id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17751 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.4.1-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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""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/core\/_serialize.cpython-311-darwin.so"", ""name"" : ""_serialize.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 13307789312, ""size"" : 131072, ""uuid"" : ""650aead6-ce16-39bb-9ba1-4bf9986b96d6"", ""path"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/msgpack\/_cmsgpack.cpython-311-darwin.so"", ""name"" : ""_cmsgpack.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 14244380672, ""size"" : 737280, ""uuid"" : ""cc06500d-d418-3365-b197-36b1304a819e"", ""path"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGL.abi3.so"", ""name"" : ""QtOpenGL.abi3.so"" }, { ""source"" : ""P"", ""arch"" : 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[ { ""rolloutId"" : ""63508950b3714d3622fc77f7"", ""factorPackIds"" : { ""SIRI_MEMORY_SYNC_CONFIG"" : ""6526e111d0c9ce2f459b54a8"" }, ""deploymentId"" : 240000015 }, { ""rolloutId"" : ""670e9bd77a111748a97092a1"", ""factorPackIds"" : { ""SIRI_TTS_DEVICE_TRAINING"" : ""67d07fb744f1a3655d87002b"" }, ""deploymentId"" : 240000016 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/annguyen/Downloads/cryosparc_P8_J115_003_volume_map.mrc Opened cryosparc_P8_J115_003_volume_map.mrc as #1, grid size 250,250,250, pixel 2.29, shown at level 0.4, step 1, values float32 > volume #1 level 0.2285 > ui tool show ""Hide Dust"" > surface dust #1 size 13.75 > volume #1 level 0.1882 > open ""/Users/annguyen/ownCloud - Anh Nguyen@oc.biophys.mpg.de/Chimera > sessions/13-02-25 fit TPR domian in map of RiboSec72.cxs"" format session Opened cryosparc_P26_J18_003_volume_map.mrc as #1, grid size 320,320,320, pixel 1.34, shown at level 0.245, step 1, values float32 Opened cryosparc_P26_J18_003_volume_map_sharp.mrc as #3, grid size 320,320,320, pixel 1.34, shown at level 1.28, step 2, values float32 Opened cryosparc_P4_J508_007_volume_map.mrc as #15, grid size 432,432,432, pixel 0.97, shown at level 0.469, step 1, values float32 Opened cryosparc_P4_J532_002_with particle substraction center.mrc as #16, grid size 432,432,432, pixel 0.97, shown at level 0.0349, step 1, values float32 Opened cryosparc_P4_J521_005_wo particle substraction side.mrc as #17, grid size 432,432,432, pixel 0.97, shown at level 0.132, step 1, values float32 Opened cryosparc_P4_J527_005_wo particle substrction center.mrc as #18, grid size 432,432,432, pixel 0.97, shown at level 0.132, step 1, values float32 Opened cryosparc_P4_J531_002_with particle substraction side.mrc as #19, grid size 432,432,432, pixel 0.97, shown at level 0.0472, step 1, values float32 Opened emd_12977 map of 7old as #20, grid size 486,486,486, pixel 1.1, shown at level 2.82, step 1, values float32 Opened cryosparc_P4_J627_004_volume_map.mrc as #21, grid size 432,432,432, pixel 1.24, shown at level 0.134, step 1, values float32 opened ChimeraX session > show #4 models > show #2 models > show #!15 models > open ""/Users/annguyen/ownCloud - Anh > Nguyen@oc.biophys.mpg.de/Alphafold/AF-P39742-F1-model_v4-Yeast Sec72.pdb"" AF-P39742-F1-model_v4-Yeast Sec72.pdb title: Alphafold monomer V2.0 prediction for translocation protein SEC72 (P39742) [more info...] Chain information for AF-P39742-F1-model_v4-Yeast Sec72.pdb #22 --- Chain | Description | UniProt A | translocation protein SEC72 | SEC72_YEAST 1-193 Computing secondary structure > show #!1 models > show #!3 models > hide #2 models > hide #!3 models > hide #4 models > show #!6 models > hide #!6 models > show #!7 models > hide #!7 models > show #!8 models > hide #14 models > hide #!15 models > show #!15 models > hide #!15 models > show #!16 models > hide #!16 models > hide #!8 models > show #!8 models > hide #!8 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #2 models > hide #2 models > hide #!1 models > show #!1 models > open > /Users/annguyen/Downloads/cryosparc_P8_J111_00011_volume_series/J111_class_00_00011_volume.mrc Opened J111_class_00_00011_volume.mrc as #23, grid size 100,100,100, pixel 5.73, shown at level 0.81, step 1, values float32 > open > /Users/annguyen/Downloads/cryosparc_P8_J111_00011_volume_series/J111_class_01_00011_volume.mrc