id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18008 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. 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swapped_out=88.6M(3%) unallocated=3.3G(97%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG image 1120K 54 \nColorSync 656K 33 \nCoreAnimation 2784K 142 \nCoreGraphics 96K 6 \nCoreUI image data 5584K 44 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 2.7G 159 \nMALLOC guard page 288K 18 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 544K 34 \nStack 190.7M 35 \nStack Guard 56.0M 1 \nVM_ALLOCATE 259.0M 389 \nVM_ALLOCATE (reserved) 160.0M 1 reserved VM address space (unallocated)\n__AUTH 5521K 698 \n__AUTH_CONST 77.4M 945 \n__CTF 824 1 \n__DATA 34.2M 1085 \n__DATA_CONST 36.9M 1103 \n__DATA_DIRTY 2778K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 646.5M 152 \n__OBJC_RO 61.4M 1 \n__OBJC_RW 2396K 1 \n__TEXT 1.3G 1122 \n__TEXT (graphics) 192K 1 \n__TPRO_CONST 128K 2 \ndyld private memory 2848K 25 \nmapped file 613.8M 101 \npage table in kernel 2265K 1 \nshared memory 3184K 25 \n=========== ======= ======= \nTOTAL 6.2G 6538 \nTOTAL, minus reserved VM space 6.0G 6538 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""c6fa742e92c9422c8ba77390c157418c29e1ebc8"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""64c17a9925d75a7281053d4c"", ""factorPackIds"" : { ""SIRI_AUDIO_DISABLE_MEDIA_ENTITY_SYNC"" : ""64d29746ad29a465b3bbeace"" }, ""deploymentId"" : 240000002 }, { ""rolloutId"" : ""60f8ddccefea4203d95cbeef"", ""factorPackIds"" : { }, ""deploymentId"" : 240000025 } ], ""experiments"" : [ { ""treatmentId"" : ""d5322b03-2bc4-481a-817e-3640bda0eeee"", ""experimentId"" : ""67f4692f84eaf455d73c6090"", ""deploymentId"" : 400000001 }, { ""treatmentId"" : ""f18344bb-554f-48ae-8449-e108a8813a55"", ""experimentId"" : ""6685b5584477001000e8c6c9"", ""deploymentId"" : 400000009 } ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/yoojoong/Downloads/cryosparc_P18_J521_class_00_00006_volume.mrc Opened cryosparc_P18_J521_class_00_00006_volume.mrc as #1, grid size 192,192,192, pixel 1.46, shown at level 0.0398, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J521_class_01_00006_volume.mrc Opened cryosparc_P18_J521_class_01_00006_volume.mrc as #2, grid size 192,192,192, pixel 1.46, shown at level 0.0395, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J521_class_02_00006_volume.mrc Opened cryosparc_P18_J521_class_02_00006_volume.mrc as #3, grid size 192,192,192, pixel 1.46, shown at level 0.0397, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J521_class_03_00006_volume.mrc Opened cryosparc_P18_J521_class_03_00006_volume.mrc as #4, grid size 192,192,192, pixel 1.46, shown at level 0.0398, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J521_class_04_00006_volume.mrc Opened cryosparc_P18_J521_class_04_00006_volume.mrc as #5, grid size 192,192,192, pixel 1.46, shown at level 0.04, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J521_class_05_00006_volume.mrc Opened cryosparc_P18_J521_class_05_00006_volume.mrc as #6, grid size 192,192,192, pixel 1.46, shown at level 0.0399, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J521_class_06_00006_volume.mrc Opened cryosparc_P18_J521_class_06_00006_volume.mrc as #7, grid size 192,192,192, pixel 1.46, shown at level 0.0396, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J521_class_07_00006_volume.mrc Opened cryosparc_P18_J521_class_07_00006_volume.mrc as #8, grid size 192,192,192, pixel 1.46, shown at level 0.0399, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J521_class_08_00006_volume.mrc Opened cryosparc_P18_J521_class_08_00006_volume.mrc as #9, grid size 192,192,192, pixel 1.46, shown at level 