id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8777 Graphics crash, macOS 13.2.1, Intel Iris Plus Graphics chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Aborted Current thread 0x00007ff8558fe680 (most recent call first): File ""/private/var/folders/q3/8zmh60_n5dz1n566d678653h0000gn/T/AppTranslocation/3CADFFCE-1F3A-4B7E-8B0E-ABDC32DA4252/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py"", line 2730 in draw_elements File ""/private/var/folders/q3/8zmh60_n5dz1n566d678653h0000gn/T/AppTranslocation/3CADFFCE-1F3A-4B7E-8B0E-ABDC32DA4252/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 1736 in draw File ""/private/var/folders/q3/8zmh60_n5dz1n566d678653h0000gn/T/AppTranslocation/3CADFFCE-1F3A-4B7E-8B0E-ABDC32DA4252/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 836 in _draw_geometry File 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""/private/var/folders/q3/8zmh60_n5dz1n566d678653h0000gn/T/AppTranslocation/3CADFFCE-1F3A-4B7E-8B0E-ABDC32DA4252/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 1538 in draw_opaque File ""/private/var/folders/q3/8zmh60_n5dz1n566d678653h0000gn/T/AppTranslocation/3CADFFCE-1F3A-4B7E-8B0E-ABDC32DA4252/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py"", line 247 in _draw_scene File ""/private/var/folders/q3/8zmh60_n5dz1n566d678653h0000gn/T/AppTranslocation/3CADFFCE-1F3A-4B7E-8B0E-ABDC32DA4252/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py"", line 177 in draw File 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""AppKit"", ""CFBundleVersion"" : ""2299.40.118"" } ], ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""6112d17137f5d11121dcd4e2"", ""factorPackIds"" : { }, ""deploymentId"" : 240000250 }, { ""rolloutId"" : ""60f8ddccefea4203d95cbeef"", ""factorPackIds"" : { }, ""deploymentId"" : 240000025 } ], ""experiments"" : [ { ""treatmentId"" : ""c28e4ee6-1b08-4f90-8e05-2809e78310a3"", ""experimentId"" : ""6317d2003d24842ff850182a"", ""deploymentId"" : 400000013 } ] }, ""reportNotes"" : [ ""dyld_process_snapshot_create_for_process failed with 5"" ] } ===== Log before crash start ===== UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/dingyongbo/Downloads/cryosparc_P3_J290_005_volume_map_sharp.mrc Opened cryosparc_P3_J290_005_volume_map_sharp.mrc as #1, grid size 224,224,224, pixel 0.825, shown at level 0.0448, step 1, values float32 > open /Users/dingyongbo/Downloads/cryosparc_P3_J288_005_volume_map_sharp.mrc Opened cryosparc_P3_J288_005_volume_map_sharp.mrc as #2, grid size 112,112,112, pixel 1.65, shown at level 0.127, step 1, values float32 > tile columns 3 spacingFactor 0.6 2 models tiled > volume #2 level 0.2095 > volume #1 level 0.07867 > ui mousemode right zoom > volume #2 level 0.202 > tile columns 3 spacingFactor 0.8 2 models tiled > open /Users/dingyongbo/Downloads/cryosparc_P3_J301_005_volume_map_sharp.mrc Opened cryosparc_P3_J301_005_volume_map_sharp.mrc as #3, grid size 224,224,224, pixel 0.825, shown at level 0.0442, step 1, values float32 > tile columns 3 spacingFactor 0.8 3 models tiled > volume #3 level 0.07665 > select add #3 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.10656,-0.12312,-0.98665,373.07,0.80081,-0.59881,-0.011765,89.136,-0.58937,-0.79137,0.1624,195.51 > view matrix models > #3,-0.03392,-0.0079143,-0.99939,357.82,0.40569,-0.91399,-0.0065317,148.17,-0.91338,-0.40567,0.034214,194.43 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.03392,-0.0079143,-0.99939,388.59,0.40569,-0.91399,-0.0065317,131.5,-0.91338,-0.40567,0.034214,194.43 > select subtract #3 Nothing selected > ui mousemode right zoom > select add #3 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.0024684,0.15393,-0.98808,372.92,-0.87731,-0.47453,-0.071735,233.01,-0.47992,0.86667,0.13622,32.012 > view matrix models > #3,0.98178,-0.18999,0.0041723,206.48,-0.088558,-0.43797,0.89461,64.752,-0.16814,-0.87868,-0.44682,226.37 > view matrix models > #3,0.98555,0.16303,0.045887,162.11,-0.16833,0.97286,0.15879,8.1128,-0.018754,-0.16422,0.98625,20.145 > view matrix models > #3,0.75394,-0.60993,-0.24404,275.75,0.64939,0.63579,0.41721,-70.762,-0.099312,-0.47303,0.87543,65.357 > view matrix models > #3,0.9203,-0.27287,-0.28033,237.11,0.2695,-0.077199,0.9599,-6.8803,-0.28357,-0.95895,0.0024905,202.77 > view matrix models > #3,0.93999,-0.064538,-0.33504,217.3,0.22914,0.84697,0.47973,-57.342,0.25281,-0.52771,0.81093,49.959 > tile columns 3 spacingFactor 0.8 3 models tiled > view matrix models > #3,0.8617,0.45592,-0.22274,131.95,0.0082645,0.4263,0.90455,-27.146,0.50735,-0.78129,0.36357,99.271 > view matrix models > #3,0.90071,0.40026,-0.16887,128.3,-0.26833,0.81829,0.50833,-1.8162,0.34165,-0.41255,0.84444,33.938 > select subtract #3 Nothing selected > ui mousemode right zoom > tile columns 3 spacingFactor 1 3 models tiled > select add #3 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.013488,-0.13326,0.99099,218.64,-0.86364,0.50104,0.055619,127.1,-0.50393,-0.85511,-0.12184,224.94 > select subtract #3 Nothing selected > ui mousemode right zoom > hide #!2 models > tile columns 3 spacingFactor 1 2 models tiled > save /Users/dingyongbo/Desktop/ChimeraX/SisAgo-Aga1/sgRNA_Compare.cxs > open /Users/dingyongbo/Desktop/ChimeraX/SisAgo-Aga1/docking_0403.cxs Opened cryosparc_P3_J291_class_00_00063_volume.mrc as #1, grid size 72,72,72, pixel 2.57, shown at level 0.148, step 1, values float32 Opened cryosparc_P3_J283_006_volume_map_sharp.mrc as #9, grid size 112,112,112, pixel 1.65, shown at level 0.128, step 1, values float32 Opened cryosparc_P3_J299_007_volume_map_sharp.mrc as #14, grid size 224,224,224, pixel 0.825, shown at level 0.0418, step 1, values float32 Opened cryosparc_P3_J299_007_volume_mask_refine.mrc as #15, grid size 224,224,224, pixel 0.825, shown at level 0.99, step 1, values float32 Opened cryosparc_P3_J300_005_volume_mask_refine.mrc as #16, grid size 224,224,224, pixel 0.825, shown at level 1, step 1, values float32 Opened cryosparc_P3_J300_005_volume_map_sharp.mrc as #17, grid size 224,224,224, pixel 0.825, shown at level 0.0344, step 1, values float32 opened ChimeraX session > hide #12 models > open /Users/dingyongbo/Desktop/ChimeraX/SisAgo- > Aga1/AgoAga1_dock_0403/Aga1.pdb Chain information for Aga1.pdb #2 --- Chain | Description B | No description available > open ""/Users/dingyongbo/Desktop/Profile in Ke Lab/Project/Aga2/Structural > Prediction/SisAga1_prediction_1/best_model.pdb"" Chain information for best_model.pdb #3 --- Chain | Description A | No description available > hide #3 models > show #3 models > hide #2 models > show #2 models > hide #2 models > show #2 models > close #2 > open ""/Users/dingyongbo/Desktop/Profile in Ke Lab/Project/Aga2/Structural > Prediction/SisAgo.pdb"" Chain information for SisAgo.pdb #2 --- Chain | Description C | No description available > tile columns 3 spacingFactor 1 3 models tiled > select add #2 3722 atoms, 3806 bonds, 459 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models > #2,0.93629,-0.35086,-0.016096,103.69,0.34752,0.9188,0.18718,30.812,-0.050886,-0.18085,0.98219,172.29 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.45875,-0.56927,-0.68226,102.26,-0.84504,-0.51688,-0.13693,28.595,-0.2747,0.63935,-0.71817,170.2 > view matrix models > #2,0.85351,-0.34328,0.39202,105.21,-0.39891,-0.91448,0.067724,26.755,0.33524,-0.21418,-0.91746,165.22 > view matrix models > #2,0.66671,0.68504,0.29361,108.64,-0.17086,-0.24298,0.95487,30.985,0.72547,-0.68679,-0.044953,165.38 > view matrix models > #2,0.44382,0.88498,-0.1408,108.53,-0.83661,0.46551,0.28877,32.97,0.3211,-0.010374,0.94699,171.69 > view matrix models > #2,0.51167,0.14816,-0.84631,103.85,-0.85374,-0.023016,-0.52019,28.976,-0.09655,0.9887,0.11471,173.39 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.51167,0.14816,-0.84631,84.528,-0.85374,-0.023016,-0.52019,79.287,-0.09655,0.9887,0.11471,74.775 > view matrix models > #2,0.77707,-0.21283,-0.59234,85.286,-0.62601,-0.35913,-0.6922,75.806,-0.06541,0.90869,-0.41231,72.478 > ui tool show ""Fit in Map"" > fitmap #2 inMap #1 Fit molecule SisAgo.pdb (#2) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms average map value = 0.1314, steps = 104 shifted from previous position = 1.9 rotated from previous position = 38.9 degrees atoms outside contour = 2172, contour level = 0.14802 Position of SisAgo.pdb (#2) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.28400201 0.60577398 -0.74322335 93.48201821 0.80409646 -0.27174838 -0.52875506 93.49394248 -0.52227573 -0.74779066 -0.40992357 97.97109234 Axis -0.59366818 -0.59885045 0.53752789 Axis point -9.66794343 0.00000000 95.49451496 Rotation angle (degrees) 169.36939025 Shift along axis -58.82399494 > select subtract #2 Nothing selected > fitmap #2 inMap #1 Fit molecule SisAgo.pdb (#2) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms average map value = 0.1314, steps = 60 shifted from previous position = 5.87 rotated from previous position = 0.019 degrees atoms outside contour = 2170, contour level = 0.14802 Position of SisAgo.pdb (#2) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.28412621 0.60551588 -0.74338618 93.48088556 0.80409617 -0.27180586 -0.52872595 93.49483757 -0.52220861 -0.74797878 -0.40966578 97.97137791 Axis -0.59360495 -0.59881597 0.53763612 Axis point -9.67819644 0.00000000 95.51239664 Rotation angle (degrees) 169.35757770 Shift along axis -58.80396710 > fitmap #2 inMap #1 Fit molecule SisAgo.pdb (#2) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms average map value = 0.1314, steps = 56 shifted from previous position = 0.00498 rotated from previous position = 0.0552 degrees atoms outside contour = 2172, contour level = 0.14802 Position of SisAgo.pdb (#2) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.28363924 0.60620423 -0.74301104 93.48397202 0.80424245 -0.27160274 -0.52860783 93.49848886 -0.52224807 -0.74749485 -0.41049793 97.97471878 Axis -0.59383131 -0.59892068 0.53726939 Axis point -9.66672790 0.00000000 95.46547348 Rotation angle (degrees) 169.37963769 Shift along axis -58.87307092 > fitmap #2 inMap #1 Fit molecule SisAgo.pdb (#2) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms average map value = 0.1314, steps = 60 shifted from previous position = 0.0412 rotated from previous position = 0.0451 degrees atoms outside contour = 2173, contour level = 0.14802 Position of SisAgo.pdb (#2) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.28408730 0.60565620 -0.74328674 93.46337618 0.80411682 -0.27171612 -0.52874067 93.53462647 -0.52219799 -0.74789778 -0.40982718 97.96877344 Axis -0.59362599 -0.59885818 0.53756587 Axis point -9.70012835 0.00000000 95.51527022 Rotation angle (degrees) 169.36265966 Shift along axis -58.83159604 > fitmap #2 inMap #1 Fit molecule SisAgo.pdb (#2) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms average map value = 0.1314, steps = 44 shifted from previous position = 0.0473 rotated from previous position = 0.01 degrees atoms outside contour = 2169, contour level = 0.14802 Position of SisAgo.pdb (#2) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.28396655 0.60568645 -0.74330823 93.48294349 0.80408184 -0.27186768 -0.52871595 93.49080711 -0.52231750 -0.74781820 -0.40982010 97.97180107 Axis -0.59368054 -0.59879756 0.53757315 Axis point -9.67462421 0.00000000 95.50288900 Rotation angle (degrees) 169.36634217 Shift along axis -58.81406225 > select add #3 2047 atoms, 2080 bonds, 243 residues, 1 model selected > view matrix models > #3,0.91167,-0.4095,0.034264,139.28,0.37681,0.79979,-0.46727,7.5823,0.16394,0.43891,0.88345,137.79 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.30221,-0.84852,0.43437,143.39,0.45603,-0.27146,-0.84755,9.9241,0.83708,0.45422,0.30492,134.44 > view matrix models > #3,0.13176,-0.96957,0.20634,145.06,0.066182,-0.19909,-0.97774,12.398,0.98907,0.14249,0.037936,134.56 > view matrix models > #3,-0.57356,-0.78122,-0.24642,149.74,-0.62852,0.61261,-0.47923,14.256,0.52534,-0.11999,-0.84239,139.34 > view matrix models > #3,-0.76881,0.62592,0.13098,147.42,0.47354,0.41959,0.77441,5.8896,0.42976,0.65739,-0.61898,137.96 > view matrix models > #3,-0.7597,-0.61576,0.20905,149.86,-0.29251,0.036472,-0.95557,14.102,0.58077,-0.78709,-0.20782,139.43 > view matrix models > #3,-0.72583,0.52773,0.44121,146.89,0.18979,0.77015,-0.60897,9.0253,-0.66117,-0.35827,-0.65916,146.95 > view matrix models > #3,-0.76534,0.59862,0.23644,147.3,0.21685,0.58572,-0.78097,9.5071,-0.60599,-0.54643,-0.57809,146.88 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.76534,0.59862,0.23644,98.232,0.21685,0.58572,-0.78097,63.49,-0.60599,-0.54643,-0.57809,100.22 > fitmap #3 inMap #1 Fit molecule best_model.pdb (#3) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms average map value = 0.1282, steps = 120 shifted from previous position = 1.91 rotated from previous position = 35.8 degrees atoms outside contour = 1145, contour level = 0.14802 Position of best_model.pdb (#3) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.03034396 0.12474393 -0.99172496 96.32008403 -0.55611859 0.82232818 0.12045204 92.30113170 0.83054894 0.55517160 0.04441972 66.53207024 Axis 0.21809060 -0.91420042 -0.34157588 Axis point 40.46471607 0.00000000 74.01783242 Rotation angle (degrees) 94.69192351 Shift along axis -86.10097881 > fitmap #3 inMap #1 Fit molecule best_model.pdb (#3) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms average map value = 0.1282, steps = 44 shifted from previous position = 0.0514 rotated from previous position = 0.0792 degrees atoms outside contour = 1139, contour level = 0.14802 Position of best_model.pdb (#3) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.03147066 0.12428715 -0.99174720 96.30093637 -0.55556539 0.82266178 0.12072662 92.31593752 0.83087717 0.55477969 0.04315993 66.57420079 Axis 0.21777476 -0.91445403 -0.34109820 Axis point 40.42980841 0.00000000 73.97166611 Rotation angle (degrees) 94.75093488 Shift along axis -86.15510832 > fitmap #3 inMap #1 Fit molecule best_model.pdb (#3) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms average map value = 0.1282, steps = 44 shifted from previous position = 0.00873 rotated from previous position = 0.0324 degrees atoms outside contour = 1140, contour level = 0.14802 Position of best_model.pdb (#3) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.03091135 0.12421481 -0.99177386 96.30411460 -0.55554957 0.82272652 0.12035769 92.31446558 0.83090874 0.55469988 0.04357589 66.56710280 Axis 0.21791040 -0.91444371 -0.34103923 Axis point 40.42535086 0.00000000 74.00717777 Rotation angle (degrees) 94.72103897 Shift along axis -86.13270789 > select subtract #3 Nothing selected > ui mousemode right zoom > fitmap #3 inMap #1 Fit molecule best_model.pdb (#3) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms average map value = 0.1282, steps = 52 shifted from previous position = 1.95 rotated from previous position = 0.0603 