Opened J111_class_01_00011_volume.mrc as #24, grid size 100,100,100, pixel 5.73, shown at level 0.824, step 1, values float32 > open > /Users/annguyen/Downloads/cryosparc_P8_J111_00011_volume_series/J111_class_02_00011_volume.mrc Opened J111_class_02_00011_volume.mrc as #25, grid size 100,100,100, pixel 5.73, shown at level 0.829, step 1, values float32 > open > /Users/annguyen/Downloads/cryosparc_P8_J111_00011_volume_series/J111_class_03_00011_volume.mrc Opened J111_class_03_00011_volume.mrc as #26, grid size 100,100,100, pixel 5.73, shown at level 0.749, step 1, values float32 > open > /Users/annguyen/Downloads/cryosparc_P8_J111_00011_volume_series/J111_class_04_00011_volume.mrc Opened J111_class_04_00011_volume.mrc as #27, grid size 100,100,100, pixel 5.73, shown at level 0.834, step 1, values float32 > open > /Users/annguyen/Downloads/cryosparc_P8_J111_00011_volume_series/J111_class_05_00011_volume.mrc Opened J111_class_05_00011_volume.mrc as #28, grid size 100,100,100, pixel 5.73, shown at level 0.832, step 1, values float32 > open > /Users/annguyen/Downloads/cryosparc_P8_J111_00011_volume_series/J111_class_06_00011_volume.mrc Opened J111_class_06_00011_volume.mrc as #29, grid size 100,100,100, pixel 5.73, shown at level 0.806, step 1, values float32 > open > /Users/annguyen/Downloads/cryosparc_P8_J111_00011_volume_series/J111_class_07_00011_volume.mrc Opened J111_class_07_00011_volume.mrc as #30, grid size 100,100,100, pixel 5.73, shown at level 0.804, step 1, values float32 > open > /Users/annguyen/Downloads/cryosparc_P8_J111_00011_volume_series/J111_class_08_00011_volume.mrc Opened J111_class_08_00011_volume.mrc as #31, grid size 100,100,100, pixel 5.73, shown at level 0.772, step 1, values float32 > open > /Users/annguyen/Downloads/cryosparc_P8_J111_00011_volume_series/J111_class_09_00011_volume.mrc Opened J111_class_09_00011_volume.mrc as #32, grid size 100,100,100, pixel 5.73, shown at level 1.34e-06, step 1, values float32 > hide #!1 models > hide #22 models > select ~sel & ##selected Nothing selected > tile #23-32 9 models tiled > volume #23-32 level 0.3 > tile #23-32 columns 10 9 models tiled > open ""/Users/annguyen/ownCloud - Anh Nguyen@oc.biophys.mpg.de/Chimera > sessions/18-05-25-scSec72-scRibo-10xbin.cxs"" format session Opened cryosparc_P8_J16_class_02_00042_volume.mrc as #2, grid size 128,128,128, pixel 4.48, shown at level 0.122, step 1, values float32 Opened cryosparc_P8_J16_class_03_00042_volume.mrc z flip as #3, grid size 128,128,128, pixel 4.48, shown at level 0.27, step 1, values float32 Opened cryosparc_P8_J16_class_00_00042_volume.mrc z flip as #5, grid size 128,128,128, pixel 4.48, shown at level 0.0367, step 1, values float32 Opened cryosparc_P5_J26_class_04_00042_volume.mrc as #1, grid size 128,128,128, pixel 4.48, shown at level 0.0781, step 1, values float32 opened ChimeraX session > show #!5 models > hide #!1 models > show #!1 models > hide #!2 models > hide #!3 models > hide #4 models > hide #!5 models > hide #!1 models > show #!2 models > volume #2 color #ffffb2d9 > volume #2 color #ffffb2 > volume #2 color #ffffb2e6 > volume #2 color #ffffb2df > hide #!2 models > show #!3 models > volume #3 color #9a6021eb > hide #!6 models > hide #!3 models > show #!3 models > hide #!3 models > show #4 models > hide #4 models > show #!5 models > show #!2 models > hide #!5 models > volume #2 level 0.3904 > volume #2 level 0.301 > volume #2 level 0.2065 > volume gasussian #2 10 Expected a density maps specifier or a keyword > hide #!2 models > open > /Users/annguyen/Downloads/cryosparc_P8_J111_00011_volume_series/J111_class_00_00011_volume.mrc > format mrc Opened J111_class_00_00011_volume.mrc as #7, grid size 100,100,100, pixel 5.73, shown at level 0.81, step 1, values float32 > hide #!7 models > close #7 > show #!1 models > show #!2 models > open ""/Users/annguyen/ownCloud - Anh > Nguyen@oc.biophys.mpg.de/Alphafold/AF-P39742-F1-model_v4-Yeast Sec72.pdb"" AF-P39742-F1-model_v4-Yeast Sec72.pdb title: Alphafold monomer V2.0 prediction for translocation protein SEC72 (P39742) [more info...] Chain information for AF-P39742-F1-model_v4-Yeast Sec72.pdb #7 --- Chain | Description | UniProt A | translocation protein SEC72 | SEC72_YEAST 1-193 Computing secondary structure > select add #7 1514 atoms, 1534 bonds, 193 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #7,1,0,0,495.18,0,1,0,-99.476,0,0,1,9.6755 > view matrix models #7,1,0,0,231.47,0,1,0,480.14,0,0,1,256.3 > hide #!1 models > show #!3 models > hide #!3 models > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.63865,-0.4328,-0.63625,235.98,0.48176,0.86963,-0.10797,479.99,0.60003,-0.23757,0.76389,256.74 > view matrix models > #7,0.26647,-0.52234,-0.81003,237.68,0.62173,0.73535,-0.26965,480.75,0.7365,-0.43177,0.52071,258 > view matrix models > #7,-0.12223,-0.51154,-0.85052,238.58,0.66361,0.59511,-0.45329,481.8,0.73803,-0.61982,0.26673,259.56 > view matrix models > #7,0.32752,-0.51535,-0.79193,237.46,0.60647,0.75737,-0.24204,480.6,0.72452,-0.40101,0.5606,257.78 > view matrix models > #7,0.58645,-0.45325,-0.6713,236.29,0.50929,0.85079,-0.12953,480.08,0.62984,-0.26592,0.72978,256.9 > ui mousemode right ""translate selected models"" > view matrix models > #7,0.58645,-0.45325,-0.6713,431.88,0.50929,0.85079,-0.12953,396.19,0.62984,-0.26592,0.72978,171.21 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.58795,-0.75187,-0.29834,432.35,0.76437,0.6371,-0.099217,396.58,0.26467,-0.1697,0.94929,170.98 > view matrix models > #7,0.58614,-0.7671,-0.26076,432.34,0.78053,0.62094,-0.072189,396.56,0.21729,-0.16122,0.9627,171.01 > view matrix models > #7,0.54838,-0.63874,-0.53971,432.52,0.61968,0.74377,-0.2506,396.77,0.56149,-0.19702,0.80368,170.84 > view matrix models > #7,0.77014,-0.44972,-0.45237,430.9,0.40794,0.89244,-0.1927,396.37,0.49038,-0.03613,0.87076,170.05 > ui tool show ""Fit in Map"" > fitmap #7 inMap #2 Fit molecule AF-P39742-F1-model_v4-Yeast Sec72.pdb (#7) to map cryosparc_P8_J16_class_02_00042_volume.mrc (#2) using 1514 atoms average map value = 0.1758, steps = 124 shifted from previous position = 20.9 rotated from previous position = 99.5 degrees atoms outside contour = 990, contour level = 0.20645 Position of AF-P39742-F1-model_v4-Yeast Sec72.pdb (#7) relative to cryosparc_P8_J16_class_02_00042_volume.mrc (#2) coordinates: Matrix rotation and translation -0.29566100 0.71916695 -0.62879525 191.95777257 0.76585194 -0.21500165 -0.60600750 317.20297658 -0.57101258 -0.66073685 -0.48720780 220.17597373 Axis -0.59314789 -0.62623923 0.50596443 Axis point -60.17408012 0.00000000 239.56782530 Rotation angle (degrees) 177.35574013 Shift along axis -201.10308507 > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.082499,-0.77168,0.63064,415.47,0.57813,-0.5525,-0.60043,412.44,0.81177,0.31505,0.49171,172.22 > ui mousemode right ""rotate selected models"" > view matrix models > #7,-0.57727,-0.81346,0.070915,418.19,0.45135,-0.39026,-0.80249,412.45,0.68047,-0.43125,0.59244,175.84 > view matrix models > #7,0.5462,-0.63153,-0.55031,416.46,0.52948,0.76936,-0.35739,405.55,0.64909,-0.096171,0.75461,173.88 > view matrix models > #7,0.68996,-0.69611,0.19848,414.53,0.36875,0.10206,-0.92391,410.57,0.62288,0.71064,0.32711,171.15 > view matrix models > #7,0.76812,-0.62559,0.1365,414.18,0.11857,-0.070524,-0.99044,412.12,0.62923,0.77696,0.020005,171.6 > view matrix models > #7,0.83432,-0.55118,0.010805,414,-0.19896,-0.31933,-0.92652,413.85,0.51413,0.77086,-0.37609,172.9 > view matrix models > #7,0.99748,-0.028643,-0.064834,411.32,-0.069382,-0.20757,-0.97576,413.16,0.014492,0.9778,-0.20903,172.57 > view matrix models > #7,0.99741,-0.027626,-0.066394,411.32,-0.070685,-0.20679,-0.97583,413.16,0.013229,0.97799,-0.20821,172.57 > view matrix models > #7,0.86645,0.4971,0.046333,408.78,0.075331,-0.03843,-0.99642,412.08,-0.49354,0.86684,-0.070745,173.86 > ui mousemode right ""translate selected models"" > view matrix models > #7,0.86645,0.4971,0.046333,411.37,0.075331,-0.03843,-0.99642,403.08,-0.49354,0.86684,-0.070745,173.25 > view matrix models > #7,0.86645,0.4971,0.046333,411.44,0.075331,-0.03843,-0.99642,402.52,-0.49354,0.86684,-0.070745,172.13 > view matrix models > #7,0.86645,0.4971,0.046333,414.95,0.075331,-0.03843,-0.99642,401.5,-0.49354,0.86684,-0.070745,165.96 > view matrix models > #7,0.86645,0.4971,0.046333,417.5,0.075331,-0.03843,-0.99642,402.68,-0.49354,0.86684,-0.070745,169.59 > view matrix models > #7,0.86645,0.4971,0.046333,422.13,0.075331,-0.03843,-0.99642,408.57,-0.49354,0.86684,-0.070745,166.36 > fitmap #7 inMap #2 Fit molecule AF-P39742-F1-model_v4-Yeast