id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17802 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.5-arm64-arm-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x0000000327c83000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000326c77000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000325c6b000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000324c5f000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000323c53000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000322c47000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000321c3b000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003156db000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003146cf000 (most 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""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003126b7000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001eeab1f00 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unallocated=5.2G(96%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 688K 35 \nColorSync 640K 32 \nCoreAnimation 1136K 60 \nCoreGraphics 48K 3 \nCoreUI image data 4848K 35 \nFoundation 32K 2 \nKernel Alloc Once 1456K 5 \nMALLOC 4.6G 144 \nMALLOC guard page 288K 18 \nMach message 64K 4 \nOpenGL GLSL 384K 4 \nSTACK GUARD 816K 51 \nStack 339.8M 51 \nStack (graphics) 544K 1 \nStack Guard 56.0M 1 \nVM_ALLOCATE 398.7M 222 \nVM_ALLOCATE (reserved) 128.0M 1 reserved VM address space (unallocated)\n__AUTH 5521K 697 \n__AUTH_CONST 77.4M 944 \n__CTF 824 1 \n__DATA 34.1M 1083 \n__DATA_CONST 36.8M 1100 \n__DATA_DIRTY 2778K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 645.8M 150 \n__OBJC_RO 61.4M 1 \n__OBJC_RW 2396K 1 \n__TEXT 1.3G 1106 \n__TEXT (graphics) 3872K 14 \n__TPRO_CONST 128K 2 \ndyld private memory 1280K 11 \nmapped file 550.0M 76 \npage table in kernel 3277K 1 \nshared memory 3808K 28 \n=========== ======= ======= \nTOTAL 8.2G 6231 \nTOTAL, minus reserved VM space 8.0G 6231 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""28a1301702f38c27286f1eb97cf349d5fd0f202d"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""61675b89201f677a9a4cbd65"", ""factorPackIds"" : { ""HEALTH_FEATURE_AVAILABILITY"" : ""65a855f5f087695cfac03d1f"" }, ""deploymentId"" : 240000187 }, { ""rolloutId"" : ""64b21a7351cbb02ce3442e4e"", ""factorPackIds"" : { ""REMINDERS_GROCERY"" : ""6647f0f7b6a75d3dc32993e7"" }, ""deploymentId"" : 240000042 } ], ""experiments"" : [ { ""treatmentId"" : ""d7ff00dd-1c5a-4dbb-85d6-7a936d671384"", ""experimentId"" : ""67f46bbc84eaf455d73c6098"", ""deploymentId"" : 400000001 } ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields 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/ivavo639/Downloads/cryosparc_P462_J16_class_00_final_volume.mrc Opened cryosparc_P462_J16_class_00_final_volume.mrc as #1, grid size 128,128,128, pixel 1.9, shown at level 0.425, step 1, values float32 > volume #1 level 0.373 > volume #1 level 0.3345 > ui tool show ""Side View"" > volume #1 level 0.3964 > open /Users/ivavo639/Downloads/cryosparc_P462_J18_006_volume_map.mrc Opened cryosparc_P462_J18_006_volume_map.mrc as #2, grid size 256,256,256, pixel 1.43, shown at level 0.19, step 1, values float32 > volume #2 level 0.5009 > volume #2 level 0.2961 > volume #2 level 0.561 > volume #2 level 0.4026 > open /Users/ivavo639/Downloads/cryosparc_P462_J19_004_volume_map.mrc Opened cryosparc_P462_J19_004_volume_map.mrc as #3, grid size 256,256,256, pixel 1.43, shown at level 0.117, step 1, values float32 > open /Users/ivavo639/Downloads/cryosparc_P462_J19_004_volume_map_sharp.mrc Opened cryosparc_P462_J19_004_volume_map_sharp.mrc as #4, grid size 256,256,256, pixel 1.43, shown at level 0.415, step 1, values float32 > close #2 > close #1 > show #!4 models > select add #4 4 models selected > select subtract #4 Nothing selected > ui tool show ""Model Panel"" > view #4 clip false > hide #!4 models > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > show #!4 models > select add #3 2 models selected > view matrix models #3,1,0,0,34.276,0,1,0,75.363,0,0,1,18.972 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models #3,1,0,0,71.765,0,1,0,162.98,0,0,1,28.784 > ui mousemode right translate > ui tool show ""Volume Viewer"" > volume #3 level 0.7817 > volume #4 level 1.37 > volume #4 level 1.106 > view sel > select add #4 5 models selected > select subtract #3 3 models selected > view sel > select subtract #4 Nothing selected > save /Users/ivavo639/Desktop/image1.png supersample 3 > volume #3 level 0.6575 > save /Users/ivavo639/Desktop/image2.png supersample 3 > open /Users/ivavo639/Downloads/cryosparc_P462_J18_006_volume_map.mrc format > mrc Opened cryosparc_P462_J18_006_volume_map.mrc as #1, grid size 256,256,256, pixel 1.43, shown at level 0.19, step 1, values float32 > volume #1 level 0.3949 > center Unknown command: center > centre Unknown command: centre > center cryosparc_P462_J18_006_volume_map_mrc Unknown command: center cryosparc_P462_J18_006_volume_map_mrc > save /Users/ivavo639/Desktop/image3.png supersample 3 > open /Users/ivavo639/Downloads/cryosparc_P462_J16_class_00_final_volume.mrc > format mrc Opened cryosparc_P462_J16_class_00_final_volume.mrc as #2, grid size 128,128,128, pixel 1.9, shown at level 0.425, step 1, values float32 > volume #2 level 0.4111 > save /Users/ivavo639/Desktop/image4.png supersample 3 > ui tool show ""Map Coordinates"" > close #3 > volume #2 level 0.4059 > volume #4 level 1.027 > save /Users/ivavo639/Desktop/image5.png supersample 3 > open 7a6a fromDatabase pdb format mmcif Summary of feedback from opening 7a6a fetched from pdb --- notes | Fetching compressed mmCIF 7a6a from http://files.rcsb.org/download/7a6a.cif Fetching CCD NA from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/NA/NA.cif 7a6a title: 1.15 A structure of human apoferritin obtained from Titan Mono- BCOR microscope [more info...] Chain information for 7a6a #3 --- Chain | Description | UniProt 1 2 4 6 A B E F G H I K M O P Q S U W X Y a e r | Ferritin heavy chain | FRIH_HUMAN 0-182 Non-standard residues in 7a6a #3 --- CSX — S-oxy cysteine NA — sodium ion 2928 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > select add #3 38685 atoms, 34728 bonds, 128 pseudobonds, 8805 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #3,1,0,0,-111.09,0,1,0,-118.46,0,0,1,-97.854 > view matrix models #3,1,0,0,-125.18,0,1,0,-121.5,0,0,1,-106.42 > view matrix models #3,1,0,0,-125.76,0,1,0,-114.03,0,0,1,-117.78 > view matrix models #3,1,0,0,-120.7,0,1,0,-120.9,0,0,1,-120.26 > view matrix models #3,1,0,0,-119.11,0,1,0,-118.37,0,0,1,-117.48 > ui mousemode right translate > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.22458,-0.72312,0.6532,-19.296,0.93216,-0.035915,-0.36025,-63.586,0.28397,0.68979,0.666,-193.03 > view matrix models > #3,-0.3056,0.85689,0.41515,-115.15,0.68738,-0.10316,0.71893,-154.17,0.65888,0.50507,-0.55748,-71.019 > view matrix models > #3,0.4436,0.66806,0.59742,-202.84,0.88822,-0.23884,-0.39244,-30.636,-0.11949,0.70473,-0.69934,14.064 > view matrix models > #3,0.45902,0.33873,0.82132,-192.21,0.86933,-0.3619,-0.3366,-20.468,0.18322,0.8685,-0.46059,-69.207 > view matrix models > #3,0.35187,0.25155,0.90162,-178.75,0.93358,-0.024349,-0.35755,-65.439,-0.067986,0.96754,-0.24341,-76.883 > ui tool show ""Fit in Map"" > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2846, steps = 52 shifted from previous position = 1.1 rotated from previous position = 1.1 degrees atoms outside contour = 32516, contour level = 1.0271 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation 0.34697531 0.26907868 0.89844577 -179.10085800 0.93450316 -0.01804092 -0.35549736 -67.28003870 -0.07944797 0.96294921 -0.25771463 -73.01404093 Axis 0.74435456 0.55208886 0.37567829 Axis point 0.00000000 32.23996227 25.74031017 Rotation angle (degrees) 117.67075879 Shift along axis -197.88889061 > view matrix models > #3,-0.49739,0.76899,0.40157,-79.755,0.57978,0.63899,-0.50552,-85.261,-0.64533,-0.018624,-0.76367,169.45 > view matrix models > #3,-0.93862,-0.019428,-0.3444,153.52,0.018567,0.99412,-0.10668,-108.02,0.34445,-0.10653,-0.93274,82.919 > ui mousemode right translate > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.3447, steps = 92 shifted from previous position = 1.95 rotated from previous position = 7.89 degrees atoms outside contour = 31586, contour level = 1.0271 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.96434137 -0.00018125 -0.26466148 145.85689349 -0.00015478 0.99999998 -0.00012088 -117.41634281 0.26466150 -0.00007560 -0.96434137 