0.0397, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J521_class_09_00006_volume.mrc Opened cryosparc_P18_J521_class_09_00006_volume.mrc as #10, grid size 192,192,192, pixel 1.46, shown at level 0.0397, step 1, values float32 > open > /Users/yoojoong/Library/CloudStorage/Dropbox/1_RothLab/Experiments/Projects/Tas2Rs/TAS2R14/2025/Prog- > TAS2R14/Structure_work/WorkingModels&Maps_SetB-2_J318(best)/WorkingModels/TwoProg- > TAS2R14_J318_J302-0612-2200noLig.pdb Chain information for TwoProg-TAS2R14_J318_J302-0612-2200noLig.pdb #11 --- Chain | Description A | No description available B | No description available C | No description available D | No description available R | No description available > set bgColor white > graphics silhouettes true > fitmap #11 inMap #1 Fit molecule TwoProg-TAS2R14_J318_J302-0612-2200noLig.pdb (#11) to map cryosparc_P18_J521_class_00_00006_volume.mrc (#1) using 8655 atoms average map value = 0.07383, steps = 232 shifted from previous position = 1.04 rotated from previous position = 2.26 degrees atoms outside contour = 1799, contour level = 0.039753 Position of TwoProg-TAS2R14_J318_J302-0612-2200noLig.pdb (#11) relative to cryosparc_P18_J521_class_00_00006_volume.mrc (#1) coordinates: Matrix rotation and translation 0.99937872 0.02123089 -0.02813207 0.56966415 -0.02172968 0.99960993 -0.01754463 5.06877401 0.02774861 0.01814503 0.99945024 -6.09632622 Axis 0.45173112 -0.70729301 -0.54376059 Axis point 220.25876810 0.00000000 15.59142798 Rotation angle (degrees) 2.26395615 Shift along axis -0.01283145 > lighting soft > molmap #11 /R/B/C/D/A 3 Opened TwoProg-TAS2R14_J318_J302-0612-2200noLig.pdb map 3 as #12, grid size 100,128,137, pixel 1, shown at level 0.11, step 1, values float32 > volume subtract #1 #12 Opened volume difference as #13, grid size 192,192,192, pixel 1.46, shown at step 1, values float32 > volume subtract #2 #12 Opened volume difference as #14, grid size 192,192,192, pixel 1.46, shown at step 1, values float32 > volume subtract #3 #12 Opened volume difference as #15, grid size 192,192,192, pixel 1.46, shown at step 1, values float32 > volume subtract #4 #12 Opened volume difference as #16, grid size 192,192,192, pixel 1.46, shown at step 1, values float32 > volume subtract #5 #12 Opened volume difference as #17, grid size 192,192,192, pixel 1.46, shown at step 1, values float32 > volume subtract #6 #12 Opened volume difference as #18, grid size 192,192,192, pixel 1.46, shown at step 1, values float32 > volume subtract #7 #12 Opened volume difference as #19, grid size 192,192,192, pixel 1.46, shown at step 1, values float32 > volume subtract #8 #12 Opened volume difference as #20, grid size 192,192,192, pixel 1.46, shown at step 1, values float32 > volume subtract #9 #12 Opened volume difference as #21, grid size 192,192,192, pixel 1.46, shown at step 1, values float32 > volume subtract #10 #12 Opened volume difference as #22, grid size 192,192,192, pixel 1.46, shown at step 1, values float32 > surface dust #13 #14 #15 #16 #17 #18 #19 #20 #21 #22 size 5 > volume level 0.09 > hide #!11 models > open > /Users/yoojoong/Library/CloudStorage/Dropbox/1_RothLab/Experiments/Projects/Tas2Rs/TAS2R14/2025/Prog- > TAS2R14/Structure_work/WorkingModels/STR_OBP_2.cif Summary of feedback from opening /Users/yoojoong/Library/CloudStorage/Dropbox/1_RothLab/Experiments/Projects/Tas2Rs/TAS2R14/2025/Prog- TAS2R14/Structure_work/WorkingModels/STR_OBP_2.cif --- warning | Atom C22 is not in the residue template for STR /R:403 > open > /Users/yoojoong/Library/CloudStorage/Dropbox/1_RothLab/Experiments/Projects/Tas2Rs/TAS2R14/2025/Prog- > TAS2R14/Structure_work/WorkingModels&Maps_SetA-combined/cmpd28p1-TAS2R14.pdb Summary of feedback from opening /Users/yoojoong/Library/CloudStorage/Dropbox/1_RothLab/Experiments/Projects/Tas2Rs/TAS2R14/2025/Prog- TAS2R14/Structure_work/WorkingModels&Maps_SetA-combined/cmpd28p1-TAS2R14.pdb --- warning | Start residue of secondary structure not found: HELIX 23 23 ALA R 226 THR R 253 1 28 Chain information for cmpd28p1-TAS2R14.pdb #24 --- Chain | Description A | No description available B | No description available C | No description available D | No description available R | No description available > hide #23#!24 atoms > select ::name=""LIG""::name=""STR"" 92 atoms, 103 bonds, 4 residues, 3 models selected > show sel & #23#!24 atoms > hide #!13-22 target m > show #!13 models > ui tool show ""Side View"" > volume #13 level 0.0719 > volume level 0.07 > volume #14 color #b2ffff81 > volume #14 level 0.0835 > volume #14 level 0.07 > volume #15 color #b2b2ff7d > volume #15 level 0.0655 > volume #16 color #ffb2ff7f > volume #16 level 0.06552 > volume #17 color #ffb2b281 > volume #17 level 0.05195 > volume #17 level 0.07451 > volume #18 color #b2ffb27f > volume #18 level 0.1155 > volume #19 color #e5bf9980 > volume #19 level 0.09699 > volume #20 color #99bfe57d > volume #20 level 0.06093 > volume #21 level 0.08353 > volume #21 color #cccc9982 > close #1-10 > close #13-22 > close #12 > open /Users/yoojoong/Downloads/cryosparc_P18_J523_class_00_00006_volume.mrc Opened cryosparc_P18_J523_class_00_00006_volume.mrc as #1, grid size 168,168,168, pixel 1.66, shown at level 0.0498, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J523_class_01_00006_volume.mrc Opened cryosparc_P18_J523_class_01_00006_volume.mrc as #2, grid size 168,168,168, pixel 1.66, shown at level 0.0499, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J523_class_02_00006_volume.mrc Opened cryosparc_P18_J523_class_02_00006_volume.mrc as #3, grid size 168,168,168, pixel 1.66, shown at level 0.0501, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J523_class_03_00006_volume.mrc Opened cryosparc_P18_J523_class_03_00006_volume.mrc as #4, grid size 168,168,168, pixel 1.66, shown at level 0.0499, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J523_class_04_00006_volume.mrc Opened cryosparc_P18_J523_class_04_00006_volume.mrc as #5, grid size 168,168,168, pixel 1.66, shown at level 0.0501, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J523_class_05_00006_volume.mrc Opened cryosparc_P18_J523_class_05_00006_volume.mrc as #6, grid size 168,168,168, pixel 1.66, shown at level 0.05, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J523_class_06_00006_volume.mrc Opened cryosparc_P18_J523_class_06_00006_volume.mrc as #7, grid size 168,168,168, pixel 1.66, shown at level 0.0499, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J523_class_07_00006_volume.mrc Opened cryosparc_P18_J523_class_07_00006_volume.mrc as #8, grid size 168,168,168, pixel 1.66, shown at level 0.05, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J523_class_08_00006_volume.mrc Opened cryosparc_P18_J523_class_08_00006_volume.mrc as #9, grid size 168,168,168, pixel 1.66, shown at level 0.0499, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J523_class_09_00006_volume.mrc Opened cryosparc_P18_J523_class_09_00006_volume.mrc as #10, grid size 168,168,168, pixel 1.66, shown at level 0.0501, step 1, values float32 > volume level 0.07 > hide #!2-10 target m > ui mousemode right zoom > volume #1 level 0.12 > volume level 0.12 > 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 #!5 models > show #!7 models > hide #!6 models > select clear > show #!8 models > hide #!7 models > select clear > show #!9 models > hide #!8 models > show #!10 models > hide #!9 models > show #!11 models > hide #!10 models > show #!10 models > show #!9 