Sec72.pdb (#7) to map cryosparc_P8_J16_class_02_00042_volume.mrc (#2) using 1514 atoms average map value = 0.232, steps = 160 shifted from previous position = 37.6 rotated from previous position = 67.3 degrees atoms outside contour = 588, contour level = 0.20645 Position of AF-P39742-F1-model_v4-Yeast Sec72.pdb (#7) relative to cryosparc_P8_J16_class_02_00042_volume.mrc (#2) coordinates: Matrix rotation and translation -0.38395242 -0.31607344 0.86757024 205.45325374 -0.90522369 0.31412465 -0.28617437 336.34493386 -0.18207308 -0.89522248 -0.40672608 204.21922377 Axis -0.45148270 0.77809256 -0.43673258 Axis point 259.91409793 0.00000000 136.29485618 Rotation angle (degrees) 137.58484244 Shift along axis 79.75971298 > undo > view matrix models > #7,0.86645,0.4971,0.046333,421.36,0.075331,-0.03843,-0.99642,404.49,-0.49354,0.86684,-0.070745,166.07 > view matrix models > #7,0.86645,0.4971,0.046333,411.19,0.075331,-0.03843,-0.99642,411.72,-0.49354,0.86684,-0.070745,165.57 > view matrix models > #7,0.86645,0.4971,0.046333,419.69,0.075331,-0.03843,-0.99642,403.55,-0.49354,0.86684,-0.070745,162.35 > view matrix models > #7,0.86645,0.4971,0.046333,419.72,0.075331,-0.03843,-0.99642,402.58,-0.49354,0.86684,-0.070745,161.28 > view matrix models > #7,0.86645,0.4971,0.046333,419.57,0.075331,-0.03843,-0.99642,402.67,-0.49354,0.86684,-0.070745,161.48 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.79617,0.26645,-0.54325,422.35,-0.60073,0.45544,-0.65703,400.9,0.072354,0.84946,0.52267,158.8 > view matrix models > #7,-0.38844,0.37591,-0.84131,425.18,-0.21376,0.85134,0.47909,395.22,0.89634,0.36594,-0.25034,161.32 > view matrix models > #7,0.33812,-0.38844,-0.8572,427.32,-0.89862,-0.40382,-0.17147,404.44,-0.27955,0.82828,-0.4856,162.27 > view matrix models > #7,0.52121,0.84885,-0.088332,418.98,0.35469,-0.30959,-0.88224,403.08,-0.77623,0.4285,-0.46244,165.22 > view matrix models > #7,0.49381,-0.38603,-0.77919,426.77,-0.86755,-0.27978,-0.4112,404.39,-0.059272,0.87904,-0.47306,161.51 > view matrix models > #7,0.9219,0.35032,-0.16545,420.7,0.33619,-0.93561,-0.10772,404.14,-0.19254,0.043681,-0.98032,167.13 > view matrix models > #7,0.97842,0.17461,-0.11046,421.29,0.14939,-0.96717,-0.20558,404.96,-0.14273,0.18464,-0.97239,166.32 > volume #2 level 0.1593 > view matrix models > #7,0.6461,0.76091,0.059758,418.75,0.6641,-0.52184,-0.5354,402.53,-0.37621,0.38561,-0.84248,165.53 > view matrix models > #7,0.72813,0.67826,0.098929,418.87,0.61827,-0.58759,-0.522,402.92,-0.29592,0.44125,-0.84719,165.1 > view matrix models > #7,0.62815,0.32171,-0.70847,422.88,-0.77253,0.14917,-0.61721,402.65,-0.092884,0.93501,0.34223,159.22 > fitmap #7 inMap #2 Fit molecule AF-P39742-F1-model_v4-Yeast Sec72.pdb (#7) to map cryosparc_P8_J16_class_02_00042_volume.mrc (#2) using 1514 atoms average map value = 0.2074, steps = 92 shifted from previous position = 29.9 rotated from previous position = 17.3 degrees atoms outside contour = 527, contour level = 0.15934 Position of AF-P39742-F1-model_v4-Yeast Sec72.pdb (#7) relative to cryosparc_P8_J16_class_02_00042_volume.mrc (#2) coordinates: Matrix rotation and translation -0.38172565 -0.71830578 0.58165482 198.20909708 -0.89890758 0.43494493 -0.05280216 329.00225981 -0.21505972 -0.54300987 -0.81172015 214.28905460 Axis -0.51453513 0.83625290 -0.18956448 Axis point 236.60478304 0.00000000 104.05931239 Rotation angle (degrees) 151.55207606 Shift along axis 132.52195625 > view matrix models > #7,0.29815,0.75481,-0.58426,403.08,-0.94016,0.12647,-0.31639,419.06,-0.16492,0.64363,0.74735,177.75 > view matrix models > #7,-0.4415,0.89545,0.056978,402.37,0.55832,0.22446,0.79869,412.45,0.7024,0.38443,-0.59904,180.56 > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for AF-P39742-F1-model_v4-Yeast Sec72.pdb_A SES surface #7.1: minimum, -17.75, mean -1.54, maximum 10.72 To also show corresponding color key, enter the above coulombic command and add key true > view matrix models > #7,-0.055832,0.99656,0.061312,400.93,0.54606,-0.020933,0.83749,413.58,0.83589,0.080238,-0.54301,181.59 > view matrix models > #7,-0.60166,0.79615,0.064393,403.22,0.52887,0.33666,0.77907,412.02,0.59858,0.50279,-0.62362,180.3 > view matrix models > #7,-0.16521,0.98459,0.057397,401.26,0.5596,0.045658,0.8275,413.25,0.81213,0.16883,-0.55852,181.26 > view matrix