83.34204308 Axis 0.00008553 -1.00000000 0.00005001 Axis point 67.30936176 0.00000000 51.49327297 Rotation angle (degrees) 164.65316042 Shift along axis 117.43298549 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.3448, steps = 44 shifted from previous position = 0.0234 rotated from previous position = 0.0165 degrees atoms outside contour = 31585, contour level = 1.0271 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.96436468 0.00006820 -0.26457656 145.81913374 0.00011534 0.99999998 -0.00016263 -117.42006990 0.26457654 -0.00018735 -0.96436467 83.37079383 Axis -0.00004672 -0.99999999 0.00008908 Axis point 67.29848720 0.00000000 51.50058751 Rotation angle (degrees) 164.65820721 Shift along axis 117.42068358 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.034394,0.26264,-0.96428,87.623,0.99937,0.017823,-0.030791,-115.82,0.0090991,-0.96473,-0.26309,144.62 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.3447, steps = 52 shifted from previous position = 0.153 rotated from previous position = 2.04 degrees atoms outside contour = 31598, contour level = 1.0271 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation 0.00001154 0.26453508 -0.96437606 83.35234254 0.99999998 -0.00020075 -0.00004310 -117.24687298 -0.00020500 -0.96437604 -0.26453508 145.84526250 Axis -0.62241297 -0.62230849 0.47469383 Axis point 0.00000000 -61.03572782 127.97921978 Rotation angle (degrees) 129.22461294 Shift along axis 90.31599147 > view matrix models > #3,-0.0058973,0.3526,-0.93576,70.273,0.98863,-0.13854,-0.058435,-92.674,-0.15025,-0.92546,-0.34777,168.8 > view matrix models > #3,0.84017,0.52934,-0.11793,-147.07,0.29684,-0.63086,-0.71687,124.89,-0.45387,0.56729,-0.68716,68.46 > view matrix models > #3,0.99964,0.018738,0.01946,-121.83,0.026059,-0.4789,-0.87748,157.89,-0.0071228,0.87767,-0.47921,-45.495 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.3085, steps = 76 shifted from previous position = 0.0928 rotated from previous position = 3.62 degrees atoms outside contour = 32294, contour level = 1.0271 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation 0.99999999 0.00001559 0.00014251 -117.34253761 0.00012922 -0.52845385 -0.84896202 163.34726123 0.00006207 0.84896203 -0.52845385 -37.13338392 Axis 1.00000000 0.00004737 0.00006692 Axis point 0.00000000 91.98688385 26.80345241 Rotation angle (degrees) 121.90104741 Shift along axis -117.33728381 > view matrix models > #3,0.23714,-0.81181,-0.53359,131.62,-0.060877,0.53576,-0.84217,44.088,0.96957,0.2322,0.077633,-150.35 > view matrix models > #3,0.30452,-0.80254,-0.51303,120.14,-0.10001,0.5087,-0.85512,53.433,0.94724,0.31171,0.074653,-156.75 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2867, steps = 80 shifted from previous position = 0.919 rotated from previous position = 0.515 degrees atoms outside contour = 32555, contour level = 1.0271 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation 0.30798630 -0.80159692 -0.51243226 118.71463833 -0.09211532 0.51095857 -0.85465555 52.44186924 0.94692091 0.31042506 0.08352888 -157.32379359 Axis 0.58323414 -0.73054566 0.35516331 Axis point 177.06222128 0.00000000 20.95088240 Rotation angle (degrees) 92.79502971 Shift along axis -24.94838988 > view matrix models > #3,0.085142,0.25521,-0.96313,73.46,-0.099465,0.96399,0.24664,-130.22,0.99139,0.074798,0.10746,-137.58 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.299, steps = 52 shifted from previous position = 1.42 rotated from previous position = 1.36 degrees atoms outside contour = 32271, contour level = 1.0271 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation 0.09471071 0.25028581 -0.96352836 74.17490298 -0.11982347 0.96370851 0.23855448 -127.48452321 0.98826728 0.09285965 0.12126364 -141.28250911 Axis -0.07314320 -0.97986029 -0.18580603 Axis point 105.61392303 0.00000000 -11.18405837 Rotation angle (degrees) 84.84551523 Shift along axis 145.74277425 > view matrix models > #3,-0.3008,0.90944,0.28712,-104.63,0.95115,0.30803,0.020776,-150.81,-0.069547,0.27934,-0.95767,89.003 > ui mousemode right rotate > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.292, steps = 68 shifted from previous position = 1.3 rotated from previous position = 2.18 degrees atoms outside contour = 32394, contour level = 1.0271 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.28539542 0.90797419 0.30680992 -108.65733855 0.95287985 0.30315602 -0.01078942 -147.50799812 -0.10280779 0.28927374 -0.95170965 90.02451015 Axis 0.58865219 0.80357203 0.08809418 Axis point 8.19750565 0.00000000 53.57344975 Rotation angle (degrees) 165.23393714 Shift along axis -174.56404726 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2921, steps = 44 shifted from previous position = 0.0269 rotated from previous position = 0.0146 degrees atoms outside contour = 32423, contour level = 1.0271 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.28555160 0.90796269 0.30669862 -108.63045428 0.95281949 0.30334165 -0.01090243 -147.49283203 -0.10293346 0.28911522 -0.95174424 90.04192977 Axis 0.58858547 0.80363104 0.08800171 Axis point 8.19430528 -0.00000000 53.57190477 Rotation angle (degrees) 165.23451613 Shift along axis -174.54428097 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2921, steps = 48 shifted from previous position = 0.00759 rotated from previous position = 0.0191 degrees atoms outside contour = 32426, contour level = 1.0271 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.28578570 0.90796782 0.30646530 -108.58037632 0.95275319 0.30355098 -0.01087003 -147.51082158 -0.10289749 0.28887929 -0.95181976 90.06899932 Axis 0.58849852 0.80370287 0.08792723 Axis point 8.20687047 -0.00000000 53.57609926 Rotation angle (degrees) 165.24579216 Shift along axis -174.53474309 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2921, steps = 44 shifted from previous position = 0.00429 rotated from previous position = 0.00825 degrees atoms outside contour = 32426, contour level = 1.0271 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.28568172 0.90797187 0.30655023 -108.60286192 0.95278694 0.30344572 -0.01085096 -147.50775922 -0.10287372 0.28897714 -0.95179263 90.05435467 Axis 0.58853978 0.80366813 0.08796859 Axis point 8.20214245 0.00000000 53.57373503 Rotation angle (degrees) 165.24288512 Shift along axis -174.54243434 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.292, steps = 44 shifted from previous position = 0.0213 rotated from previous position = 0.0217 degrees atoms outside contour = 32401, contour level = 1.0271 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.28541078 0.90797810 0.30678407 -108.65651544 0.95287336 0.30317568 -0.01081069 -147.50267779 -0.10282534 0.28924087 -0.95171775 90.02503483 Axis 0.58864609 0.80357846 0.08807626 Axis point 8.19442954 0.00000000 53.57185131 Rotation angle (degrees) 165.23436394 Shift along axis -174.56113998 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.292, steps = 40 shifted from previous position = 0.0066 rotated from previous position = 0.00318 degrees atoms outside contour = 32389, contour level = 1.0271 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.28538480 0.90797474 0.30681818 -108.66062652 0.95288362 0.30314435 -0.01078459 -147.50682861 -0.10280234 0.28928425 -0.95170705 90.02084895 Axis 0.58865656 0.80356825 0.08809948 Axis point 8.19601437 0.00000000 53.57225548 Rotation angle (degrees) 165.23376273 Shift along axis -174.56480491 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2921, steps = 60 shifted from previous position = 0.0206 rotated from previous position = 0.0224 degrees atoms outside contour = 32428, contour level = 1.0271 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.28564852 0.90797520 0.30657130 -108.60681782 0.95279745 0.30341277 -0.01084928 -147.50855599 -0.10286853 0.28900127 -0.95178587 90.05604072 Axis 0.58855313 0.80365731 0.08797809 Axis point 8.20326345 0.00000000 53.57567919 Rotation angle (degrees) 165.24209703 Shift along axis -174.54425302 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.292, steps = 40 shifted from previous position = 0.0182 rotated from previous position = 0.0138 degrees atoms outside contour = 32406, contour level = 1.0271 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.28548753 0.90797124 0.30673294 -108.63708139 0.95284833 0.30325393 -0.01082220 -147.50836578 -0.10284422 0.28918036 -0.95173409 90.03969849 Axis 0.58861504 0.80360405 0.08805034 Axis point 8.20119680 0.00000000 53.57591693 Rotation angle (degrees) 165.23603382 Shift along axis -174.55571388 