and translation -0.42419484 0.90557094 -0.00006576 107.25563594 0.90557093 0.42419484 0.00009474 -68.20119474 0.00011369 -0.00001936 -0.99999999 426.16157095 Axis -0.53656523 -0.84385885 -0.00002983 Axis point 75.29716123 0.00000000 213.08536916 Rotation angle (degrees) 179.99390807 Shift along axis -0.01017496 > fitmap #3 inMap #2 Fit map 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc in map 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc using 105956 points correlation = 0.7774, correlation about mean = 0.4363, overlap = 1.157e+04 steps = 36, shift = 0.0233, angle = 0.00882 degrees Position of 301_46FAB_GT1-1_RM20A3_J311_C3_map_sharp_2.96A.mrc (#3) relative to 301_06FAB_GT11_RM20A3_J333_C3_map_sharp_3.14A.mrc (#2) coordinates: Matrix rotation and translation -0.42409073 0.90561970 -0.00008804 107.22896438 0.90561970 0.42409073 -0.00000517 -68.17397669 0.00003265 -0.00008193 -0.99999999 426.21410292 Axis -0.53661358 -0.84382810 0.00001466 Axis point 75.28230841 0.00000000 213.10873106 Rotation angle (degrees) 179.99590239 Shift along axis -0.00715236 [deleted to fit within ticket limits] > color #1 #54164eff > color #1 #671b60ff > color #1 #7f2175ff > color #1 #a02a94ff > color #1 #c333b5ff > color #1 #d036c0ff > color #1 #ce36bfff > color #1 #c533b6ff > color #1 #b02ea3ff > color #1 #8d2583ff > color #1 #6a1c63ff > color #1 #591752ff > color #1 #52154cff > color #1 #51154bff > color #1 #53164dff > color #1 #6a1c62ff > color #1 #7b2072ff > color #1 #98288dff > color #1 #c032b2ff > color #1 #c834baff > color #1 #cf36bfff > color #1 #3036bfff > color #1 #3029bfff > color #1 #30295dff > color #1 #332c64ff > color #1 #39316eff > color #1 #3a3271ff > color #1 #3c3374ff > color #1 #3e3578ff > color #1 #40377cff > color #1 #41387eff > color #1 #423880ff > color #1 #443a84ff > color #1 #443a85ff > color #1 #453b86ff > color #1 #453b87ff > color #1 #463c88ff > color #1 #473c89ff > color #1 #473d8aff > color #1 #483e8cff > color #1 #493f8eff > color #1 #4a3f90ff > color #1 #4b4092ff > color #1 #4d4296ff > color #1 #4f4499ff > color #1 #51459cff > color #1 #5347a1ff > color #1 #5548a4ff > color #1 #5549a6ff > color #1 #574ba9ff > color #1 #584babff > color #1 #594cacff > color #1 #5a4dafff > color #1 #5b4eb1ff > color #1 #5c4eb2ff > color #1 #5c4fb3ff > color #1 #5d4fb4ff > color #1 #5e50b6ff > color #1 #5e51b7ff > color #1 #6053bbff > color #1 #6153bdff > color #1 #6254beff > color #1 #6355c0ff > color #1 #6556c3ff > color #1 #6557c4ff > color #1 #6758c7ff > color #1 #6758c8ff > color #1 #6859caff > color #1 #695accff > color #1 #6a5acdff > color #1 #6a5bceff > color #1 #6a5bcfff > color #1 #6b5cd0ff > color #1 #6c5cd1ff > color #1 #6c5dd2ff > color #1 #6d5dd3ff > color #1 #6d5dd4ff > color #1 #6e5ed5ff > color #1 #6e5ed6ff > color #1 #6f5fd7ff > color #1 #6f5fd8ff > color #1 #7060d9ff > color #1 #7060daff > color #1 #7160daff > color #1 #7161dbff > color #1 #7261ddff > color #1 #7262ddff > color #1 #7262deff > color #1 #7362dfff > color #1 #7363e0ff > color #1 #7463e1ff > color #1 #7464e2ff > color #1 #7564e3ff > color #1 #7564e4ff > color #1 #7665e4ff > color #1 #7665e5ff > color #1 #7766e7ff > color #1 #7766e8ff > color #1 #7867e9ff > color #1 #7967eaff > color #1 #7968ebff > color #1 #7968ecff > color #1 #7a68ecff > color #1 #7a69edff > color #1 #7b69eeff > color #1 #7b69efff > color #1 #7b6aefff > color #1 #7c6af0ff > color #1 #7c6af1ff > color #1 #7d6bf3ff > color #1 #7e6cf5ff > color #1 #7f6df6ff > color #1 #806df8ff > color #1 #816efaff > color #1 #826ffcff > color #1 #826ffdff > color #1 #8370feff > color #1 #8370ffff > select #7 /L 762 atoms, 780 bonds, 101 residues, 1 model selected > ui windowfill toggle > select #7 /L 762 atoms, 780 bonds, 101 residues, 1 model selected > select up 21175 atoms, 21715 bonds, 2672 residues, 1 model