models > hide #!11 models > hide #!9 models > hide #!10 models > show #!1 models > volume #1 level 0.09855 > show #!2 models > hide #!1 models > volume level 0.09 > volume #2 level 0.108 > volume level 0.1 > show #!1 models > hide #!2 models > show #!3 models > hide #!1 models > volume #3 level 0.09344 > show #!4 models > hide #!3 models > volume #4 level 0.1 > show #!5 models > hide #!4 models > volume #5 level 0.1108 > volume #6 level 0.101 > volume #7 level 0.09482 > open /Users/yoojoong/Downloads/cryosparc_P18_J524_class_00_00005_volume.mrc Opened cryosparc_P18_J524_class_00_00005_volume.mrc as #12, grid size 120,120,120, pixel 2.33, shown at level 0.0832, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J524_class_01_00005_volume.mrc Opened cryosparc_P18_J524_class_01_00005_volume.mrc as #13, grid size 120,120,120, pixel 2.33, shown at level 0.083, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J524_class_02_00005_volume.mrc Opened cryosparc_P18_J524_class_02_00005_volume.mrc as #14, grid size 120,120,120, pixel 2.33, shown at level 0.0829, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J524_class_03_00005_volume.mrc Opened cryosparc_P18_J524_class_03_00005_volume.mrc as #15, grid size 120,120,120, pixel 2.33, shown at level 0.0831, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J524_class_04_00005_volume.mrc Opened cryosparc_P18_J524_class_04_00005_volume.mrc as #16, grid size 120,120,120, pixel 2.33, shown at level 0.0831, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J524_class_05_00005_volume.mrc Opened cryosparc_P18_J524_class_05_00005_volume.mrc as #17, grid size 120,120,120, pixel 2.33, shown at level 0.083, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J524_class_06_00005_volume.mrc Opened cryosparc_P18_J524_class_06_00005_volume.mrc as #18, grid size 120,120,120, pixel 2.33, shown at level 0.0828, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J524_class_07_00005_volume.mrc Opened cryosparc_P18_J524_class_07_00005_volume.mrc as #19, grid size 120,120,120, pixel 2.33, shown at level 0.0832, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J524_class_08_00005_volume.mrc Opened cryosparc_P18_J524_class_08_00005_volume.mrc as #20, grid size 120,120,120, pixel 2.33, shown at level 0.0832, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J524_class_09_00005_volume.mrc Opened cryosparc_P18_J524_class_09_00005_volume.mrc as #21, grid size 120,120,120, pixel 2.33, shown at level 0.0829, step 1, values float32 > volume level 0.1 > hide #!13-21 target m > show #!13 models > hide #!12 models > show #!14 models > hide #!13 models > show #!15 models > hide #!14 models > show #!16 models > hide #!15 models > show #!17 models > hide #!16 models > show #!18 models > hide #!17 models > volume level 0.12 > show #!19 models > hide #!18 models > show #!20 models > hide #!19 models > show #!21 models > hide #!20 models > volume level 0.13 > volume level 0.15 > hide #!21 models > show #!12 models > volume #12 step 2 > volume #12 step 1 > show #!13 models > hide #!12 models > show #!14 models > hide #!13 models > volume #14 level 0.1524 > show #!15 models > hide #!14 models > volume #15 level 0.1399 > show #!16 models > hide #!15 models > volume #16 level 0.1239 > volume #16 level 0.1273 > show #!17 models > hide #!16 models > volume #17 level 0.1523 > show #!18 models > hide #!17 models > volume #18 level 0.1477 > show #!19 models > hide #!18 models > volume #19 level 0.1478 > show #!20 models > hide #!19 models > volume #20 level 0.139 > open /Users/yoojoong/Downloads/cryosparc_P18_J525_class_00_00010_volume.mrc Opened cryosparc_P18_J525_class_00_00010_volume.mrc as #22, grid size 168,168,168, pixel 1.66, shown at level 