models > #7,-0.55223,0.83143,0.06136,402.94,0.54075,0.3012,0.78541,412.15,0.63453,0.4669,-0.61593,180.37 > view matrix models > #7,-0.19703,0.97876,0.056635,401.37,0.56213,0.065453,0.82446,413.15,0.80324,0.19428,-0.56309,181.16 > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.19703,0.97876,0.056635,417.45,0.56213,0.065453,0.82446,399.43,0.80324,0.19428,-0.56309,168.22 > view matrix models > #7,-0.19703,0.97876,0.056635,419.8,0.56213,0.065453,0.82446,398.11,0.80324,0.19428,-0.56309,167.29 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.62471,0.2148,-0.75073,423.14,-0.72578,0.51439,-0.45677,401.7,0.28805,0.83022,0.47724,163.34 > view matrix models > #7,0.076393,0.91561,0.39474,418.74,0.98476,-0.13133,0.11405,399.48,0.15626,0.38001,-0.91169,168.68 > show #!6 models > view matrix models > #7,-0.40791,0.85234,0.32732,420.37,0.89861,0.31133,0.30915,397.15,0.1616,0.42024,-0.89291,168.43 > view matrix models > #7,0.62067,0.26302,-0.73864,422.89,-0.72586,0.54897,-0.41444,401.45,0.29649,0.79338,0.53164,163.38 > view matrix models > #7,0.787,0.4945,-0.36892,420.61,-0.57145,0.80967,-0.13375,399.24,0.23257,0.31608,0.91979,165.05 > view matrix models > #7,0.64509,0.28852,-0.70754,422.65,-0.3065,0.94592,0.10628,397.44,0.69994,0.1483,0.69863,165.18 > view matrix models > #7,0.97784,0.073831,-0.19589,421.82,0.045789,0.83766,0.54428,396.21,0.20428,-0.54119,0.81571,169.47 > view matrix models > #7,0.87693,-0.22396,-0.42525,423.98,0.40975,0.81081,0.41796,395.71,0.25119,-0.54077,0.80279,169.38 > view matrix models > #7,0.56262,0.041042,-0.82569,424.28,0.064642,0.99353,0.093431,396.33,0.82418,-0.10594,0.55633,166.39 > fitmap #7 inMap #2 Fit molecule AF-P39742-F1-model_v4-Yeast Sec72.pdb (#7) to map cryosparc_P8_J16_class_02_00042_volume.mrc (#2) using 1514 atoms average map value = 0.1998, steps = 164 shifted from previous position = 38.2 rotated from previous position = 52.9 degrees atoms outside contour = 574, contour level = 0.15934 Position of AF-P39742-F1-model_v4-Yeast Sec72.pdb (#7) relative to cryosparc_P8_J16_class_02_00042_volume.mrc (#2) coordinates: Matrix rotation and translation -0.99704805 0.00838735 -0.07632046 205.41510085 -0.06490415 0.43898253 0.89614830 333.43347542 0.04101965 0.89845645 -0.43714231 209.14419648 Axis 0.01668121 -0.84802994 -0.52968572 Axis point 105.93579805 0.00000000 4.76705404 Rotation angle (degrees) 176.03288284 Shift along axis -390.11569049 > ui mousemode right ""translate selected models"" > view matrix models > #7,0.95276,0.093927,-0.28883,413.68,0.14353,0.69886,0.70071,402.81,0.26767,-0.70906,0.65237,170.71 > view matrix models > #7,0.95276,0.093927,-0.28883,415.53,0.14353,0.69886,0.70071,403.48,0.26767,-0.70906,0.65237,170.06 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.4107,-0.42511,-0.80661,420.42,0.38014,-0.72427,0.57526,410.04,-0.82875,-0.54288,-0.13586,173.54 > fitmap #7 inMap #2 Fit molecule AF-P39742-F1-model_v4-Yeast Sec72.pdb (#7) to map cryosparc_P8_J16_class_02_00042_volume.mrc (#2) using 1514 atoms average map value = 0.5909, steps = 152 shifted from previous position = 75.6 rotated from previous position = 53.2 degrees atoms outside contour = 189, contour level = 0.15934 Position of AF-P39742-F1-model_v4-Yeast Sec72.pdb (#7) relative to cryosparc_P8_J16_class_02_00042_volume.mrc (#2) coordinates: Matrix rotation and translation -0.36537732 0.82900503 0.42337935 253.70171638 0.67542842 -0.07686771 0.73340834 343.65826821 0.64054340 0.55393322 -0.53184784 200.71086084 Axis -0.55933969 -0.67679840 -0.47862620 Axis point -13.69521201 0.00000000 -21.72737954 Rotation angle (degrees) 170.76786469 Shift along axis -470.55828152 > undo > view matrix models > #7,0.67451,0.27265,-0.68608,416.16,-0.71574,0.46932,-0.51716,409.18,0.18099,0.83988,0.51171,163.07 > fitmap #7 inMap #2 Fit molecule AF-P39742-F1-model_v4-Yeast Sec72.pdb (#7) to map cryosparc_P8_J16_class_02_00042_volume.mrc (#2) using 1514 atoms average map value = 0.2074, steps = 80 shifted from previous position = 19.8 rotated from previous position = 11.4 degrees atoms outside contour = 526, contour level = 0.15934 Position of AF-P39742-F1-model_v4-Yeast Sec72.pdb (#7) relative to cryosparc_P8_J16_class_02_00042_volume.mrc (#2) coordinates: Matrix rotation and translation -0.38026206 -0.71895260 0.58181434 198.23758393 -0.89952691 0.43377184 -0.05189727 329.06031594 -0.21506299 -0.54309222 -0.81166418 214.34129831 Axis -0.51522568 0.83586297 -0.18940855 Axis point 236.86349273 0.00000000 104.02709263 Rotation angle (degrees) 151.53124705 Shift along axis 132.31416225 > view matrix models > #7,0.20052,0.3051,-0.93097,406.31,-0.91895,0.38797,-0.070785,417.39,0.33959,0.86971,0.35817,176.36 > view matrix models > #7,0.42815,0.34344,-0.83591,405.37,-0.90043,0.24089,-0.36222,418.66,0.076957,0.90776,0.41238,176.7 > ui mousemode right ""translate selected models"" > view matrix models > #7,0.42815,0.34344,-0.83591,407.73,-0.90043,0.24089,-0.36222,401.27,0.076957,0.90776,0.41238,151.51 > view matrix models > #7,0.42815,0.34344,-0.83591,405.33,-0.90043,0.24089,-0.36222,407.53,0.076957,0.90776,0.41238,153.19 > view matrix models > #7,0.42815,0.34344,-0.83591,412.88,-0.90043,0.24089,-0.36222,414.29,0.076957,0.90776,0.41238,160.47 > view matrix models > #7,0.42815,0.34344,-0.83591,413.05,-0.90043,0.24089,-0.36222,414.28,0.076957,0.90776,0.41238,160.13 > fitmap #7 inMap #2 Fit molecule AF-P39742-F1-model_v4-Yeast Sec72.pdb (#7) to map cryosparc_P8_J16_class_02_00042_volume.mrc (#2) using 1514 atoms average map value = 0.2074, steps = 84 shifted from previous position = 19 rotated from previous position = 11.2 degrees atoms outside contour = 524, contour level = 0.15934 Position of AF-P39742-F1-model_v4-Yeast Sec72.pdb (#7) relative to cryosparc_P8_J16_class_02_00042_volume.mrc (#2) coordinates: Matrix rotation and translation -0.38228232 -0.71820425 0.58141454 198.20777711 -0.89867229 0.43540176 -0.05304159 328.99776277 -0.21505421 -0.54277801 -0.81187666 214.27532541 Axis -0.51429597 0.83641048 -0.18951825 Axis point 236.50941442 0.00000000 104.06276879 Rotation angle (degrees) 151.56749759 Shift along axis 132.63063037 > view matrix models > #7,0.55184,0.40864,-0.72697,445.4,-0.82916,0.36216,-0.42584,386.56,0.089261,0.83777,0.53868,145.48 > save ""/Users/annguyen/ownCloud - Anh Nguyen@oc.biophys.mpg.de/Chimera > sessions/18-05-25-scSec72-scRibo-10xbin.cxs"" > open > /Users/annguyen/Downloads/cryosparc_P8_J110_00018_volume_series/J110_class_00_00018_volume.mrc Opened J110_class_00_00018_volume.mrc as #8, grid size 100,100,100, pixel 5.73, shown at level 0.794, step 1, values float32 > open > /Users/annguyen/Downloads/cryosparc_P8_J110_00018_volume_series/J110_class_01_00018_volume.mrc Opened J110_class_01_00018_volume.mrc as #9, grid size 100,100,100, pixel 5.73, shown at level 0.839, step 1, values float32 > open > /Users/annguyen/Downloads/cryosparc_P8_J110_00018_volume_series/J110_class_02_00018_volume.mrc Opened J110_class_02_00018_volume.mrc as #10, grid size 100,100,100, pixel 5.73, shown at level 0.805, step 1, values float32 > open > /Users/annguyen/Downloads/cryosparc_P8_J110_00018_volume_series/J110_class_03_00018_volume.mrc Opened J110_class_03_00018_volume.mrc as #11, grid size 100,100,100, pixel 5.73, shown at level 0.806, step 1, values float32 > open > /Users/annguyen/Downloads/cryosparc_P8_J110_00018_volume_series/J110_class_04_00018_volume.mrc Opened J110_class_04_00018_volume.mrc as #12, grid size 100,100,100, pixel 5.73, shown at level 0.813, step 1, values float32 > open > /Users/annguyen/Downloads/cryosparc_P8_J110_00018_volume_series/J110_class_05_00018_volume.mrc Opened J110_class_05_00018_volume.mrc as #13, grid size 100,100,100, pixel 5.73, shown at level 0.778, step 1, values float32 > open > /Users/annguyen/Downloads/cryosparc_P8_J110_00018_volume_series/J110_class_06_00018_volume.mrc Opened J110_class_06_00018_volume.mrc as #14, grid size 100,100,100, pixel 5.73, shown at level 0.775, step 1, values float32 > open > /Users/annguyen/Downloads/cryosparc_P8_J110_00018_volume_series/J110_class_07_00018_volume.mrc Opened J110_class_07_00018_volume.mrc as #15, grid size 100,100,100, pixel 5.73, shown at level 0.816, step 1, values float32 > open > /Users/annguyen/Downloads/cryosparc_P8_J110_00018_volume_series/J110_class_08_00018_volume.mrc Opened J110_class_08_00018_volume.mrc as #16, grid size 100,100,100, pixel 5.73, shown at level 0.794, step 1, values float32 > open > /Users/annguyen/Downloads/cryosparc_P8_J110_00018_volume_series/J110_class_09_00018_volume.mrc Opened J110_class_09_00018_volume.mrc as #17, grid size 100,100,100, pixel 5.73, shown at level 0.818, step 1, values float32 > hide #!6 models > hide #!7 models > select subtract #7 1 model selected > hide #!2 models > tile columns 5 rows 2 models #8-17 Expected a keyword > tile columns 5 rows 2 models #8-17 Expected a keyword > hide ~ Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > tile columns 5 rows 2 Expected a keyword > modeldisplay #8-17 Unknown command: modeldisplay #8-17 > tile columns 5 rows 2 Expected a keyword > hide #!8 models > hide #!9 models > hide #!10 models > hide #!12 models > hide #!13 models > hide #!14 models > hide #!15 models > hide #!16 models > hide #!17 models > hide #!11 models > show #!8 models > show #!9 models > hide #!9 models > hide #!8 models > show #!9 models > hide #!9 models > show #!10 models > hide #!10 models > show #!11 models > volume #11 level 0.4579 > volume #12 level 0.3937 > volume #13 level 0.4076 > volume #14 level 0.4802 > volume #15 level 0.4586 > volume #16 level 0.4684 > volume #17 level 0.4663 > show #!8 models > volume #8 level 0.4239 > volume #9 level 0.5066 > volume gaussian #9 sDev 4 Opened J110_class_01_00018_volume.mrc gaussian as #18, grid size 100,100,100, pixel 5.73, shown at step 1, values float32 > undo > close #18 > volume gaussian #9 sDev 9 Opened J110_class_01_00018_volume.mrc gaussian as #18, grid size 100,100,100, pixel 5.73, shown at step 1, values float32 > volume gaussian #9 sDev 6 Opened J110_class_01_00018_volume.mrc gaussian as #19, grid size 100,100,100, pixel 5.73, shown at step 1, values float32 > close #18 > volume #19 level 0.3162 > close #19 > volume gaussian #9 sDev 5 Opened J110_class_01_00018_volume.mrc gaussian as #18, grid size 100,100,100, pixel 5.73, shown at step 1, values float32 > volume #18 level 0.2342 > ui tool show ""Segment Map"" Segmenting J110_class_01_00018_volume.mrc gaussian, density threshold 0.234190 Showing 15 region surfaces 235 watershed regions, grouped to 15 regions Showing J110_class_01_00018_volume gaussian.seg - 15 regions, 15 surfaces > undo > close #19 > hide #!10 models > volume save ~/Desktop/mask_60S.mrc #18 Expected a density maps specifier or a keyword > volume save ~/Desktop/mask_60S.mrc models #18 Expected a density maps specifier or a keyword > info models #18 model id #18 type Volume name ""J110_class_01_00018_volume.mrc gaussian"" model id #18.1 type VolumeSurface name surface > volume save ~/Desktop/mask_60S.mrc map #18 Expected a density maps specifier or a keyword > volume save ~/Desktop/mask_60S.mrc Expected a density maps specifier or a keyword > hide #!10 models > volume save ~/Desktop/mask_60S.mrc Expected a density maps specifier or a keyword > volume #18 level 0.1919 > volume #18 level 0.18 > volume #18 level 0.19 > hide #!18 models > show #!9 models > volume #9 level 0.8736 > hide #!9 models > show #!18 models > show #!9 models > volume gaussian #9 sDev 4 Opened J110_class_01_00018_volume.mrc gaussian as #19, grid size 100,100,100, pixel 5.73, shown at step 1, values float32 > hide #!18 models > volume #19 level 0.3912 > volume #19 level 0.3064 > ui tool show ""Segment Map"" Segmenting J110_class_01_00018_volume.mrc gaussian, density threshold 0.306386 Showing 14 region surfaces 300 watershed regions, grouped to 14 regions Showing J110_class_01_00018_volume gaussian.seg - 14 regions, 14 surfaces > volume #19 level 0.2126 > hide #!19 models > show #!19 models > hide #!19 models Drag select of 402, 3000 of 45968 triangles, 400, 391, 96 of 176 triangles, 143 > view matrix models > #20.1,1,0,0,-107.1,0,1,0,78.908,0,0,1,451.03,#20.3,1,0,0,-107.1,0,1,0,78.908,0,0,1,451.03,#20.7,1,0,0,-107.1,0,1,0,78.908,0,0,1,451.03,#20.14,1,0,0,-107.1,0,1,0,78.908,0,0,1,451.03 Drag select of 399, 401, 291, 148 of 160 triangles, 61, 289, 43 of 44 triangles, 158 > select clear Drag select of 398, 401, 291, 396, 61, 287, 158 Deleted 7 regions Drag select of 399, 300, 289 Deleted 3 regions Showing 4 region surfaces > hide #!20 models > show #!20 models Drag select of 402, 344 of 45968 triangles, 400, 391, 143 Drag select of 402, 161 of 45968 triangles, 400, 391, 143 Drag select of 400, 276 of 316 triangles, 391, 166 of 176 triangles, 143 Deleted 3 regions > open /Users/annguyen/Downloads/cryosparc_P8_J123_001_volume_map.mrc Opened cryosparc_P8_J123_001_volume_map.mrc as #21, grid size 250,250,250, pixel 2.29, shown at level 0.226, step 1, values float32 > hide #!20 models > volume #21 level 0.008316 > ui tool show ""Side View"" > volume #21 level 0.1258 > volume #21 level 0.08917 > volume #21 level 0.1319 > close #21 > show #!20 models Saving 1 regions to mrc file... Opened mask_60S.mrc as #21, grid size 68,51,62, pixel 5.73, shown at step 1, values float32 Wrote mask_60S.mrc > volume #21 level 0.3666 > volume resample #21 onGrid #1 Opened mask_60S.mrc resampled as #22, grid size 128,128,128, pixel 4.48, shown at step 1, values float32 > volume resample #21 onGrid #9 Opened mask_60S.mrc resampled as #23, grid size 100,100,100, pixel 5.73, shown at step 1, values float32 > save /Users/annguyen /Desktop/60S_mask_resample128.mrc #22 Cannot determine format for '/Users/annguyen' > save /Users/annguyen/Desktop/60S_mask_resample128.mrc #22 > save /Users/annguyen/Desktop/60S_mask_resample100.mrc #23 > hide #!20 models > hide #!22 models > hide #!23 models > show #!23 models > show #!9 models > hide #!23 models > volume copy #9 Opened J110_class_01_00018_volume.mrc copy as #24, grid size 100,100,100, pixel 5.73, shown at step 1, values float32 > volume #24 level 0.5002 > close #24 > close #23 > show #!22 models > ui tool show ""Side View"" > volume #22 level 0.5978 > volume #22 level 1.008 > close #22 > show #!21 models > ui mousemode right ""map eraser"" > volume #21 level 0.3895 > hide #!21 models > show #!21 models > hide #!21 models > show #!21 models > volume erase #21 center 366.49,382.85,188.29 radius 47.926 > volume erase #21 center 414.79,314.84,262.52 radius 47.926 > volume erase #21 center 380,207.63,280.69 radius 34.873 > volume erase #21 center 377.45,206.56,278.46 radius 34.873 > volume erase #21 center 414.77,268.23,315.92 radius 34.873 > volume erase #21 center 342.16,390.7,312.31 radius 34.873 > volume erase #21 center 327.15,404.07,300.25 radius 34.873 > volume erase #21 center 311.52,413.31,270.86 radius 34.873 > volume erase #21 center 331.81,371.6,435.54 radius 34.873 > volume erase #21 center 363.69,370.71,340.24 radius 34.873 > volume erase #21 center 411.47,344.75,295.78 radius 34.873 > volume erase #21 center 326.97,410.67,238.63 radius 34.873 > volume erase #21 center 291.82,422.85,276.21 radius 34.873 > volume erase #21 center 302.06,399.23,336.25 radius 34.873 > volume erase #21 center 391.69,329.81,350.06 radius 34.873 > volume erase #21 center 277.23,431.84,247.82 radius 34.873 > volume erase #21 center 241.97,413.04,254.94 radius 34.873 > volume #21 level 0.3601 > volume erase #21 center 378.08,372.05,278.19 radius 34.873 > volume erase #21 center 353.27,368.85,289.09 radius 34.873 > volume erase #21 center 300.53,327.59,452.97 radius 34.873 > volume resample #21 onGrid #9 Opened mask_60S.mrc resampled as #23, grid size 100,100,100, pixel 5.73, shown at step 1, values float32 > volume resample #21 onGrid #1 Opened mask_60S.mrc resampled as #24, grid size 128,128,128, pixel 4.48, shown at step 1, values float32 > rename #23 ""mask_60S.mrc resampledb 100"" > rename #23 ""mask_60S.mrc resampled 100"" > rename #24 ""mask_60S.mrc resampled 120"" > save /Users/annguyen/Desktop/60S_mask_resample100.mrc #23 > save /Users/annguyen/Desktop/60S_mask_resample128.mrc #24 > volume #23 level 0.3994 > volume #24 level 0.3539 ===== 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/annguyen/Downloads/cryosparc_P8_J137_mask.mrc Opened cryosparc_P8_J137_mask.mrc as #1, grid size 128,128,128, pixel 4.48, shown at level 1, step 1, values float32 > open /Users/annguyen/Downloads/cryosparc_P8_J137_mask.mrc Opened cryosparc_P8_J137_mask.mrc as #2, grid size 128,128,128, pixel 4.48, shown at level 1, step 1, values float32 OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,7 Model Number: Z16U000NJD/A Chip: Apple M2 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 15.4.1 (24E263) Kernel Version: Darwin 24.4.0 Time since boot: 21 hours, 4 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL P3223QE: Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus) UI Looks like: 2560 x 1440 @ 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-EMalign: 0.1.1 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 finufft: 2.3.1 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