selected > select up 145807 atoms, 149542 bonds, 18287 residues, 18 models selected > select up 145807 atoms, 149542 bonds, 18287 residues, 18 models selected > select up 145807 atoms, 149542 bonds, 18287 residues, 18 models selected > select clear > hide #!1 models > show #!7 models > color zone #1 near #7 distance 5 > show #!1 models > hide #!1 models > color #!7 bychain > color #7 /A,B,C,D,E,F gray > color #7 /G,I,O,Q,M,J darkslategray > color zone #1 near #7 distance 5 > show #!1 models > color zone #1 near #7 distance 4.62 > color zone #1 near #7 distance 11.89 > color zone #1 near #7 distance 4.7 > color zone #1 near #7 distance 7.61 > color zone #1 near #7 distance 5 > hide #!1 models > show #!1 models > hide #!7 models > color (:NAG, NAM, BMA) lavender > color zone #1 near #7 distance 5 > ui tool show ""Color Actions"" > color (:NAG, NAM, BMA) voilet Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color (:NAG, NAM, BMA) violet > color zone #1 near #7 distance 5 > color (:NAG, NAM, BMA) lavender > color zone #1 near #7 distance 5 > select ~sel & ##selected Nothing selected > color (:NAG, NAM, BMA) #E6E6FA > color zone #1 near #7 distance 5 > select ~sel & ##selected Nothing selected > color (:NAG, NAM, BMA) violet > color zone #1 near #7 distance 5 > color (:NAG, NAM, BMA) magenta > color zone #1 near #7 distance 5 > color (:NAG, NAM, BMA) pink > color zone #1 near #7 distance 5 > color (:NAG, NAM, BMA) lavender > color zone #1 near #7 distance 5 > color (:NAG, NAM, BMA) magenta > color zone #1 near #7 distance 5 > select ~sel & ##selected Nothing selected > color (:NAG, NAM, BMA) pink > color zone #1 near #7 distance 5 > color #7 /H yellowgreen > color #7 /H olivegreen Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #7 /H olive > color #7 /H yellowgreen > color #7 /L greenyellow > color zone #1 near #7 distance 5 > color #7 /H olive > color zone #1 near #7 distance 5 > color #7 /H green > color zone #1 near #7 distance 5 > color #7 /H chartreuse > color zone #1 near #7 distance 5 > color #7 /H green > color #7 /L chartreuse > color zone #1 near #7 distance 5 > color #7 /H green > color zone #1 near #7 distance 5 > ui tool show ""Side View"" > view name top > view list Named views: top > view top > lighting soft > lighting full > lighting soft > lighting simple > color zone #1 near #7 distance 5.09 > color zone #1 near #7 distance 6.11 > lighting soft > lighting full > set bgColor gray > set bgColor #80808000 > set bgColor black > set bgColor transparent > lighting soft > lighting full > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting full > lighting shadows false > lighting shadows true > set bgColor white > set bgColor #ffffff00 > lighting simple > lighting soft > lighting flat > lighting shadows true intensity 0.5 > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > lighting soft > graphics silhouettes false > 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 Unsupported scale factor (0.000000) detected on Display0 QPainter::begin: Paint device returned engine == 0, type: 2 QPainter::translate: Painter not active QPainter::setPen: Painter not active QPainter::setBrush: Painter not active QPainter::drawPoints: Painter not active QPainter::end: Painter not active, aborted QPainter::begin: Paint device returned engine == 0, type: 2 QPainter::translate: Painter not active QPainter::setPen: Painter not active QPainter::setBrush: Painter not active QPainter::drawPoints: Painter not active QPainter::end: Painter not active, aborted Unsupported scale factor (0.000000) detected on Display0 > view name top > show #!2 models > hide #!1 models > show #!8 models > color zone #2 near #8 distance 6.2 > hide #!8 models > show #!8 models > volume #2 level 0.21 > hide #!8 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > view top > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!2 models > show #!8 models > select #8 /A,B,C,D,E,F 14085 atoms, 14370 bonds, 15 pseudobonds, 1740 residues, 2 models selected > select #8 24630 atoms, 25167 bonds, 15 pseudobonds, 3123 residues, 2 models selected > color sel bychain > select clear > select #8 /C 3656 atoms, 3733 bonds, 4 pseudobonds, 452 residues, 2 models selected > select #8 /D 1039 atoms, 1057 bonds, 1 pseudobond, 128 residues, 2 models selected > select #8 /E 3656 atoms, 3733 bonds, 4 pseudobonds, 452 residues, 2 models selected > select #8 /F 1039 atoms, 1057 bonds, 1 pseudobond, 128 residues, 2 models selected > select #8 /A,B,C,D,E,F 14085 atoms, 14370 bonds, 15 pseudobonds, 1740 residues, 2 models selected > color #8 /A,B,C,D,E,F gray > select clear > color #8 /G,I,O,Q,M,J darkslategray > select #8 /H 1022 atoms, 1050 bonds, 128 residues, 1 model selected > select clear > color #8 /A,B,C,D,E,F gray > color #8 /G,I,O,Q,M,J darkslategray > color (:NAG, NAM, BMA) pink > color #8 /N,L,R teal > color #8 /H,K,P navy > color zone #2 near #8 distance 6.2 > show #!2 models > show #!1 models > hide #!2 models > show #!2 models > hide #!8 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!1 models > show #!1 models > view list Named views: top > view top > show #!2 models > hide #!1 models > view name front > ui tool show Log > view list Named views: front, top > view top > save /Users/sphulera/Desktop/HVTN301/Map_session_042325.cxs > ui tool show ""Show Volume Menu"" > ui tool show ""Volume Viewer"" > volume #2 level 0.215 > volume #2 level 0.216 > volume #2 level 0.217 > volume #2 level 0.218 > volume #2 level 0.219 > volume #2 level 0.22 > volume #2 level 0.225 > volume #1 level 0.225 > volume #2 level 0.22 > volume #2 level 0.221 > volume #2 level 0.222 > view front > view top > view name top > view list Named views: front, top > view front > view top > ui tool show ""Model Panel"" > show #!9 models > hide #!3 models > show #!3 models > hide #!3 models > color #9 /A,B,C,D,E,F gray > color #9 /G,I,O,Q,M,J darkslategray > color (:NAG, NAM, BMA) pink > color #9 /N,L,R maroon > color #9 /H,K,P brown > ui tool show ""Color Actions"" > color #9 /H,K,P #9A6324 > color #9 /N,L,R #800000 > ui tool show ""Color Zone"" > color zone #1 near #9 distance 1.03 > color zone #3 near #9 distance 6.2 > show #!3 models > hide #!9 models > show #!2 models > show #!1 models > hide #!2 models > hide #!3 models > show #!4 models > hide #!4 models > show #!3 models > show #!2 models > hide #!2 models > hide #!1 models > show #!2 models > hide #!3 models > show #!1 models > hide #!2 models > color zone #1 near #7 distance 1.03 > show #!7 models > hide #!1 models > color zone #1 near #7 distance 1.04 > color zone #1 near #7 distance 3.51 > show #!1 models > show #!2 models > hide #!1 models > hide #!7 models > show #!3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!1 models > show #!2 models > hide #!2 models > hide #!3 models > show #!2 models > hide #!1 models > show #!3 models > hide #!2 models > volume #3 level 0.22 > color #9 /H,K,P #800000 > color zone #3 near #9 distance 6.34 > color zone #3 near #9 distance 4.79 > color #9 /N,L,R #9A6324 > color zone #3 near #9 distance 4.79 > color #9 /H,K,P maroon > color #9 /N,L,R brown > color zone #3 near #9 distance 4.79 > color #9 /N,L,R #9A6324 > color zone #3 near #9 distance 4.79 > volume #3 level 0.225 > volume #3 level 0.229 > volume #3 level 0.23 > ui tool show ""Hide Dust"" > surface dust #3 size 1.03 > surface dust #3 size 1.07 > surface dust #3 size 14.5 > show #!2 models > hide #!3 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > show #!3 models > hide #!2 models > view top > view front > show #!2 models > hide #!3 models > show #!1 models > hide #!2 models > ui tool show ""Side