0.0499, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J525_class_01_00010_volume.mrc Opened cryosparc_P18_J525_class_01_00010_volume.mrc as #25, grid size 168,168,168, pixel 1.66, shown at level 0.05, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J525_class_02_00010_volume.mrc Opened cryosparc_P18_J525_class_02_00010_volume.mrc as #26, grid size 168,168,168, pixel 1.66, shown at level 0.0497, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J525_class_03_00010_volume.mrc Opened cryosparc_P18_J525_class_03_00010_volume.mrc as #27, grid size 168,168,168, pixel 1.66, shown at level 0.0499, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J525_class_04_00010_volume.mrc Opened cryosparc_P18_J525_class_04_00010_volume.mrc as #28, grid size 168,168,168, pixel 1.66, shown at level 0.0498, step 1, values float32 > hide #23#!20-22,24-28 target m > show #!22 models > volume level 0.15 > volume level 0.12 > show #!25 models > hide #!22 models > show #!26 models > hide #!25 models > show #!27 models > hide #!26 models > show #!28 models > hide #!27 models > volume level 0.11 > volume level 0.1 > hide #!27 models > hide #!28 models > show #!22 models > show #!25 models > hide #!22 models > show #!26 models > hide #!25 models > show #!27 models > hide #!26 models > show #!28 models > hide #!27 models > volume #28 level 0.119 > volume #27 level 0.1202 > hide #!28 models > hide #!27 models > show #!25 models > show #!22 models > hide #!25 models > volume #22 level 0.123 > show #!25 models > hide #!22 models > volume #25 level 0.1208 > volume level 0.12 > show #!26 models > hide #!25 models > show #!25 models > hide #!25 models > show #!27 models > hide #!26 models > show #!28 models > hide #!27 models > show #!25 models > hide #!28 models > show #!22 models > hide #!25 models > show #!25 models > hide #!22 models > show #!26 models > hide #!25 models > volume #26 level 0.1088 > show #!27 models > hide #!26 models > volume #27 level 0.09343 > volume #28 level 0.09254 > hide #!27 models > volume #28 level 0.08831 > open /Users/yoojoong/Downloads/cryosparc_P18_J526_class_00_00010_volume.mrc Opened cryosparc_P18_J526_class_00_00010_volume.mrc as #29, grid size 120,120,120, pixel 2.33, shown at level 0.0828, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J526_class_01_00010_volume.mrc Opened cryosparc_P18_J526_class_01_00010_volume.mrc as #30, grid size 120,120,120, pixel 2.33, shown at level 0.0833, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J526_class_02_00010_volume.mrc Opened cryosparc_P18_J526_class_02_00010_volume.mrc as #31, grid size 120,120,120, pixel 2.33, shown at level 0.083, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J526_class_03_00010_volume.mrc Opened cryosparc_P18_J526_class_03_00010_volume.mrc as #32, grid size 120,120,120, pixel 2.33, shown at level 0.0829, step 1, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J526_class_04_00010_volume.mrc Opened cryosparc_P18_J526_class_04_00010_volume.mrc as #33, grid size 120,120,120, pixel 2.33, shown at level 0.0829, step 1, values float32 > hide #!28-33 target m > show #!28 models > hide #!28 models > show #!29 models > volume level 0.1 > volume level 0.13 > show #!30 models > hide #!29 models > show #!31 models > hide #!30 models > show #!32 models > hide #!31 models > show #!33 models > hide #!32 models > show #!32 models > hide #!33 models > volume #32 level 0.1359 > show #!31 models > hide #!32 models > volume #31 level 0.1524 > show #!30 models > hide #!31 models > volume #30 level 0.1384 > volume #30 level 0.1324 > show #!29 models > hide #!30 models > volume #29 level 0.1278 > volume #30 level 0.1372 > hide #!29 models > volume #30 level 0.1396 > volume #31 level 0.1578 > volume #32 level 0.1561 > volume #33 level 0.1233 > volume #32 level 0.1359 > show #23 models > show #!24 models > volume #32 level 0.1288 > hide #!32 models > show #!29 models > volume #29 level 0.1201 > show #!30 models > hide #!29 models > volume #30 level 0.1324 > show #!31 models > hide #!30 models > volume #31 level 0.145 > volume #32 level 0.1347 > hide #!31 models > volume #32 level 0.1371 > volume #33 level 0.1132 > volume #30 level 0.1061 > volume #29 level 0.09597 > volume #29 level 0.09 > volume level 0.09 > volume level 0.1 > volume level 0.11 > hide #!33 models > volume #32 level 0.1159 > volume #33 level 0.11 > show #!31 models > show #!32 models > hide #!33 models > hide #!32 models > show #!32 models > hide #!31 models > show #!31 models > show #!30 models > show #!29 models > hide #!32 models > hide #!31 models > show #!31 models > hide #!31 models > hide #!30 models > show #!30 models > hide #!29 models > show #!29 models > hide #!30 models > volume level 0.13 > volume level 0.14 > show #!30 models > hide #!29 models > show #!33 models > hide #!30 models > show #!29 models > hide #!29 models > show #!29 models > hide #!33 models > show #!33 models > hide #!29 models > show #!29 models > hide #!33 models > show #!33 models > hide #!29 models > show #!31 models > show #!32 models > hide #!32 models > hide #!33 models > show #!32 models > hide #!31 models > show #!30 models > hide #!32 models > show #!32 models > hide #!30 models > show #!31 models > hide #!32 models > open /Users/yoojoong/Downloads/cryosparc_P18_J533_004_volume_map_sharp.mrc Opened cryosparc_P18_J533_004_volume_map_sharp.mrc as #34, grid size 320,320,320, pixel 0.874, shown at level 0.0226, step 2, values float32 > hide #!31 models > surface dust #34 > volume #34 step 1 > volume #34 level 0.08992 > ui mousemode right translate > ui tool show ""Side View"" > hide #!24 models > volume #34 color #b2b2b27a > volume #34 level 0.1112 > volume #34 level 0.1006 > volume #34 level 0.08637 > volume #34 color #b2b2b2 > volume #34 level 0.1254 > volume #34 level 0.09346 > show #!32 models > show #!31 models > hide #!34 models > hide #!32 models > hide #!31 models > show #!30 models > show #!32 models > hide #!32 models > show #!33 models > hide #!33 models > hide #!30 models > open /Users/yoojoong/Downloads/cryosparc_P18_J534_004_volume_map_sharp.mrc Opened cryosparc_P18_J534_004_volume_map_sharp.mrc as #35, grid size 320,320,320, pixel 0.874, shown at level 0.021, step 2, values float32 > volume #35 step 1 > volume #35 level 0.1312 > volume #35 level 0.1178 > show #!24 models > hide #23 models > volume #35 level 0.07776 > surface dust #35 > volume #35 level 0.1011 ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/yoojoong/Downloads/cryosparc_P18_J534_004_volume_map_sharp.mrc Opened cryosparc_P18_J534_004_volume_map_sharp.mrc as #1, grid size 320,320,320, pixel 0.874, shown at level 0.021, step 2, values float32 > open /Users/yoojoong/Downloads/cryosparc_P18_J533_004_volume_map_sharp.mrc Opened cryosparc_P18_J533_004_volume_map_sharp.mrc as #2, grid size 320,320,320, pixel 0.874, shown at level 0.0226, step 2, values float32 OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M1 Pro 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: MacBookPro18,3 Model Number: MKGR3LL/A Chip: Apple M1 Pro Total Number of Cores: 8 (6 performance and 2 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: 1 day, 4 hours, 29 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: LG ULTRAFINE: Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus) UI Looks like: 2560 x 1440 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal T24i-10: 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