degrees atoms outside contour = 1148, contour level = 0.14802 Position of best_model.pdb (#3) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.03026880 0.12474466 -0.99172717 96.32323800 -0.55608092 0.82235938 0.12041300 92.29775611 0.83057691 0.55512523 0.04447629 66.51685765 Axis 0.21808546 -0.91420943 -0.34155505 Axis point 40.46938096 0.00000000 74.01663685 Rotation angle (degrees) 94.68724036 Shift along axis -86.09195021 > fitmap #3 inMap #1 Fit molecule best_model.pdb (#3) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms average map value = 0.1282, steps = 36 shifted from previous position = 0.0551 rotated from previous position = 0.0436 degrees atoms outside contour = 1141, contour level = 0.14802 Position of best_model.pdb (#3) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.03088814 0.12517885 -0.99165336 96.30076219 -0.55604695 0.82227879 0.12111810 92.31928918 0.83057684 0.55514687 0.04420665 66.56194635 Axis 0.21775129 -0.91420894 -0.34176951 Axis point 40.45442142 0.00000000 73.97971727 Rotation angle (degrees) 94.71511001 Shift along axis -86.17834763 > fitmap #3 inMap #1 Fit molecule best_model.pdb (#3) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms average map value = 0.1282, steps = 60 shifted from previous position = 0.041 rotated from previous position = 0.0703 degrees atoms outside contour = 1141, contour level = 0.14802 Position of best_model.pdb (#3) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.03091934 0.12411592 -0.99178599 96.32718411 -0.55557788 0.82271897 0.12027859 92.29326547 0.83088952 0.55473322 0.04351812 66.53880821 Axis 0.21796747 -0.91444293 -0.34100485 Axis point 40.44348164 0.00000000 74.00610448 Rotation angle (degrees) 94.72314618 Shift along axis -86.09078845 > fitmap #3 inMap #1 Fit molecule best_model.pdb (#3) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms average map value = 0.1282, steps = 48 shifted from previous position = 0.0215 rotated from previous position = 0.0781 degrees atoms outside contour = 1147, contour level = 0.14802 Position of best_model.pdb (#3) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.03012875 0.12484847 -0.99171837 96.32431088 -0.55626317 0.82223630 0.12041166 92.29857214 0.83045995 0.55528418 0.04467565 66.51862786 Axis 0.21816393 -0.91413821 -0.34169552 Axis point 40.47591112 0.00000000 74.02331174 Rotation angle (degrees) 94.68102233 Shift along axis -86.08827869 > fitmap #3 inMap #1 Fit molecule best_model.pdb (#3) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms average map value = 0.1282, steps = 36 shifted from previous position = 0.0527 rotated from previous position = 0.0511 degrees atoms outside contour = 1141, contour level = 0.14802 Position of best_model.pdb (#3) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.03090425 0.12521443 -0.99164837 96.30211389 -0.55604425 0.82227494 0.12115667 92.31812837 0.83057805 0.55514455 0.04421297 66.56121462 Axis 0.21773090 -0.91420755 -0.34178619 Axis point 40.45536992 0.00000000 73.97833226 Rotation angle (degrees) 94.71550223 Shift along axis -86.17968845 > fitmap #3 inMap #1 Fit molecule best_model.pdb (#3) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms average map value = 0.1282, steps = 60 shifted from previous position = 0.0444 rotated from previous position = 0.0366 degrees atoms outside contour = 1145, contour level = 0.14802 Position of best_model.pdb (#3) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.03040462 0.12483764 -0.99171132 96.32280480 -0.55615262 0.82228912 0.12056154 92.29439711 0.83052393 0.55520840 0.04442739 66.53024273 Axis 0.21805495 -0.91418450 -0.34164125 Axis point 40.46778075 0.00000000 74.01260719 Rotation angle (degrees) 