View"" > show #!2 models > hide #!1 models > show #!3 models > hide #!2 models > view name top > show #!1 models > hide #!3 models > color #9 /H,K,P #800000 > color zone #3 near #9 distance 4.79 > show #!3 models > hide #!1 models > show #!1 models > show #!2 models > hide #!1 models > hide #!2 models > hide #!3 models > show #!10 models > color #10 /H,K,P purple > color #10 /H,K,P lavender > color #10 /H,K,P purple > color #10 /N,L,R #dcbeff > color zone #4 near #10 distance 6.2 > show #!4 models > volume #4 level 0.08196 > volume #4 level 0.1 > volume #4 level 0.15 > hide #!10 models > surface dust #4 size 10.3 > surface dust #4 size 10.05 > surface dust #4 size 20.62 > surface dust #4 size 21.28 > surface dust #4 size 115.02 > list view Unknown command: list view > view list Named views: front, top > view front > view top > view front > view top > volume #4 level 0.17 > volume #4 level 0.2 > surface dust #4 size 109.75 > surface dust #4 size 3.14 > surface dust #4 size 10 > surface dust #4 size 10.53 > surface dust #4 size 5.29 > save /Users/sphulera/Desktop/HVTN301/Map_session_042325.cxs > show #!5 models > hide #!4 models > show #!4 models > hide #!4 models > show #!6 models > hide #!6 models > show #!11 models > hide #!11 models > hide #!5 models > show #!1 models > show #!2 models > hide #!1 models > show #!3 models > hide #!2 models > show #!4 models > show #!5 models > hide #!4 models > hide #!3 models > show #!4 models > hide #!5 models > show #!5 models > hide #!4 models > show #!11 models > hide #!5 models > color #11 /A,B,C,D,E,F gray > color #11 /G,I,O,Q,M,J darkslategray > color (:NAG, NAM, BMA) pink > color #11 /N,L,R lime > color #11 /H,K,P green > show #!1 models > hide #!1 models > color #11 /H,K,P blue > color #11 /N,L,R cyan > color zone #5 near #11 distance 5 > show #!5 models > hide #!11 models > show #!1 models > hide #!1 models > show #!2 models > hide #!5 models > show #!11 models > hide #!2 models > ui tool show ""Color Actions"" > show #!1 models > hide #!11 models > show #!2 models > hide #!1 models > show #!3 models > hide #!2 models > show #!4 models > hide #!3 models > show #!5 models > hide #!4 models > show #!6 models > hide #!6 models > show #!4 models > hide #!5 models > show #!3 models > hide #!4 models > show #!2 models > hide #!2 models > show #!5 models > hide #!3 models > color #11 /N,L,R pink > color zone #5 near #11 distance 5 > color #11 /N,L,R deeppink > color zone #5 near #11 distance 5 > color #11 /H,K,P red > color zone #5 near #11 distance 5 > color zone #5 near #11 distance 4.9 > color zone #5 near #11 distance 4.8 > color zone #5 near #11 distance 5 > color #11 /H,K,P #e6194B > color zone #5 near #11 distance 5 > color #11 /N,L,R #fabed4 > color zone #5 near #11 distance 5 > color #11 /H,K,P orange > color zone #5 near #11 distance 5 > color #11 /N,L,R apricot Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #11 /N,L,R #ffd8b1 > color zone #5 near #11 distance 5 > color #11 /H,K,P #f58231 > color zone #5 near #11 distance 5 > show #!2 models > show #!1 models > show #!4 models > show #!3 models > show #!6 models > hide #!5 models > hide #!4 models > hide #!3 models > hide #!2 models > hide #!1 models > show #!1 models > hide #!6 models > show #!2 models > show #!3 models > show #!4 models > hide #!3 models > hide #!2 models > hide #!1 models > show #!5 models > hide #!4 models > color #12 /A,B,C,D,E,F gray > color #12 /G,I,O,Q,M,J darkslategray > color (:NAG, NAM, BMA) pink > color #12 /N,L,R yellow > color #12 /H,K,P beige > color zone #5 near #11 distance 5 > color zone #6 near #12 distance 6.2 > show #!6 models > hide #!5 models > color #12 /A,B,C,D,E,F gray > color #12 /G,I,O,Q,M,J darkslategray > color (:NAG, NAM, BMA) pink > color #12 /N,L,R beige > color #12 /H,K,P yellow > color zone #6 near #12 distance 5 > save /Users/sphulera/Desktop/HVTN301/Map_session_042425.cxs > ui tool show ""Side View"" > view name front > view name top > hide #!6 models > show #!1 models > save /Users/sphulera/Desktop/HVTN301/map_figs/02_top.png width 704 height > 850 supersample 3 transparentBackground true > view name top > save /Users/sphulera/Desktop/HVTN301/map_figs/02_top.png width 1822 height > 850 supersample 3 transparentBackground true > save /Users/sphulera/Desktop/HVTN301/map_figs/02_top.png width 2000 height > 933 supersample 3 > save /Users/sphulera/Desktop/HVTN301/map_figs/02_top.png width 4287 height > 2000 supersample 3 transparentBackground true > ui tool show ""Side View"" > save /Users/sphulera/Desktop/HVTN301/map_figs/02_top.png width 4287 height > 2000 supersample 4 > ui tool show ""Model Panel"" > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > view name top > ui tool show ""Volume Viewer"" > volume #2 level 0.21 > volume #1 level 0.21 > volume #1 level 0.2 > volume #1 level 0.21 > ui tool show ""Surface Zone"" > surface zone #1 nearAtoms #7 distance 7.71 > surface unzone #1 > ui tool show ""Hide Dust"" > surface dust #1 size 6.2 > surface dust #1 size 10 > volume #1 level 0.2195 > volume #1 level 0.2272 > ui tool show ""Color Zone"" > color zone #1 near #7 distance 1.03 > color zone #1 near #7 distance 1.05 > color zone #1 near #7 distance 1.22 > color zone #1 near #7 distance 1.18 > color zone #1 near #7 distance 5.99 > color zone #1 near #7 distance 5 > show #!2 models > hide #!2 models > save /Users/sphulera/Desktop/HVTN301/map_figs/02_top.png width 4287 height > 2000 supersample 4 transparentBackground true > show #!2 models > hide #!1 models > save /Users/sphulera/Desktop/HVTN301/map_figs/06_top.png width 4287 height > 2000 supersample 4 > surface dust #2 size 10.3 > color zone #2 near #7 distance 6.2 > color zone #2 near #8 distance 6.2 > color zone #2 near #8 distance 6.27 > color zone #2 near #8 distance 5.48 > color zone #2 near #8 distance 5 > volume #2 level 0.215 > volume #2 level 0.216 > volume #2 level 0.218 > volume #2 level 0.22 > volume #2 level 0.225 > volume #2 level 0.224 > volume #2 level 0.223 > volume #2 level 0.222 > volume #2 level 0.221 > volume #2 level 0.2215 > volume #2 level 0.2216 > volume #2 level 0.2217 > volume #2 level 0.2218 > volume #2 level 0.2219 > volume #2 level 0.22 > volume #2 level 0.229 > volume #2 level 0.228 > volume #2 level 0.227 > volume #2 level 0.226 > volume #2 level 0.225 > volume #2 level 0.224 > volume #2 level 0.223 > volume #2 level 0.222 > volume #2 level 0.221 > volume #2 level 0.222 > save /Users/sphulera/Desktop/HVTN301/map_figs/06_top.png width 4287 height > 2000 supersample 4 > view name top > show #!3 models > hide #!2 models > volume #3 level 0.22 > volume #3 level 0.21 > volume #3 level 0.215 > volume #3 level 0.216 > save /Users/sphulera/Desktop/HVTN301/map_figs/46_top.png width 4287 height > 2000 supersample 4 > show #!4 models > hide #!3 models > volume #4 level 0.1 > volume #4 level 0.15 > volume #4 level 0.17 > volume #4 level 0.18 > color zone #4 near #10 distance 6.2 > color zone #4 near #10 distance 5 > surface dust #4 size 10 > volume #4 level 0.19 > volume #4 level 0.2 > show #!10 models > hide #!4 models > show #!4 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > volume #4 level 0.21 > volume #4 level 0.215 > volume #4 color darkgrey > color zone #4 near #10 distance 5 > volume #4 level 0.2 > save /Users/sphulera/Desktop/HVTN301/map_figs/48_top.png width 4287 height > 2000 supersample 4 > show #!6 models > hide #!5 models > show #!5 models > hide #!6 models > volume #5 level 0.2 > volume #5 level 0.21 > volume #5 level 0.212 > ui tool show ""Side View"" > color zone #5 near #11 distance 5 > color zone #5 near #11 distance 5.1 > color zone #5 near #11 