id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17496 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.0-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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unmapped memory 161.3M 1 \npage table in kernel 2955K 1 \nshared memory 3184K 25 \n=========== ======= ======= \nTOTAL 7.1G 6816 \nTOTAL, minus reserved VM space 7.0G 6816 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""efc98aed5d7d559e914647cf3c375014ef2a0f97"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""6246d6a916a70b047e454124"", ""factorPackIds"" : { }, ""deploymentId"" : 240000010 }, { ""rolloutId"" : ""654d8c0661e7447155256fcd"", ""factorPackIds"" : { ""SIRI_TEXT_TO_SPEECH"" : ""67612d1806e0ec00e1336c09"" }, ""deploymentId"" : 240000311 } ], ""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/carolin/Downloads/cryosparc_P170_J161_class_00_00400_volume.mrc Opened cryosparc_P170_J161_class_00_00400_volume.mrc as #1, grid size 96,96,96, pixel 6.75, shown at level 0.244, step 1, values float32 > volume #1 level 0.4187 > volume #1 level 0.9611 > open /Users/carolin/Downloads/cryosparc_P170_J161_class_00_00800_volume.mrc Opened cryosparc_P170_J161_class_00_00800_volume.mrc as #2, grid size 96,96,96, pixel 6.75, shown at level 0.37, step 1, values float32 > volume #2 level 0.5144 > volume #2 level 1.092 > close > open /Users/carolin/Downloads/cryosparc_P313_J24_class_00_final_volume.mrc Opened cryosparc_P313_J24_class_00_final_volume.mrc as #1, grid size 128,128,128, pixel 3.68, shown at level 0.552, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P313_J24_class_01_final_volume.mrc Opened cryosparc_P313_J24_class_01_final_volume.mrc as #2, grid size 128,128,128, pixel 3.68, shown at level 0.459, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P313_J24_class_02_final_volume.mrc Opened cryosparc_P313_J24_class_02_final_volume.mrc as #3, grid size 128,128,128, pixel 3.68, shown at level 0.307, step 1, values float32 > set bgColor white > lighting soft > fitmap #2 inMap #1 Fit map cryosparc_P313_J24_class_01_final_volume.mrc in map cryosparc_P313_J24_class_00_final_volume.mrc using 20970 points correlation = 0.8535, correlation about mean = 0.1809, overlap = 1.039e+04 steps = 288, shift = 7.36, angle = 80.6 degrees Position of cryosparc_P313_J24_class_01_final_volume.mrc (#2) relative to cryosparc_P313_J24_class_00_final_volume.mrc (#1) coordinates: Matrix rotation and translation 0.93342460 0.16182889 -0.32020294 50.44659688 -0.34639681 0.17410728 -0.92178951 492.12860007 -0.09342251 0.97133829 0.21857303 -30.93970909 Axis 0.95940321 -0.11492825 -0.25755967 Axis point 0.00000000 268.12418385 293.62963449 Rotation angle (degrees) 80.61588390 Shift along axis -0.19203228 > fitmap #3 inMap #1 Fit map cryosparc_P313_J24_class_02_final_volume.mrc in map cryosparc_P313_J24_class_00_final_volume.mrc using 20965 points correlation = 0.9003, correlation about mean = 0.5101, overlap = 1.12e+04 steps = 444, shift = 12.1, angle = 89 degrees Position of cryosparc_P313_J24_class_02_final_volume.mrc (#3) relative to cryosparc_P313_J24_class_00_final_volume.mrc (#1) coordinates: Matrix rotation and translation 0.54900639 -0.83579120 -0.00671240 306.07420262 0.26929761 0.16927952 0.94806289 -87.80598230 -0.79124635 -0.52230022 0.31801211 455.59507496 Axis -0.73530266 0.39233159 0.55263543 Axis point 0.00000000 356.18518988 401.51795660 Rotation angle (degrees) 88.96008101 Shift along axis -7.72825732 > volume #1 level 0.4 > volume #2 level 0.4 > volume #3 level 0.4 > fitmap #3 inMap #1 Fit map cryosparc_P313_J24_class_02_final_volume.mrc in map cryosparc_P313_J24_class_00_final_volume.mrc using 15693 points correlation = 0.9173, correlation about mean = 0.411, overlap = 1.043e+04 steps = 44, shift = 0.305, angle = 0.562 degrees Position of cryosparc_P313_J24_class_02_final_volume.mrc (#3) relative to cryosparc_P313_J24_class_00_final_volume.mrc (#1) coordinates: Matrix rotation and translation 0.54220002 -0.84017963 -0.01083193 309.74521129 0.26991031 0.16194638 0.94916900 -86.20486811 -0.79571827 -0.51756310 0.31458047 456.21017006 Axis -0.73339820 0.39246038 0.55506930 Axis point 0.00000000 356.69293757 402.54489425 Rotation angle (degrees) 89.46350678 Shift along axis -7.77031512 > hide #!3 models > hide #!2 models > view name frontal > show #!2 models > select add #2 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.014805,0.98597,-0.16627,25.297,-0.89163,-0.062239,-0.44847,561.81,-0.45252,0.15489,0.8782,92.01 > fitmap #2 inMap #1 Fit map cryosparc_P313_J24_class_01_final_volume.mrc in map cryosparc_P313_J24_class_00_final_volume.mrc using 23144 points correlation = 0.9109, correlation about mean = 0.4148, overlap = 1.265e+04 steps = 948, shift = 19.4, angle = 51.8 degrees Position of cryosparc_P313_J24_class_01_final_volume.mrc (#2) relative to cryosparc_P313_J24_class_00_final_volume.mrc (#1) coordinates: Matrix rotation and translation 0.03891606 0.79184154 0.60948545 -98.98328561 -0.99346808 0.09613877 -0.06146958 464.41357453 -0.10726935 -0.60311218 0.79041064 214.54557259 Axis -0.27100956 0.35862652 -0.89327534 Axis point 168.06499965 328.39841344 0.00000000 Rotation angle (degrees) 92.13575157 Shift along axis 1.72817351 > select subtract #2 Nothing selected > hide #!2 models > show #!3 models > hide #!1 models > show #!1 models > fitmap #3 inMap #1 Fit map cryosparc_P313_J24_class_02_final_volume.mrc in map cryosparc_P313_J24_class_00_final_volume.mrc using 15693 points correlation = 0.9173, correlation about mean = 0.411, overlap = 1.043e+04 steps = 44, shift = 0.00026, angle = 0.00275 degrees Position of cryosparc_P313_J24_class_02_final_volume.mrc (#3) relative to cryosparc_P313_J24_class_00_final_volume.mrc (#1) coordinates: Matrix rotation and translation 0.54223846 -0.84015490 -0.01082598 309.72876905 0.26988892 0.16195635 0.94917338 -86.20339367 -0.79569933 -0.51760012 0.31456746 456.21739952 Axis -0.73341903 0.39245395 0.55504633 Axis point 0.00000000 356.68692335 402.53259190 Rotation angle (degrees) 89.46249264 Shift along axis -7.77003862 > tile 2 models tiled > show #!2 models > tile 3 models tiled > lighting soft > graphics silhouettes true > volume #1 level 0.5 > volume #2 level 0.5 > volume #3 level 0.5 > volume #3 level 0.6 > volume #2 level 0.6 > volume #1 level 0.6 > view frotnal Expected an objects specifier or a view name or a keyword > view frontal > view name frontal > save alfj24.tiff > open /Users/carolin/Downloads/cryosparc_P313_J26_class_00_00182_volume.mrc Opened cryosparc_P313_J26_class_00_00182_volume.mrc as #4, grid size 128,128,128, pixel 3.68, shown at level 0.513, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P313_J26_class_01_00182_volume.mrc Opened cryosparc_P313_J26_class_01_00182_volume.mrc as #5, grid size 128,128,128, pixel 3.68, shown at level 0.578, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P313_J26_class_02_00182_volume.mrc Opened cryosparc_P313_J26_class_02_00182_volume.mrc as #6, grid size 128,128,128, pixel 3.68, shown at level 0.337, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P313_J26_class_03_00182_volume.mrc Opened cryosparc_P313_J26_class_03_00182_volume.mrc as #7, grid size 128,128,128, pixel 3.68, shown at level 0.267, step 1, values float32 > hide #!1 models > hide #!2 models > hide #!3 models > hide #!5 models > hide #!6 models > hide #!7 models > fitmap #5 inMap #4 Fit map cryosparc_P313_J26_class_01_00182_volume.mrc in map cryosparc_P313_J26_class_00_00182_volume.mrc using 20967 points correlation = 0.966, correlation about mean = 0.7158, overlap = 1.533e+04 steps = 84, shift = 5.14, angle = 16.6 degrees Position of cryosparc_P313_J26_class_01_00182_volume.mrc (#5) relative to cryosparc_P313_J26_class_00_00182_volume.mrc (#4) coordinates: Matrix rotation and translation 0.99999687 0.00026556 -0.00248890 0.30498300 -0.00026739 0.99999969 -0.00073678 -0.00577093 0.00248871 0.00073744 0.99999663 -0.63168237 Axis 0.28249362 -0.95381744 -0.10212562 Axis point 247.55249374 0.00000000 104.49995885 Rotation angle (degrees) 0.14950254 Shift along axis 0.15617112 > show #!5 models > show #!6 models > fitmap #6 inMap #4 Fit map cryosparc_P313_J26_class_02_00182_volume.mrc in map cryosparc_P313_J26_class_00_00182_volume.mrc using 20958 points correlation = 0.6926, correlation about mean = 0.1425, overlap = 6006 steps = 108, shift = 16.5, angle = 20.6 degrees Position of cryosparc_P313_J26_class_02_00182_volume.mrc (#6) relative to cryosparc_P313_J26_class_00_00182_volume.mrc (#4) coordinates: Matrix rotation and translation 0.92557940 -0.01515344 -0.37825011 109.76812398 0.05148124 0.99495422 0.08611498 -40.35635960 0.37503661 -0.09917904 0.92168924 -53.58177125 Axis -0.23798417 -0.96749114 0.08558290 Axis point 198.31676511 0.00000000 256.42563724 Rotation angle (degrees) 22.91089002 Shift along axis 8.33566090 > hide #!5 models > select add #6 2 models selected > view matrix models > #6,0.58298,-0.10085,-0.8062,312.08,0.77142,0.38016,0.51028,-152.91,0.25503,-0.91941,0.29942,347.03 > view matrix models > #6,0.58195,-0.10658,-0.80621,313.82,0.77119,0.38694,0.50552,-153.46,0.25808,-0.91592,0.30738,343.45 > view matrix models > #6,0.57105,-0.61634,-0.54225,384.7,0.6201,0.7567,-0.20707,-39.555,0.53795,-0.218,0.8143,-29.053 > view matrix models > #6,0.64768,0.15676,-0.74561,214.72,0.75242,0.022431,0.65831,-91.368,0.11992,-0.98738,-0.10342,495.44 > view matrix models > #6,0.44053,0.83593,-0.32735,-17.864,-0.88444,0.3416,-0.31793,445.97,-0.15394,0.42958,0.88981,-56.3 > view matrix models > #6,-0.0027187,0.94797,-0.31835,53.607,-0.5664,-0.26382,-0.78076,644.47,-0.82412,0.17819,0.53765,251.95 > fitmap #6 inMap #4 Fit map cryosparc_P313_J26_class_02_00182_volume.mrc in map cryosparc_P313_J26_class_00_00182_volume.mrc using 20958 points correlation = 0.8253, correlation about mean = 0.4489, overlap = 7078 steps = 200, shift = 40.4, angle = 34.9 degrees Position of cryosparc_P313_J26_class_02_00182_volume.mrc (#6) relative to cryosparc_P313_J26_class_00_00182_volume.mrc (#4) coordinates: Matrix rotation and translation -0.17342439 0.92003506 -0.35136801 149.48055412 -0.74976995 -0.35467009 -0.55861808 635.19365797 -0.63856794 0.16656717 0.75132309 162.32619812 Axis 0.39348219 0.15583337 -0.90602855 Axis point 342.03443449 278.35146692 0.00000000 Rotation angle (degrees) 112.85408977 Shift along axis 10.73013342 > view matrix models > #6,0.77084,0.43155,0.46858,-148.12,-0.63702,0.51988,0.56914,119.04,0.0020013,-0.73722,0.67565,273.55 > fitmap #6 inMap #4 Fit map cryosparc_P313_J26_class_02_00182_volume.mrc in map cryosparc_P313_J26_class_00_00182_volume.mrc using 20958 points correlation = 0.8252, correlation about mean = 0.4485, overlap = 7078 steps = 664, shift = 28, angle = 28.8 degrees Position of cryosparc_P313_J26_class_02_00182_volume.mrc (#6) relative to cryosparc_P313_J26_class_00_00182_volume.mrc (#4) coordinates: Matrix rotation and translation -0.17375721 0.92121670 -0.34809227 148.48970991 -0.75074022 -0.35266898 -0.55858187 634.90692161 -0.63733630 0.16426924 0.75287322 162.21965244 Axis 0.39192794 0.15682734 -0.90653057 Axis point 341.56041706 278.56335346 0.00000000 Rotation angle (degrees) 112.75407122 Shift along axis 10.71095329 > select subtract #6 Nothing selected > show #!7 models > hide #!6 models > ui mousemode right ""translate selected models"" > undo > select add #7 2 models selected > view matrix models > #7,0.94439,-0.2983,-0.1384,191.22,0.29724,0.95437,-0.028706,-196.82,0.14065,-0.014028,0.98996,-0.16014 > view matrix models > #7,0.94439,-0.2983,-0.1384,199.14,0.29724,0.95437,-0.028706,-212.61,0.14065,-0.014028,0.98996,5.7348 > view matrix models > #7,0.94439,-0.2983,-0.1384,221.02,0.29724,0.95437,-0.028706,-255.94,0.14065,-0.014028,0.98996,21.532 > view matrix models > #7,0.94439,-0.2983,-0.1384,218.89,0.29724,0.95437,-0.028706,-252.08,0.14065,-0.014028,0.98996,20.589 > view matrix models > #7,0.94439,-0.2983,-0.1384,219.01,0.29724,0.95437,-0.028706,-251.61,0.14065,-0.014028,0.98996,19.495 > view matrix models > #7,0.94439,-0.2983,-0.1384,95.413,0.29724,0.95437,-0.028706,-108.38,0.14065,-0.014028,0.98996,99.44 > fitmap #7 inMap #4 Fit map cryosparc_P313_J26_class_03_00182_volume.mrc in map cryosparc_P313_J26_class_00_00182_volume.mrc using 20957 points correlation = 0.5582, correlation about mean = -0.1764, overlap = 2563 steps = 176, shift = 22.9, angle = 23.7 degrees Position of cryosparc_P313_J26_class_03_00182_volume.mrc (#7) relative to cryosparc_P313_J26_class_00_00182_volume.mrc (#4) coordinates: Matrix rotation and translation 0.12232188 0.92143162 -0.36878330 -10.85760242 -0.88910551 0.26685850 0.37185741 358.16569773 0.44105413 0.28240097 0.85189257 -61.74986031 Axis -0.04505673 -0.40789271 -0.91191745 Axis point 195.22295961 202.10265994 0.00000000 Rotation angle (degrees) 83.07693490 Shift along axis -89.29319235 > volume #4 level 0.55 > volume #5 level 0.55 > volume #6 level 0.55 > volume #7 level 0.55 > fitmap #7 inMap #4 Fit map cryosparc_P313_J26_class_03_00182_volume.mrc in map cryosparc_P313_J26_class_00_00182_volume.mrc using 1798 points correlation = 0.1022, correlation about mean = -0.1825, overlap = 26.81 steps = 220, shift = 32.2, angle = 13.3 degrees Position of cryosparc_P313_J26_class_03_00182_volume.mrc (#7) relative to cryosparc_P313_J26_class_00_00182_volume.mrc (#4) coordinates: Matrix rotation and translation -0.00991176 0.97369900 -0.22762252 -52.73881789 -0.94464926 0.06553432 0.32147011 427.00775447 0.32793221 0.21820978 0.91915448 -24.23946071 Axis -0.05163427 -0.27779946 -0.95925042 Axis point 180.81985053 246.62108688 0.00000000 Rotation angle (degrees) 90.72260359 Shift along axis -92.64767943 > view matrix models > #7,0.99338,-0.10641,-0.043393,38.243,0.11314,0.83944,0.53155,-133.75,-0.020134,-0.53293,0.84592,177.95 > fitmap #7 inMap #4 Fit map cryosparc_P313_J26_class_03_00182_volume.mrc in map cryosparc_P313_J26_class_00_00182_volume.mrc using 1798 points correlation = 0.8999, correlation about mean = 0.1705, overlap = 1017 steps = 104, shift = 12.9, angle = 9.32 degrees Position of cryosparc_P313_J26_class_03_00182_volume.mrc (#7) relative to cryosparc_P313_J26_class_00_00182_volume.mrc (#4) coordinates: Matrix rotation and translation 0.14316274 0.97286121 -0.18178421 16.46971930 -0.94509923 0.18890269 0.26665188 343.97859816 0.29375480 0.13362950 0.94649420 -94.50375756 Axis -0.06716585 -0.24010984 -0.96841934 Axis point 216.95278673 173.60980625 0.00000000 Rotation angle (degrees) 81.99382531 Shift along axis 7.82041852 > select subtract #7 Nothing selected > show #!5 models > fitmap #5 inMap #4 Fit map cryosparc_P313_J26_class_01_00182_volume.mrc in map cryosparc_P313_J26_class_00_00182_volume.mrc using 22321 points correlation = 0.9625, correlation about mean = 0.7176, overlap = 1.566e+04 steps = 200, shift = 16.7, angle = 78.9 degrees Position of cryosparc_P313_J26_class_01_00182_volume.mrc (#5) relative to cryosparc_P313_J26_class_00_00182_volume.mrc (#4) coordinates: Matrix rotation and translation 0.99999760 0.00039245 -0.00215542 0.14520985 -0.00039299 0.99999989 -0.00025252 -0.09099416 0.00215533 0.00025337 0.99999764 -0.46703298 Axis 0.11469422 -0.97731055 -0.17807114 Axis point 201.15592837 0.00000000 57.10177919 Rotation angle (degrees) 0.12636110 Shift along axis 0.18874938 > fitmap #6 inMap #4 Fit map cryosparc_P313_J26_class_02_00182_volume.mrc in map cryosparc_P313_J26_class_00_00182_volume.mrc using 10373 points correlation = 0.8997, correlation about mean = 0.324, overlap = 5510 steps = 80, shift = 19.7, angle = 2.87 degrees Position of cryosparc_P313_J26_class_02_00182_volume.mrc (#6) relative to cryosparc_P313_J26_class_00_00182_volume.mrc (#4) coordinates: Matrix rotation and translation -0.13710967 0.91585143 -0.37738190 150.20626048 -0.74138841 -0.34754093 -0.57407189 635.81192410 -0.65692022 0.20107577 0.72665286 165.17839057 Axis 0.41881892 0.15103695 -0.89542088 Axis point 351.35983782 277.28356282 0.00000000 Rotation angle (degrees) 112.27168393 Shift along axis 11.03613400 > tile 4 models tiled > lighting soft > save alfj26.tiff > open /Users/carolin/Downloads/cryosparc_P313_J27_class_00_00182_volume.mrc Opened cryosparc_P313_J27_class_00_00182_volume.mrc as #8, grid size 128,128,128, pixel 3.68, shown at level 0.525, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P313_J27_class_01_00182_volume.mrc Opened cryosparc_P313_J27_class_01_00182_volume.mrc as #9, grid size 128,128,128, pixel 3.68, shown at level 0.586, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P313_J27_class_02_00182_volume.mrc Opened cryosparc_P313_J27_class_02_00182_volume.mrc as #10, grid size 128,128,128, pixel 3.68, shown at level 0.421, step 1, values float32 > hide #!4 models > hide #!5 models > hide #!6 models > hide #!7 models > volume #8 level 0.6 > volume #9 level 0.6 > volume #10 level 0.6 > fitmap #9 inMap #8 Fit map cryosparc_P313_J27_class_01_00182_volume.mrc in map cryosparc_P313_J27_class_00_00182_volume.mrc using 20279 points correlation = 0.9664, correlation about mean = 0.7352, overlap = 1.581e+04 steps = 52, shift = 10.7, angle = 0.335 degrees Position of cryosparc_P313_J27_class_01_00182_volume.mrc (#9) relative to cryosparc_P313_J27_class_00_00182_volume.mrc (#8) coordinates: Matrix rotation and translation 0.99998705 -0.00468447 0.00199101 0.47177414 0.00467873 0.99998492 0.00287574 -1.65980585 -0.00200445 -0.00286639 0.99999388 0.95787959 Axis -0.49129197 0.34184832 0.80110669 Axis point 352.74167076 96.39802506 0.00000000 Rotation angle (degrees) 0.33483345 Shift along axis -0.03181695 > fitmap #10 inMap #8 Fit map cryosparc_P313_J27_class_02_00182_volume.mrc in map cryosparc_P313_J27_class_00_00182_volume.mrc using 9831 points correlation = 0.8033, correlation about mean = 0.3653, overlap = 5284 steps = 244, shift = 14.4, angle = 34.3 degrees Position of cryosparc_P313_J27_class_02_00182_volume.mrc (#10) relative to cryosparc_P313_J27_class_00_00182_volume.mrc (#8) coordinates: Matrix rotation and translation 0.92599708 0.35693024 0.12300496 -96.38902583 -0.37446706 0.82694130 0.41945501 14.07179096 0.04799829 -0.43447542 0.89940384 121.08751775 Axis -0.75781079 0.06656381 -0.64907016 Axis point 0.00000000 255.35096138 71.07283542 Rotation angle (degrees) 34.29259599 Shift along axis -4.61297835 > tile 3 models tiled > lighting full > lighting soft > volume #8 level 0.8292 > volume #8 level 0.8 > volume #9 level 0.8 > volume #10 level 0.8 > save alfj27.tiff > open /Users/carolin/Downloads/cryosparc_P313_J37_002_volume_map_sharp(1).mrc Opened cryosparc_P313_J37_002_volume_map_sharp(1).mrc as #11, grid size 128,128,128, pixel 3.68, shown at level 0.497, step 1, values float32 > fitmap #11 inMap #8 Fit map cryosparc_P313_J37_002_volume_map_sharp(1).mrc in map cryosparc_P313_J27_class_00_00182_volume.mrc using 20961 points correlation = 0.9828, correlation about mean = 0.8461, overlap = 1.89e+04 steps = 116, shift = 1.99, angle = 26.8 degrees Position of cryosparc_P313_J37_002_volume_map_sharp(1).mrc (#11) relative to cryosparc_P313_J27_class_00_00182_volume.mrc (#8) coordinates: Matrix rotation and translation 0.99999875 -0.00147230 0.00058343 0.03399388 0.00147261 0.99999877 -0.00053461 -0.35823122 -0.00058264 0.00053547 0.99999969 -0.11545666 Axis 0.32007048 0.34878321 0.88085479 Axis point 192.21714372 69.83138098 0.00000000 Rotation angle (degrees) 0.09577705 Shift along axis -0.21576515 > hide #!8 models > hide #!9 models > hide #!10 models > volume #11 color silver > volume #11 level 1.186 > volume #11 level 1.1 > save alfj37.tiff > open /Users/carolin/Downloads/cryosparc_P313_J40_004_volume_map_sharp.mrc Opened cryosparc_P313_J40_004_volume_map_sharp.mrc as #12, grid size 256,256,256, pixel 1.84, shown at level 0.163, step 1, values float32 > fitmap #12 inMap #11 Fit map cryosparc_P313_J40_004_volume_map_sharp.mrc in map cryosparc_P313_J37_002_volume_map_sharp(1).mrc using 167639 points correlation = 0.9648, correlation about mean = 0.8088, overlap = 6.194e+04 steps = 132, shift = 1.31, angle = 28.5 degrees Position of cryosparc_P313_J40_004_volume_map_sharp.mrc (#12) relative to cryosparc_P313_J37_002_volume_map_sharp(1).mrc (#11) coordinates: Matrix rotation and translation 0.99997707 -0.00655375 0.00170552 0.88818000 0.00655254 0.99997828 0.00071678 -1.85209056 -0.00171018 -0.00070559 0.99999829 0.39582132 Axis -0.10444334 0.25081234 0.96238493 Axis point 276.33879720 131.74501883 0.00000000 Rotation angle (degrees) 0.39014566 Shift along axis -0.17635918 > volume #12 level 0.5014 > save alfj40.tiff > volume #12 color silver > lighting soft > save alfj40.tiff > open /Users/carolin/Downloads/cryosparc_P313_J41_005_volume_map_sharp(3).mrc Opened cryosparc_P313_J41_005_volume_map_sharp(3).mrc as #13, grid size 256,256,256, pixel 1.84, shown at level 0.152, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P313_J41_005_volume_mask_refine.mrc Opened cryosparc_P313_J41_005_volume_mask_refine.mrc as #14, grid size 256,256,256, pixel 1.84, shown at level 1, step 1, values float32 > fitmap #13 inMap #12 Fit map cryosparc_P313_J41_005_volume_map_sharp(3).mrc in map cryosparc_P313_J40_004_volume_map_sharp.mrc using 167626 points correlation = 0.9768, correlation about mean = 0.8998, overlap = 2.552e+04 steps = 200, shift = 1.22, angle = 28.4 degrees Position of cryosparc_P313_J41_005_volume_map_sharp(3).mrc (#13) relative to cryosparc_P313_J40_004_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation 0.99999194 0.00022343 0.00400860 -0.75781601 -0.00021402 0.99999722 -0.00234724 0.37933142 -0.00400911 0.00234636 0.99998921 0.94349376 Axis 0.50464459 0.86204505 -0.04703372 Axis point 233.69016955 0.00000000 176.95312719 Rotation angle (degrees) 0.26644944 Shift along axis -0.09980300 > hide #!12 models > volume #14 level 0.9704 > fitmap #14 inMap #13 Fit map cryosparc_P313_J41_005_volume_mask_refine.mrc in map cryosparc_P313_J41_005_volume_map_sharp(3).mrc using 713468 points correlation = 0.3897, correlation about mean = 0.1341, overlap = 5.33e+04 steps = 696, shift = 66.7, angle = 84.7 degrees Position of cryosparc_P313_J41_005_volume_mask_refine.mrc (#14) relative to cryosparc_P313_J41_005_volume_map_sharp(3).mrc (#13) coordinates: Matrix rotation and translation -0.24666088 0.86566485 0.43564065 40.12599692 -0.96533965 -0.25905026 -0.03181709 514.07278220 0.08530989 -0.42838922 0.89955817 129.71312169 Axis -0.20807250 0.18381069 -0.96068698 Axis point 204.37564473 257.21944083 0.00000000 Rotation angle (degrees) 107.64247810 Shift along axis -38.47075069 > volume #14 color #b2b2ff33 > volume #13 color silver > select add #14 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #14,-0.53395,-0.77424,-0.33977,655.73,-0.61754,0.082627,0.78219,190.91,-0.57753,0.62747,-0.52225,350.92 > view matrix models > #14,-0.12344,-0.80767,0.57656,370.89,0.2891,0.52654,0.79949,-126.1,-0.94931,0.26537,0.1685,372.37 > view matrix models > #14,0.63447,-0.19692,-0.74745,338.59,-0.36207,0.77864,-0.51248,249.06,0.6829,0.59578,0.42272,-137.65 > view matrix models > #14,0.2404,0.0085662,-0.97064,430.41,-0.77024,0.61021,-0.18538,312.36,0.59071,0.79219,0.1533,-103.79 > view matrix models > #14,0.51626,0.73511,-0.43942,83.464,0.35521,-0.65066,-0.67116,448.41,-0.77929,0.19041,-0.59703,515.21 > view matrix models > #14,0.52742,-0.3603,-0.76943,406.06,0.53549,-0.56213,0.63029,105.73,-0.65961,-0.74444,-0.10354,598.01 > view matrix models > #14,0.58211,-0.44652,-0.67953,394.01,0.48562,-0.47939,0.731,76.407,-0.65217,-0.75552,-0.062219,589.95 > view matrix models > #14,-0.2291,-0.9714,0.062454,544.11,-0.042398,0.074058,0.99635,13.352,-0.97248,0.22562,-0.058152,435.78 > view matrix models > #14,-0.48691,-0.87109,-0.064139,607.91,-0.18481,0.030976,0.98229,59.409,-0.85368,0.49014,-0.17607,372.26 > ui mousemode right ""translate selected models"" > view matrix models > #14,-0.48691,-0.87109,-0.064139,603.66,-0.18481,0.030976,0.98229,86.404,-0.85368,0.49014,-0.17607,338.25 > volume #14 level 0.9889 > ui mousemode right ""rotate selected models"" > view matrix models > #14,0.92193,-0.2561,0.2906,57.787,0.37732,0.76338,-0.52429,110.63,-0.087566,0.59301,0.80042,-73.651 > view matrix models > #14,-0.20063,-0.97108,0.12941,518.76,0.53455,0.0021833,0.84514,-44.242,-0.82098,0.23874,0.51865,239.35 > ui mousemode right ""translate selected models"" > view matrix models > #14,-0.20063,-0.97108,0.12941,525.21,0.53455,0.0021833,0.84514,-75.802,-0.82098,0.23874,0.51865,275.3 > view matrix models > #14,0.40962,-0.24878,-0.87768,461.57,0.63112,-0.61742,0.46956,92.97,-0.65871,-0.74626,-0.095891,580.67 > view matrix models > #14,0.52144,-0.67182,0.52607,200.13,0.28927,0.7192,0.63173,-129.94,-0.80276,-0.17723,0.56936,348.11 > view matrix models > #14,-0.49072,-0.86126,-0.132,623.67,-0.26823,0.0051885,0.96334,76.768,-0.829,0.50813,-0.23356,388.31 > select subtract #14 Nothing selected > select add #14 2 models selected > view matrix models > #14,0.80577,-0.58315,0.10332,200.5,0.58819,0.80834,-0.024829,-61.41,-0.069036,0.080776,0.99434,8.7593 > view matrix models > #14,0.25407,0.6588,0.70812,-99.076,-0.54452,0.70252,-0.45822,328.2,-0.79934,-0.26917,0.53722,366.54 > select subtract #14 Nothing selected > lighting soft > graphics silhouettes false > graphics silhouettes true > volume #13 level 0.4695 > save alfj41.tiff > save /Users/carolin/Documents/SPF1_Paper/ChimeraSessions/alfprocessing.cxs > includeMaps true > open /Users/carolin/Downloads/cryosparc_P170_J160_class_00_final_volume.mrc Opened cryosparc_P170_J160_class_00_final_volume.mrc as #15, grid size 96,96,96, pixel 6.75, shown at level 0.393, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J160_class_01_final_volume.mrc Opened cryosparc_P170_J160_class_01_final_volume.mrc as #16, grid size 96,96,96, pixel 6.75, shown at level 0.41, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J160_class_02_final_volume.mrc Opened cryosparc_P170_J160_class_02_final_volume.mrc as #17, grid size 96,96,96, pixel 6.75, shown at level 0.399, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J161_class_00_final_volume.mrc Opened cryosparc_P170_J161_class_00_final_volume.mrc as #18, grid size 96,96,96, pixel 6.75, shown at level 0.337, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J161_class_01_final_volume.mrc Opened cryosparc_P170_J161_class_01_final_volume.mrc as #19, grid size 96,96,96, pixel 6.75, shown at level 0.326, step 1, values float32 > hide #!13 models > hide #!14 models > tile 5 models tiled > volume #15 level 0.6793 > volume #16 level 0.8266 > volume #17 level 0.8412 > volume #18 level 0.7429 > volume #19 level 0.7241 > fitmap #15 inMap #18 Fit map cryosparc_P170_J160_class_00_final_volume.mrc in map cryosparc_P170_J161_class_00_final_volume.mrc using 4903 points correlation = 0, correlation about mean = 0, overlap = 0 steps = 24, shift = 0, angle = 0 degrees Position of cryosparc_P170_J160_class_00_final_volume.mrc (#15) relative to cryosparc_P170_J161_class_00_final_volume.mrc (#18) coordinates: Matrix rotation and translation 1.00000000 -0.00000000 0.00000000 -122.46418334 0.00000000 1.00000000 -0.00000000 -246.05862001 0.00000000 -0.00000000 1.00000000 845.55959585 Axis -0.46867849 -0.32807494 0.82018736 Axis point -110274440588900864.00000000 1100658185752776960.00000000 0.00000000 Rotation angle (degrees) 0.00000000 Shift along axis 831.63928820 > fitmap #15 inMap #18 Fit map cryosparc_P170_J160_class_00_final_volume.mrc in map cryosparc_P170_J161_class_00_final_volume.mrc using 4903 points correlation = 0.9157, correlation about mean = 0.5077, overlap = 2.583e+04 steps = 88, shift = 11.3, angle = 15.4 degrees Position of cryosparc_P170_J160_class_00_final_volume.mrc (#15) relative to cryosparc_P170_J161_class_00_final_volume.mrc (#18) coordinates: Matrix rotation and translation 0.98397639 -0.17099991 0.05049257 44.53835069 0.17762453 0.96473254 -0.19426951 14.24268666 -0.01549176 0.20012533 0.97964782 -50.67939871 Axis 0.74342667 0.12437919 0.65715036 Axis point 0.00000000 260.95690670 24.92963105 Rotation angle (degrees) 15.38208772 Shift along axis 1.57850653 > fitmap #16 inMap #18 Fit map cryosparc_P170_J160_class_01_final_volume.mrc in map cryosparc_P170_J161_class_00_final_volume.mrc using 5402 points correlation = 0.892, correlation about mean = 0.4338, overlap = 2.677e+04 steps = 124, shift = 20.9, angle = 40.5 degrees Position of cryosparc_P170_J160_class_01_final_volume.mrc (#16) relative to cryosparc_P170_J161_class_00_final_volume.mrc (#18) coordinates: Matrix rotation and translation 0.96768637 -0.12023160 -0.22164714 121.99494111 0.23104853 0.77483785 0.58842406 -201.08016838 0.10099343 -0.62062119 0.77757936 241.84711240 Axis -0.93023158 -0.24823757 0.27027266 Axis point 0.00000000 234.54123185 430.71649652 Rotation angle (degrees) 40.53123599 Shift along axis 1.79676667 > fitmap #17 inMap #18 Fit map cryosparc_P170_J160_class_02_final_volume.mrc in map cryosparc_P170_J161_class_00_final_volume.mrc using 4068 points correlation = 0.8942, correlation about mean = 0.2993, overlap = 2.249e+04 steps = 60, shift = 6.59, angle = 18.7 degrees Position of cryosparc_P170_J160_class_02_final_volume.mrc (#17) relative to cryosparc_P170_J161_class_00_final_volume.mrc (#18) coordinates: Matrix rotation and translation 0.96016765 -0.27840820 -0.02381104 111.78264293 0.27858221 0.94717932 0.15888136 -131.03933140 -0.02168055 -0.15918608 0.98701051 59.39785254 Axis -0.49588609 -0.00332156 0.86838123 Axis point 530.98991206 319.45182554 0.00000000 Rotation angle (degrees) 18.70563537 Shift along axis -3.41622239 > fitmap #19 inMap #18 Fit map cryosparc_P170_J161_class_01_final_volume.mrc in map cryosparc_P170_J161_class_00_final_volume.mrc using 4454 points correlation = 0.9103, correlation about mean = 0.4402, overlap = 2.386e+04 steps = 80, shift = 2.79, angle = 22.6 degrees Position of cryosparc_P170_J161_class_01_final_volume.mrc (#19) relative to cryosparc_P170_J161_class_00_final_volume.mrc (#18) coordinates: Matrix rotation and translation 0.92755971 -0.33720936 -0.16100570 186.53285073 0.32012087 0.93934187 -0.12312388 -43.81231890 0.19275792 0.06266346 0.97924342 -72.36787407 Axis 0.24151687 -0.45988001 0.85450569 Axis point 227.14865079 501.96271354 0.00000000 Rotation angle (degrees) 22.62052432 Shift along axis 3.36047915 > select add #15 2 models selected > view matrix models > #15,0.47906,-0.81799,-0.31842,584.23,0.6813,0.57523,-0.45271,-30.737,0.55348,-6.2955e-05,0.83287,-115.01 > ui mousemode right ""rotate selected models"" > view matrix models > #15,-0.17056,-0.14142,-0.97515,778.38,-0.88106,-0.42123,0.21519,588.83,-0.44119,0.89586,-0.052751,190.39 > view matrix models > #15,-0.19704,-0.18889,-0.96203,798.64,-0.84499,-0.46489,0.26434,575.97,-0.49716,0.86499,-0.068006,223.78 > ui mousemode right ""translate selected models"" > view matrix models > #15,-0.19704,-0.18889,-0.96203,750.05,-0.84499,-0.46489,0.26434,649.45,-0.49716,0.86499,-0.068006,222.19 > fitmap #15 inMap #18 Fit map cryosparc_P170_J160_class_00_final_volume.mrc in map cryosparc_P170_J161_class_00_final_volume.mrc using 4903 points correlation = 0.9289, correlation about mean = 0.584, overlap = 2.644e+04 steps = 52, shift = 13.5, angle = 5.01 degrees Position of cryosparc_P170_J160_class_00_final_volume.mrc (#15) relative to cryosparc_P170_J161_class_00_final_volume.mrc (#18) coordinates: Matrix rotation and translation -0.88077912 0.13820892 -0.45290886 713.49847656 -0.47003455 -0.37113353 0.80082921 331.71615403 -0.05740792 0.91823646 0.39184963 -77.30080868 Axis 0.15974654 -0.53812612 -0.82758765 Axis point 387.41297743 108.90338089 0.00000000 Rotation angle (degrees) 158.43972716 Shift along axis -0.55301830 > select subtract #15 Nothing selected > show #!16 models > hide #!15 models > select add #16 2 models selected > view matrix models > #16,0.37878,-0.26936,-0.88542,612.92,0.67368,0.73622,0.064232,-267.69,0.63457,-0.62082,0.46033,242.13 > ui mousemode right ""rotate selected models"" > view matrix models > #16,0.78634,0.52697,-0.32245,34.877,0.54113,-0.83932,-0.05205,329.73,-0.29807,-0.13356,-0.94515,846.68 > view matrix models > #16,0.72824,0.62551,0.28,-175.72,0.54574,-0.77644,0.31514,187.4,0.41453,-0.076693,-0.9068,583.22 > view matrix models > #16,0.73896,0.64978,0.17812,-153.81,0.52117,-0.71881,0.4601,129.07,0.427,-0.24716,-0.86982,622.89 > ui mousemode right ""translate selected models"" > view matrix models > #16,0.73896,0.64978,0.17812,-192.36,0.52117,-0.71881,0.4601,233.38,0.427,-0.24716,-0.86982,550.14 > fitmap #16 inMap #18 Fit map cryosparc_P170_J160_class_01_final_volume.mrc in map cryosparc_P170_J161_class_00_final_volume.mrc using 5402 points correlation = 0.9954, correlation about mean = 0.9661, overlap = 3.148e+04 steps = 64, shift = 5.51, angle = 14.5 degrees Position of cryosparc_P170_J160_class_01_final_volume.mrc (#16) relative to cryosparc_P170_J161_class_00_final_volume.mrc (#18) coordinates: Matrix rotation and translation 0.99826601 -0.05254094 0.02654119 8.79348161 -0.05884331 -0.90270647 0.42621416 498.59146817 0.00156521 -0.42703687 -0.90423286 754.94601245 Axis -0.99954462 0.02925822 -0.00738294 Axis point 0.00000000 334.06636771 321.54104058 Rotation angle (degrees) 154.73408968 Shift along axis 0.22469910 > select subtract #16 Nothing selected > show #!17 models > hide #!16 models > select add #17 2 models selected > view matrix models > #17,0.40304,-0.69708,-0.59299,659.83,0.74744,0.62462,-0.22624,-172.42,0.5281,-0.35204,0.77277,81.643 > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #17,-0.6504,0.62528,-0.43129,525.71,-0.12196,-0.64638,-0.7532,694.43,-0.74974,-0.43728,0.49667,617.97 > view matrix models > #17,-0.98955,0.14325,-0.016669,656.35,0.073947,0.40474,-0.91144,343.34,-0.12382,-0.90314,-0.4111,860.35 > view matrix models > #17,-0.99187,0.117,-0.050008,676.49,0.091959,0.38753,-0.91726,344.9,-0.087941,-0.9144,-0.39514,847.01 > view matrix models > #17,-0.31488,0.75375,0.57681,44.36,0.021197,0.61315,-0.78968,253.59,-0.94889,-0.23643,-0.20905,849.53 > ui mousemode right ""translate selected models"" > view matrix models > #17,-0.31488,0.75375,0.57681,-4.7819,0.021197,0.61315,-0.78968,372.37,-0.94889,-0.23643,-0.20905,781.65 > view matrix models > #17,-0.31488,0.75375,0.57681,-4.4468,0.021197,0.61315,-0.78968,371.92,-0.94889,-0.23643,-0.20905,781.48 > fitmap #17 inMap #18 Fit map cryosparc_P170_J160_class_02_final_volume.mrc in map cryosparc_P170_J161_class_00_final_volume.mrc using 4068 points correlation = 0.9383, correlation about mean = 0.5788, overlap = 2.377e+04 steps = 84, shift = 8.48, angle = 25.8 degrees Position of cryosparc_P170_J160_class_02_final_volume.mrc (#17) relative to cryosparc_P170_J161_class_00_final_volume.mrc (#18) coordinates: Matrix rotation and translation -0.85786747 0.50328251 0.10377924 406.54378787 -0.12956879 -0.01641727 -0.99143452 688.05563444 -0.49726788 -0.86396597 0.07929355 744.14697858 Axis 0.14451449 0.68142313 -0.71748037 Axis point 390.35631130 631.40624488 0.00000000 Rotation angle (degrees) 153.83080214 Shift along axis -6.30235703 > select subtract #17 Nothing selected > hide #!17 models > show #!19 models > select add #19 2 models selected > view matrix models > #19,0.25337,-0.83421,-0.48979,721.18,0.68859,0.51115,-0.51437,-72.241,0.67945,-0.20694,0.70394,67.226 > ui mousemode right ""rotate selected models"" > view matrix models > #19,0.44937,-0.18646,-0.87367,574.25,0.88136,-0.067137,0.46765,-265.91,-0.14586,-0.98017,0.13417,764.97 > view matrix models > #19,-0.75971,-0.2833,-0.5853,901.68,-0.19694,-0.75758,0.62232,252.91,-0.61972,0.58805,0.51975,290.23 > ui mousemode right ""translate selected models"" > view matrix models > #19,-0.75971,-0.2833,-0.5853,845.41,-0.19694,-0.75758,0.62232,412.25,-0.61972,0.58805,0.51975,181.96 > view matrix models > #19,-0.75971,-0.2833,-0.5853,848.52,-0.19694,-0.75758,0.62232,417.51,-0.61972,0.58805,0.51975,187.84 > fitmap #19 inMap #18 Fit map cryosparc_P170_J161_class_01_final_volume.mrc in map cryosparc_P170_J161_class_00_final_volume.mrc using 4454 points correlation = 0.9715, correlation about mean = 0.7924, overlap = 2.623e+04 steps = 76, shift = 15.9, angle = 28.6 degrees Position of cryosparc_P170_J161_class_01_final_volume.mrc (#19) relative to cryosparc_P170_J161_class_00_final_volume.mrc (#18) coordinates: Matrix rotation and translation -0.99299705 0.10972681 -0.04378224 625.34178817 -0.09206803 -0.48652913 0.86879968 223.59050050 0.07402928 0.86674646 0.49322432 -132.24940590 Axis -0.00878655 -0.50416402 -0.86356322 Axis point 320.86382330 129.17668191 -0.00000000 Rotation angle (degrees) 173.29032233 Shift along axis -4.01515912 > select subtract #19 Nothing selected > show #!17 models > show #!16 models > show #!15 models > tile 5 models tiled > volume #19 level 0.775 > volume #19 level 0.78 > volume #18 level 0.78 > volume #17 level 0.78 > volume #16 level 0.78 > volume #15 level 0.78 > volume #15 level 0.5 > volume #15 level 0.9 > volume #16 level 0.9 > volume #16 level 1.1 > volume #16 level 1.256 > volume #16 level 1.2 > volume #15 level 1.2 > volume #17 level 1.2 > volume #18 level 1.2 > volume #19 level 1.2 > open /Users/carolin/Downloads/cryosparc_P170_J164_class_00_final_volume.mrc Opened cryosparc_P170_J164_class_00_final_volume.mrc as #20, grid size 96,96,96, pixel 6.75, shown at level 0.404, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J164_class_01_final_volume.mrc Opened cryosparc_P170_J164_class_01_final_volume.mrc as #21, grid size 96,96,96, pixel 6.75, shown at level 0.421, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J164_class_02_final_volume.mrc Opened cryosparc_P170_J164_class_02_final_volume.mrc as #22, grid size 96,96,96, pixel 6.75, shown at level 0.405, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J165_class_00_final_volume.mrc Opened cryosparc_P170_J165_class_00_final_volume.mrc as #23, grid size 96,96,96, pixel 6.75, shown at level 0.335, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J165_class_01_final_volume.mrc Opened cryosparc_P170_J165_class_01_final_volume.mrc as #24, grid size 96,96,96, pixel 6.75, shown at level 0.344, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J166_class_00_final_volume.mrc Opened cryosparc_P170_J166_class_00_final_volume.mrc as #25, grid size 96,96,96, pixel 6.75, shown at level 0.343, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J166_class_01_final_volume.mrc Opened cryosparc_P170_J166_class_01_final_volume.mrc as #26, grid size 96,96,96, pixel 6.75, shown at level 0.345, step 1, values float32 > hide #!15 models > hide #!17 models > hide #!16 models > hide #!18 models > hide #!19 models > hide #!26 models > hide #!25 models > hide #!24 models > hide #!23 models > hide #!22 models > hide #!21 models > volume #20 level 1.026 > show #!21 models > hide #!20 models > volume #21 level 0.7912 > show #!22 models > hide #!21 models > volume #22 level 0.7831 > show #!23 models > hide #!22 models > volume #23 level 0.8271 > show #!24 models > hide #!23 models > volume #24 level 0.8703 > show #!25 models > hide #!24 models > volume #25 level 0.7353 > show #!26 models > hide #!25 models > volume #26 level 0.7099 > fitmap #26 inMap #18 Fit map cryosparc_P170_J166_class_01_final_volume.mrc in map cryosparc_P170_J161_class_00_final_volume.mrc using 5398 points correlation = 0.9264, correlation about mean = 0.5791, overlap = 2.686e+04 steps = 252, shift = 302, angle = 10.4 degrees Position of cryosparc_P170_J166_class_01_final_volume.mrc (#26) relative to cryosparc_P170_J161_class_00_final_volume.mrc (#18) coordinates: Matrix rotation and translation 0.99997120 -0.00750197 0.00115438 2.34328074 -0.00428302 -0.43213738 0.90179762 172.24202384 -0.00626640 -0.90177659 -0.43215707 756.37390447 Axis -0.99998994 0.00411445 0.00178474 Axis point 0.00000000 324.26320426 323.95989297 Rotation angle (degrees) 115.60482048 Shift along axis -0.28464568 > show #!18 models > fitmap #25 inMap #18 Fit map cryosparc_P170_J166_class_00_final_volume.mrc in map cryosparc_P170_J161_class_00_final_volume.mrc using 4354 points correlation = 0.9317, correlation about mean = 0.5575, overlap = 2.346e+04 steps = 288, shift = 332, angle = 10.3 degrees Position of cryosparc_P170_J166_class_00_final_volume.mrc (#25) relative to cryosparc_P170_J161_class_00_final_volume.mrc (#18) coordinates: Matrix rotation and translation -0.86533285 -0.41657377 -0.27868508 831.92429569 -0.27672862 -0.06648937 0.95864512 120.86256105 -0.41787600 0.90666724 -0.05774245 188.84105468 Axis -0.25474309 0.68217338 0.68537978 Axis point 446.54583073 -2.50860669 0.00000000 Rotation angle (degrees) 174.14448590 Shift along axis -0.04990361 > fitmap #24 inMap #18 Fit map cryosparc_P170_J165_class_01_final_volume.mrc in map cryosparc_P170_J161_class_00_final_volume.mrc using 5072 points correlation = 0.8929, correlation about mean = 0.3822, overlap = 2.502e+04 steps = 300, shift = 323, angle = 107 degrees Position of cryosparc_P170_J165_class_01_final_volume.mrc (#24) relative to cryosparc_P170_J161_class_00_final_volume.mrc (#18) coordinates: Matrix rotation and translation 0.97763125 0.02394357 0.20895901 -67.67808066 0.15607934 -0.74854069 -0.64445799 717.13579063 0.14098369 0.66265645 -0.73553386 303.10628934 Axis 0.99360019 0.05167129 0.10044272 Axis point 0.00000000 303.10715987 290.36401160 Rotation angle (degrees) 138.87022234 Shift along axis 0.25519723 > select add #24 2 models selected > view matrix models > #24,-0.98482,0.091382,0.14758,687.66,-0.11239,-0.98362,-0.14091,520.44,0.13228,-0.15536,0.97896,299.43 > ui mousemode right ""rotate selected models"" > view matrix models > #24,0.56823,-0.81255,-0.12993,562.35,0.82087,0.57074,0.020624,-335.11,0.057396,-0.11837,0.99131,307.93 > view matrix models > #24,-0.94528,-0.32565,-0.019886,862.87,-0.29537,0.8801,-0.37174,55.203,0.13856,-0.34552,-0.92813,973.43 > view matrix models > #24,-0.56572,-0.82443,-0.016935,898.76,-0.69392,0.48706,-0.53033,362.41,0.44546,-0.28826,-0.84762,829.19 > ui mousemode right ""translate selected models"" > view matrix models > #24,-0.56572,-0.82443,-0.016935,931.59,-0.69392,0.48706,-0.53033,285.79,0.44546,-0.28826,-0.84762,597.35 > fitmap #24 inMap #18 Fit map cryosparc_P170_J165_class_01_final_volume.mrc in map cryosparc_P170_J161_class_00_final_volume.mrc using 5072 points correlation = 0.9956, correlation about mean = 0.9631, overlap = 2.964e+04 steps = 52, shift = 6.16, angle = 4.52 degrees Position of cryosparc_P170_J165_class_01_final_volume.mrc (#24) relative to cryosparc_P170_J161_class_00_final_volume.mrc (#18) coordinates: Matrix rotation and translation 0.99905189 -0.00909148 -0.04257562 17.07347720 -0.00703309 0.93140249 -0.36392302 142.25131501 0.04296364 0.36387742 0.93045547 -109.54049754 Axis 0.99316003 -0.11672729 0.00280888 Axis point 0.00000000 362.68011391 322.53398358 Rotation angle (degrees) 21.49416197 Shift along axis 0.04439774 > select subtract #24 Nothing selected > hide #!24 models > show #!23 models > fitmap #23 inMap #18 Fit map cryosparc_P170_J165_class_00_final_volume.mrc in map cryosparc_P170_J161_class_00_final_volume.mrc using 4178 points correlation = 0.9133, correlation about mean = 0.4551, overlap = 2.249e+04 steps = 468, shift = 317, angle = 113 degrees Position of cryosparc_P170_J165_class_00_final_volume.mrc (#23) relative to cryosparc_P170_J161_class_00_final_volume.mrc (#18) coordinates: Matrix rotation and translation -0.74545362 0.61263126 0.26264396 283.22707961 -0.20683456 0.16197812 -0.96487438 646.24052153 -0.63365478 -0.77359294 0.00596615 785.38627247 Axis 0.15558721 0.72904418 -0.66654873 Axis point 256.45745591 0.00000000 621.05786709 Rotation angle (degrees) 142.06928571 Shift along axis -8.29382405 > ui mousemode right ""rotate selected models"" > select add #23 2 models selected > view matrix models > #23,0.51216,-0.84345,-0.16212,631.41,-0.64542,-0.2534,-0.72057,565.12,0.56668,0.47368,-0.67416,239.95 > fitmap #23 inMap #18 Fit map cryosparc_P170_J165_class_00_final_volume.mrc in map cryosparc_P170_J161_class_00_final_volume.mrc using 4178 points correlation = 0.9718, correlation about mean = 0.7672, overlap = 2.511e+04 steps = 96, shift = 18.8, angle = 48.4 degrees Position of cryosparc_P170_J165_class_00_final_volume.mrc (#23) relative to cryosparc_P170_J161_class_00_final_volume.mrc (#18) coordinates: Matrix rotation and translation 0.99820375 0.05909519 0.00985106 -21.10758573 0.03736970 -0.48564134 -0.87335904 746.00912457 -0.04682724 0.87215839 -0.48697737 223.21169342 Axis 0.99939592 0.03245116 -0.01243893 Axis point 0.00000000 307.77160154 330.63144588 Rotation angle (degrees) 119.15720170 Shift along axis 0.33751103 > select subtract #23 Nothing selected > hide #!23 models > show #!22 models > select add #22 2 models selected > fitmap #232in #18 Missing or invalid ""atomsOrMap"" argument: only initial part ""#232"" of atom specifier valid > fitmap #22 inMap #18 Fit map cryosparc_P170_J164_class_02_final_volume.mrc in map cryosparc_P170_J161_class_00_final_volume.mrc using 4150 points correlation = 0.9314, correlation about mean = 0.5697, overlap = 2.273e+04 steps = 364, shift = 327, angle = 50.2 degrees Position of cryosparc_P170_J164_class_02_final_volume.mrc (#22) relative to cryosparc_P170_J161_class_00_final_volume.mrc (#18) coordinates: Matrix rotation and translation 0.61550187 0.78358917 -0.08453098 -101.48924653 0.03665490 0.07867745 0.99622602 -40.50012442 0.78728259 -0.61627745 0.01970373 266.44140142 Axis -0.81463083 -0.44043701 -0.37734844 Axis point -0.00000000 148.77639578 178.25589806 Rotation angle (degrees) 98.22486577 Shift along axis -0.02722550 > select subtract #22 Nothing selected > hide #!22 models > show #!22 models > hide #!22 models > show #!21 models > fitmap #21 inMap #18 Fit map cryosparc_P170_J164_class_01_final_volume.mrc in map cryosparc_P170_J161_class_00_final_volume.mrc using 5449 points correlation = 0.9935, correlation about mean = 0.9541, overlap = 3.058e+04 steps = 296, shift = 326, angle = 12.6 degrees Position of cryosparc_P170_J164_class_01_final_volume.mrc (#21) relative to cryosparc_P170_J161_class_00_final_volume.mrc (#18) coordinates: Matrix rotation and translation -0.99937338 0.03182502 -0.01549288 643.03467131 0.01998390 0.86858067 0.49514471 -123.68141243 0.02921481 0.49452483 -0.86867238 435.44855463 Axis -0.01340186 -0.96658241 -0.25600554 Axis point 319.77059691 0.00000000 237.95000492 Rotation angle (degrees) 178.67482066 Shift along axis -0.54682171 > hide #!21 models > show #!21 models > hide #!21 models > show #!20 models > fitmap #20 inMap #18 Fit map cryosparc_P170_J164_class_00_final_volume.mrc in map cryosparc_P170_J161_class_00_final_volume.mrc using 4250 points correlation = 0.9048, correlation about mean = 0.3349, overlap = 2.357e+04 steps = 292, shift = 320, angle = 106 degrees Position of cryosparc_P170_J164_class_00_final_volume.mrc (#20) relative to cryosparc_P170_J161_class_00_final_volume.mrc (#18) coordinates: Matrix rotation and translation 0.98156158 -0.19088914 0.00991061 64.16460095 0.17223040 0.86074816 -0.47900868 144.59089826 0.08290701 0.47188342 0.87775423 -136.07929223 Axis 0.93180838 -0.07153142 0.35583199 Axis point 0.00000000 341.65524968 202.68545367 Rotation angle (degrees) 30.67982711 Shift along axis 1.02495491 > select add #20 2 models selected > view matrix models > #20,0.39966,-0.42116,-0.81418,742,0.011618,-0.8858,0.46391,187.88,-0.91659,-0.19487,-0.34913,836.59 > view matrix models > #20,0.38651,-0.56061,0.73234,292.22,-0.4433,0.58338,0.68055,-217.47,-0.80876,-0.58769,-0.02304,825.32 > ui mousemode right ""move picked models"" > ui mousemode right ""translate selected models"" > view matrix models > #20,0.38651,-0.56061,0.73234,327.43,-0.4433,0.58338,0.68055,-233.76,-0.80876,-0.58769,-0.02304,828.42 > view matrix models > #20,0.38651,-0.56061,0.73234,321.54,-0.4433,0.58338,0.68055,-230.89,-0.80876,-0.58769,-0.02304,824.33 > ui mousemode right ""rotate selected models"" > view matrix models > #20,-0.91192,-0.30408,0.27557,804.34,0.13646,0.4086,0.90246,-432.5,-0.38702,0.86057,-0.33112,312.27 > fitmap #20 inMap #18 Fit map cryosparc_P170_J164_class_00_final_volume.mrc in map cryosparc_P170_J161_class_00_final_volume.mrc using 4250 points correlation = 0.9848, correlation about mean = 0.8418, overlap = 2.751e+04 steps = 92, shift = 25.8, angle = 30.1 degrees Position of cryosparc_P170_J164_class_00_final_volume.mrc (#20) relative to cryosparc_P170_J161_class_00_final_volume.mrc (#18) coordinates: Matrix rotation and translation 0.99951585 0.01778590 -0.02552915 3.00359073 0.01735596 0.36227174 0.93191092 -105.84564586 0.02582336 -0.93190282 0.36178765 504.63830918 Axis -0.99962062 -0.02754193 -0.00023059 Axis point 0.00000000 315.74761153 329.65857932 Rotation angle (degrees) 68.78997953 Shift along axis -0.20362193 > select subtract #20 Nothing selected > hide #!18 models > show #!21 models > show #!22 models > show #!23 models > show #!24 models > show #!25 models > show #!26 models > tile 7 models tiled > volume #20 level 1.2 > volume #21 level 1.2 > volume #22 level 1.2 > volume #23 level 1.2 > volume #24 level 1.2 > volume #25 level 1.2 > volume #26 level 1.2 > hide #!26 models > hide #!24 models > show #!24 models > hide #!25 models > hide #!23 models > hide #!22 models > hide #!20 models > show #!18 models > show #!16 models > tile 4 models tiled > tit #18 in #16 Unknown command: tit #18 in #16 > fitmap #18 inMap #16 Fit map cryosparc_P170_J161_class_00_final_volume.mrc in map cryosparc_P170_J160_class_01_final_volume.mrc using 4425 points correlation = 0.9963, correlation about mean = 0.9535, overlap = 3.048e+04 steps = 240, shift = 296, angle = 56.4 degrees Position of cryosparc_P170_J161_class_00_final_volume.mrc (#18) relative to cryosparc_P170_J160_class_01_final_volume.mrc (#16) coordinates: Matrix rotation and translation 0.99817024 -0.06039319 0.00297116 19.38332307 -0.05335972 -0.90290525 -0.42651477 772.99806949 0.02844127 0.42557581 -0.90447571 469.70357103 Axis 0.99951953 -0.02987695 0.00825040 Axis point 0.00000000 334.20385186 321.31224703 Rotation angle (degrees) 154.77018435 Shift along axis 0.15442694 > fitmap #21 inMap #16 Fit map cryosparc_P170_J164_class_01_final_volume.mrc in map cryosparc_P170_J160_class_01_final_volume.mrc using 4542 points correlation = 0.9377, correlation about mean = 0.446, overlap = 2.753e+04 steps = 300, shift = 302, angle = 95 degrees Position of cryosparc_P170_J164_class_01_final_volume.mrc (#21) relative to cryosparc_P170_J160_class_01_final_volume.mrc (#16) coordinates: Matrix rotation and translation 0.88253918 -0.45203187 -0.12958312 229.11996825 -0.43025246 -0.66502744 -0.61042716 876.98162011 0.18975620 0.59447934 -0.78140060 324.78015538 Axis 0.96647958 -0.25614845 0.01746970 Axis point 0.00000000 410.08430542 319.14413181 Rotation angle (degrees) 141.43895195 Shift along axis 2.47610288 > select add #21 2 models selected > view matrix models > #21,-0.29531,-0.95176,0.083343,688.46,0.88837,-0.30564,-0.34262,270.25,0.35156,-0.027138,0.93577,248.45 > view matrix models > #21,-0.31437,-0.93396,-0.16994,771.4,-0.93185,0.26945,0.243,479.86,-0.18116,0.23475,-0.95502,951.63 > fitmap #21 inMap #16 Fit map cryosparc_P170_J164_class_01_final_volume.mrc in map cryosparc_P170_J160_class_01_final_volume.mrc using 4542 points correlation = 0.995, correlation about mean = 0.936, overlap = 3.041e+04 steps = 76, shift = 3.19, angle = 23.9 degrees Position of cryosparc_P170_J164_class_01_final_volume.mrc (#21) relative to cryosparc_P170_J160_class_01_final_volume.mrc (#16) coordinates: Matrix rotation and translation -0.99886427 -0.01798741 -0.04412064 668.52405715 0.02114980 -0.99715942 -0.07228958 664.26784872 -0.04269501 -0.07314062 0.99640734 38.93631522 Axis -0.02172553 -0.03639371 0.99910135 Axis point 331.42946920 336.11982297 0.00000000 Rotation angle (degrees) 178.87772121 Shift along axis 0.20211296 > fitmap #24 inMap #16 Fit map cryosparc_P170_J165_class_01_final_volume.mrc in map cryosparc_P170_J160_class_01_final_volume.mrc using 4350 points correlation = 0.198, correlation about mean = 0.0127, overlap = 1.487e-05 steps = 2000, shift = 81.9, angle = 88.7 degrees Position of cryosparc_P170_J165_class_01_final_volume.mrc (#24) relative to cryosparc_P170_J160_class_01_final_volume.mrc (#16) coordinates: Matrix rotation and translation -0.03911952 -0.07930860 0.99608224 -95.09807352 -0.62972049 -0.77202437 -0.08620025 1152.03171196 0.77583618 -0.63062550 -0.01974103 -54.63059500 Axis -0.67639055 0.27363233 -0.68382832 Axis point 138.92526652 536.37317403 0.00000000 Rotation angle (degrees) 156.26864036 Shift along axis 416.91451284 > select subtract #21 Nothing selected > select add #24 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #24,-0.49343,-0.58355,0.64498,444.57,0.32983,0.56062,0.75955,-187.15,-0.80482,0.58752,-0.084154,739.12 > ui mousemode right ""rotate selected models"" > view matrix models > #24,0.44536,-0.893,-0.064789,467.45,0.881,0.42417,0.20957,-145.29,-0.15966,-0.15041,0.97564,424.78 > fitmap #24 inMap #16 Fit map cryosparc_P170_J165_class_01_final_volume.mrc in map cryosparc_P170_J160_class_01_final_volume.mrc using 4350 points correlation = 0.9957, correlation about mean = 0.9432, overlap = 2.939e+04 steps = 76, shift = 21, angle = 15.7 degrees Position of cryosparc_P170_J165_class_01_final_volume.mrc (#24) relative to cryosparc_P170_J160_class_01_final_volume.mrc (#16) coordinates: Matrix rotation and translation 0.99787402 -0.06254412 -0.01832153 27.23724148 -0.06365651 -0.99563733 -0.06822144 690.69059592 -0.01397475 0.06924268 -0.99750196 629.12252532 Axis 0.99946773 -0.03160438 -0.00808793 Axis point 0.00000000 334.94132893 326.56650507 Rotation angle (degrees) 176.05673357 Shift along axis 0.30559875 > select subtract #24 Nothing selected > tile 4 models tiled > volume #16 level 1.937 > volume #16 level 2 > volume #18 level 2 > volume #21 level 2 > volume #24 level 2 > close #15-26 > open > /Users/carolin/Downloads/cryosparc_P313_J42_class_00_00202_volume(1).mrc Opened cryosparc_P313_J42_class_00_00202_volume(1).mrc as #15, grid size 168,168,168, pixel 2.81, shown at level 0.201, step 1, values float32 > open > /Users/carolin/Downloads/cryosparc_P313_J42_class_01_00202_volume(1).mrc Opened cryosparc_P313_J42_class_01_00202_volume(1).mrc as #16, grid size 168,168,168, pixel 2.81, shown at level 0.224, step 1, values float32 > open > /Users/carolin/Downloads/cryosparc_P313_J42_class_02_00202_volume(1).mrc Opened cryosparc_P313_J42_class_02_00202_volume(1).mrc as #17, grid size 168,168,168, pixel 2.81, shown at level 0.225, step 1, values float32 > tile 3 models tiled > lighting soft > volume #15 level 0.3 > volume #15 level 0.5 > volume #16 level 0.5 > volume #17 level 0.5 > save alfj42.tiff > view frontal > tile 3 models tiled > lighting soft > save alfj42.tiff > open > /Users/carolin/Downloads/cryosparc_P170_J179_class_01_00122_volume_sharp.mrc Opened cryosparc_P170_J179_class_01_00122_volume_sharp.mrc as #18, grid size 128,128,128, pixel 5.07, shown at level 0.16, step 1, values float32 > hide #!15 models > hide #!16 models > hide #!17 models > volume #18 level 0.8477 > volume #18 level 2.04 > close #18 > open /Users/carolin/Downloads/cryosparc_P170_J180_002_volume_map_sharp.mrc Opened cryosparc_P170_J180_002_volume_map_sharp.mrc as #18, grid size 96,96,96, pixel 6.75, shown at level 0.249, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J180_002_volume_mask_refine.mrc Opened cryosparc_P170_J180_002_volume_mask_refine.mrc as #19, grid size 96,96,96, pixel 6.75, shown at level 1, step 1, values float32 > volume #19 level 0.9484 > volume #19 color #ffffb21f > volume #19 level 0.9484 > close #19 > volume #18 level 2.547 > volume #18 level 1.943 > close #18 > open /Users/carolin/Downloads/cryosparc_P170_J181_002_volume_map_sharp.mrc Opened cryosparc_P170_J181_002_volume_map_sharp.mrc as #18, grid size 96,96,96, pixel 6.75, shown at level 0.196, step 1, values float32 > volume #18 level 2.723 > volume #18 level 1.789 > close #18 > open /Users/carolin/Documents/SPF1_Paper/maps_models/APO20241220.pdb Chain information for APO20241220.pdb #18 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available > open /Users/carolin/Downloads/cryosparc_P170_J180_002_volume_mask_refine.mrc Opened cryosparc_P170_J180_002_volume_mask_refine.mrc as #19, grid size 96,96,96, pixel 6.75, shown at level 1, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J181_002_volume_map_sharp.mrc Opened cryosparc_P170_J181_002_volume_map_sharp.mrc as #20, grid size 96,96,96, pixel 6.75, shown at level 0.196, step 1, values float32 > close #19 > volume #20 level 0.6357 > fitmap #18 inMap #20 Fit molecule APO20241220.pdb (#18) to map cryosparc_P170_J181_002_volume_map_sharp.mrc (#20) using 23607 atoms average map value = 0.02718, steps = 140 shifted from previous position = 20.7 rotated from previous position = 36.5 degrees atoms outside contour = 23607, contour level = 0.63567 Position of APO20241220.pdb (#18) relative to cryosparc_P170_J181_002_volume_map_sharp.mrc (#20) coordinates: Matrix rotation and translation -0.32116171 -0.64710050 0.69145941 177.04936005 -0.23164981 0.76163793 0.60518265 120.60403837 -0.91825570 0.03418506 -0.39450965 487.38293015 Axis -0.32483863 0.91576157 0.23634851 Axis point 255.35184537 0.00000000 152.86284711 Rotation angle (degrees) 118.49073947 Shift along axis 168.12430317 > select add #20 2 models selected > view matrix models > #20,-0.1209,-0.42225,-0.89838,806.91,0.77435,-0.60638,0.18079,202.13,-0.6211,-0.67381,0.40028,599.22 > view matrix models > #20,0.0076028,0.21617,-0.97633,581.72,0.91374,-0.39813,-0.081033,174.88,-0.40622,-0.8915,-0.20055,798.62 > select add #18 23607 atoms, 24130 bonds, 10 pseudobonds, 3005 residues, 4 models selected > select subtract #20 23607 atoms, 24130 bonds, 10 pseudobonds, 3005 residues, 2 models selected > view matrix models > #18,0.97801,0.19311,0.078768,-37.674,0.18476,-0.97745,0.10224,355.78,0.096735,-0.085437,-0.99164,364.42 > view matrix models > #18,-0.04733,-0.86845,0.49351,274.12,-0.9075,0.24383,0.34205,261.63,-0.41739,-0.43167,-0.79965,487.04 > close #20 > open /Users/carolin/Downloads/cryosparc_P170_J181_002_volume_map_sharp.mrc Opened cryosparc_P170_J181_002_volume_map_sharp.mrc as #19, grid size 96,96,96, pixel 6.75, shown at level 0.196, step 1, values float32 > volume #19 level 0.8005 > view matrix models > #18,0.93705,0.01427,0.3489,-44.747,0.26948,-0.66497,-0.69656,425.65,0.22207,0.74674,-0.62695,111.95 > view matrix models > #18,0.91012,-0.23006,0.3446,8.8537,0.24301,-0.37722,-0.89367,409.65,0.33559,0.8971,-0.28741,0.43178 > ui mousemode right ""translate selected models"" > view matrix models > #18,0.91012,-0.23006,0.3446,-27.09,0.24301,-0.37722,-0.89367,405.62,0.33559,0.8971,-0.28741,99.801 > view matrix models > #18,-0.46826,-0.063637,0.8813,77.542,0.15219,0.97669,0.15139,-0.94279,-0.87038,0.20501,-0.44766,427.94 > view matrix models > #18,0.67558,-0.69292,0.25191,128.43,0.19306,0.496,0.84659,-58.552,-0.71156,-0.5233,0.46887,377.48 > fitmap #18 inMap #19 Fit molecule APO20241220.pdb (#18) to map cryosparc_P170_J181_002_volume_map_sharp.mrc (#19) using 23607 atoms average map value = 0.08262, steps = 92 shifted from previous position = 40 rotated from previous position = 11.8 degrees atoms outside contour = 23607, contour level = 0.80046 Position of APO20241220.pdb (#18) relative to cryosparc_P170_J181_002_volume_map_sharp.mrc (#19) coordinates: Matrix rotation and translation -0.77565110 -0.17717289 0.60578472 260.19474098 0.62385221 -0.36086093 0.69324441 302.89541302 0.09577992 0.91563593 0.39043186 43.16094273 Axis 0.22802442 0.52292260 0.82131408 Axis point 97.08109933 169.79780489 0.00000000 Rotation angle (degrees) 150.81386134 Shift along axis 253.17030073 > select subtract #18 Nothing selected > close #19 > close #18 > save /Users/carolin/Documents/SPF1_Paper/ChimeraSessions/alfprocessing.cxs > includeMaps true > close session > open /Users/carolin/Documents/SPF1_Paper/maps_models/APO20241220.pdb Chain information for APO20241220.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available > open /Users/carolin/Downloads/cryosparc_P170_J181_002_volume_map_sharp.mrc Opened cryosparc_P170_J181_002_volume_map_sharp.mrc as #2, grid size 96,96,96, pixel 6.75, shown at level 0.196, step 1, values float32 > volume #2 level 0.6337 > select add #2 2 models selected > select subtract #2 Nothing selected > select add #1 23607 atoms, 24130 bonds, 10 pseudobonds, 3005 residues, 2 models selected > view matrix models #1,1,0,0,100.32,0,1,0,154.16,0,0,1,165.97 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.61621,-0.52694,0.58534,378.54,0.77246,-0.25945,0.57964,161.58,-0.15357,0.80934,0.56691,112.57 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.61621,-0.52694,0.58534,421.45,0.77246,-0.25945,0.57964,126.48,-0.15357,0.80934,0.56691,111.59 > fitmap #1 inMap #2 Fit molecule APO20241220.pdb (#1) to map cryosparc_P170_J181_002_volume_map_sharp.mrc (#2) using 23607 atoms average map value = 2.392, steps = 132 shifted from previous position = 13.6 rotated from previous position = 54.4 degrees atoms outside contour = 2536, contour level = 0.63372 Position of APO20241220.pdb (#1) relative to cryosparc_P170_J181_002_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation -0.71094814 0.37654396 0.59394225 270.36247369 0.56938839 -0.18746887 0.80040758 117.18744789 0.41273432 0.90723210 -0.08111912 104.50174480 Axis 0.37433520 0.63499009 0.67576678 Axis point 108.31565871 18.94998707 0.00000000 Rotation angle (degrees) 171.79671728 Shift along axis 246.23786714 > color #2 #b2b2b288 models > color #2 #b2b2b287 models > open /Users/carolin/Downloads/cryosparc_P170_J183_map.mrc Opened cryosparc_P170_J183_map.mrc as #3, grid size 128,128,128, pixel 5.07, shown at level 0.154, step 1, values float32 > select subtract #1 Nothing selected > hide #!2 models > volume #3 level 1.214 > select add #1 23607 atoms, 24130 bonds, 10 pseudobonds, 3005 residues, 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.95641,0.11261,-0.26943,523.09,0.25447,-0.13116,-0.95814,482.75,-0.14324,-0.98494,0.096789,541.47 > view matrix models > #1,-0.97183,0.019915,-0.23484,537.7,0.23452,0.1805,-0.95521,424.3,0.023365,-0.98337,-0.18008,562.8 > fitmap #1 inMap #3 Fit molecule APO20241220.pdb (#1) to map cryosparc_P170_J183_map.mrc (#3) using 23607 atoms average map value = 1.835, steps = 100 shifted from previous position = 35.7 rotated from previous position = 14.7 degrees atoms outside contour = 3555, contour level = 1.2144 Position of APO20241220.pdb (#1) relative to cryosparc_P170_J183_map.mrc (#3) coordinates: Matrix rotation and translation -0.99017523 0.12203678 -0.06826457 484.52972895 0.07232097 0.02911947 -0.99695624 486.84717979 -0.11967750 -0.99209833 -0.03765919 528.06068899 Axis 0.06776871 0.71721944 -0.69354429 Axis point 226.00034819 0.00000000 493.37663767 Rotation angle (degrees) 177.94597407 Shift along axis 15.77874268 > molmap #1 16 onGrid #3 Opened APO20241220.pdb map 16 as #4, grid size 128,128,128, pixel 5.07, shown at level 0.0443, step 1, values float32 > molmap #1 20 onGrid #3 Opened APO20241220.pdb map 20 as #4, grid size 128,128,128, pixel 5.07, shown at level 0.0371, step 1, values float32 > molmap #1 30 onGrid #3 Opened APO20241220.pdb map 30 as #4, grid size 128,128,128, pixel 5.07, shown at level 0.0253, step 1, values float32 > molmap #1 40 onGrid #3 Opened APO20241220.pdb map 40 as #4, grid size 128,128,128, pixel 5.07, shown at level 0.019, step 1, values float32 > molmap #1 60 onGrid #3 Opened APO20241220.pdb map 60 as #4, grid size 128,128,128, pixel 5.07, shown at level 0.0114, step 1, values float32 > molmap #1 50 onGrid #3 Opened APO20241220.pdb map 50 as #4, grid size 128,128,128, pixel 5.07, shown at level 0.0145, step 1, values float32 > volume #4 level 0.01452 > save /Users/carolin/Desktop/masks/20250426_test1_apo50.mrc models #4 > open /Users/carolin/Downloads/cryosparc_P170_J185_mask.mrc Opened cryosparc_P170_J185_mask.mrc as #5, grid size 128,128,128, pixel 5.07, shown at level 0.933, step 1, values float32 > hide #!3 models > show #!3 models > volume #5 level 0.7338 > volume #5 level 0.793 > volume #5 level 0.9094 > open /Users/carolin/Downloads/cryosparc_P170_J186_mask.mrc Opened cryosparc_P170_J186_mask.mrc as #6, grid size 128,128,128, pixel 5.07, shown at level 1, step 1, values float32 > hide #!5 models > volume #6 level 1 > hide #!6 models > open /Users/carolin/Downloads/cryosparc_P170_J187_004_volume_map_sharp.mrc Opened cryosparc_P170_J187_004_volume_map_sharp.mrc as #7, grid size 96,96,96, pixel 6.75, shown at level 0.0712, step 1, values float32 > hide #!4 models > hide #!3 models > hide #!1 models > select subtract #1 Nothing selected > volume #7 level 3.43 > volume #7 level 2.342 > open /Users/carolin/Downloads/cryosparc_P170_J190_007_volume_map_sharp.mrc Opened cryosparc_P170_J190_007_volume_map_sharp.mrc as #8, grid size 344,344,344, pixel 1.89, shown at level 0.162, step 2, values float32 > hide #!7 models > open /Users/carolin/Downloads/cryosparc_P170_J191_004_volume_map_sharp.mrc Opened cryosparc_P170_J191_004_volume_map_sharp.mrc as #9, grid size 344,344,344, pixel 1.89, shown at level 0.0393, step 2, values float32 > volume #8 level 0.9666 > hide #!9 models > volume #8 level 1.178 > show #!1 models > show cartoons > hide atoms > volume #8 level 0.8819 > volume #8 level 0.628 > show #!9 models > hide #!8 models > volume #9 level 0.6361 > volume #9 level 0.285 > open /Users/carolin/Downloads/cryosparc_P170_J192_class_00_00073_volume.mrc Opened cryosparc_P170_J192_class_00_00073_volume.mrc as #10, grid size 144,144,144, pixel 4.5, shown at level 0.1, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J192_class_01_00073_volume.mrc Opened cryosparc_P170_J192_class_01_00073_volume.mrc as #11, grid size 144,144,144, pixel 4.5, shown at level 0.11, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J192_class_02_00073_volume.mrc Opened cryosparc_P170_J192_class_02_00073_volume.mrc as #12, grid size 144,144,144, pixel 4.5, shown at level 0.117, step 1, values float32 > hide #!9 models > hide #!12 models > hide #!11 models > volume #10 level 1.88 > volume #11 level 1.928 > volume #12 level 1.879 > open > /Users/carolin/Downloads/cryosparc_P170_J193_class_00_00142_volume_sharp.mrc Opened cryosparc_P170_J193_class_00_00142_volume_sharp.mrc as #13, grid size 128,128,128, pixel 5.07, shown at level 0.156, step 1, values float32 > open > /Users/carolin/Downloads/cryosparc_P170_J193_class_01_00142_volume_sharp.mrc Opened cryosparc_P170_J193_class_01_00142_volume_sharp.mrc as #14, grid size 128,128,128, pixel 5.07, shown at level 0.155, step 1, values float32 > open > /Users/carolin/Downloads/cryosparc_P170_J193_class_02_00142_volume_sharp.mrc Opened cryosparc_P170_J193_class_02_00142_volume_sharp.mrc as #15, grid size 128,128,128, pixel 5.07, shown at level 0.315, step 1, values float32 > hide #!10 models > hide #!15 models > hide #!14 models > volume #13 level 1.413 > volume #14 level 1.41 > volume #15 level 1.549 > volume #15 level 2.535 > open /Users/carolin/Downloads/cryosparc_P170_J194_class_00_00072_volume.mrc Opened cryosparc_P170_J194_class_00_00072_volume.mrc as #16, grid size 144,144,144, pixel 4.5, shown at level 0.125, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J194_class_01_00072_volume.mrc Opened cryosparc_P170_J194_class_01_00072_volume.mrc as #17, grid size 144,144,144, pixel 4.5, shown at level 0.108, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J194_class_02_00072_volume.mrc Opened cryosparc_P170_J194_class_02_00072_volume.mrc as #18, grid size 144,144,144, pixel 4.5, shown at level 0.103, step 1, values float32 > hide #!15 models > hide #!17 models > hide #!18 models > volume #16 level 1.921 > volume #17 level 2.053 > volume #18 level 1.938 > show #!15 models > hide #!15 models > show #!13 models > hide #!18 models > volume #13 level 2.033 > show #!14 models > hide #!13 models > volume #14 level 2.054 > hide #!14 models > show #!8 models > molmap #1/a-h 40 onGrid #8 Opened APO20241220.pdb map 40 as #19, grid size 172,172,172, pixel 3.77, shown at level 0.0162, step 1, values float32 > molmap #1/a-g/h:1-155 40 onGrid #8 Opened APO20241220.pdb map 40 as #20, grid size 172,172,172, pixel 3.77, shown at level 0.0171, step 1, values float32 > molmap #1/a-g/h:1-150 40 onGrid #8 Opened APO20241220.pdb map 40 as #21, grid size 172,172,172, pixel 3.77, shown at level 0.0172, step 1, values float32 > hide #!19 models > hide #!20 models > show #!20 models > hide #!20 models > save /Users/carolin/Desktop/masks/20250426_EMC40A.mrc models #21 > open /Users/carolin/Downloads/cryosparc_P170_J195_class_00_00044_volume.mrc Opened cryosparc_P170_J195_class_00_00044_volume.mrc as #22, grid size 144,144,144, pixel 4.5, shown at level 0.152, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J195_class_01_00044_volume.mrc Opened cryosparc_P170_J195_class_01_00044_volume.mrc as #23, grid size 144,144,144, pixel 4.5, shown at level 0.137, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J195_class_02_00044_volume.mrc Opened cryosparc_P170_J195_class_02_00044_volume.mrc as #24, grid size 144,144,144, pixel 4.5, shown at level 0.113, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J195_class_03_00044_volume.mrc Opened cryosparc_P170_J195_class_03_00044_volume.mrc as #25, grid size 144,144,144, pixel 4.5, shown at level 0.136, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J195_class_04_00044_volume.mrc Opened cryosparc_P170_J195_class_04_00044_volume.mrc as #26, grid size 144,144,144, pixel 4.5, shown at level 0.127, step 1, values float32 > hide #!21 models > hide #!26 models > hide #!25 models > hide #!24 models > hide #!23 models > volume #22 level 1.808 > hide #!8 models > hide #!1 models > volume #22 level 1.799 > volume #22 level 1.789 > volume #22 level 1.78 > volume #22 level 1.742 > volume #22 level 1.733 > volume #22 level 1.676 > volume #22 level 1.638 > volume #22 level 1.628 > volume #22 level 1.619 > volume #22 level 1.609 > volume #22 level 1.6 > volume #22 level 1.591 > volume #22 level 1.581 > volume #22 level 1.572 > volume #22 level 1.562 > volume #22 level 1.553 > volume #22 level 1.543 > volume #23 level 1.482 > volume #23 level 1.945 > volume #24 level 1.992 > volume #25 level 1.904 > volume #26 level 1.898 > open /Users/carolin/Downloads/cryosparc_P170_J200_003_volume_map_sharp.mrc Opened cryosparc_P170_J200_003_volume_map_sharp.mrc as #27, grid size 344,344,344, pixel 1.89, shown at level 0.107, step 2, values float32 > hide #!27 models > hide #!26 models > show #!27 models > volume #27 level 0.8784 > volume #27 step 1 > volume #27 level 1.09 > open /Users/carolin/Downloads/cryosparc_P170_J201_003_volume_map_sharp.mrc Opened cryosparc_P170_J201_003_volume_map_sharp.mrc as #28, grid size 344,344,344, pixel 1.89, shown at level 0.0953, step 2, values float32 > hide #!27 models > volume #28 level 0.8289 > volume #28 step 1 > show #!27 models > volume #28 level 0.7666 > lighting soft > volume #28 level 0.6794 > show #!19 models > hide #!19 models > open /Users/carolin/Downloads/cryosparc_P170_J202_002_volume_map_sharp.mrc Opened cryosparc_P170_J202_002_volume_map_sharp.mrc as #29, grid size 344,344,344, pixel 1.89, shown at level 0.0145, step 2, values float32 > volume #29 level 0.3244 > volume #29 level 0.5104 > close #29 > show #!1 models > show #!27 models > molmap #1/i 40 onGrid #27 Opened APO20241220.pdb map 40 as #29, grid size 344,344,344, pixel 1.89, shown at level 0.015, step 1, values float32 > save /Users/carolin/Desktop/masks/20250426_spf140A.mrc models #29 > show #!13 models > show #!14 models > show #!15 models > hide #!27 models > hide #!29 models > open /Users/carolin/Downloads/cryosparc_P170_J208_class_00_00071_volume.mrc Opened cryosparc_P170_J208_class_00_00071_volume.mrc as #30, grid size 144,144,144, pixel 4.5, shown at level 0.088, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J208_class_01_00071_volume.mrc Opened cryosparc_P170_J208_class_01_00071_volume.mrc as #31, grid size 144,144,144, pixel 4.5, shown at level 0.101, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J208_class_02_00071_volume.mrc Opened cryosparc_P170_J208_class_02_00071_volume.mrc as #32, grid size 144,144,144, pixel 4.5, shown at level 0.0999, step 1, values float32 > hide #!13 models > hide #!14 models > hide #!15 models > hide #!32 models > hide #!31 models > volume #30 level 1.551 > volume #30 level 1.969 > volume #31 level 1.835 > volume #32 level 0.3419 > volume #32 level 2.025 > show #!31 models > hide #!32 models > volume #31 level 2.153 > volume #30 level 2.148 > show #!32 models > hide #!30 models > open /Users/carolin/Downloads/cryosparc_P170_J207_class_00_00072_volume.mrc Opened cryosparc_P170_J207_class_00_00072_volume.mrc as #33, grid size 144,144,144, pixel 4.5, shown at level 0.153, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J207_class_01_00072_volume.mrc Opened cryosparc_P170_J207_class_01_00072_volume.mrc as #34, grid size 144,144,144, pixel 4.5, shown at level 0.0968, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J207_class_02_00072_volume.mrc Opened cryosparc_P170_J207_class_02_00072_volume.mrc as #35, grid size 144,144,144, pixel 4.5, shown at level 0.116, step 1, values float32 > hide #!32 models > volume #33 level 1.951 > volume #34 level 1.958 > volume #35 level 2.092 > volume #35 level 1.991 > open /Users/carolin/Downloads/cryosparc_P170_J205_005_volume_map_sharp.mrc Opened cryosparc_P170_J205_005_volume_map_sharp.mrc as #36, grid size 344,344,344, pixel 1.89, shown at level 0.111, step 2, values float32 > volume #36 level 0.9435 > close #36 > open /Users/carolin/Downloads/cryosparc_P170_J209_002_volume_map_sharp.mrc Opened cryosparc_P170_J209_002_volume_map_sharp.mrc as #36, grid size 344,344,344, pixel 1.89, shown at level 0.0328, step 2, values float32 > volume #36 level 0.4467 > hide #!34 models > volume #36 level 0.6287 > volume #36 level 0.5847 > volume #36 level 0.57 > open > /Users/carolin/Downloads/cryosparc_P170_J211_class_01_00122_volume_sharp.mrc Opened cryosparc_P170_J211_class_01_00122_volume_sharp.mrc as #37, grid size 128,128,128, pixel 5.07, shown at level 0.142, step 1, values float32 > open > /Users/carolin/Downloads/cryosparc_P170_J211_class_00_00122_volume_sharp.mrc Opened cryosparc_P170_J211_class_00_00122_volume_sharp.mrc as #38, grid size 128,128,128, pixel 5.07, shown at level 0.167, step 1, values float32 > hide #!36 models > volume #37 level 0.5175 > volume #38 level 1.005 > volume #37 level 0.8162 > volume #38 level 1.682 > volume #37 level 1.651 > hide #!37 models > hide #!38 models > show #!27 models > open /Users/carolin/Downloads/cryosparc_P170_J213_002_volume_map_sharp.mrc Opened cryosparc_P170_J213_002_volume_map_sharp.mrc as #39, grid size 344,344,344, pixel 1.89, shown at level 0.217, step 2, values float32 > volume #39 level 0.9873 > volume #39 level 1.062 > hide #!27 models > show #!27 models > hide #!27 models > show #!27 models > hide #!27 models > volume #39 level 0.931 > volume #39 color silver > volume #39 color #c0c0c081 > volume #39 color #c0c0c082 > show #!27 models > hide #!27 models > volume #39 level 0.9686 > volume #39 step 1 > volume #39 level 1.235 > open 7kra 7kra title: Cryo-EM structure of Saccharomyces cerevisiae ER membrane protein complex bound to Fab-DH4 in lipid nanodiscs [more info...] Chain information for 7kra #40 --- Chain | Description | UniProt A | ER membrane protein complex subunit 1 | EMC1_YEAST 1-760 B | ER membrane protein complex subunit 2 | EMC2_YEAST 1-292 C | ER membrane protein complex subunit 3 | EMC3_YEAST 1-253 D | ER membrane protein complex subunit 4 | EMC4_YEAST 1-190 E | ER membrane protein complex subunit 5 | EMC5_YEAST 1-141 F | ER membrane protein complex subunit 6 | EMC6_YEAST 1-108 G | Protein SOP4 | SOP4_YEAST 1-234 H | Endoplasmic reticulum membrane protein complex subunit 10 | EMC10_YEAST 1-205 I | Fab DH4 heavy chain | J | Fab DH4 light chain | M N | Unassigned helix | Non-standard residues in 7kra #40 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) X3P — [(2~{R})-1-octanoyloxy-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy- propan-2-yl] nonanoate > matchmaker #40 to #1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker APO20241220.pdb, chain A (#1) with 7kra, chain A (#40), sequence alignment score = 3137.5 RMSD between 611 pruned atom pairs is 0.934 angstroms; (across all 685 pairs: 1.508) > show cartoons > style stick Changed 40900 atom styles > hide #!40 models > ui tool show ""Side View"" > fitmap #1 inMap #39 Fit molecule APO20241220.pdb (#1) to map cryosparc_P170_J213_002_volume_map_sharp.mrc (#39) using 23607 atoms average map value = 0.6934, steps = 68 shifted from previous position = 1.2 rotated from previous position = 1.17 degrees atoms outside contour = 18053, contour level = 1.2347 Position of APO20241220.pdb (#1) relative to cryosparc_P170_J213_002_volume_map_sharp.mrc (#39) coordinates: Matrix rotation and translation -0.99001667 0.11310033 -0.08411492 489.56979553 0.08669399 0.01807300 -0.99607104 486.07985759 -0.11113575 -0.99341919 -0.02769768 524.02542093 Axis 0.07001742 0.71343708 -0.69721237 Axis point 224.48307530 -0.00000000 496.28380955 Rotation angle (degrees) 178.91492016 Shift along axis 15.70880406 > open /Users/carolin/Downloads/cryosparc_P170_J215_003_volume_map_sharp.mrc Opened cryosparc_P170_J215_003_volume_map_sharp.mrc as #41, grid size 344,344,344, pixel 1.89, shown at level 0.211, step 2, values float32 > volume #41 level 1.015 > open /Users/carolin/Downloads/cryosparc_P170_J216_volume_map_sharp.mrc Opened cryosparc_P170_J216_volume_map_sharp.mrc as #42, grid size 344,344,344, pixel 1.89, shown at level 0.0128, step 2, values float32 > close #41 > volume #42 level 0.1239 > close #42 > show #!35 models > show #!34 models > show #!33 models > show #!32 models > hide #!32 models > hide #!39 models > volume #35 level 1.677 > volume #34 level 1.67 > volume #33 level 1.682 > open /Users/carolin/Downloads/cryosparc_P170_J219_class_00_00035_volume.mrc Opened cryosparc_P170_J219_class_00_00035_volume.mrc as #41, grid size 144,144,144, pixel 4.5, shown at level 0.119, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J219_class_01_00035_volume.mrc Opened cryosparc_P170_J219_class_01_00035_volume.mrc as #42, grid size 144,144,144, pixel 4.5, shown at level 0.128, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J219_class_02_00035_volume.mrc Opened cryosparc_P170_J219_class_02_00035_volume.mrc as #43, grid size 144,144,144, pixel 4.5, shown at level 0.122, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J219_class_03_00035_volume.mrc Opened cryosparc_P170_J219_class_03_00035_volume.mrc as #44, grid size 144,144,144, pixel 4.5, shown at level 0.124, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J219_class_04_00035_volume.mrc Opened cryosparc_P170_J219_class_04_00035_volume.mrc as #45, grid size 144,144,144, pixel 4.5, shown at level 0.123, step 1, values float32 > volume #41 level 0.5144 > volume #42 level 0.7609 > volume #43 level 0.9581 > volume #44 level 0.9443 > volume #45 level 1.147 > open /Users/carolin/Downloads/cryosparc_P170_J220_class_00_00036_volume.mrc Opened cryosparc_P170_J220_class_00_00036_volume.mrc as #46, grid size 270,270,270, pixel 2.4, shown at level 0.0475, step 2, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J220_class_01_00036_volume.mrc Opened cryosparc_P170_J220_class_01_00036_volume.mrc as #47, grid size 270,270,270, pixel 2.4, shown at level 0.0487, step 2, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J220_class_04_00036_volume.mrc Opened cryosparc_P170_J220_class_04_00036_volume.mrc as #48, grid size 270,270,270, pixel 2.4, shown at level 0.0502, step 2, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J220_class_02_00036_volume.mrc Opened cryosparc_P170_J220_class_02_00036_volume.mrc as #49, grid size 270,270,270, pixel 2.4, shown at level 0.0499, step 2, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J220_class_03_00036_volume.mrc Opened cryosparc_P170_J220_class_03_00036_volume.mrc as #50, grid size 270,270,270, pixel 2.4, shown at level 0.0508, step 2, values float32 > volume #46 level 0.425 > volume #47 level 0.4348 > volume #48 level 0.4562 > volume #49 level 0.2485 > volume #50 level 0.2246 > open /Users/carolin/Downloads/cryosparc_P170_J217_class_00_00162_volume.mrc Opened cryosparc_P170_J217_class_00_00162_volume.mrc as #51, grid size 128,128,128, pixel 5.07, shown at level 0.203, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J217_class_01_00162_volume.mrc Opened cryosparc_P170_J217_class_01_00162_volume.mrc as #52, grid size 128,128,128, pixel 5.07, shown at level 0.151, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J217_class_02_00162_volume.mrc Opened cryosparc_P170_J217_class_02_00162_volume.mrc as #53, grid size 128,128,128, pixel 5.07, shown at level 0.145, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J217_class_03_00162_volume.mrc Opened cryosparc_P170_J217_class_03_00162_volume.mrc as #54, grid size 128,128,128, pixel 5.07, shown at level 0.291, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J217_class_04_00162_volume.mrc Opened cryosparc_P170_J217_class_04_00162_volume.mrc as #55, grid size 128,128,128, pixel 5.07, shown at level 0.334, step 1, values float32 > volume #51 level 0.5933 > volume #51 level 0.6323 > volume #52 level 0.5785 > volume #53 level 0.6455 > volume #54 level 0.9569 > volume #55 level 0.9983 > open /Users/carolin/Downloads/cryosparc_P170_J218_class_00_00162_volume.mrc Opened cryosparc_P170_J218_class_00_00162_volume.mrc as #56, grid size 128,128,128, pixel 5.07, shown at level 0.238, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J218_class_01_00162_volume.mrc Opened cryosparc_P170_J218_class_01_00162_volume.mrc as #57, grid size 128,128,128, pixel 5.07, shown at level 0.274, step 1, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J218_class_02_00162_volume.mrc Opened cryosparc_P170_J218_class_02_00162_volume.mrc as #58, grid size 128,128,128, pixel 5.07, shown at level 0.157, step 1, values float32 > volume #56 level 0.492 > volume #57 level 0.6287 > volume #58 level 0.5978 > open /Users/carolin/Downloads/cryosparc_P170_J210_mask.mrc Opened cryosparc_P170_J210_mask.mrc as #59, grid size 344,344,344, pixel 1.89, shown at level 0.412, step 2, values float32 > volume #59 level 0.009242 > open /Users/carolin/Downloads/cryosparc_P170_J204_mask.mrc Opened cryosparc_P170_J204_mask.mrc as #60, grid size 344,344,344, pixel 1.89, shown at level 5e-05, step 2, values float32 > hide #!59 models > volume #60 level 0.01484 > show #!29 models > hide #!60 models > hide #!58 models > volume #29 level 0.08033 > open /Users/carolin/Downloads/cryosparc_P170_J221_002_volume_map_sharp.mrc Opened cryosparc_P170_J221_002_volume_map_sharp.mrc as #61, grid size 344,344,344, pixel 1.89, shown at level 0.0121, step 2, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J222_002_volume_map_sharp.mrc Opened cryosparc_P170_J222_002_volume_map_sharp.mrc as #62, grid size 344,344,344, pixel 1.89, shown at level 0.00848, step 2, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J224_003_volume_map_sharp.mrc Opened cryosparc_P170_J224_003_volume_map_sharp.mrc as #63, grid size 344,344,344, pixel 1.89, shown at level 0.0226, step 2, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J223_001_volume_map_sharp.mrc Opened cryosparc_P170_J223_001_volume_map_sharp.mrc as #64, grid size 344,344,344, pixel 1.89, shown at level 0.00816, step 2, values float32 > open /Users/carolin/Downloads/cryosparc_P170_J225_002_volume_map_sharp.mrc Opened cryosparc_P170_J225_002_volume_map_sharp.mrc as #65, grid size 344,344,344, pixel 1.89, shown at level 0.0571, step 2, values float32 > hide #!29 models > hide #!62 models > hide #!63 models > hide #!64 models > hide #!65 models > volume #61 level 0.03005 > volume #62 level 0.03962 > volume #63 level 0.0656 > volume #64 level 0.01838 > open /Users/carolin/Downloads/cryosparc_P170_J226_005_volume_map_sharp.mrc Opened cryosparc_P170_J226_005_volume_map_sharp.mrc as #66, grid size 344,344,344, pixel 1.89, shown at level 0.0911, step 2, values float32 > volume #66 level 0.4862 > open /Users/carolin/Downloads/cryosparc_P170_J227_004_volume_map_sharp.mrc Opened cryosparc_P170_J227_004_volume_map_sharp.mrc as #67, grid size 344,344,344, pixel 1.89, shown at level 0.00696, step 2, values float32 > volume #67 level 0.2846 > volume #67 level 0.06693 > volume #67 level 0.2091 > hide #!67 models > show #!4 models > hide #!1 models > show #!2 models > open /Users/carolin/Downloads/cryosparc_P170_J230_002_volume_map_sharp.mrc Opened cryosparc_P170_J230_002_volume_map_sharp.mrc as #68, grid size 344,344,344, pixel 1.89, shown at level 0.014, step 2, values float32 > hide #!2 models > open /Users/carolin/Downloads/cryosparc_P170_J232_002_volume_map_sharp.mrc Opened cryosparc_P170_J232_002_volume_map_sharp.mrc as #69, grid size 344,344,344, pixel 1.89, shown at level 0.00476, step 2, values float32 > volume #68 level 0.07975 > open /Users/carolin/Downloads/cryosparc_P170_J231_002_volume_map_sharp.mrc Opened cryosparc_P170_J231_002_volume_map_sharp.mrc as #70, grid size 344,344,344, pixel 1.89, shown at level 0.00517, step 2, values float32 > volume #69 level 0.04329 > hide #!4 models > show #!1 models > hide #!70 models > hide #!69 models > volume #68 level 0.4587 > volume #69 level 0.2076 > volume #70 level 0.2004 > hide #!70 models > show #!2 models > hide #!1 models > show #!39 models > color #39 silver models > color #39 #fffb00ff models > select add #2 2 models selected > view matrix models > #2,0.57817,-0.61801,-0.53271,516.3,-0.43525,-0.78586,0.4393,581.63,-0.69013,-0.022124,-0.72335,802.57 > view matrix models > #2,0.54168,-0.8206,-0.18219,478.71,-0.74107,-0.5685,0.35723,637.73,-0.39672,-0.058489,-0.91607,782.11 > view matrix models > #2,0.42012,-0.64918,-0.63409,611.73,-0.39021,-0.76008,0.51963,531.9,-0.81929,0.029124,-0.57264,778.29 > show #!3 models > hide #!2 models > select subtract #2 Nothing selected > volume copy #3 Opened cryosparc_P170_J183_map.mrc copy as #71, grid size 128,128,128, pixel 5.07, shown at step 1, values float32 > ui mousemode right ""map eraser"" > hide #!39 models > hide #!71 models > show #!71 models > show #!3 models > hide #!3 models > volume erase #71 center 323.88,308.64,265.06 radius 34.692 > volume erase #71 center 322.95,366.56,267.18 radius 34.692 > volume erase #71 center 335.35,367.77,245.17 radius 34.692 > volume erase #71 center 356.91,296.37,268.66 radius 23.344 > volume erase #71 center 349.48,286.65,273.14 radius 23.344 > volume erase #71 center 294.68,320.76,267.39 radius 23.344 > volume erase #71 center 289.47,338.66,269.12 radius 23.344 > volume erase #71 center 285.2,308.92,278.9 radius 23.344 > volume erase #71 center 279.51,335.63,285 radius 17.832 > volume erase #71 center 360.51,323.06,273.64 radius 17.832 > volume erase #71 center 333.99,335.67,277.06 radius 17.832 > volume erase #71 center 310.85,337.95,273.99 radius 17.832 > volume erase #71 center 289.07,360.29,278.22 radius 17.832 > volume #71 level 0.8455 > ui mousemode right ""map eraser"" > volume erase #71 center 358.39,364.19,262.79 radius 26.407 > volume erase #71 center 356.5,336.32,249.66 radius 26.407 > volume erase #71 center 323.39,309.41,232.56 radius 26.407 > volume erase #71 center 304.36,321.89,245.91 radius 26.407 > volume erase #71 center 334.64,397.4,282.27 radius 19.013 > volume erase #71 center 330.7,278.36,285.29 radius 10.431 > save /Users/carolin/Desktop/masks/20250417_EMCmaskbasedonj183.mrc models #71 > hide #!71 models > hide #72 models > open /Users/carolin/Downloads/cryosparc_P170_J229_004_volume_map_sharp.mrc Opened cryosparc_P170_J229_004_volume_map_sharp.mrc as #72, grid size 344,344,344, pixel 1.89, shown at level 0.111, step 2, values float32 > volume #72 level 0.8747 > volume #72 step 1 > volume #72 level 1 > volume #72 level 0.5295 > show #!1 models > volume #72 level 1.079 > open /Users/carolin/Downloads/cryosparc_P170_J235_002_volume_map_sharp.mrc Opened cryosparc_P170_J235_002_volume_map_sharp.mrc as #73, grid size 344,344,344, pixel 1.89, shown at level 0.0914, step 2, values float32 > hide #!72 models > volume #73 level 0.8491 > volume #73 level 0.7165 > open /Users/carolin/Downloads/cryosparc_P170_J238_volume_map.mrc Opened cryosparc_P170_J238_volume_map.mrc as #74, grid size 344,344,344, pixel 1.89, shown at level 0.00971, step 2, values float32 > volume #74 level 0.03086 ===== 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 - 89.3 OpenGL renderer: Apple M1 Max OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,4 Model Number: Z15G0009HD/A Chip: Apple M1 Max Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 32 GB System Firmware Version: 11881.1.1 OS Loader Version: 11881.1.1 Software: System Software Overview: System Version: macOS 15.0 (24A335) Kernel Version: Darwin 24.0.0 Time since boot: 3 days, 16 hours, 48 minutes Graphics/Displays: Apple M1 Max: Chipset Model: Apple M1 Max Type: GPU Bus: Built-In Total Number of Cores: 32 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal PL2792QN: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 75.00Hz 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: 3.10.0 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: 2.2.2 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 plotly: 5.24.1 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 pyKVFinder: 0.7.2 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 tenacity: 9.0.0 tifffile: 2024.7.24 tinyarray: 1.2.4 toml: 0.10.2 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