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2921, steps = 60 shifted from previous position = 0.02 rotated from previous position = 0.0119 degrees atoms outside contour = 32416, contour level = 1.0271 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.28553902 0.90794621 0.30675911 -108.63735596 0.95281170 0.30336284 -0.01099307 -147.48515715 -0.10304043 0.28914471 -0.95172370 90.05076991 Axis 0.58858324 0.80363470 0.08798318 Axis point 8.19155211 0.00000000 53.57499596 Rotation angle (degrees) 165.22841162 Shift along axis -174.54336355 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.292, steps = 28 shifted from previous position = 0.0272 rotated from previous position = 0.0107 degrees atoms outside contour = 32403, contour level = 1.0271 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.28553843 0.90798813 0.30663555 -108.61870794 0.95282973 0.30331068 -0.01086955 -147.50961044 -0.10287526 0.28906779 -0.95176494 90.06680175 Axis 0.58859659 0.80362340 0.08799708 Axis point 8.20739383 0.00000000 53.58344081 Rotation angle (degrees) 165.23884356 Shift along axis -174.54915985 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2921, steps = 44 shifted from previous position = 0.0275 rotated from previous position = 0.00934 degrees atoms outside contour = 32417, contour level = 1.0271 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.28550839 0.90795192 0.30677071 -108.64291566 0.95282630 0.30331859 -0.01094888 -147.48670486 -0.10299032 0.28917320 -0.95172047 90.04086214 Axis 0.58859793 0.80362129 0.08800741 Axis point 8.19061358 0.00000000 53.57256207 Rotation angle (degrees) 165.22957910 Shift along axis -174.54618789 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.292, steps = 28 shifted from previous position = 0.0206 rotated from previous position = 0.0163 degrees atoms outside contour = 32407, contour level = 1.0271 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.28566870 0.90797552 0.30655155 -108.59899059 0.95279403 0.30342438 -0.01082520 -147.52477725 -0.10284423 0.28898806 -0.95179250 90.06818495 Axis 0.58854656 0.80366184 0.08798070 Axis point 8.21223300 -0.00000000 53.58190095 Rotation angle (degrees) 165.24380571 Shift along axis -174.55133360 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.292, steps = 44 shifted from previous position = 0.00609 rotated from previous position = 0.0107 degrees atoms outside contour = 32414, contour level = 1.0271 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.28559557 0.90799802 0.30655303 -108.61075293 0.95283344 0.30330554 -0.01068599 -147.53566205 -0.10268209 0.28904210 -0.95179360 90.04752085 Axis 0.58858475 0.80362687 0.08804460 Axis point 8.21280848 0.00000000 53.57813450 Rotation angle (degrees) 165.24907160 Shift along axis -174.56205619 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.292, steps = 60 shifted from previous position = 0.00723 rotated from previous position = 0.0172 degrees atoms outside contour = 32400, contour level = 1.0271 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.28541856 0.90797596 0.30678314 -108.65410318 0.95287142 0.30318198 -0.01080490 -147.50589115 -0.10282171 0.28924097 -0.95171811 90.02759865 Axis 0.58864299 0.80358056 0.08807785 Axis point 8.19647888 0.00000000 53.57323909 Rotation angle (degrees) 165.23457120 Shift along axis -174.56190555 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.292, steps = 48 shifted from previous position = 0.000558 rotated from previous position = 0.00271 degrees atoms outside contour = 32399, contour level = 1.0271 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.28545921 0.90796835 0.30676786 -108.64643454 0.95285797 0.30322411 -0.01080884 -147.50858079 -0.10283349 0.28922071 -0.95172299 90.03243782 Axis 0.58862592 0.80359408 0.08806864 Axis point 8.19870412 0.00000000 53.57451232 Rotation angle (degrees) 165.23495449 Shift along axis -174.56009452 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.292, steps = 40 shifted from previous position = 0.00712 rotated from previous position = 0.00183 degrees atoms outside contour = 32394, contour level = 1.0271 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.28543405 0.90797095 0.30678356 -108.64618984 0.95286617 0.30319846 -0.01080548 -147.50975817 -0.10282736 0.28923942 -0.95171797 90.03260738 Axis 0.58863614 0.80358571 0.08807664 Axis point 8.20127008 0.00000000 53.57534061 Rotation angle (degrees) 165.23444430 Shift along axis -174.56003819 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.292, steps = 60 shifted from previous position = 0.0108 rotated from previous position = 0.00493 degrees atoms outside contour = 32399, contour level = 1.0271 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.28549471 0.90796925 0.30673216 -108.63913347 0.95284630 0.30326040 -0.01081902 -147.50803517 -0.10284306 0.28917983 -0.95173438 90.03638326 Axis 0.58861208 0.80360615 0.08805093 Axis point 8.19929935 -0.00000000 53.57442062 Rotation angle (degrees) 165.23614457 Shift along axis -174.55688390 > volume #4 level 0.6203 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.037011,0.99871,-0.03484,-117.1,0.95715,-0.025408,0.28846,-144.55,0.28721,-0.044024,-0.95686,83.928 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.3447, steps = 60 shifted from previous position = 1.65 rotated from previous position = 3.22 degrees atoms outside contour = 27303, contour level = 0.6203 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.00002228 0.99999996 -0.00026965 -117.42618837 0.96432168 0.00009287 0.26473324 -144.42501953 0.26473325 -0.00025414 -0.96432165 83.35640079 Axis -0.70390330 -0.70394455 -0.09477455 Axis point 6.74498714 0.00000000 51.85632991 Rotation angle (degrees) 169.15066128 Shift along axis 176.42382153 > view matrix models > #3,0.9259,0.36874,0.082098,-161.95,0.26488,-0.78865,0.55486,-2.9592,0.26934,-0.492,-0.82788,124.77 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2793, steps = 60 shifted from previous position = 1.21 rotated from previous position = 2.8 degrees atoms outside contour = 28882, contour level = 0.6203 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation 0.90882826 0.40172656 0.11245879 -168.21201322 0.27468767 -0.77915570 0.56343862 -5.70680173 0.31397116 -0.48117789 -0.81846805 117.83967245 Axis -0.97497091 -0.18807735 -0.11856908 Axis point 0.00000000 33.59280801 65.76508169 Rotation angle (degrees) 147.60746703 Shift along axis 151.10299868 > view matrix models > #3,0.9409,-0.33868,-0.0013345,-71.137,-0.23711,-0.66151,0.71147,23.356,-0.24184,-0.6691,-0.70272,191.99 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2778, steps = 88 shifted from previous position = 1.07 rotated from previous position = 2.98 degrees atoms outside contour = 28961, contour level = 0.6203 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation 0.92808317 -0.37024560 -0.03974703 -60.38365680 -0.23632945 -0.66813810 0.70550681 24.67857675 -0.28776730 -0.64537561 -0.70758767 194.74668224 Axis -0.97891806 0.17972809 0.09704244 Axis point 0.00000000 44.97506202 92.36435372 Rotation angle (degrees) 136.37088211 Shift along axis 82.44477970 > view matrix models > #3,0.84088,0.25159,-0.47919,-71.624,0.061475,-0.92405,-0.37729,147.59,-0.53772,0.2878,-0.79248,124.1 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2731, steps = 76 shifted from previous position = 1.84 rotated from previous position = 3.1 degrees atoms outside contour = 29115, contour level = 0.6203 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation 0.85047981 0.28108977 -0.44460391 -79.80695663 0.08066145 -0.90493837 -0.41782804 149.58610292 -0.51978633 0.31949192 -0.79230492 117.89756008 Axis 0.96034464 0.09792361 -0.26105391 Axis point 0.00000000 69.12727373 64.58986126 Rotation angle (degrees) 157.42558701 Shift along axis -92.77179086 > view matrix models > #3,-0.030378,0.99874,0.039997,-117.75,-0.74474,0.0040732,-0.66735,169.18,-0.66667,-0.05006,0.74367,-2.4874 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.030378,0.99874,0.039997,-116.25,-0.74474,0.0040732,-0.66735,168.21,-0.66667,-0.05006,0.74367,-3.0155 > view matrix models > #3,-0.030378,0.99874,0.039997,-115.91,-0.74474,0.0040732,-0.66735,167.78,-0.66667,-0.05006,0.74367,-2.4523 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.3, steps = 60 shifted from previous position = 2.59 rotated from previous position = 4.25 degrees atoms outside contour = 28488, contour level = 0.6203 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.00003011 1.00000000 -0.00004023 -117.37144723 -0.70723655 -0.00004974 -0.70697699 167.70929188 -0.70697699 0.00000717 0.70723655 0.68418308 Axis 0.35734343 0.35731947 -0.86291858 Axis point 22.19929373 145.78685742 0.00000000 Rotation angle (degrees) 98.41961243 Shift along axis 17.39348584 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.3, steps = 28 shifted from previous position = 0.0248 rotated from previous position = 0.0247 degrees atoms outside contour = 28493, contour level = 0.6203 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.00013013 0.99999999 -0.00008030 -117.33017514 -0.70694171 -0.00014879 -0.70727180 167.72077497 -0.70727180 -0.00003527 0.70694172 0.75700651 Axis 0.35748421 0.35746145 -0.86280145 Axis point 22.23672182 145.77460313 0.00000000 Rotation angle (degrees) 98.43391628 Shift along axis 17.35688046 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.3, steps = 40 shifted from previous position = 0.00177 rotated from previous position = 0.0112 degrees atoms outside contour = 28492, contour level = 0.6203 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.00002494 1.00000000 -0.00002846 -117.34833213 -0.70705304 -0.00003776 -0.70716052 167.70609726 -0.70716052 0.00000248 0.70705304 0.72697607 Axis 0.35743827 0.35742264 -0.86283657 Axis point 22.22229579 145.77985241 0.00000000 Rotation angle (degrees) 98.42443024 Shift along axis 17.36990850 > volume #4 level 0.8576 > volume #4 level 1.117 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.3, steps = 28 shifted from previous position = 0.0341 rotated from previous position = 0.0181 degrees atoms outside contour = 32723, contour level = 1.1175 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation 0.00003635 1.00000000 0.00002444 -117.39553171 -0.70726947 0.00004298 -0.70694406 167.69838570 -0.70694406 0.00000841 0.70726947 0.68025121 Axis 0.35732228 0.35733038 -0.86292282 Axis point 22.18926678 145.79735661 0.00000000 Rotation angle (degrees) 98.41404933 Shift along axis 17.38868486 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.3, steps = 44 shifted from previous position = 0.0349 rotated from previous position = 0.0239 degrees atoms outside contour = 32732, contour level = 1.1175 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.00002177 1.00000000 -0.00004663 -117.34583643 -0.70698203 -0.00004837 -0.70723152 167.70714803 -0.70723152 0.00001757 0.70698202 0.74197998 Axis 0.35748389 0.35745144 -0.86280574 Axis point 22.22877579 145.78020563 0.00000000 Rotation angle (degrees) 98.42670258 Shift along axis 17.35773122 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.3, steps = 28 shifted from previous position = 0.0295 rotated from previous position = 0.0333 degrees atoms outside contour = 32725, contour level = 1.1175 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation 0.00001119 1.00000000 0.00001188 -117.38600076 -0.70739055 0.00001631 -0.70682291 167.70074111 -0.70682291 -0.00000050 0.70739054 0.65031115 Axis 0.35725469 0.35726095 -0.86297955 Axis point 22.18242438 145.78977512 0.00000000 Rotation angle (degrees) 98.41204402 Shift along axis 17.41502149 > view matrix models > #3,1.1187e-05,1,1.1885e-05,-113.37,-0.70739,1.6313e-05,-0.70682,146.73,-0.70682,-4.9979e-07,0.70739,49.209 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.03135, steps = 176 shifted from previous position = 11.6 rotated from previous position = 7.15 degrees atoms outside contour = 37126, contour level = 1.1175 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation 0.07123834 0.99636257 -0.04676254 -122.21338861 -0.76785559 0.02485657 -0.64014056 150.99573625 -0.63664974 0.08150943 0.76683331 18.64432364 Axis 0.36167542 0.29563875 -0.88418811 Axis point 24.93327501 140.07636034 0.00000000 Rotation angle (degrees) 93.92989790 Shift along axis -16.04647780 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.03135, steps = 48 shifted from previous position = 0.0258 rotated from previous position = 0.0147 degrees atoms outside contour = 37133, contour level = 1.1175 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation 0.07098734 0.99638246 -0.04672042 -122.17856753 -0.76787667 0.02469209 -0.64012165 150.99930429 -0.63665236 0.08131606 0.76685167 18.64947726 Axis 0.36157398 0.29566522 -0.88422075 Axis point 24.92931701 140.05186751 0.00000000 Rotation angle (degrees) 93.94130169 Shift along axis -16.02160349 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.03135, steps = 40 shifted from previous position = 0.00673 rotated from previous position = 0.00506 degrees atoms outside contour = 37129, contour level = 1.1175 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation 0.07107105 0.99637565 -0.04673842 -122.18811707 -0.76788584 0.02474648 -0.64010855 150.99748018 -0.63663196 0.08138296 0.76686150 18.64159786 Axis 0.36159910 0.29564447 -0.88421742 Axis point 24.92898611 140.05845337 0.00000000 Rotation angle (degrees) 93.93705334 Shift along axis -16.02476915 > view matrix models > #3,0.071071,0.99638,-0.046738,-125.52,-0.76789,0.024746,-0.64011,167.98,-0.63663,0.081383,0.76686,-20.825 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.297, steps = 96 shifted from previous position = 7.46 rotated from previous position = 5.37 degrees atoms outside contour = 33036, contour level = 1.1175 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation 0.13705350 0.98803502 -0.07073289 -124.02590878 -0.80147463 0.06864554 -0.59407593 157.64621997 -0.58211232 0.13811080 0.80129311 -41.52040981 Axis 0.36609560 0.25569128 -0.89476029 Axis point 13.29950571 149.02061519 0.00000000 Rotation angle (degrees) 89.79968907 Shift along axis 32.05423809 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.297, steps = 48 shifted from previous position = 0.00599 rotated from previous position = 0.00523 degrees atoms outside contour = 33035, contour level = 1.1175 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation 0.13698982 0.98804240 -0.07075319 -124.01953672 -0.80151922 0.06859120 -0.59402205 157.65415280 -0.58206592 0.13808502 0.80133126 -41.53202398 Axis 0.36605572 0.25565789 -0.89478615 Axis point 13.29854338 149.01752201 0.00000000 Rotation angle (degrees) 89.80197716 Shift along axis 32.06974706 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.98024,-0.09091,0.17568,106.21,0.032741,-0.95045,-0.30915,145.83,0.19508,-0.29729,0.93465,-97.63 > view matrix models > #3,-0.82349,-0.47366,0.31226,116.76,0.22603,-0.77876,-0.58519,135.33,0.52035,-0.41132,0.74836,-100.58 > view matrix models > #3,-0.22585,0.45135,0.86329,-128.09,0.85674,-0.32978,0.39655,-108.08,0.46368,0.82917,-0.31221,-115.13 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.3235, steps = 116 shifted from previous position = 0.361 rotated from previous position = 11.3 degrees atoms outside contour = 32489, contour level = 1.1175 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.23475830 0.31523721 0.91951838 -117.33976631 0.91954698 -0.23467214 0.31521793 -117.34841197 0.31515376 0.91954037 -0.23478419 -117.32419490 Axis 0.57734087 0.57738116 0.57732877 Axis point 0.00240505 0.00000000 0.00781647 Rotation angle (degrees) 148.44161741 Shift along axis -203.23443886 > view matrix models > #3,-0.53473,0.80761,0.24866,-60.845,0.82015,0.56688,-0.07746,-153.89,-0.20352,0.16252,-0.96549,119.59 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2845, steps = 68 shifted from previous position = 1.69 rotated from previous position = 0.574 degrees atoms outside contour = 33218, contour level = 1.1175 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.52933731 0.81307423 0.24230626 -60.75954838 0.82459914 0.56024133 -0.07852337 -152.37685052 -0.19959531 0.15824018 -0.96701694 118.72260114 Axis 0.47214405 0.88122177 0.02298249 Axis point 19.28897725 0.00000000 60.27159421 Rotation angle (degrees) 165.47914834 Shift along axis -160.23651509 > view matrix models > #3,0.51886,0.51963,-0.6788,-41.121,-0.15878,-0.72165,-0.67381,185.39,-0.83998,0.45739,-0.29193,79.304 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2882, steps = 100 shifted from previous position = 2.16 rotated from previous position = 5.17 degrees atoms outside contour = 33244, contour level = 1.1175 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation 0.45619216 0.55239396 -0.69767444 -34.88159396 -0.20435812 -0.69802351 -0.68629509 187.80996682 -0.86609842 0.45565788 -0.20554666 73.70006506 Axis 0.82735078 0.12202404 -0.54827076 Axis point 0.00000000 84.79336214 72.10397976 Rotation angle (degrees) 136.35989709 Shift along axis -46.34957458 > view matrix models > #3,0.37286,-0.62821,-0.68288,112.61,-0.8933,-0.44208,-0.081073,167.48,-0.25096,0.64025,-0.72602,40.723 > view matrix models > #3,0.093343,-0.89504,-0.43611,147.99,-0.97428,-0.17235,0.14519,118.47,-0.20511,0.41134,-0.8881,81.479 > view matrix models > #3,0.3626,-0.88643,-0.28769,97.653,-0.75793,-0.46011,0.46242,89.447,-0.54227,0.050378,-0.83869,158.08 > view matrix models > #3,0.41098,-0.89044,-0.19549,81.528,-0.79663,-0.45503,0.39789,101.04,-0.44325,-0.0077907,-0.89636,160.06 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.3037, steps = 84 shifted from previous position = 1.22 rotated from previous position = 6.55 degrees atoms outside contour = 33018, contour level = 1.1175 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation 0.45881359 -0.88046599 -0.11945597 64.63352994 -0.76106414 -0.45880737 0.45855989 90.61162485 -0.45855367 -0.11947985 -0.88059815 172.97753192 Axis -0.84916458 0.49814871 0.17540632 Axis point 0.00000000 81.75714292 84.86487295 Rotation angle (degrees) 160.10131953 Shift along axis 20.59491209 > view matrix models > #3,0.26763,-0.78281,-0.56177,127.9,-0.95867,-0.2748,-0.073779,155.07,-0.096621,0.55829,-0.824,43.527 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2913, steps = 80 shifted from previous position = 1.27 rotated from previous position = 1.64 degrees atoms outside contour = 33094, contour level = 1.1175 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation 0.28616711 -0.79022605 -0.54189591 125.40517393 -0.95435504 -0.28554516 -0.08758102 157.69388776 -0.08552696 0.54222390 -0.83586984 45.05030793 Axis 0.79230762 -0.57412160 -0.20647766 Axis point -0.00000000 118.40296378 59.45549727 Rotation angle (degrees) 156.58115431 Shift along axis -0.47787388 > view #3 clip false > view matrix models > #3,0.24196,-0.67263,-0.6993,135.33,-0.70634,-0.61623,0.34834,115.98,-0.66524,0.40966,-0.62421,104.16 > view matrix models > #3,0.48381,-0.69138,-0.53658,89.768,-0.84162,-0.53569,-0.068621,171.68,-0.24,0.4848,-0.84105,70.683 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2902, steps = 76 shifted from previous position = 1.7 rotated from previous position = 4.2 degrees atoms outside contour = 33198, contour level = 1.1175 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation 0.51841646 -0.66956725 -0.53190608 80.89862870 -0.83398209 -0.53335632 -0.14143873 179.47786978 -0.18899273 0.51692431 -0.83490778 60.00192182 Axis 0.86591964 -0.45102078 -0.21624854 Axis point 0.00000000 104.55364473 59.34139489 Rotation angle (degrees) 157.65687048 Shift along axis -23.87186405 > view matrix models > #3,0.35079,0.88471,-0.30697,-109.39,0.36471,-0.43099,-0.82537,106.6,-0.86251,0.17757,-0.47385,136.97 > view matrix models > #3,0.36873,0.87367,-0.3174,-108.98,0.17093,-0.39936,-0.90072,134.65,-0.91369,0.27787,-0.2966,110.24 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2952, steps = 84 shifted from previous position = 0.544 rotated from previous position = 5.34 degrees atoms outside contour = 33066, contour level = 1.1175 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation 0.34682443 0.90312148 -0.25314899 -117.86644097 0.14504638 -0.31829911 -0.93682828 132.54015964 -0.92664685 0.28819659 -0.24138841 104.35672880 Axis 0.77032440 0.42351126 -0.47669543 Axis point 0.00000000 78.07077364 69.77576612 Rotation angle (degrees) 127.33192515 Shift along axis -84.40952041 > view matrix models > #3,-0.18848,0.96459,0.18452,-113.59,-0.1194,0.16399,-0.97921,111.82,-0.97479,-0.20659,0.084263,130.01 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.3244, steps = 68 shifted from previous position = 1.17 rotated from previous position = 4.31 degrees atoms outside contour = 32523, contour level = 1.1175 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.15622731 0.96993321 0.18660815 -117.40629742 -0.18630064 0.15660047 -0.96993215 118.76479917 -0.96999233 -0.18629510 0.15623390 118.80892999 Axis 0.43211923 0.63778162 -0.63757946 Axis point -55.70671860 0.00000000 166.50910625 Rotation angle (degrees) 114.94173889 Shift along axis -50.73764608 > view matrix models > #3,-0.68475,0.66576,-0.29645,37.956,-0.46997,-0.71429,-0.51857,201.8,-0.55699,-0.21577,0.802,-2.7289 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2732, steps = 68 shifted from previous position = 1.55 rotated from previous position = 1.64 degrees atoms outside contour = 33442, contour level = 1.1175 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.68310137 0.65692033 -0.31910533 42.41935990 -0.44966153 -0.72261169 -0.52501130 199.98752326 -0.57547984 -0.21514655 0.78900882 1.33778981 Axis 0.26317745 0.21774657 -0.93985321 Axis point 54.01685105 95.23852537 0.00000000 Rotation angle (degrees) 143.93523929 Shift along axis 53.45309017 > ui mousemode right translate > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.66511,0.33426,-0.66775,-37.512,-0.68627,0.62612,-0.37013,50.383,0.29437,0.70444,0.64584,-193.05 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.3027, steps = 60 shifted from previous position = 1.52 rotated from previous position = 3.34 degrees atoms outside contour = 32965, contour level = 1.1175 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation 0.66651455 0.33327788 -0.66684647 -38.59022408 -0.66670351 0.66671731 -0.33315833 40.04070169 0.33356378 0.66664375 0.66657431 -196.11243014 Axis 0.57719871 -0.57754982 -0.57730222 Axis point 236.04410538 0.00000000 -234.61329332 Rotation angle (degrees) 60.00641171 Shift along axis 67.81641464 > view matrix models > #3,0.86109,-0.45486,0.22723,-74.074,0.0127,-0.42752,-0.90392,156.42,0.5083,0.78124,-0.36236,-108.78 > view matrix models > #3,0.80928,-0.53866,0.23434,-58.901,-0.46945,-0.83286,-0.2932,189.1,0.3531,0.12727,-0.92689,53.42 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2793, steps = 64 shifted from previous position = 1.27 rotated from previous position = 3.33 degrees atoms outside contour = 33205, contour level = 1.1175 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation 0.77931739 -0.56327826 0.27455786 -56.67715275 -0.48121475 -0.81860989 -0.31354460 190.48814809 0.40136863 0.11222947 -0.90901473 48.28895445 Axis 0.94245109 -0.28069571 0.18164761 Axis point 0.00000000 82.79060001 39.49812696 Rotation angle (degrees) 166.94498347 Shift along axis -98.11307716 > view matrix models > #3,-0.024142,-0.99409,-0.10581,133.98,-0.92465,0.062441,-0.37566,146.15,0.38004,0.088773,-0.9207,54.956 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2949, steps = 60 shifted from previous position = 1.32 rotated from previous position = 2.68 degrees atoms outside contour = 33181, contour level = 1.1175 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation 0.01989966 -0.99366744 -0.11058489 128.85658268 -0.93031134 0.02211267 -0.36610359 151.62904284 0.36623055 0.11016371 -0.92398006 54.87005756 Axis 0.70359770 -0.70440746 0.09359703 Axis point 133.23676822 0.00000000 54.41631890 Rotation angle (degrees) 160.21744478 Shift along axis -11.00975935 > view matrix models > #3,-0.21221,-0.97223,-0.098681,152.33,-0.96719,0.22339,-0.12099,103.28,0.13967,0.069769,-0.98774,93.92 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.21221,-0.97223,-0.098681,213.24,-0.96719,0.22339,-0.12099,82.932,0.13967,0.069769,-0.98774,162.69 > select add #4 38685 atoms, 34728 bonds, 128 pseudobonds, 8805 residues, 4 models selected > view matrix models > #4,1,0,0,-5.246,0,1,0,1.365,0,0,1,-5.802,#3,-0.21221,-0.97223,-0.098681,208,-0.96719,0.22339,-0.12099,84.297,0.13967,0.069769,-0.98774,156.88 > select subtract #3 2 models selected > view matrix models #4,1,0,0,-21.632,0,1,0,-0.31027,0,0,1,-22.084 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.21848,-0.18204,0.95871,-21.628,-0.91102,0.31406,0.26724,0.63915,-0.34974,-0.93179,-0.097223,-20.385 > view matrix models > #4,-0.69436,-0.104,0.71208,-20.856,-0.65577,-0.31606,-0.68562,1.5871,0.29636,-0.94302,0.15126,-21.016 > volume #4 level 1.682 > view matrix models > #4,0.28001,0.74043,0.61103,-22.083,-0.8133,0.52113,-0.2588,0.79711,-0.51005,-0.42448,0.74811,-21.237 > view matrix models > #4,0.39908,-0.28372,0.87192,-21.623,0.18903,0.95595,0.22454,-0.57413,-0.89722,0.075211,0.43513,-21.094 > view matrix models > #4,0.031896,-0.86436,-0.50186,-19.965,0.98981,-0.042402,0.13594,-0.36979,-0.13878,-0.50108,0.8542,-21.523 > view matrix models > #4,-0.50674,-0.018246,-0.8619,-19.928,0.85998,0.059379,-0.50687,0.1092,0.060428,-0.99807,-0.014399,-20.69 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.50674,-0.018246,-0.8619,-31.483,0.85998,0.059379,-0.50687,-1.4918,0.060428,-0.99807,-0.014399,-31.689 > view matrix models > #4,-0.50674,-0.018246,-0.8619,-31.09,0.85998,0.059379,-0.50687,2.6298,0.060428,-0.99807,-0.014399,-32.755 > view matrix models > #4,-0.50674,-0.018246,-0.8619,-31.373,0.85998,0.059379,-0.50687,3.1925,0.060428,-0.99807,-0.014399,-32.825 > view matrix models > #4,-0.50674,-0.018246,-0.8619,-36.642,0.85998,0.059379,-0.50687,5.6209,0.060428,-0.99807,-0.014399,-39.189 > ui mousemode right translate > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.24362,-0.46207,-0.85272,-36.867,0.73933,-0.48058,0.47164,5.3939,-0.62773,-0.74534,0.22454,-39.049 > select add #3 38685 atoms, 34728 bonds, 128 pseudobonds, 8805 residues, 4 models selected > select subtract #4 38685 atoms, 34728 bonds, 128 pseudobonds, 8805 residues, 2 models selected > view matrix models > #3,0.58669,-0.34158,-0.73425,114.24,0.33703,0.92743,-0.16214,-147.98,0.73635,-0.15234,0.65923,-81.815 > view matrix models > #3,0.85054,-0.34485,0.39706,-50.106,-0.010534,0.74368,0.66846,-183.32,-0.5258,-0.57273,0.6289,120.44 > view matrix models > #3,-0.26019,0.86516,-0.42872,35.679,-0.5693,0.22116,0.79182,-70.206,0.77987,0.45009,0.43499,-131.61 > view matrix models > #3,0.90771,0.29074,-0.30253,-49.3,0.3365,-0.073715,0.93879,-159.7,0.25064,-0.95396,-0.16475,167.48 > view matrix models > #3,-0.41195,-0.89195,0.18633,188.45,0.26298,0.07941,0.96153,-171.78,-0.87243,0.4451,0.20185,91.612 > view matrix models > #3,0.060078,-0.59251,-0.80332,214.21,0.38791,-0.72766,0.56572,-44.501,-0.91974,-0.3456,0.18613,192.42 > view matrix models > #3,-0.96557,-0.24865,-0.076493,208.9,0.25832,-0.88156,-0.39512,102.43,0.030816,-0.40128,0.91544,0.63602 > view matrix models > #3,-0.96389,-0.2521,-0.085816,210.21,0.26477,-0.87263,-0.41039,102.41,0.028573,-0.41829,0.90786,3.8046 > view matrix models > #3,-0.91568,-0.28025,-0.28809,231.72,0.40176,-0.6184,-0.6754,87.511,0.011125,-0.73419,0.67885,70.207 > view matrix models > #3,-0.22391,0.92659,-0.30214,9.1953,0.011624,-0.30745,-0.95149,129.46,-0.97454,-0.21656,0.05807,198.77 > view matrix models > #3,-0.32933,0.91524,0.2321,-40.097,-0.86889,-0.19756,-0.45387,161.7,-0.36955,-0.35114,0.86031,48.502 > view matrix models > #3,-0.43039,0.88915,0.15547,-16.036,-0.84207,-0.33347,-0.42392,171.05,-0.32509,-0.31337,0.89225,35.019 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.43039,0.88915,0.15547,-60.981,-0.84207,-0.33347,-0.42392,170.39,-0.32509,-0.31337,0.89225,-72.68 > view matrix models > #3,-0.43039,0.88915,0.15547,-65.058,-0.84207,-0.33347,-0.42392,170.6,-0.32509,-0.31337,0.89225,-82.713 > ui mousemode right translate > ui mousemode right rotate > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.43039,0.88915,0.15547,-112.58,-0.84207,-0.33347,-0.42392,193.69,-0.32509,-0.31337,0.89225,-72.483 > ui mousemode right rotate > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2997, steps = 100 shifted from previous position = 3.38 rotated from previous position = 4.56 degrees atoms outside contour = 36528, contour level = 1.6825 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.51360048 0.10006770 -0.85217428 149.55196307 0.85198833 -0.05817071 -0.52031918 -31.07186909 -0.10163873 -0.99327873 -0.05538001 136.47369345 Axis -0.40670058 -0.64538975 0.64658078 Axis point 117.80469701 94.44053984 0.00000000 Rotation angle (degrees) 144.44676286 Shift along axis 47.47186410 > volume #4 level 0.5751 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2998, steps = 104 shifted from previous position = 0.00736 rotated from previous position = 0.0177 degrees atoms outside contour = 27831, contour level = 0.5751 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.51352489 0.09995655 -0.85223288 149.56376358 0.85206789 -0.05791159 -0.52021780 -31.12427516 -0.10135334 -0.99330506 -0.05543072 136.44177954 Axis -0.40667148 -0.64546505 0.64652392 Axis point 117.81225854 94.43693214 0.00000000 Rotation angle (degrees) 144.43277296 Shift along axis 47.47918965 > volume #4 level 0.5073 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2997, steps = 100 shifted from previous position = 0.0189 rotated from previous position = 0.0244 degrees atoms outside contour = 26977, contour level = 0.50731 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.51372281 0.09997024 -0.85211198 149.56566350 0.85191241 -0.05824218 -0.52043550 -31.04275823 -0.10165692 -0.99328435 -0.05524555 136.47126872 Axis -0.40663443 -0.64536662 0.64664548 Axis point 117.79381438 94.43858689 0.00000000 Rotation angle (degrees) 144.44968662 Shift along axis 47.46394019 > volume #4 level 0.6768 > volume flip #4 Opened cryosparc_P462_J19_004_volume_map_sharp.mrc z flip as #5, grid size 256,256,256, pixel 1.43, shown at step 1, values float32 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2998, steps = 56 shifted from previous position = 0.0225 rotated from previous position = 0.0233 degrees atoms outside contour = 29055, contour level = 0.6768 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.51348420 0.09984300 -0.85227071 149.57682048 0.85208933 -0.05801421 -0.52017125 -31.12131349 -0.10137927 -0.99331049 -0.05528577 136.42450899 Axis -0.40667558 -0.64541087 0.64657543 Axis point 117.81246537 94.42236117 0.00000000 Rotation angle (degrees) 144.42868417 Shift along axis 47.46552988 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2997, steps = 84 shifted from previous position = 0.0262 rotated from previous position = 0.0217 degrees atoms outside contour = 29060, contour level = 0.6768 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.51376309 0.09988856 -0.85209728 149.57580929 0.85190091 -0.05816394 -0.52046306 -31.04584081 -0.10154964 -0.99329715 -0.05521267 136.45931715 Axis -0.40658708 -0.64539121 0.64665071 Axis point 117.79047963 94.43899988 0.00000000 Rotation angle (degrees) 144.44619616 Shift along axis 47.46263547 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2998, steps = 84 shifted from previous position = 0.0227 rotated from previous position = 0.015 degrees atoms outside contour = 29043, contour level = 0.6768 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.51362402 0.09992017 -0.85217741 149.57252742 0.85200304 -0.05797628 -0.52031680 -31.09472019 -0.10139622 -0.99330495 -0.05535428 136.43750993 Axis -0.40662899 -0.64544830 0.64656736 Axis point 117.80295932 94.43530932 0.00000000 Rotation angle (degrees) 144.43707669 Shift along axis 47.46554971 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.75206,0.39954,0.52418,-58.223,-0.60931,-0.72467,-0.32185,200.7,0.25127,-0.56144,0.78844,-96.355 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2889, steps = 76 shifted from previous position = 1.35 rotated from previous position = 3.55 degrees atoms outside contour = 29388, contour level = 0.6768 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.81247832 -0.13013873 -0.56828066 179.54258201 0.40877639 0.56783392 -0.71446939 -30.42012621 0.41566917 -0.81279060 -0.40815510 96.23905150 Axis -0.08730601 -0.87371514 0.47853893 Axis point 79.12040634 0.00000000 72.34329359 Rotation angle (degrees) 145.73066196 Shift along axis 56.95751227 > view matrix models > #3,-0.90765,-0.24815,0.33851,58.685,-0.31568,-0.1279,-0.94021,169.92,0.27661,-0.96024,0.037756,36.361 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2715, steps = 92 shifted from previous position = 2.52 rotated from previous position = 0.6 degrees atoms outside contour = 29672, contour level = 0.6768 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.63222516 0.45142058 -0.62969105 95.61175260 0.37123793 0.88985982 0.26520162 -178.47708576 0.68005423 -0.06609807 -0.73017621 13.03688059 Axis -0.24479535 -0.96776293 -0.05924648 Axis point 65.98151889 0.00000000 38.55601954 Rotation angle (degrees) 137.41470377 Shift along axis 148.54580602 > show sel atoms > hide sel atoms > show sel atoms > show sel cartoons > hide sel atoms > view matrix models > #3,-0.39995,-0.91621,0.024328,115.43,0.64539,-0.30038,-0.70232,46.354,0.65078,-0.26519,0.71145,-169.99 > view matrix models > #3,-0.269,-0.95892,0.090037,97.25,0.96307,-0.26665,0.037403,-82.486,-0.011858,0.096773,0.99524,-167.99 > view matrix models > #3,-0.54071,-0.37338,-0.7538,159.83,0.46699,-0.87857,0.10021,40.93,-0.69968,-0.29783,0.64941,0.65451 > view matrix models > #3,-0.035701,0.97335,0.22654,-174.58,-0.61387,0.15752,-0.77353,149.39,-0.7886,-0.16668,0.59189,2.4602 > view matrix models > #3,-0.0027605,0.648,0.76164,-203.24,-0.21109,0.7441,-0.63384,16.068,-0.97746,-0.16252,0.13473,78.251 > view matrix models > #3,-0.41628,0.80809,0.41679,-132.59,0.097691,0.49549,-0.8631,36.035,-0.90397,-0.31858,-0.2852,137.59 > ui tool show ""Fit in Map"" > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2857, steps = 76 shifted from previous position = 1.92 rotated from previous position = 2.99 degrees atoms outside contour = 29359, contour level = 0.6768 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation 0.49871396 0.79431318 -0.34691636 -111.07678519 0.83784043 -0.33923765 0.42771630 -108.99303866 0.22205360 -0.50396864 -0.83469025 132.30768119 Axis -0.85276442 -0.52077405 0.03984018 Axis point 0.00000000 1.39293111 68.32792155 Rotation angle (degrees) 146.88827749 Shift along axis 156.75423728 > view matrix models > #3,-0.54366,0.53224,-0.64897,40.697,0.72678,-0.088199,-0.68118,10.928,-0.41979,-0.84199,-0.33887,149.37 > view matrix models > #3,0.95156,0.075823,-0.29796,-123.41,0.30724,-0.27072,0.91231,-106.14,-0.011489,-0.95967,-0.2809,108.21 > view matrix models > #3,0.16162,-0.9645,-0.20885,82.185,0.18323,-0.17863,0.96671,-108.79,-0.96969,-0.1945,0.14785,80.374 > view matrix models > #3,-0.0045944,-0.86308,0.50504,5.5388,0.73076,0.34186,0.59087,-190.53,-0.68262,0.37178,0.62913,-77.22 > volume flip #4 Opened cryosparc_P462_J19_004_volume_map_sharp.mrc z flip as #6, grid size 256,256,256, pixel 1.43, shown at step 1, values float32 > volume flip #4 Opened cryosparc_P462_J19_004_volume_map_sharp.mrc z flip as #7, grid size 256,256,256, pixel 1.43, shown at step 1, values float32 > volume flip #1 Opened cryosparc_P462_J18_006_volume_map.mrc z flip as #8, grid size 256,256,256, pixel 1.43, shown at step 1, values float32 > volume flip #4 Opened cryosparc_P462_J19_004_volume_map_sharp.mrc z flip as #9, grid size 256,256,256, pixel 1.43, shown at step 1, values float32 > view matrix models > #3,0.96293,-0.19082,-0.19065,-105.94,0.24796,0.90445,0.3471,-171.16,0.1062,-0.38151,0.91825,-115.55 > view matrix models > #3,0.64957,-0.2291,-0.72496,-1.3258,0.52632,0.82361,0.21131,-178.45,0.54868,-0.51882,0.65557,-120.57 > view matrix models > #3,0.20466,-0.23867,-0.94929,78.828,0.58626,0.80651,-0.076382,-149.54,0.78385,-0.5409,0.30498,-104.33 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #3,0.20466,-0.23867,-0.94929,299.55,0.58626,0.80651,-0.076382,32.588,0.78385,-0.5409,0.30498,110.89 > view matrix models > #3,0.20466,-0.23867,-0.94929,111.69,0.58626,0.80651,-0.076382,-155.83,0.78385,-0.5409,0.30498,-133.16 > view matrix models > #3,0.20466,-0.23867,-0.94929,84.519,0.58626,0.80651,-0.076382,-144.29,0.78385,-0.5409,0.30498,-105.77 > view matrix models > #3,0.20466,-0.23867,-0.94929,81.812,0.58626,0.80651,-0.076382,-146.1,0.78385,-0.5409,0.30498,-108.26 > ui mousemode right translate > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2856, steps = 136 shifted from previous position = 7.08 rotated from previous position = 9.3 degrees atoms outside contour = 29334, contour level = 0.6768 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation 0.06343041 0.93481053 -0.34943649 -75.98136717 -0.96777508 0.14311689 0.20719304 73.16732664 0.24369650 0.32503359 0.91376430 -172.25869083 Axis 0.05902718 -0.29710455 -0.95301872 Axis point 20.28156886 110.30986267 0.00000000 Rotation angle (degrees) 86.55124462 Shift along axis 137.94244563 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.088339,0.17841,-0.97998,65.866,0.9539,0.29844,-0.031656,-137.09,0.28682,-0.93761,-0.19655,61.045 > view matrix models > #3,-0.77958,-0.14753,-0.60869,142.13,0.30925,0.75445,-0.57893,-50.189,0.54463,-0.63956,-0.54253,36.263 > view matrix models > #3,-0.68488,-0.25892,-0.6811,152.65,0.2539,0.79135,-0.55615,-50.7,0.68299,-0.55383,-0.47624,1.9746 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2953, steps = 100 shifted from previous position = 2.26 rotated from previous position = 5.75 degrees atoms outside contour = 29144, contour level = 0.6768 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.32717486 0.90369714 -0.27620301 -34.58229907 -0.27739724 0.18756298 0.94226902 -99.89819895 0.90333127 0.38490469 0.18931720 -173.86815125 Axis -0.31671802 -0.67026134 -0.67114785 Axis point 37.30300004 24.84897922 0.00000000 Rotation angle (degrees) 118.36894362 Shift along axis 194.60197360 > ui tool show ""Side View"" > view matrix models > #3,0.30701,-0.80724,0.5041,-37.972,-0.576,-0.57925,-0.57679,210.48,0.7576,-0.11328,-0.64281,-40.21 > view matrix models > #3,0.33618,-0.64954,0.68197,-81.039,-0.38259,-0.75586,-0.53132,203.13,0.86059,-0.082294,-0.50261,-72.584 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2775, steps = 92 shifted from previous position = 1.45 rotated from previous position = 2.21 degrees atoms outside contour = 29565, contour level = 0.6768 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.72657730 -0.68421690 0.06271102 160.38527020 -0.63948266 0.70679767 0.30248798 -44.23086362 -0.25129140 0.17967829 -0.95108799 121.86194393 Axis -0.36107867 0.92321357 0.13152528 Axis point 77.70077385 0.00000000 58.02708945 Rotation angle (degrees) 170.20872327 Shift along axis -82.71830678 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2775, steps = 100 shifted from previous position = 0.00323 rotated from previous position = 0.00407 degrees atoms outside contour = 29553, contour level = 0.6768 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.72655483 -0.68423547 0.06276870 160.37500085 -0.63948256 0.70678552 0.30251660 -44.23399047 -0.25135659 0.17965541 -0.95107508 121.87102156 Axis -0.36108730 0.92320979 0.13152815 Axis point 77.69770694 0.00000000 58.02996888 Rotation angle (degrees) 170.20481351 Shift along axis -82.71715791 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2775, steps = 120 shifted from previous position = 0.02 rotated from previous position = 0.0172 degrees atoms outside contour = 29580, contour level = 0.6768 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.72675794 -0.68401773 0.06279054 160.36864597 -0.63926531 0.70697972 0.30252197 -44.30257504 -0.25132204 0.17972043 -0.95107193 121.85435159 Axis -0.36094736 0.92326287 0.13153960 Axis point 77.68353108 0.00000000 58.02801973 Rotation angle (degrees) 170.20578263 Shift along axis -82.75888932 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2775, steps = 104 shifted from previous position = 0.00103 rotated from previous position = 0.0014 degrees atoms outside contour = 29579, contour level = 0.6768 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.72677405 -0.68400043 0.06279257 160.36839398 -0.63924993 0.70699657 0.30251509 -44.30629574 -0.25131458 0.17971997 -0.95107398 121.85305272 Axis -0.36093652 0.92326750 0.13153690 Axis point 77.68275458 0.00000000 58.02773068 Rotation angle (degrees) 170.20600307 Shift along axis -82.76120028 > fitmap #3 inMap #9 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc z flip (#9) using 38685 atoms average map value = 0.2844, steps = 104 shifted from previous position = 3.1 rotated from previous position = 7.24 degrees atoms outside contour = 29462, contour level = 0.6768 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc z flip (#9) coordinates: Matrix rotation and translation -0.79862444 -0.60054520 0.03929974 162.15132244 -0.57546193 0.78112175 0.24226511 -51.80182762 -0.17618903 0.17086333 -0.96941382 113.61075455 Axis -0.31262851 0.94350503 0.10982564 Axis point 76.23277418 0.00000000 55.72429923 Rotation angle (degrees) 173.44275319 Shift along axis -87.09103837 > hide #!9 models > show #!9 models > hide #!9 models > show #!4 models > hide #!4 models > show #!9 models > open /Users/ivavo639/Downloads/cryosparc_P462_J19_004_volume_map.mrc format > mrc Opened cryosparc_P462_J19_004_volume_map.mrc as #10, grid size 256,256,256, pixel 1.43, shown at level 0.117, step 1, values float32 > hide #!9 models > ui mousemode right ""translate selected models"" > view matrix models > #3,0.22159,-0.65294,0.72427,126.92,-0.39698,-0.7388,-0.54458,389.3,0.89068,-0.16685,-0.42292,152.53 > ui mousemode right translate > ui mousemode right ""move picked models"" > ui mousemode right ""translate selected models"" > view matrix models > #3,0.22159,-0.65294,0.72427,149.47,-0.39698,-0.7388,-0.54458,379.21,0.89068,-0.16685,-0.42292,146.39 > volume #10 level 0.459 > fitmap #3 inMap #9 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc z flip (#9) using 38685 atoms average map value = 0, steps = 24 shifted from previous position = 0 rotated from previous position = 0 degrees atoms outside contour = 38685, contour level = 0.6768 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc z flip (#9) coordinates: Matrix rotation and translation -0.79862444 -0.60054520 0.03929974 205.35595314 -0.57546193 0.78112175 0.24226511 -403.96175953 -0.17618903 0.17086333 -0.96941382 59.05108160 Axis -0.31262851 0.94350503 0.10982564 Axis point 39.00783590 0.00000000 50.96736470 Rotation angle (degrees) 173.44275319 Shift along axis -438.85475582 > fitmap #3 inMap #9 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc z flip (#9) using 38685 atoms average map value = 0, steps = 24 shifted from previous position = 0 rotated from previous position = 0 degrees atoms outside contour = 38685, contour level = 0.6768 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc z flip (#9) coordinates: Matrix rotation and translation -0.79862444 -0.60054520 0.03929974 205.35595314 -0.57546193 0.78112175 0.24226511 -403.96175953 -0.17618903 0.17086333 -0.96941382 59.05108160 Axis -0.31262851 0.94350503 0.10982564 Axis point 39.00783590 0.00000000 50.96736470 Rotation angle (degrees) 173.44275319 Shift along axis -438.85475582 > fitmap #3 inMap #10 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map.mrc (#10) using 38685 atoms average map value = 0.2711, steps = 60 shifted from previous position = 2.66 rotated from previous position = 4.9 degrees atoms outside contour = 28711, contour level = 0.459 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map.mrc (#10) coordinates: Matrix rotation and translation 0.22846480 -0.61166240 0.75741201 138.62521316 -0.44429074 -0.75775573 -0.47792469 381.37369831 0.86626184 -0.22732217 -0.44487645 159.78664818 Axis 0.78212842 -0.33971946 0.52236561 Axis point 0.00000000 214.23550519 54.34878348 Rotation angle (degrees) 170.78117674 Shift along axis 62.32969998 > ui tool show ""Side View"" > fitmap #3 inMap #10 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map.mrc (#10) using 38685 atoms average map value = 0.2711, steps = 40 shifted from previous position = 0.0107 rotated from previous position = 0.0156 degrees atoms outside contour = 28718, contour level = 0.459 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map.mrc (#10) coordinates: Matrix rotation and translation 0.22826062 -0.61161282 0.75751360 138.63232964 -0.44441216 -0.75772130 -0.47786637 381.36961334 0.86625338 -0.22757018 -0.44476611 159.81151092 Axis 0.78206644 -0.33976442 0.52242915 Axis point 0.00000000 214.24749571 54.32716021 Rotation angle (degrees) 170.79180776 Shift along axis 62.33405901 > view matrix models > #3,0.22826,-0.61161,0.75751,138.55,-0.44441,-0.75772,-0.47787,381.29,0.86625,-0.22757,-0.44477,159.57 > fitmap #3 inMap #10 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map.mrc (#10) using 38685 atoms average map value = 0.2711, steps = 48 shifted from previous position = 0.279 rotated from previous position = 0.0142 degrees atoms outside contour = 28705, contour level = 0.459 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map.mrc (#10) coordinates: Matrix rotation and translation 0.22805286 -0.61162252 0.75756834 138.63745857 -0.44453412 -0.75764869 -0.47786807 381.36036125 0.86624553 -0.22778579 -0.44467103 159.84625757 Axis 0.78200210 -0.33983131 0.52248196 Axis point 0.00000000 214.25534210 54.31954274 Rotation angle (degrees) 170.79898206 Shift along axis 62.33337730 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.58611,-0.3393,-0.73576,240.53,-0.72545,-0.62417,-0.29005,376.59,-0.36083,0.70376,-0.61198,214.5 > view matrix models > #3,-0.47084,-0.21482,-0.85566,364.8,-0.022948,-0.96659,0.25529,269.68,-0.88192,0.13984,0.45018,217.2 > fitmap #3 inMap #10 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map.mrc (#10) using 38685 atoms average map value = 0.2784, steps = 96 shifted from previous position = 0.357 rotated from previous position = 8.9 degrees atoms outside contour = 28477, contour level = 0.459 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map.mrc (#10) coordinates: Matrix rotation and translation -0.41815089 -0.12620603 -0.89956761 352.96886359 0.03095733 -0.99170606 0.12474266 281.55731057 -0.90784992 0.02431304 0.41858977 237.61160163 Axis -0.53793411 0.04436283 0.84181876 Axis point 244.60852697 144.66253492 0.00000000 Rotation angle (degrees) 174.64378383 Shift along axis 22.64258944 > ui mousemode right translate > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.012553,0.99443,-0.1047,78.894,-0.11922,-0.10545,-0.98725,325.94,-0.99279,8.8711e-05,0.11988,285.77 > view matrix models > #3,0.18802,0.55359,-0.81129,190.7,0.61843,-0.70844,-0.34009,233.63,-0.76301,-0.43778,-0.47556,380.65 > view matrix models > #3,0.25619,0.60119,-0.75692,170.61,0.62495,-0.70041,-0.34478,232.46,-0.73743,-0.38471,-0.55515,380.77 > view matrix models > #3,0.54104,0.32576,-0.77534,171.67,0.72616,-0.64602,0.23529,145.6,-0.42424,-0.69032,-0.58607,383.52 > view matrix models > #3,0.60604,0.31544,-0.73021,159.89,0.73328,-0.57729,0.35921,122.01,-0.30824,-0.75315,-0.58117,376.66 > fitmap #3 inMap #10 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map.mrc (#10) using 38685 atoms average map value = 0.2779, steps = 68 shifted from previous position = 0.332 rotated from previous position = 2.06 degrees atoms outside contour = 28364, contour level = 0.459 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map.mrc (#10) coordinates: Matrix rotation and translation 0.58100248 0.32641636 -0.74557929 163.67997195 0.74558018 -0.58083501 0.32671225 124.74297500 -0.32641433 -0.74570977 -0.58083615 377.95369949 Axis -0.87519534 -0.34207729 0.34207636 Axis point 0.00000000 108.06375287 200.36414483 Rotation angle (degrees) 142.21676669 Shift along axis -56.63466097 > ui tool show ""Fit in Map"" > open /Users/ivavo639/Downloads/cryosparc_P462_J16_class_00_final_volume.mrc > format mrc Opened cryosparc_P462_J16_class_00_final_volume.mrc as #11, grid size 128,128,128, pixel 1.9, shown at level 0.425, step 1, values float32 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.581,0.32642,-0.74558,-48.02,0.74558,-0.58084,0.32671,-33.715,-0.32641,-0.74571,-0.58084,142.52 > view matrix models > #3,0.581,0.32642,-0.74558,-56.669,0.74558,-0.58084,0.32671,-40.244,-0.32641,-0.74571,-0.58084,132.84 > ui mousemode right translate > ui mousemode right ""rotate selected models"" > ui mousemode right rotate > ui mousemode right ""translate selected models"" > view matrix models > #3,0.581,0.32642,-0.74558,-65.736,0.74558,-0.58084,0.32671,-52.449,-0.32641,-0.74571,-0.58084,143.82 > ui tool show ""Side View"" > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #3,0.581,0.32642,-0.74558,-61.359,0.74558,-0.58084,0.32671,-56.764,-0.32641,-0.74571,-0.58084,148.89 > view matrix models > #3,0.581,0.32642,-0.74558,-58.769,0.74558,-0.58084,0.32671,-51.236,-0.32641,-0.74571,-0.58084,154.26 > fitmap #3 inMap #4 Fit molecule 7a6a (#3) to map cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) using 38685 atoms average map value = 0.2834, steps = 96 shifted from previous position = 2.42 rotated from previous position = 5.08 degrees atoms outside contour = 29347, contour level = 0.6768 Position of 7a6a (#3) relative to cryosparc_P462_J19_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation 0.92676236 0.14672688 0.34580741 -166.76742165 -0.34597786 0.69198091 0.63361008 -114.80420674 -0.14632449 -0.70684768 0.69206611 19.63278500 Axis -0.88739375 0.32579525 -0.32617448 Axis point 0.00000000 -21.80414135 224.16012045 Rotation angle (degrees) 49.04965719 Shift along axis 104.18198896 > hide #3:HOH > show sel atoms > hide sel cartoons > view #3/A > view #3/A:159-163 > volume #!4 style mesh > ui tool show ""Volume Viewer"" > volume #4 > volume #4 level 1.219 > volume #4 style surface > volume #4 level 0.7446 > volume #4 level 0.7107 > volume #4 step 2 > volume #4 level 0.5936 > volume #4 step 1 > volume #4 level 0.6727 > save /Users/ivavo639/Desktop/image6.png supersample 3 ===== 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 OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M3 OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac15,12 Model Number: MXCV3KS/A Chip: Apple M3 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 11881.121.1 OS Loader Version: 11881.121.1 Software: System Software Overview: System Version: macOS 15.5 (24F74) Kernel Version: Darwin 24.5.0 Time since boot: 3 days, 42 minutes Graphics/Displays: Apple M3: Chipset Model: Apple M3 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: DELL P2723DE: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal 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