distance 5.2 > color zone #5 near #11 distance 5.3 > color zone #5 near #11 distance 5.4 > color zone #5 near #11 distance 5.5 > color zone #5 near #11 distance 5.6 > color zone #5 near #11 distance 5.7 > color zone #5 near #11 distance 5.8 > color zone #5 near #11 distance 5.9 > color zone #5 near #11 distance 6 > color zone #5 near #11 distance 6.1 > color zone #5 near #11 distance 6.2 > color zone #5 near #11 distance 6.3 > color zone #5 near #11 distance 6.32 > color zone #5 near #11 distance 6.76 > color zone #5 near #11 distance 12.55 > color zone #5 near #11 distance 5 > volume #5 color #ff9300 > color #11 /A,B,C,D,E,F gray > color #11 /G,I,O,Q,M,J darkslategray > color (:NAG, NAM, BMA) pink > color #11 /N,L,R #ffd8b1 > color #11 /H,K,P #f58231 > color zone #5 near #11 distance 5 > save /Users/sphulera/Desktop/HVTN301/map_figs/56_top.png width 4369 height > 2000 supersample 4 transparentBackground true > hide #!5 models > show #!2 models > save /Users/sphulera/Desktop/HVTN301/map_figs/06_top.png width 4369 height > 2000 supersample 4 transparentBackground true > show #!3 models > hide #!2 models > save /Users/sphulera/Desktop/HVTN301/map_figs/46_top.png width 4369 height > 2000 supersample 4 transparentBackground true > show #!4 models > hide #!3 models > save /Users/sphulera/Desktop/HVTN301/map_figs/48_top.png width 4369 height > 2000 supersample 4 transparentBackground true > show #!5 models > hide #!4 models > show #!6 models > hide #!5 models > save /Users/sphulera/Desktop/HVTN301/map_figs/61_top.png width 4369 height > 2000 supersample 4 transparentBackground true > save /Users/sphulera/Desktop/HVTN301/Map_session_top_042425.cxs > ui tool show Log > view list Named views: front, top > view front > show #!1 models > hide #!6 models > show #!2 models > show #!3 models > show #!4 models > show #!5 models > show #!6 models > hide #!6 models > hide #!5 models > hide #!4 models > show #!4 models > hide #!3 models > hide #!2 models > hide #!1 models > show #!5 models > hide #!4 models > color #11 /A,B,C,D,E,F gray > color #11 /G,I,O,Q,M,J darkslategray > color (:NAG, NAM, BMA) pink > color #11 /N,L,R #ffd8b1 > color #11 /H,K,P #f58231 > color zone #5 near #11 distance 5 > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!3 models > hide #!3 models > show #!4 models > hide #!5 models > show #!5 models > hide #!5 models > show #!2 models > hide #!2 models > color #10 /A,B,C,D,E,F gray > color #10 /G,I,O,Q,M,J darkslategray > color (:NAG, NAM, BMA) pink > color #10 /N,L,R #dcbeff > color #10 /H,K,P #purple Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color zone #4 near #10 distance 5 > show #!3 models > show #!2 models > show #!1 models > show #!5 models > show #!6 models > show #!7 models > show #!8 models > show #!9 models > show #!10 models > hide #!10 models > hide #!9 models > hide #!8 models > hide #!7 models > view top > hide #!5 models > hide #!6 models > hide #!3 models > hide #!2 models > hide #!1 models > save /Users/sphulera/Desktop/HVTN301/map_figs/48_top.png width 4369 height > 2000 supersample 4 transparentBackground true > view front > show #!1 models > hide #!4 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > view name front ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M3 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 Air Model Identifier: Mac15,12 Model Number: Z1B600163LL/A Chip: Apple M3 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 11881.101.1 OS Loader Version: 11881.101.1 Software: System Software Overview: System Version: macOS 15.4 (24E248) Kernel Version: Darwin 24.4.0 Time since boot: 16 days, 2 hours, 34 minutes Graphics/Displays: Apple M3: Chipset Model: Apple M3 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal LG HDR 4K: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX