id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18161 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.1.1-x86_64-i386-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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Total=10.5G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=10.5G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG image 2068K 45 \nCG raster data 8K 1 \nColorSync 264K 35 \nCoreAnimation 1276K 120 \nCoreGraphics 16K 3 \nCoreImage 24K 2 \nCoreUI image data 5144K 40 \nDispatch continuations 96.0M 1 \nFoundation 32K 2 \nIOKit 15.5M 2 \nKernel Alloc Once 8K 1 \nMALLOC 9.0G 648 \nMALLOC guard page 96K 24 \nMach message 16K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 160K 40 \nStack 163.3M 41 \nStack Guard 56.0M 1 \nVM_ALLOCATE 1.2G 423 \nVM_ALLOCATE (reserved) 96.0M 2 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 45.5M 789 \n__DATA_CONST 65.1M 460 \n__DATA_DIRTY 1849K 231 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 211.0M 149 \n__OBJC_RO 70.8M 1 \n__OBJC_RW 2157K 3 \n__TEXT 1.0G 795 \ndyld private memory 292K 4 \nmapped file 538.0M 94 \nshared memory 3512K 32 \n=========== ======= ======= \nTOTAL 12.5G 4003 \nTOTAL, minus reserved VM space 12.5G 4003 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""80dbd6617593c7ca9402bff45d4eacc1c423943e"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""62745b8e85854550ad70b6e4"", ""factorPackIds"" : { }, ""deploymentId"" : 240000073 }, { ""rolloutId"" : ""644114de41e7236e6177f9bd"", ""factorPackIds"" : { }, ""deploymentId"" : 240000013 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/tessasmith/Downloads/cryosparc_P45_EscVc_monomer_16.mrc Opened cryosparc_P45_EscVc_monomer_16.mrc as #1, grid size 288,288,288, pixel 1.11, shown at level 1.78e-05, step 2, values float32 > open ""/Users/tessasmith/Downloads/cryosparc_P45_J213_011_volume_map (1).mrc"" Opened cryosparc_P45_J213_011_volume_map (1).mrc as #2, grid size 288,288,288, pixel 1.11, shown at level 0.0821, step 2, values float32 > volume #1 step 1 > volume #2 step 1 > volume #1 level 0.05753 > volume #2 level 0.08591 > volume #2 level 0.06588 > open ""/Users/tessasmith/Nextcloud/Tess/Phenix > Data/EscV_325-675/EscVc_Final.pdb"" Chain information for EscVc_Final.pdb #3 --- Chain | Description A B C D E F G H I | No description available > hide #3 models > show #3 models > hide atoms > show cartoons > ui mousemode right ""translate selected models"" > select add #3 23976 atoms, 24363 bonds, 2970 residues, 1 model selected > view matrix models > #3,-0.56576,0.81393,0.13205,107.76,0.82023,0.57192,-0.010999,-67.348,-0.084476,0.10209,-0.99118,380.09 > view matrix models > #3,-0.56576,0.81393,0.13205,93.518,0.82023,0.57192,-0.010999,-88.972,-0.084476,0.10209,-0.99118,375.26 Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 1 atomic models, 2 maps. > view matrix models > #3,-0.56576,0.81393,0.13205,89.354,0.82023,0.57192,-0.010999,-83.258,-0.084476,0.10209,-0.99118,376.67 > view matrix models > #3,-0.87829,0.443,0.17988,200.3,0.46729,0.87496,0.12681,-100.73,-0.10121,0.19543,-0.97548,360.23 Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 1 atomic models, 2 maps. > hide #!1 models > fitmap #3 inMap #2 Fit molecule EscVc_Final.pdb (#3) to map cryosparc_P45_J213_011_volume_map (1).mrc (#2) using 23976 atoms average map value = 0.1286, steps = 120 shifted from previous position = 2.49 rotated from previous position = 13.4 degrees atoms outside contour = 4277, contour level = 0.065877 Position of EscVc_Final.pdb (#3) relative to cryosparc_P45_J213_011_volume_map (1).mrc (#2) coordinates: Matrix rotation and translation -0.91971052 0.39259694 0.00045105 252.51848360 0.39259709 0.91971052 0.00031027 -73.03445419 -0.00029302 0.00046244 -0.99999985 381.98409842 Axis 0.20036319 0.97972167 0.00019695 Axis point 133.76440556 0.00000000 190.97451615 Rotation angle (degrees) 179.97824291 Shift along axis -20.88279594 > select subtract #3 Nothing selected > show #!1 models > color #2 #ffffb288 models > volume #2 level 0.09467 > volume #2 level 0.06963 > hide #3 models > hide #!1 models > volume gaussian #2 sDev 2 Opened cryosparc_P45_J213_011_volume_map (1).mrc gaussian as #4, grid size 288,288,288, pixel 1.11, shown at step 1, values float32 > volume #4 level 0.04306 > volume copy #4 Opened cryosparc_P45_J213_011_volume_map (1).mrc gaussian copy as #5, grid size 288,288,288, pixel 1.11, shown at step 1, values float32 > volume #5 level 0.0463 > volume #5 level 0.03217 > ui mousemode right ""map eraser"" > volume erase #5 center 210.71,170.58,189.5 radius 50.828 outside true > volume erase #5 center 189.03,140.56,198.97 radius 20.876 > volume erase #5 center 203.8,127.53,209.74 radius 20.876 > volume erase #5 center 225.79,125.06,191.8 radius 20.876 > volume erase #5 center 207.41,129,179.08 radius 20.876 > volume erase #5 center 187.92,120.07,181.26 radius 20.876 > show #3 models > volume erase #5 center 193.43,128.62,156.76 radius 20.868 > volume erase #5 center 208.12,136.95,155.57 radius 20.868 > volume erase #5 center 217.06,142.08,175.67 radius 17.682 > volume erase #5 center 219.27,135.88,185.21 radius 17.682 > volume erase #5 center 193.97,142.96,184.37 radius 17.682 > volume erase #5 center 208.02,146.92,141.18 radius 17.682 > volume erase #5 center 201.1,161.63,139.34 radius 17.682 > volume erase #5 center 221.57,167.14,142.41 radius 17.682 > volume erase #5 center 229.74,167.98,144.6 radius 17.682 > volume erase #5 center 206.1,157.53,142.67 radius 17.682 > volume erase #5 center 204.09,178.34,140.04 radius 17.682 > volume erase #5 center 211.82,188.87,138.88 radius 17.682 > volume erase #5 center 192.14,172.26,143.68 radius 17.682 > color #5 #b2ffffbb models > color #5 #b2ffffbd models > volume erase #5 center 195.54,199.27,148.45 radius 17.682 > volume erase #5 center 206.93,213.16,149.09 radius 17.682 > volume erase #5 center 194.89,215.55,163.43 radius 17.682 > volume erase #5 center 186.05,205.04,167.57 radius 17.682 > volume erase #5 center 184.49,188.09,172.13 radius 7.3278 > volume erase #5 center 199.19,214.35,192.49 radius 14.974 > volume erase #5 center 211.59,212.4,201.4 radius 14.974 > volume erase #5 center 209.66,202.05,212.58 radius 14.974 > volume erase #5 center 192.64,200.25,215.72 radius 14.974 > volume erase #5 center 173.36,195.88,209.28 radius 14.974 > volume erase #5 center 166.31,189.98,199.1 radius 14.974 > volume erase #5 center 173.37,194.72,188.31 radius 14.974 > volume erase #5 center 187.24,204.55,195.07 radius 14.974 > volume erase #5 center 181.62,189.35,202.17 radius 8.7615 > volume erase #5 center 173.07,182.67,192.51 radius 8.7615 > volume erase #5 center 184.13,192.38,182.04 radius 8.7615 > volume erase #5 center 180.71,188.4,192.45 radius 8.7615 > volume erase #5 center 189.64,195.12,195.5 radius 8.7615 > volume erase #5 center 187.03,211.66,180.21 radius 8.7615 > volume erase #5 center 197.2,202.88,179.14 radius 8.7615 > volume erase #5 center 202.59,202.18,191.58 radius 8.7615 > volume erase #5 center 200.14,200.34,193.86 radius 8.7615 > volume erase #5 center 206.24,219.51,185.09 radius 8.7615 > volume erase #5 center 207.99,196.07,200.96 radius 8.7615 > volume erase #5 center 197.37,191.8,205.95 radius 8.7615 > volume erase #5 center 201.34,191.57,200.78 radius 8.7615 > volume erase #5 center 204.18,191.19,202.39 radius 8.7615 > hide #3 models > hide #6 models > ui mousemode right ""translate selected models"" > ui mousemode right zoom > ui mousemode right ""translate selected models"" > show #6 models > ui mousemode right ""map eraser"" > volume erase #5 center 172.3,205.49,187.88 radius 8.7615 > hide #6 models > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > save /Users/tessasmith/Desktop/EscVc-EspA_monomer.mrc models #5 > open > /Users/tessasmith/Downloads/cryosparc_P45_J216_class_00_00270_volume.mrc Opened cryosparc_P45_J216_class_00_00270_volume.mrc as #7, grid size 72,72,72, pixel 4.42, shown at level 0.586, step 1, values float32 > hide #!5 models > volume #7 level 0.4026 > open > /Users/tessasmith/Downloads/cryosparc_P45_J216_class_01_00270_volume.mrc Opened cryosparc_P45_J216_class_01_00270_volume.mrc as #6, grid size 72,72,72, pixel 4.42, shown at level 0.586, step 1, values float32 > volume #7 level 0.3259 > open ""/Users/tessasmith/Downloads/cryosparc_P45_J216_class_01_00270_volume > (1).mrc"" Opened cryosparc_P45_J216_class_01_00270_volume (1).mrc as #8, grid size 72,72,72, pixel 4.42, shown at level 0.586, step 1, values float32 > hide #!7 models > hide #!6 models > hide #!8 models > show #!7 models > hide #!7 models > show #!8 models > volume #8 level 0.3492 > hide #!8 models > show #!5 models > open ""/Users/tessasmith/Downloads/cryosparc_P45_J213_011_volume_map (2).mrc"" Opened cryosparc_P45_J213_011_volume_map (2).mrc as #9, grid size 288,288,288, pixel 1.11, shown at level 0.0821, step 2, values float32 > hide #!5 models > volume #9 step 1 > volume #9 level 0.05895 > open > /Users/tessasmith/Downloads/cryosparc_P45_J219_class_00_00270_volume.mrc Opened cryosparc_P45_J219_class_00_00270_volume.mrc as #10, grid size 72,72,72, pixel 4.42, shown at level 0.586, step 1, values float32 > open > /Users/tessasmith/Downloads/cryosparc_P45_J219_class_01_00270_volume.mrc Opened cryosparc_P45_J219_class_01_00270_volume.mrc as #11, grid size 72,72,72, pixel 4.42, shown at level 0.586, step 1, values float32 > hide #!9 models > hide #!11 models > show #!11 models > volume #10 level 0.3894 > volume #11 level 0.3494 > volume #10 level 0.3594 > hide #!11 models > hide #!10 models > show #!4 models > show #3 models > hide #!4 models > show #!5 models > hide #3 models > show #!1 models > open /Users/tessasmith/Downloads/cryosparc_P45_J231_006_volume_map.mrc Opened cryosparc_P45_J231_006_volume_map.mrc as #12, grid size 288,288,288, pixel 1.11, shown at level 0.0814, step 2, values float32 > hide #!5 models > hide #!1 models > volume #12 step 1 > volume #12 level 0.05559 > volume #12 level 0.0543 > open > /Users/tessasmith/Downloads/cryosparc_P45_J229_class_00_00966_volume.mrc Opened cryosparc_P45_J229_class_00_00966_volume.mrc as #13, grid size 84,84,84, pixel 3.79, shown at level 0.482, step 1, values float32 > hide #!12 models > open > /Users/tessasmith/Downloads/cryosparc_P45_J229_class_01_00966_volume.mrc Opened cryosparc_P45_J229_class_01_00966_volume.mrc as #14, grid size 84,84,84, pixel 3.79, shown at level 0.482, step 1, values float32 > show #!2 models > hide #!2 models > show #!5 models > hide #!5 models > volume #13 level 0.4529 > volume #14 level 0.4851 > open /Users/tessasmith/Downloads/cryosparc_P45_J233_map_all_classes.cs Unrecognized file suffix '.cs' > open > /Users/tessasmith/Downloads/cryosparc_P45_J233_map_all_classes/J233_volume_class_01_map.mrc Opened J233_volume_class_01_map.mrc as #15, grid size 288,288,288, pixel 1.11, shown at level 0.0826, step 2, values float32 > open > /Users/tessasmith/Downloads/cryosparc_P45_J233_map_all_classes/J233_volume_class_00_map.mrc Opened J233_volume_class_00_map.mrc as #16, grid size 288,288,288, pixel 1.11, shown at level 0.0828, step 2, values float32 > hide #!13 models > hide #!14 models > volume #15 step 1 > volume #16 step 1 > hide #!15 models > volume #16 level 0.06426 > hide #!16 models > show #!15 models > volume #15 level 0.06731 > volume #15 level 0.05476 > hide #!15 models > show #!16 models > hide #!16 models > show #!15 models > open /Users/tessasmith/Downloads/cryosparc_P45_J232_003_volume_map.mrc Opened cryosparc_P45_J232_003_volume_map.mrc as #17, grid size 288,288,288, pixel 1.11, shown at level 0.0819, step 2, values float32 > hide #!15 models > volume #17 step 1 > show #!1 models > hide #!1 models > volume #17 level 0.05888 > close #2 > close #4 > close #6 > close #7 > close #8 > close #10 > close #11 > close #12 > close #13 > close #14 > close #15 > close #16 > volume #17 level 0.1292 > toolshed show > open > /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_018.mrc > /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_019.mrc > /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_009.mrc > /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_010.mrc > /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_011.mrc > /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_012.mrc > /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_013.mrc > /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_014.mrc > /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_015.mrc > /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_016.mrc > /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_017.mrc > /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_000.mrc > /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_001.mrc > /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_002.mrc > /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_003.mrc > /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_004.mrc > /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_005.mrc > /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_006.mrc > /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_007.mrc > /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_008.mrc Opened J235_component_000_frame_018.mrc as #2.1, grid size 288,288,288, pixel 1.11, shown at level 0.0755, step 2, values float32 Opened J235_component_000_frame_019.mrc as #2.2, grid size 288,288,288, pixel 1.11, shown at level 0.0757, step 2, values float32 Opened J235_component_000_frame_009.mrc as #2.3, grid size 288,288,288, pixel 1.11, shown at level 0.0743, step 2, values float32 Opened J235_component_000_frame_010.mrc as #2.4, grid size 288,288,288, pixel 1.11, shown at level 0.0743, step 2, values float32 Opened J235_component_000_frame_011.mrc as #2.5, grid size 288,288,288, pixel 1.11, shown at level 0.0744, step 2, values float32 Opened J235_component_000_frame_012.mrc as #2.6, grid size 288,288,288, pixel 1.11, shown at level 0.0745, step 2, values float32 Opened J235_component_000_frame_013.mrc as #2.7, grid size 288,288,288, pixel 1.11, shown at level 0.0747, step 2, values float32 Opened J235_component_000_frame_014.mrc as #2.8, grid size 288,288,288, pixel 1.11, shown at level 0.0749, step 2, values float32 Opened J235_component_000_frame_015.mrc as #2.9, grid size 288,288,288, pixel 1.11, shown at level 0.075, step 2, values float32 Opened J235_component_000_frame_016.mrc as #2.10, grid size 288,288,288, pixel 1.11, shown at level 0.0752, step 2, values float32 Opened J235_component_000_frame_017.mrc as #2.11, grid size 288,288,288, pixel 1.11, shown at level 0.0753, step 2, values float32 Opened J235_component_000_frame_000.mrc as #2.12, grid size 288,288,288, pixel 1.11, shown at level 0.0755, step 2, values float32 Opened J235_component_000_frame_001.mrc as #2.13, grid size 288,288,288, pixel 1.11, shown at level 0.0753, step 2, values float32 Opened J235_component_000_frame_002.mrc as #2.14, grid size 288,288,288, pixel 1.11, shown at level 0.0753, step 2, values float32 Opened J235_component_000_frame_003.mrc as #2.15, grid size 288,288,288, pixel 1.11, shown at level 0.0751, step 2, values float32 Opened J235_component_000_frame_004.mrc as #2.16, grid size 288,288,288, pixel 1.11, shown at level 0.0749, step 2, values float32 Opened J235_component_000_frame_005.mrc as #2.17, grid size 288,288,288, pixel 1.11, shown at level 0.0748, step 2, values float32 Opened J235_component_000_frame_006.mrc as #2.18, grid size 288,288,288, pixel 1.11, shown at level 0.0746, step 2, values float32 Opened J235_component_000_frame_007.mrc as #2.19, grid size 288,288,288, pixel 1.11, shown at level 0.0745, step 2, values float32 Opened J235_component_000_frame_008.mrc as #2.20, grid size 288,288,288, pixel 1.11, shown at level 0.0744, step 2, values float32 > hide #!17 models > open /Downloads/cryosparc_P45_J235_component_000 Unknown command: vseries open /Downloads/cryosparc_P45_J235_component_000 > open > /Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_*.mrc Unknown command: vseries open /Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_*.mrc > /Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_*.mrc Unknown command: vseries /Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_*.mrc > vseries play #2 loop true No volume series specified > open > /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_0*.mrc Unknown command: vseries open /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_0*.mrc > toolshed show > open > /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_000_frame_0*.mrc > vseries true Opened map series J235_component_000_frame_000.mrc as #4, 20 images, grid size 288,288,288, pixel 1.11, shown at level 0.0755, step 2, values float32 > hide #!2 models > open > /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_002_frame_0*.mrc > vseries true No such file/path: /Users/tessasmith/Downloads/cryosparc_P45_J235_component_000/J235_component_002_frame_0*.mrc > open > /Users/tessasmith/Downloads/cryosparc_P45_J235_component_001/J235_component_001_frame_0*.mrc > vseries true Opened map series J235_component_001_frame_000.mrc as #6, 20 images, grid size 288,288,288, pixel 1.11, shown at level 0.075, step 2, values float32 > hide #!4 models > hide #!2 models > show #3 models > hide #3 models > hide #!6 models > show #!5 models > hide #!5 models > show #!4 models > hide #!4 models > show #!6 models > hide #!6 models > close #6 > open > /Users/tessasmith/Downloads/cryosparc_P45_J235_component_001/J235_component_001_frame_0*.mrc > vseries true Opened map series J235_component_001_frame_000.mrc as #6, 20 images, grid size 288,288,288, pixel 1.11, shown at level 0.075, step 2, values float32 > hide #!6 models > open > /Users/tessasmith/Downloads/cryosparc_P45_J235_component_002/J235_component_002_frame_0*.mrc > vseries true Opened map series J235_component_002_frame_000.mrc as #7, 20 images, grid size 288,288,288, pixel 1.11, shown at level 0.0753, step 2, values float32 > hide #!7 models > show #!6 models > hide #!6 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!7 models > volume #7.7 step 1 > volume #6.7 step 1 > volume #4.3 step 1 > volume #2.20 step 1 > volume #2.19 step 1 > volume #2.18 step 1 > volume #2.17 step 1 > volume #2.16 step 1 > volume #2.15 step 1 > volume #2.14 step 1 > volume #2.13 step 1 > volume #2.12 step 1 > volume #2.11 step 1 > volume #2.10 step 1 > volume #2.9 step 1 > volume #2.8 step 1 > volume #2.7 step 1 > volume #2.6 step 1 > volume #2.5 step 1 > volume #2.4 step 1 > volume #2.3 step 1 > volume #2.2 step 1 > volume #2.1 step 1 > open ""/Users/tessasmith/Downloads/cryosparc_P45_J232_003_volume_map (1).mrc"" Opened cryosparc_P45_J232_003_volume_map (1).mrc as #8, grid size 288,288,288, pixel 1.11, shown at level 0.0819, step 2, values float32 > hide #!7 models > close #8 > show #!17 models > volume #17 level 0.05618 > hide #!17 models > show #!9 models > volume #9 level 0.1066 > volume #9 level 0.06668 > volume #9 level 0.04477 > open ""/Users/tessasmith/Downloads/cryosparc_P45_J207_006_volume_map (1).mrc"" Opened cryosparc_P45_J207_006_volume_map (1).mrc as #8, grid size 288,288,288, pixel 1.11, shown at level 0.0847, step 2, values float32 > hide #!9 models > volume #8 step 1 > volume #8 level 0.04188 > hide #!8 models > show #!9 models > open ""/Users/tessasmith/Downloads/cryosparc_P45_J208_009_volume_map (1).mrc"" Opened cryosparc_P45_J208_009_volume_map (1).mrc as #10, grid size 288,288,288, pixel 1.11, shown at level 0.085, step 2, values float32 > hide #!9 models > volume #10 step 1 > volume #10 level 0.07053 > volume #10 level 0.06658 > volume #10 level 0.05344 > hide #!10 models > show #!17 models > close #2 > show #!9 models > hide #!17 models > show #!17 models > hide #!9 models > show #!5 models > hide #!5 models > show #!9 models > show #!5 models > volume #5 level 0.01029 > volume #5 level 0.01496 > hide #!5 models > hide #!17 models > hide #!9 models > show #!17 models > hide #!17 models > show #!9 models > volume #9 level 0.07699 > volume #9 level 0.03575 > hide #!9 models > show #!6 models > show #3 models > hide #3 models > show #!1 models > hide #!1 models > hide #!6 models > show #!7 models > hide #!7 models > show #!4 models > hide #!4 models > show #!8 models > hide #!8 models > show #!17 models > open /Users/tessasmith/Downloads/cryosparc_P45_J237_005_volume_map.mrc Opened cryosparc_P45_J237_005_volume_map.mrc as #2, grid size 288,288,288, pixel 1.11, shown at level 0.0822, step 2, values float32 > hide #!17 models > volume #2 step 1 > volume #2 level 0.06456 > volume #2 level 0.04569 > open > /Users/tessasmith/Downloads/cryosparc_P45_J239_map_all_classes/J239_volume_class_00_map.mrc Opened J239_volume_class_00_map.mrc as #11, grid size 288,288,288, pixel 1.11, shown at level 0.083, step 2, values float32 > open > /Users/tessasmith/Downloads/cryosparc_P45_J239_map_all_classes/J239_volume_class_01_map.mrc Opened J239_volume_class_01_map.mrc as #12, grid size 288,288,288, pixel 1.11, shown at level 0.0828, step 2, values float32 > open > /Users/tessasmith/Downloads/cryosparc_P45_J239_map_all_classes/J239_volume_class_02_map.mrc Opened J239_volume_class_02_map.mrc as #13, grid size 288,288,288, pixel 1.11, shown at level 0.083, step 2, values float32 > open > /Users/tessasmith/Downloads/cryosparc_P45_J239_map_all_classes/J239_volume_class_03_map.mrc Opened J239_volume_class_03_map.mrc as #14, grid size 288,288,288, pixel 1.11, shown at level 0.0834, step 2, values float32 > open > /Users/tessasmith/Downloads/cryosparc_P45_J239_map_all_classes/J239_volume_class_04_map.mrc Opened J239_volume_class_04_map.mrc as #15, grid size 288,288,288, pixel 1.11, shown at level 0.0832, step 2, values float32 > open > /Users/tessasmith/Downloads/cryosparc_P45_J239_map_all_classes/J239_volume_class_05_map.mrc Opened J239_volume_class_05_map.mrc as #16, grid size 288,288,288, pixel 1.11, shown at level 0.0832, step 2, values float32 > open > /Users/tessasmith/Downloads/cryosparc_P45_J239_map_all_classes/J239_volume_class_06_map.mrc Opened J239_volume_class_06_map.mrc as #18, grid size 288,288,288, pixel 1.11, shown at level 0.0829, step 2, values float32 > open > /Users/tessasmith/Downloads/cryosparc_P45_J239_map_all_classes/J239_volume_class_07_map.mrc Opened J239_volume_class_07_map.mrc as #19, grid size 288,288,288, pixel 1.11, shown at level 0.0827, step 2, values float32 > open > /Users/tessasmith/Downloads/cryosparc_P45_J239_map_all_classes/J239_volume_class_08_map.mrc Opened J239_volume_class_08_map.mrc as #20, grid size 288,288,288, pixel 1.11, shown at level 0.0828, step 2, values float32 > open > /Users/tessasmith/Downloads/cryosparc_P45_J239_map_all_classes/J239_volume_class_09_map.mrc Opened J239_volume_class_09_map.mrc as #21, grid size 288,288,288, pixel 1.11, shown at level 0.0833, step 2, values float32 > hide #!21 models > hide #!20 models > hide #!19 models > hide #!18 models > hide #!16 models > hide #!15 models > hide #!14 models > hide #!12 models > hide #!13 models > hide #!2 models > volume #11 step 1 > volume #12 step 1 > volume #13 step 1 > volume #14 step 1 > volume #15 step 1 > volume #16 step 1 > volume #18 step 1 > volume #19 step 1 > volume #20 step 1 > volume #21 step 1 > show #!1 models > hide #!1 models > hide #!11 models > show #!12 models > hide #!12 models > show #!13 models > hide #!13 models > show #!14 models > hide #!14 models > show #!15 models > show #!16 models > hide #!15 models > hide #!16 models > show #!18 models > hide #!18 models > show #!19 models > hide #!19 models > show #!20 models > hide #!20 models > show #!21 models > hide #!21 models > show #!11 models > hide #!11 models > show #!12 models > hide #!12 models > show #!14 models > show #!13 models > hide #!13 models > show #!13 models > hide #!14 models > hide #!13 models > show #!14 models > hide #!14 models > show #!15 models > hide #!15 models > show #!16 models > hide #!16 models > show #!18 models > show #!19 models > hide #!18 models > hide #!19 models > show #!20 models > hide #!20 models > show #!21 models > hide #!21 models > show #!20 models > show #!11 models > hide #!20 models > show #!20 models > show #!10 models > hide #!10 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > hide #!20 models > show #!11 models > hide #!11 models > show #!12 models > hide #!12 models > show #!13 models > hide #!13 models > show #!14 models > hide #!14 models > show #!15 models > hide #!15 models > show #!16 models > hide #!16 models > show #!18 models > hide #!18 models > show #!19 models > hide #!19 models > show #!20 models > show #!21 models > hide #!20 models > open ""/Users/tessasmith/Downloads/cryosparc_P45_J212_009_volume_map (1).mrc"" Opened cryosparc_P45_J212_009_volume_map (1).mrc as #22, grid size 288,288,288, pixel 1.11, shown at level 0.0397, step 2, values float32 > hide #!21 models > volume #22 step 1 > volume #22 level 0.1172 > volume #22 level 0.1079 > show #3 models > select add #3 23976 atoms, 24363 bonds, 2970 residues, 1 model selected > view matrix models > #3,0.99822,-0.020185,-0.05607,-2.2089,0.03097,0.97957,0.1987,-57.974,0.050914,-0.20009,0.97845,27.476 > view matrix models > #3,0.99822,-0.020185,-0.05607,0.60597,0.03097,0.97957,0.1987,-64.584,0.050914,-0.20009,0.97845,-3.3197 > fitmap #3 inMap #22 Fit molecule EscVc_Final.pdb (#3) to map cryosparc_P45_J212_009_volume_map (1).mrc (#22) using 23976 atoms average map value = 0.1674, steps = 176 shifted from previous position = 10.1 rotated from previous position = 18.6 degrees atoms outside contour = 7426, contour level = 0.10793 Position of EscVc_Final.pdb (#3) relative to cryosparc_P45_J212_009_volume_map (1).mrc (#22) coordinates: Matrix rotation and translation 0.97510444 0.22174603 -0.00016921 -52.49615510 -0.22174594 0.97510438 0.00042526 25.87509294 0.00025930 -0.00037716 0.99999989 -40.01666926 Axis -0.00180932 -0.00096623 -0.99999790 Axis point 89.19609953 246.42701815 0.00000000 Rotation angle (degrees) 12.81163118 Shift along axis 40.08656620 > view matrix models > #3,0.9751,0.22175,-0.00016921,-52.503,-0.22175,0.9751,0.00042526,25.834,0.0002593,-0.00037716,1,-39.98 > select clear > color #22 #b2b2ffac models > color #22 #b2b2ffab models > volume #22 level 0.09862 Drag select of 5 residues, 22 cryosparc_P45_J212_009_volume_map (1).mrc > select clear > hide #!22 models > select /A:593 6 atoms, 5 bonds, 1 residue, 1 model selected > select /A:594 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > select add /A:593 6 atoms, 5 bonds, 1 residue, 1 model selected > select add /A:594 14 atoms, 12 bonds, 2 residues, 1 model selected > select add /A:595 25 atoms, 22 bonds, 3 residues, 1 model selected > select add /A:596 34 atoms, 30 bonds, 4 residues, 1 model selected > select add /A:597 41 atoms, 36 bonds, 5 residues, 1 model selected > select add /A:598 47 atoms, 41 bonds, 6 residues, 1 model selected > select add /A:600 51 atoms, 44 bonds, 7 residues, 1 model selected > select add /A:599 57 atoms, 49 bonds, 8 residues, 1 model selected > select add /A:601 63 atoms, 54 bonds, 9 residues, 1 model selected > select add /A:602 75 atoms, 66 bonds, 10 residues, 1 model selected > select add /A:603 83 atoms, 73 bonds, 11 residues, 1 model selected > show sel atoms > style sel stick Changed 83 atom styles > select clear > show #!22 models > select /A:605 8 atoms, 7 bonds, 1 residue, 1 model selected > hide #!22 models > select add /A:604 16 atoms, 14 bonds, 2 residues, 1 model selected > show sel atoms > style sel stick Changed 16 atom styles > select clear > show #!22 models Drag select of 220 residues, 22 cryosparc_P45_J212_009_volume_map (1).mrc > select clear > volume #22 level 0.09 > volume #22 level 0.11 > volume #22 level 0.085 > volume #22 level 0.08 > volume #22 level 0.065 > volume #22 level 0.06 > volume #22 level 0.055 > volume #22 level 0.065 > open /Users/tessasmith/Downloads/cryosparc_P45_J241_005_volume_map.mrc Opened cryosparc_P45_J241_005_volume_map.mrc as #23, grid size 288,288,288, pixel 1.11, shown at level 0.0393, step 2, values float32 > hide #!22 models > hide #3 models > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > volume #23 step 1 > volume #23 level 0.09136 > volume #23 level 0.06926 > volume #23 level 0.04242 > hide #!23 models > show #!22 models > hide #!22 models > show #!20 models > volume #20 level 0.03738 > volume #20 level 0.1056 > hide #!20 models > show #!23 models > hide #!23 models > show #!19 models > hide #!19 models > show #!20 models > show #!23 models > hide #!23 models > show #!23 models > hide #!23 models > show #!9 models > volume #9 level 0.09633 > show #3 models > select add #3 23976 atoms, 24363 bonds, 2970 residues, 1 model selected > view matrix models > #3,-0.38353,-0.69956,-0.60292,464.52,-0.70502,0.64348,-0.29814,226.62,0.59654,0.31073,-0.74,135.14 > view matrix models > #3,0.99193,0.12665,0.0055187,-39.882,0.12673,-0.99176,-0.018552,313.09,0.0031236,0.019102,-0.99981,340.87 > view matrix models > #3,0.99193,0.12665,0.0055187,-41.187,0.12673,-0.99176,-0.018552,306.77,0.0031236,0.019102,-0.99981,375.45 Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 1 atomic models, 2 maps. > hide #!20 models > fitmap #3 inMap #9 Fit molecule EscVc_Final.pdb (#3) to map cryosparc_P45_J213_011_volume_map (2).mrc (#9) using 23976 atoms average map value = 0.1286, steps = 100 shifted from previous position = 9.65 rotated from previous position = 10.5 degrees atoms outside contour = 8929, contour level = 0.096327 Position of EscVc_Final.pdb (#3) relative to cryosparc_P45_J213_011_volume_map (2).mrc (#9) coordinates: Matrix rotation and translation 0.99851990 -0.05438755 -0.00011933 -7.77777912 -0.05438760 -0.99851983 -0.00037562 345.73121958 -0.00009872 0.00038156 -0.99999992 381.96453630 Axis 0.99962987 -0.02720504 -0.00005436 Axis point 0.00000000 172.72359468 191.01475903 Rotation angle (degrees) 179.97830045 Shift along axis -17.20129833 > show #!8 models > hide #!8 models > save /Users/tessasmith/EscV325-aligned.pdb relModel #9 > hide #3 models > select subtract #3 Nothing selected > open /Users/tessasmith/EscV325-aligned.pdb Chain information for EscV325-aligned.pdb #24 --- Chain | Description A B C D E F G H I | No description available > hide #24 atoms > show #24 cartoons > open /Users/tessasmith/Downloads/1xou.pdb 1xou.pdb title: Crystal structure of the cesa-ESPA complex [more info...] Chain information for 1xou.pdb #25 --- Chain | Description | UniProt A | ESPA | Q47184_ECOLI 1-192 B | Z5138 gene product | O52124_ECOLI 1-95 > select #25/A:31-190 565 atoms, 569 bonds, 1 pseudobond, 72 residues, 2 models selected > ui tool show ""Selection Inspector"" > color sel #a35c87 target r > view matrix models #25,1,0,0,-0.020978,0,1,0,0.00017177,0,0,1,0.0169 > select clear > open /Users/tessasmith/Downloads/7k7k.pdb 7k7k.pdb title: Structure of the epec type III secretion injectisome ESPA filament [more info...] Chain information for 7k7k.pdb #26 --- Chain | Description | UniProt A B C D E F G H I J K L M N O P Q R S T U V W X Y Z a b | translocon ESPA | B7UM94_ECO27 1-192 > select add #26 36204 atoms, 36484 bonds, 4788 residues, 1 model selected > hide sel atoms > show sel cartoons > hide sel cartoons > select #26/A:22-192 1293 atoms, 1303 bonds, 171 residues, 1 model selected > show sel cartoons > view matrix models #26,1,0,0,-155.43,0,1,0,-158.53,0,0,1,-72.769 > select clear Drag select of 9 cryosparc_P45_J213_011_volume_map (2).mrc > select clear > volume #9 level 0.05251 > hide #!9 models > hide #24 models > hide #26 models > show #26 models > hide #!25 models > hide #26 models > show #!21 models > show #!1 models > hide #!1 models > hide #!21 models > show #!20 models > show #!21 models > hide #!20 models > show #!20 models > hide #!21 models > show #!21 models > show #!19 models > hide #!19 models > hide #!21 models > hide #!20 models > show #!19 models > hide #!19 models > show #!18 models > volume #18 level 0.07869 > hide #!18 models > show #!16 models > hide #!16 models > show #!22 models > show #!21 models > hide #!22 models > hide #!21 models > show #!20 models > hide #!20 models > show #!19 models > hide #!19 models > show #!18 models > hide #!18 models > show #!16 models > hide #!16 models > show #!15 models > volume #15 level 0.07244 > hide #!15 models > show #!14 models > hide #!14 models > show #!13 models > hide #!13 models > show #!12 models > hide #!12 models > show #!11 models > hide #!11 models > show #!9 models > volume #9 level 0.08859 > show #!5 models > show #24 models > hide #!5 models > hide #!9 models > show #!9 models > volume #9 level 0.05122 > hide #!9 models > log metadata #24 The model has no metadata > log chains #24 Chain information for EscV325-aligned.pdb #24 --- Chain | Description A B C D E F G H I | No description available > select #24/A:346-675 2664 atoms, 2707 bonds, 330 residues, 1 model selected > select clear > select #24/A:346-675 2664 atoms, 2707 bonds, 330 residues, 1 model selected > select clear > select #24/B:346-675 2664 atoms, 2707 bonds, 330 residues, 1 model selected > select clear > hide #24 cartoons > select #24/A:346-675 2664 atoms, 2707 bonds, 330 residues, 1 model selected > show sel cartoons > select #24/B:346-675 2664 atoms, 2707 bonds, 330 residues, 1 model selected > show sel cartoons Drag select of 660 residues > show #!9 models > volume zone #24 nearAtoms #9 range 15 newMap true no atoms specified for zone > volume zone #9 nearAtoms #24 range 15 newMap true Opened cryosparc_P45_J213_011_volume_map (2).mrc zone as #27, grid size 288,288,288, pixel 1.11, shown at step 1, values float32 > hide #24 models > show #24 models > volume zone #9 nearAtoms #24 A/B range 15 newMap true Expected a keyword > hide #!27 models > save /Users/tessasmith/Desktop/EscV325-A/B.pdb models #24 selectedOnly true Cannot save '/Users/tessasmith/Desktop/EscV325-A/B.pdb': Unable to open file '/Users/tessasmith/Desktop/EscV325-A/B.pdb' for writing > save /Users/tessasmith/Desktop/EscVc-dimer.pdb models #24 selectedOnly true > open /Users/tessasmith/Desktop/EscVc-dimer.pdb Summary of feedback from opening /Users/tessasmith/Desktop/EscVc-dimer.pdb --- warnings | Start residue of secondary structure not found: HELIX 25 25 ASP C 365 SER C 381 1 17 Start residue of secondary structure not found: HELIX 26 26 THR C 465 SER C 479 1 15 Start residue of secondary structure not found: HELIX 27 27 ALA C 481 PHE C 484 1 4 Start residue of secondary structure not found: HELIX 28 28 VAL C 487 ARG C 499 1 13 Start residue of secondary structure not found: HELIX 29 29 ASN C 502 GLN C 511 1 10 168 messages similar to the above omitted Chain information for EscVc-dimer.pdb #28 --- Chain | Description A B | No description available > hide #24 models > hide #28 models > show #28 models > select add #24 23976 atoms, 24363 bonds, 2970 residues, 1 model selected > select subtract #24 Nothing selected > show #!9 models > volume zone #9 nearAtoms #28 range 15 newMap true Opened cryosparc_P45_J213_011_volume_map (2).mrc zone as #29, grid size 288,288,288, pixel 1.11, shown at step 1, values float32 > volume #29 level 0.0166 > hide #28 models > open /Users/tessasmith/Downloads/cryosparc_P45_J236_010_volume_map.mrc Opened cryosparc_P45_J236_010_volume_map.mrc as #30, grid size 288,288,288, pixel 1.11, shown at level 0.0375, step 2, values float32 > hide #!29 models > volume #30 step 1 > volume #30 level 0.05788 > open /Users/tessasmith/Downloads/cryosparc_P45_J245_018_volume_map.mrc Opened cryosparc_P45_J245_018_volume_map.mrc as #31, grid size 288,288,288, pixel 1.11, shown at level 0.0373, step 2, values float32 > hide #!30 models > volume #31 step 1 > volume #31 level 0.09313 > hide #!31 models > show #!30 models > show #!31 models > hide #!31 models > hide #!30 models > show #!30 models > show #3 models > hide #!30 models > hide #3 models > show #28 models > show #!29 models > hide #28 models > save /Users/tessasmith/Desktop/EscVc-dimer.mrc models #29 > volume #29 level 0.05 > volume #29 level 0.01 > volume #29 level 0.005 > volume #29 level 0.01 > hide #!29 models > show #!5 models > volume #5 level 0.05 > hide #!5 models > show #!29 models > volume #29 level 0.05 > volume #29 level 0.01 > show #28 models > volume #29 level 0.04974 > volume #29 level 0.05 > volume #29 level 0.04 > volume #29 level 0.03 > open > /Users/tessasmith/Downloads/cryosparc_P45_J247_component_000/J247_component_000_frame_0*.mrc > vseries true Opened map series J247_component_000_frame_000.mrc as #32, 20 images, grid size 288,288,288, pixel 1.11, shown at level 0.0793, step 2, values float32 > hide #28 models > hide #!29 models > volume #32.1 step 1 > hide #!32 models > show #!1 models > hide #!1 models > show #!2 models > hide #!2 models > show #!2 models > volume #5 level 0.05408 > hide #!5 models > hide #!2 models > show #!4 models > hide #!4 models > show #!4 models > close #4 > show #!5 models > hide #!5 models > close #5 > close #1 > show #!2 models > hide #!2 models > show #!6 models > hide #!6 models > show #!6 models > close #2 > undo > close #6 > show #!7 models > hide #!7 models > close #7 > show #!8 models > close #8 > close #10 > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!12 models > hide #!12 models > show #!13 models > close #11 > close #12-16 > show #!17 models > close #17 > close #18-21 > close #22 > show #!23 models > close #23 > show #24 models > hide #24 models > show #!27 models > close #27 > show #28 models > show #!29 models > hide #!29 models > hide #28 models > show #!30 models > close #30 > show #!31 models > close #31 > show #!32 models > volume #32.20 level 0.06555 > volume #32.20 level 0.06568 > volume #32.1 level 0.05765 > volume #32.1 level 0.04696 > show #28 models > color #32 #cccc99b9 models > color #32 #cccc9990 models > color #32 #cccc9991 models > volume #32.5 level 0.04512 > open > /Users/tessasmith/Downloads/cryosparc_P45_J250_00193_volume_series/J250_class_00_00193_volume.mrc Opened J250_class_00_00193_volume.mrc as #1, grid size 112,112,112, pixel 2.84, shown at level 0.329, step 1, values float32 > open > /Users/tessasmith/Downloads/cryosparc_P45_J250_00193_volume_series/J250_class_01_00193_volume.mrc Opened J250_class_01_00193_volume.mrc as #2, grid size 112,112,112, pixel 2.84, shown at level 0.336, step 1, values float32 > open > /Users/tessasmith/Downloads/cryosparc_P45_J250_00193_volume_series/J250_class_02_00193_volume.mrc Opened J250_class_02_00193_volume.mrc as #4, grid size 112,112,112, pixel 2.84, shown at level 0.324, step 1, values float32 > open > /Users/tessasmith/Downloads/cryosparc_P45_J250_00193_volume_series/J250_class_03_00193_volume.mrc Opened J250_class_03_00193_volume.mrc as #5, grid size 112,112,112, pixel 2.84, shown at level 0.33, step 1, values float32 > open > /Users/tessasmith/Downloads/cryosparc_P45_J250_00193_volume_series/J250_class_04_00193_volume.mrc Opened J250_class_04_00193_volume.mrc as #6, grid size 112,112,112, pixel 2.84, shown at level 0.33, step 1, values float32 > open > /Users/tessasmith/Downloads/cryosparc_P45_J250_00193_volume_series/J250_class_05_00193_volume.mrc Opened J250_class_05_00193_volume.mrc as #7, grid size 112,112,112, pixel 2.84, shown at level 0.333, step 1, values float32 > open > /Users/tessasmith/Downloads/cryosparc_P45_J250_00193_volume_series/J250_class_06_00193_volume.mrc Opened J250_class_06_00193_volume.mrc as #8, grid size 112,112,112, pixel 2.84, shown at level 0.336, step 1, values float32 > open > /Users/tessasmith/Downloads/cryosparc_P45_J250_00193_volume_series/J250_class_07_00193_volume.mrc Opened J250_class_07_00193_volume.mrc as #10, grid size 112,112,112, pixel 2.84, shown at level 0.336, step 1, values float32 > open > /Users/tessasmith/Downloads/cryosparc_P45_J250_00193_volume_series/J250_class_08_00193_volume.mrc Opened J250_class_08_00193_volume.mrc as #11, grid size 112,112,112, pixel 2.84, shown at level 0.333, step 1, values float32 > open > /Users/tessasmith/Downloads/cryosparc_P45_J250_00193_volume_series/J250_class_09_00193_volume.mrc Opened J250_class_09_00193_volume.mrc as #12, grid size 112,112,112, pixel 2.84, shown at level 0.321, step 1, values float32 > show #!29 models > hide #!29 models > hide #!32 models > hide #28 models > hide #!12 models > hide #!11 models > hide #!10 models > hide #!8 models > hide #!7 models > hide #!6 models > hide #!5 models > hide #!4 models > hide #!2 models > hide #!1 models > show #!2 models > hide #!2 models > show #3 models > hide #3 models > close #1-2 > close #4-8 > close #10-12 > open /Users/tessasmith/Downloads/cryosparc_P45_J255_volume_class_00_map.mrc Opened cryosparc_P45_J255_volume_class_00_map.mrc as #1, grid size 288,288,288, pixel 1.11, shown at level 0.0859, step 2, values float32 > volume #1 step 1 > volume #1 level 0.06882 > open /Users/tessasmith/Downloads/cryosparc_P45_J255_volume_class_01_map.mrc Opened cryosparc_P45_J255_volume_class_01_map.mrc as #2, grid size 288,288,288, pixel 1.11, shown at level 0.0866, step 2, values float32 > volume #2 step 1 > hide #!1 models > volume #2 level 0.06146 > volume #1 level 0.0615 > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > open /Users/tessasmith/Downloads/cryosparc_P45_J255_volume_class_02_map.mrc Opened cryosparc_P45_J255_volume_class_02_map.mrc as #4, grid size 288,288,288, pixel 1.11, shown at level 0.084, step 2, values float32 > hide #!2 models > volume #4 step 1 > volume #4 level 0.08398 > volume #4 level 0.07346 > volume #4 level 0.06689 > open /Users/tessasmith/Downloads/cryosparc_P45_J255_volume_class_03_map.mrc Opened cryosparc_P45_J255_volume_class_03_map.mrc as #5, grid size 288,288,288, pixel 1.11, shown at level 0.0759, step 2, values float32 > hide #!4 models > volume #5 step 1 > volume #5 level 0.05189 > show #!29 models > hide #!29 models > close #5 > open /Users/tessasmith/Downloads/cryosparc_P45_J255_volume_class_04_map.mrc Opened cryosparc_P45_J255_volume_class_04_map.mrc as #5, grid size 288,288,288, pixel 1.11, shown at level 0.087, step 2, values float32 > volume #5 step 1 > volume #5 level 0.06451 > hide #!5 models > show #!5 models > hide #!5 models > show #!4 models > hide #!4 models > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > show #!5 models > open /Users/tessasmith/Downloads/cryosparc_P45_J255_volume_class_05_map.mrc Opened cryosparc_P45_J255_volume_class_05_map.mrc as #6, grid size 288,288,288, pixel 1.11, shown at level 0.0842, step 2, values float32 > hide #!5 models > volume #6 step 1 > volume #6 level 0.05659 > open /Users/tessasmith/Downloads/cryosparc_P45_J255_volume_class_06_map.mrc Opened cryosparc_P45_J255_volume_class_06_map.mrc as #7, grid size 288,288,288, pixel 1.11, shown at level 0.087, step 2, values float32 > hide #!6 models > volume #7 step 1 > volume #7 level 0.07861 > volume #7 level 0.06887 > open /Users/tessasmith/Downloads/cryosparc_P45_J255_volume_class_08_map.mrc Opened cryosparc_P45_J255_volume_class_08_map.mrc as #8, grid size 288,288,288, pixel 1.11, shown at level 0.0857, step 2, values float32 > hide #!7 models > volume #8 step 1 > volume #8 level 0.06739 > open /Users/tessasmith/Downloads/cryosparc_P45_J255_volume_class_09_map.mrc Opened cryosparc_P45_J255_volume_class_09_map.mrc as #10, grid size 288,288,288, pixel 1.11, shown at level 0.0868, step 2, values float32 > hide #!8 models > volume #10 step 1 > volume #10 level 0.06496 > hide #!10 models > show #!8 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > hide #!8 models > show #!8 models > show #!7 models > hide #!8 models > hide #!7 models > show #!6 models > show #!5 models > hide #!6 models > show #!4 models > hide #!4 models > show #!4 models > hide #!5 models > hide #!4 models > show #!4 models > hide #!4 models > show #!2 models > show #!4 models > hide #!4 models > hide #!2 models > show #!1 models > hide #!1 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!1 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!1 models > show #!2 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!2 models > hide #!4 models > show #!1 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > show #!4 models > hide #!2 models > show #!5 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > hide #!5 models > show #!4 models > show #!29 models > hide #!29 models > show #28 models > color #4 #b2ffff93 models > color #4 #b2ffff94 models > hide #!4 models > show #26 models > log metadata #26 Metadata for 7k7k.pdb #26 --- Title | Structure of the epec type III secretion injectisome ESPA filament Citation | Cryo-em structure of the ESPA filament from enteropathogenicescherichia coli: revealing the mechanism of effectortranslocation In the T3SS. PMID: 33453150 Source (natural) | Escherichia coli O127:H6 (strain E2348/69 / epec) Experimental method | Electron microscopy Resolution | 3.56Å > log chains #26 Chain information for 7k7k.pdb #26 --- Chain | Description | UniProt A B C D E F G H I J K L M N O P Q R S T U V W X Y Z a b | translocon ESPA | B7UM94_ECO27 1-192 > select #26/B:22-192 1293 atoms, 1303 bonds, 171 residues, 1 model selected > show sel cartoons > hide sel cartoons > select add #26 36204 atoms, 36484 bonds, 4788 residues, 1 model selected > select subtract #26 Nothing selected > hide #26 models > show #!4 models > volume #4 level 0.06952 > open /Users/tessasmith/Downloads/cryosparc_P45_J258_004_volume_map.mrc Opened cryosparc_P45_J258_004_volume_map.mrc as #11, grid size 288,288,288, pixel 1.11, shown at level 0.0753, step 2, values float32 > volume #11 step 1 > hide #!4 models > volume #11 level 0.06961 > volume #11 level 0.06392 > volume #11 level 0.0412 > volume #11 level 0.045 > volume #11 level 0.05 > volume #11 level 0.055 > volume #11 level 0.06 > open /Users/tessasmith/Downloads/cryosparc_P45_J256_004_volume_map.mrc Opened cryosparc_P45_J256_004_volume_map.mrc as #12, grid size 288,288,288, pixel 1.11, shown at level 0.082, step 2, values float32 > hide #!11 models > hide #!12 models > show #!12 models > hide #28 models > volume #12 step 1 > volume #12 level 0.06923 > volume #12 level 0.0514 > hide #!12 models > show #!11 models > open ""/Users/tessasmith/Downloads/cryosparc_P45_J208_009_volume_map (2).mrc"" Opened cryosparc_P45_J208_009_volume_map (2).mrc as #13, grid size 288,288,288, pixel 1.11, shown at level 0.085, step 2, values float32 > hide #!11 models > volume #13 step 1 > volume #13 level 0.07579 > volume #13 level 0.06658 > volume #13 level 0.1534 > volume #13 level 0.0771 > hide #!13 models > show #!9 models > volume #9 level 0.03446 > volume #9 level 0.05508 > volume #9 level 0.05122 > volume #9 level 0.1131 > hide #!9 models > open /Users/tessasmith/Downloads/cryosparc_P45_J259_004_volume_map.mrc Opened cryosparc_P45_J259_004_volume_map.mrc as #14, grid size 288,288,288, pixel 1.11, shown at level 0.078, step 2, values float32 > show #!1 models > hide #!1 models > volume #14 step 1 > show #!29 models > hide #!29 models > show #!29 models > hide #!29 models > volume #14 level 0.07369 > volume #14 level 0.06063 > hide #!14 models > show #26 models > log metadata #26 Metadata for 7k7k.pdb #26 --- Title | Structure of the epec type III secretion injectisome ESPA filament Citation | Cryo-em structure of the ESPA filament from enteropathogenicescherichia coli: revealing the mechanism of effectortranslocation In the T3SS. PMID: 33453150 Source (natural) | Escherichia coli O127:H6 (strain E2348/69 / epec) Experimental method | Electron microscopy Resolution | 3.56Å > log chains #26 Chain information for 7k7k.pdb #26 --- Chain | Description | UniProt A B C D E F G H I J K L M N O P Q R S T U V W X Y Z a b | translocon ESPA | B7UM94_ECO27 1-192 > select #26/B:22-192 1293 atoms, 1303 bonds, 171 residues, 1 model selected > show sel cartoons > select add #26 36204 atoms, 36484 bonds, 4788 residues, 1 model selected > show sel cartoons > hide sel cartoons > select subtract #26 Nothing selected > select #26/A:22-192 1293 atoms, 1303 bonds, 171 residues, 1 model selected > show sel cartoons > select #26/F:22-192 1293 atoms, 1303 bonds, 171 residues, 1 model selected > show sel cartoons > select add #26 36204 atoms, 36484 bonds, 4788 residues, 1 model selected > select subtract #26 Nothing selected > show #28 models > select add #26 36204 atoms, 36484 bonds, 4788 residues, 1 model selected > view matrix models #26,1,0,0,-39.582,0,1,0,-71.057,0,0,1,9.0374 > view matrix models #26,1,0,0,-35.4,0,1,0,-77.43,0,0,1,-46.352 > view matrix models #26,1,0,0,-42.602,0,1,0,-64.863,0,0,1,-42.101 > view matrix models #26,1,0,0,-39.026,0,1,0,-71.05,0,0,1,-48.144 > select subtract #26 Nothing selected > show #!9 models > select add #28 5328 atoms, 5414 bonds, 660 residues, 1 model selected > select add #26 41532 atoms, 41898 bonds, 5448 residues, 2 models selected > select subtract #28 36204 atoms, 36484 bonds, 4788 residues, 1 model selected > view matrix models #26,1,0,0,36.224,0,1,0,-85.69,0,0,1,-60.629 > view matrix models #26,1,0,0,47.345,0,1,0,-116.38,0,0,1,-75.699 Drag select of 10 residues > select clear > select add #28 5328 atoms, 5414 bonds, 660 residues, 1 model selected > select subtract #28 Nothing selected > select add #26 36204 atoms, 36484 bonds, 4788 residues, 1 model selected > view matrix models #26,1,0,0,40.568,0,1,0,-64.131,0,0,1,-77.533 > view matrix models > #26,-0.55081,0.47711,-0.68482,374.17,-0.20722,0.71664,0.66595,-87.68,0.8085,0.50872,-0.29586,-117.51 > view matrix models > #26,-0.55081,0.47711,-0.68482,345.65,-0.20722,0.71664,0.66595,-107.28,0.8085,0.50872,-0.29586,-90.467 > view matrix models > #26,-0.55081,0.47711,-0.68482,344.05,-0.20722,0.71664,0.66595,-99.642,0.8085,0.50872,-0.29586,-48.418 > view matrix models > #26,-0.55081,0.47711,-0.68482,372.73,-0.20722,0.71664,0.66595,-78.07,0.8085,0.50872,-0.29586,-61.479 > view matrix models > #26,-0.43358,-0.49501,-0.75298,595.27,-0.1922,0.86718,-0.45941,96.875,0.88038,-0.054474,-0.47113,92.477 > view matrix models > #26,-0.43358,-0.49501,-0.75298,587.3,-0.1922,0.86718,-0.45941,110.46,0.88038,-0.054474,-0.47113,81.479 > view matrix models > #26,-0.43358,-0.49501,-0.75298,600.43,-0.1922,0.86718,-0.45941,119.95,0.88038,-0.054474,-0.47113,71.226 > view matrix models > #26,-0.43358,-0.49501,-0.75298,591.87,-0.1922,0.86718,-0.45941,131.09,0.88038,-0.054474,-0.47113,85.839 > view matrix models > #26,-0.43358,-0.49501,-0.75298,592.39,-0.1922,0.86718,-0.45941,127.85,0.88038,-0.054474,-0.47113,92.777 > view matrix models > #26,-0.42929,-0.11615,-0.89567,528,-0.8231,0.45853,0.33505,198.83,0.37177,0.88106,-0.29245,-64.963 > view matrix models > #26,-0.42929,-0.11615,-0.89567,544.9,-0.8231,0.45853,0.33505,201.55,0.37177,0.88106,-0.29245,-57.926 > view matrix models > #26,-0.94922,-0.12542,-0.28852,534.06,-0.28599,-0.038157,0.95747,96.359,-0.1311,0.99137,0.00035018,-40.991 > view matrix models > #26,-0.94922,-0.12542,-0.28852,533.37,-0.28599,-0.038157,0.95747,92.988,-0.1311,0.99137,0.00035018,-22.286 > view matrix models > #26,0.6269,0.41396,-0.66002,164.61,-0.50697,-0.42652,-0.74904,553.85,-0.59159,0.80418,-0.057525,124.17 > view matrix models > #26,-0.18673,-0.33544,-0.92337,554.2,-0.98122,0.017376,0.19211,362.06,-0.048398,0.9419,-0.33238,36.525 > view matrix models > #26,-0.18673,-0.33544,-0.92337,552.78,-0.98122,0.017376,0.19211,360.83,-0.048398,0.9419,-0.33238,44.341 > volume #9 level 0.05895 > view matrix models > #26,-0.18673,-0.33544,-0.92337,542.85,-0.98122,0.017376,0.19211,356.6,-0.048398,0.9419,-0.33238,35.638 > view matrix models > #26,-0.18673,-0.33544,-0.92337,541.13,-0.98122,0.017376,0.19211,358.96,-0.048398,0.9419,-0.33238,35.472 > view matrix models > #26,0.053822,-0.26224,-0.9635,483.88,-0.99273,0.089947,-0.079936,395.57,0.10763,0.9608,-0.25549,-14.385 > view matrix models > #26,0.053822,-0.26224,-0.9635,473.81,-0.99273,0.089947,-0.079936,395.88,0.10763,0.9608,-0.25549,-24.71 > view matrix models > #26,0.053822,-0.26224,-0.9635,473.59,-0.99273,0.089947,-0.079936,395.55,0.10763,0.9608,-0.25549,-24.896 > view matrix models > #26,0.053822,-0.26224,-0.9635,475.62,-0.99273,0.089947,-0.079936,405.55,0.10763,0.9608,-0.25549,-36.738 > view matrix models > #26,0.053822,-0.26224,-0.9635,474.61,-0.99273,0.089947,-0.079936,408.44,0.10763,0.9608,-0.25549,-23.704 > view matrix models > #26,0.053822,-0.26224,-0.9635,477.91,-0.99273,0.089947,-0.079936,406.11,0.10763,0.9608,-0.25549,-19.121 > view matrix models > #26,0.053822,-0.26224,-0.9635,477.67,-0.99273,0.089947,-0.079936,405.81,0.10763,0.9608,-0.25549,-19.869 > color #9 #e5bf99b1 models > color #9 #e5bf9982 models > view matrix models > #26,0.15889,-0.099731,-0.98225,421.66,-0.95867,0.22226,-0.17764,386.02,0.23603,0.96987,-0.060295,-84.425 > view matrix models > #26,0.15889,-0.099731,-0.98225,418.81,-0.95867,0.22226,-0.17764,389.02,0.23603,0.96987,-0.060295,-91.713 > view matrix models > #26,0.12545,-0.18708,-0.9743,444.79,-0.92568,0.33121,-0.18278,357.42,0.35689,0.92483,-0.13163,-91.166 > view matrix models > #26,0.16632,-0.028972,-0.98565,401.06,-0.87657,0.45347,-0.16124,314.4,0.45163,0.8908,0.050025,-136.21 > view matrix models > #26,0.16632,-0.028972,-0.98565,403.45,-0.87657,0.45347,-0.16124,314.81,0.45163,0.8908,0.050025,-143.06 > view matrix models > #26,0.16632,-0.028972,-0.98565,402.77,-0.87657,0.45347,-0.16124,317.38,0.45163,0.8908,0.050025,-146.71 > view matrix models > #26,0.16632,-0.028972,-0.98565,405.66,-0.87657,0.45347,-0.16124,316.8,0.45163,0.8908,0.050025,-147.52 > open /Users/tessasmith/Downloads/cryosparc_P45_J260_004_volume_map.mrc Opened cryosparc_P45_J260_004_volume_map.mrc as #15, grid size 288,288,288, pixel 1.11, shown at level 0.0792, step 2, values float32 > hide #!9 models > hide #28 models > select subtract #26 Nothing selected > hide #26 models > volume #15 step 1 > show #28 models > hide #28 models > volume #15 level 0.0703 > show #28 models > show #26 models > hide #!15 models > select #28/A:657 9 atoms, 8 bonds, 1 residue, 1 model selected > select #28/A:606 6 atoms, 5 bonds, 1 residue, 1 model selected > select add #28/A:605 14 atoms, 12 bonds, 2 residues, 1 model selected > select add #28/A:604 22 atoms, 19 bonds, 3 residues, 1 model selected > select add #28/A:603 30 atoms, 26 bonds, 4 residues, 1 model selected > select add #28/A:602 42 atoms, 38 bonds, 5 residues, 1 model selected > select add #28/A:601 48 atoms, 43 bonds, 6 residues, 1 model selected > select add #28/A:600 52 atoms, 46 bonds, 7 residues, 1 model selected > select add #28/A:599 58 atoms, 51 bonds, 8 residues, 1 model selected > select add #28/A:598 64 atoms, 56 bonds, 9 residues, 1 model selected > select add #28/A:597 71 atoms, 62 bonds, 10 residues, 1 model selected > select add #28/A:596 80 atoms, 70 bonds, 11 residues, 1 model selected > select add #28/A:595 91 atoms, 80 bonds, 12 residues, 1 model selected > select add #28/A:594 99 atoms, 87 bonds, 13 residues, 1 model selected > select add #28/A:593 105 atoms, 92 bonds, 14 residues, 1 model selected > style sel stick Changed 105 atom styles > show sel atoms > select clear > select #26/F:192 10 atoms, 9 bonds, 1 residue, 1 model selected > select add #26/F:190 18 atoms, 16 bonds, 2 residues, 1 model selected > select add #26/F:191 22 atoms, 19 bonds, 3 residues, 1 model selected > select clear > show #!15 models > color #15 #b2b2ff76 models > color #15 #b2b2ff75 models Drag select of 1 residues, 15 cryosparc_P45_J260_004_volume_map.mrc > select #26/A:136 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear > hide #!15 models > select #28/A:641 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #28/A:642 17 atoms, 15 bonds, 2 residues, 1 model selected > select add #28/A:644 26 atoms, 23 bonds, 3 residues, 1 model selected > select add #28/A:643 34 atoms, 30 bonds, 4 residues, 1 model selected > show sel atoms > style sel stick Changed 34 atom styles > select clear > show #!15 models > select #26/F:192 10 atoms, 9 bonds, 1 residue, 1 model selected > select add #26/F:191 14 atoms, 12 bonds, 2 residues, 1 model selected > hide #!15 models > select add #26/F:190 22 atoms, 19 bonds, 3 residues, 1 model selected > select add #26/F:189 28 atoms, 24 bonds, 4 residues, 1 model selected > select clear > select add #26 36204 atoms, 36484 bonds, 4788 residues, 1 model selected > select clear > select add #26 36204 atoms, 36484 bonds, 4788 residues, 1 model selected > view matrix models > #26,0.16632,-0.028972,-0.98565,405.28,-0.87657,0.45347,-0.16124,317.63,0.45163,0.8908,0.050025,-144.72 > show #!15 models > select subtract #26 Nothing selected > hide #!15 models > select #28/A:638 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > select clear > show #!15 models > show #!25 models > open /Users/tessasmith/Downloads/cryosparc_P45_J263_005_volume_map.mrc Opened cryosparc_P45_J263_005_volume_map.mrc as #16, grid size 288,288,288, pixel 1.11, shown at level 0.0816, step 2, values float32 > hide #!15 models > hide #!25 models > hide #26 models > hide #28 models > volume #16 step 1 > volume #16 level 0.05421 > volume #16 level 0.03779 > volume #16 level 0.05011 > open /Users/tessasmith/Downloads/cryosparc_P45_J254_005_volume_map.mrc Opened cryosparc_P45_J254_005_volume_map.mrc as #17, grid size 288,288,288, pixel 1.11, shown at level 0.0714, step 2, values float32 > hide #!16 models > volume #17 step 1 > show #28 models > hide #28 models > show #!29 models > hide #!29 models > volume #17 level 0.05787 > hide #!17 models > show #!16 models > hide #!16 models > show #!17 models > show #!29 models > hide #!29 models > show #!29 models > hide #!29 models > hide #!17 models > show #!16 models > volume #16 level 0.05011 > hide #!16 models > show #!17 models > color #17 #ffb2b297 models > color #17 #ffb2b296 models > show #28 models > show #26 models > hide #28 models > hide #26 models > show #28 models > hide #!17 models > show #!15 models > hide #!15 models > show #!14 models > hide #!14 models > show #!11 models > show #!4 models > hide #!4 models > show #!4 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > volume #11 level 0.07563 > volume #4 level 0.07346 > volume #11 level 0.0735 > hide #!4 models > lighting soft > set bgColor white > show #!16 models > hide #!11 models > volume #16 level 0.01316 > volume #16 level 0.03506 > color #16 #941100ff models > color #16 #0433ffff models > color #16 #005493ff models > volume #16 level 0.0419 > save /Users/tessasmith/Desktop/image2.png supersample 3 > volume #16 level 0.06516 > volume #16 level 0.05148 > save /Users/tessasmith/Desktop/image3.png supersample 3 > volume #16 level 0.07337 > hide #28 models > show #28 models > show #26 models > show #!17 models > hide #!16 models > color #17 #ffb2b2b2 models > color #17 #ffb2b2df models > color #17 #ffb2b2c8 models > color #17 #ffb2b2c7 models > open /Users/tessasmith/Downloads/cryosparc_P45_J253_006_volume_map.mrc Opened cryosparc_P45_J253_006_volume_map.mrc as #18, grid size 288,288,288, pixel 1.11, shown at level 0.064, step 2, values float32 > hide #!17 models > hide #26 models > hide #28 models > volume #18 step 1 > show #!29 models > hide #!29 models > volume #18 level 0.04923 > volume #18 level 0.03818 > volume #18 level 0.05291 > volume #18 level 0.07502 > volume #18 level 0.05476 > show #!9 models > hide #!18 models > show #!18 models > hide #!18 models > show #!18 models > hide #!18 models > color #9 #e5bf99ff models > show #!18 models > hide #!18 models > show #!18 models > hide #!18 models > show #!18 models > hide #!18 models > show #!18 models > volume #18 level 0.06 > volume #18 level 0.07105 > hide #!9 models > hide #!18 models > show #!16 models > ui tool show ""Surface Color"" > open /Users/tessasmith/Downloads/cryosparc_P45_J266_map_locres.mrc Opened cryosparc_P45_J266_map_locres.mrc as #19, grid size 288,288,288, pixel 1.11, shown at level 5.51, step 2, values float32 > hide #!19 models > color sample #16.1 map #19 palette #ff0000:#ffffff:#0000ff Map values for surface ""surface"": minimum 2.478, mean 2.685, maximum 4.185 > volume #16 level 0.05781 > volume #16 level 0.07207 > volume #16 level 0.03966 > volume #16 level 0.02022 > volume #16 level 0.025 > volume #16 level 0.0613 > hide #!17 models > volume #16 level 0.09242 > volume #16 level 0.05223 > open /Users/tessasmith/Downloads/cryosparc_P45_J265_004_volume_map.mrc Opened cryosparc_P45_J265_004_volume_map.mrc as #20, grid size 288,288,288, pixel 1.11, shown at level 0.0388, step 2, values float32 > hide #!16 models > volume #20 step 1 > volume #20 level 0.0544 > volume #20 level 0.07155 > volume #20 level 0.05128 > hide #!20 models > show #!20 models > volume #20 level 0.05284 > volume #20 level 0.05 > volume #20 level 0.04 > volume #20 level 0.03 > volume #20 level 0.02 > volume #20 level 0.05 > volume #20 level 0.06559 > volume #20 level 0.07651 > hide #!20 models > show #!17 models > show #!18 models > hide #!17 models > hide #!18 models > show #!17 models > hide #!17 models > show #!16 models > volume #18 level 0.04836 > hide #!18 models > volume #16 level 0.04574 > volume #16 level 0.03019 > volume #16 level 0.05093 > open /Users/tessasmith/Downloads/cryosparc_P45_J267_005_volume_map.mrc Opened cryosparc_P45_J267_005_volume_map.mrc as #21, grid size 288,288,288, pixel 1.11, shown at level 0.0458, step 2, values float32 > hide #!16 models > volume #21 step 1 > volume #21 level 0.02739 > volume #21 level 0.03581 > hide #!21 models > show #!11 models > show #!14 models > show #!15 models > hide #!15 models > show #!15 models > hide #!15 models > hide #!14 models > hide #!11 models ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/tessasmith/Downloads/cryosparc_P45_J268_010_volume_map.mrc Opened cryosparc_P45_J268_010_volume_map.mrc as #1, grid size 288,288,288, pixel 1.11, shown at level 0.0421, step 2, values float32 > open /Users/tessasmith/Downloads/cryosparc_P45_J268_010_volume_map.mrc Opened cryosparc_P45_J268_010_volume_map.mrc as #2, grid size 288,288,288, pixel 1.11, shown at level 0.0421, step 2, values float32 OpenGL version: 4.1 ATI-5.1.35 OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 6-Core Intel Core i7 Processor Speed: 2.6 GHz Number of Processors: 1 Total Number of Cores: 6 L2 Cache (per Core): 256 KB L3 Cache: 12 MB Hyper-Threading Technology: Enabled Memory: 32 GB System Firmware Version: 2020.41.1.0.0 (iBridge: 21.16.1069.0.0,0) OS Loader Version: 580~743 Software: System Software Overview: System Version: macOS 14.1.1 (23B81) Kernel Version: Darwin 23.1.0 Time since boot: 8 days, 18 hours, 40 minutes Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0000 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 AMD Radeon Pro 5300M: Chipset Model: AMD Radeon Pro 5300M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0043 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32207P1-019 Option ROM Version: 113-D32207P1-019 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal SAMSUNG: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Mirror: Off Online: Yes Rotation: Supported Adapter Type: DVI or HDMI Adapter Firmware Version: 15.75 Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 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: 2.2.4 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: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 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: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 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-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 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: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 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: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 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: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 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: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Window Toolkit duplicate all ChimeraX