94.69456951 Shift along axis -86.09991763 > volume #1 level 0.1818 > fitmap #3 inMap #1 Fit molecule best_model.pdb (#3) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms average map value = 0.1282, steps = 60 shifted from previous position = 0.00867 rotated from previous position = 0.00355 degrees atoms outside contour = 1405, contour level = 0.1818 Position of best_model.pdb (#3) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.03044689 0.12481011 -0.99171348 96.31967382 -0.55612281 0.82230896 0.12056373 92.30115537 0.83054235 0.55518520 0.04437299 66.53438976 Axis 0.21804291 -0.91419771 -0.34161357 Axis point 40.46547457 0.00000000 74.01085212 Rotation angle (degrees) 94.69677781 Shift along axis -86.10873389 > fitmap #3 inMap #1 Fit molecule best_model.pdb (#3) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms average map value = 0.1282, steps = 48 shifted from previous position = 0.019 rotated from previous position = 0.0318 degrees atoms outside contour = 1407, contour level = 0.1818 Position of best_model.pdb (#3) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.02989607 0.12474754 -0.99173811 96.32579565 -0.55612275 0.82236129 0.12020656 92.29597037 0.83056240 0.55512175 0.04478957 66.51795423 Axis 0.21818112 -0.91418183 -0.34156784 Axis point 40.46637714 0.00000000 74.04223242 Rotation angle (degrees) 94.66746684 Shift along axis -86.07922291 > fitmap #3 inMap #1 Fit molecule best_model.pdb (#3) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms average map value = 0.1282, steps = 40 shifted from previous position = 0.0434 rotated from previous position = 0.0725 degrees atoms outside contour = 1407, contour level = 0.1818 Position of best_model.pdb (#3) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.03092581 0.12501259 -0.99167316 96.31937975 -0.55666630 0.82188171 0.12096820 92.29110726 0.83016047 0.55577200 0.04417294 66.55917110 Axis 0.21814435 -0.91402772 -0.34200346 Axis point 40.48263271 0.00000000 73.98495774 Rotation angle (degrees) 94.72857650 Shift along axis -86.10856836 > fitmap #3 inMap #1 Fit molecule best_model.pdb (#3) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms average map value = 0.1282, steps = 40 shifted from previous position = 0.0254 rotated from previous position = 0.0331 degrees atoms outside contour = 1407, contour level = 0.1818 Position of best_model.pdb (#3) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.03081906 0.12483506 -0.99169885 96.32007201 -0.55622600 0.82220666 0.12078523 92.30216456 0.83045951 0.55533109 0.04409686 66.53710687 Axis 0.21801173 -0.91417716 -0.34168845 Axis point 40.47434283 0.00000000 73.98696111 Rotation angle (degrees) 94.71835384 Shift along axis -86.11658614 > fitmap #3 inMap #1 Fit molecule best_model.pdb (#3) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms average map value = 0.1282, steps = 48 shifted from previous position = 0.0371 rotated from previous position = 0.0678 degrees atoms outside contour = 1405, contour level = 0.1818 Position of best_model.pdb (#3) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.03084428 0.12415442 -0.99178351 96.30416353 -0.55544174 0.82281125 0.12027610 92.31436989 0.83098333 0.55458771 0.04358152 66.56594749 Axis 0.21789363 -0.91448001 -0.34095261 Axis point 40.41994322 0.00000000 74.01312137 Rotation angle (degrees) 94.71651312 Shift along axis -86.13141537 > fitmap #3 inMap #1 Fit molecule best_model.pdb (#3) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms average map value = 0.1282, steps = 44 shifted from previous position = 0.00718 rotated from previous position = 0.0195 degrees atoms outside contour = 1405, contour level = 0.1818 Position of best_model.pdb (#3) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.03112604 0.12426149 -0.99176129 96.30205885 -0.55556301 0.82269447 0.12051461 92.31585861 0.83089174 0.55473696 0.04342786 66.57242477 Axis 0.21785384 -0.91444386 -0.34107498 Axis point 40.42618061 -0.00000000 73.99401579 Rotation angle (degrees) 94.73238660 Shift along axis -86.14408463 > fitmap #3 inMap #1 Fit molecule best_model.pdb (#3) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms average map value = 0.1282, steps = 44 shifted from previous position = 0.00345 rotated from previous position = 0.00849 degrees atoms outside contour = 1406, contour level = 0.1818 Position of best_model.pdb (#3) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.03098418 0.12422201 -0.99177068 96.30323341 -0.55555574 0.82271562 0.12040367 92.31511825 0.83090191 0.55471443 0.04352107 66.56944203 Axis 0.21789588 -0.91444394 -0.34104789 Axis point 40.42537610 0.00000000 74.00305735 Rotation angle (degrees) 94.72502128 Shift along axis -86.13629092 > fitmap #3 inMap #1 Fit molecule best_model.pdb (#3) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms average map value = 0.1282, steps = 44 shifted from previous position = 0.00234 rotated from previous position = 0.00478 degrees atoms outside contour = 1405, contour level = 0.1818 Position of best_model.pdb (#3) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.03106601 0.12423713 -0.99176623 96.30245936 -0.55555725 0.82270614 0.12046145 92.31563255 0.83089784 0.55472510 0.04346263 66.57148290 Axis 0.21787360 -0.91444535 -0.34105836 Axis point 40.42551502 -0.00000000 73.99814036 Rotation angle (degrees) 94.72932598 Shift along axis -86.14059811 > fitmap #2 inMap #1 Fit molecule SisAgo.pdb (#2) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms average map value = 0.1314, steps = 48 shifted from previous position = 1.2 rotated from previous position = 0.055 degrees atoms outside contour = 2589, contour level = 0.1818 Position of SisAgo.pdb (#2) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.28456287 0.60558376 -0.74316383 93.45934088 0.80431278 -0.27100185 -0.52880919 93.54855022 -0.52163696 -0.74821553 -0.40996164 97.96417915 Axis -0.59340959 -0.59914481 0.53748541 Axis point -9.68077486 0.00000000 95.49724955 Rotation angle (degrees) 169.34649252 Shift along axis -58.85448039 > fitmap #2 inMap #1 Fit molecule SisAgo.pdb (#2) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms average map value = 0.1314, steps = 48 shifted from previous position = 0.00392 rotated from previous position = 0.0655 degrees atoms outside contour = 2590, contour level = 0.1818 Position of SisAgo.pdb (#2) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.28409377 0.60550306 -0.74340902 93.45612538 0.80393542 -0.27207820 -0.52883031 93.54565869 -0.52247369 -0.74789014 -0.40948959 97.96928578 Axis -0.59362750 -0.59870988 0.53772937 Axis point -9.71837129 0.00000000 95.54341878 Rotation angle (degrees) 169.36746374 Shift along axis -58.80387376 > fitmap #2 inMap #1 Fit molecule SisAgo.pdb (#2) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms average map value = 0.1314, steps = 44 shifted from previous position = 0.0623 rotated from previous position = 0.0262 degrees atoms outside contour = 2597, contour level = 0.1818 Position of SisAgo.pdb (#2) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.28385514 0.60578501 -0.74327046 93.48370305 0.80406828 -0.27193044 -0.52870431 93.49026184 -0.52239894 -0.74771554 -0.40990360 97.97163795 Axis -0.59373266 -0.59877584 0.53753979 Axis point -9.67503261 0.00000000 95.49884568 Rotation angle (degrees) 169.37175459 Shift along axis -58.82038312 > fitmap #2 inMap #1 Fit molecule SisAgo.pdb (#2) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms average map value = 0.1314, steps = 44 shifted from previous position = 0.0595 rotated from previous position = 0.0265 degrees atoms outside contour = 2591, contour level = 0.1818 Position of SisAgo.pdb (#2) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.28415449 0.60547007 -0.74341268 93.45771539 0.80400623 -0.27193843 -0.52879454 93.54414748 -0.52233168 -0.74796768 -0.40952913 97.96536741 Axis -0.59359627 -0.59876341 0.53770424 Axis point -9.71504073 0.00000000 95.53725117 Rotation angle (degrees) 169.36133405 Shift along axis -58.81057026 > fitmap #2 inMap #1 Fit molecule SisAgo.pdb (#2) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms average map value = 0.1314, steps = 44 shifted from previous position = 0.059 rotated from previous position = 0.0254 degrees atoms outside contour = 2597, contour level = 0.1818 Position of SisAgo.pdb (#2) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.28386637 0.60576994 -0.74327845 93.48329051 0.80406861 -0.27192925 -0.52870442 93.49086076 -0.52239233 -0.74772818 -0.40988897 97.97244855 Axis -0.59372725 -0.59877572 0.53754589 Axis point -9.67583480 0.00000000 95.50037031 Rotation angle (degrees) 169.37104182 Shift along axis -58.81894804 > fitmap #3 inMap #1 Fit molecule best_model.pdb (#3) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms average map value = 0.1282, steps = 72 shifted from previous position = 6.31 rotated from previous position = 0.054 degrees atoms outside contour = 1404, contour level = 0.1818 Position of best_model.pdb (#3) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.03062542 0.12477300 -0.99171266 96.29758495 -0.55607889 0.82232832 0.12063426 92.32080113 0.83056519 0.55516487 0.04419948 66.56267412 Axis 0.21800032 -0.91422131 -0.34157761 Axis point 40.44839524 0.00000000 74.00339199 Rotation angle (degrees) 94.70634104 Shift along axis -86.14505866 > fitmap #3 inMap #1 Fit molecule best_model.pdb (#3) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms average map value = 0.1282, steps = 60 shifted from previous position = 0.00889 rotated from previous position = 0.0507 degrees atoms outside contour = 1405, contour level = 0.1818 Position of best_model.pdb (#3) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.03103521 0.12429930 -0.99175940 96.30395985 -0.55556537 0.82269567 0.12049553 92.31427512 0.83089356 0.55472671 0.04352385 66.56786778 Axis 0.21785657 -0.91443668 -0.34109246 Axis point 40.42775437 -0.00000000 73.99767909 Rotation angle (degrees) 94.72698175 Shift along axis -86.14090768 > fitmap #3 inMap #1 Fit molecule best_model.pdb (#3) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms average map value = 0.1282, steps = 44 shifted from previous position = 0.00704 rotated from previous position = 0.00531 degrees atoms outside contour = 1403, contour level = 0.1818 Position of best_model.pdb (#3) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.03096377 0.12427425 -0.99176477 96.30211072 -0.55561143 0.82267376 0.12043278 92.31610524 0.83086543 0.55476482 0.04357511 66.57450729 Axis 0.21790626 -0.91442144 -0.34110158 Axis point 40.42531631 0.00000000 74.00490304 Rotation angle (degrees) 94.72408447 Shift along axis -86.13966327 > volume #1 level 0.1301 > ui tool show AlphaFold > alphafold predict #8/B Please cite ColabFold: Making protein folding accessible to all. Nature Methods (2022) if you use these predictions. > alphafold predict > MSEYATILPENKINVIFRSNNKYHVPEFITVFKPYEGRDINLQVLVVNGDNEIYDLTKLLFYEIYVKDDTKYPWPYTKTRGGISRVFGIRYNFDPSTISRININSENDFISSISNQLDMNRFNVAVIIANRKLTKEFHDKTKAALIGSRIRTQFVTFTTLKRLKNRKYKATIPLPLAVQLIAKAGGTPWIVDSSIYNDLSKNVSSNGMLMGIAFARTRKDKITYSVGYFTTLNNYYQRFDVQPINESAPITDSTEGLYVPKEAMVKTLESGIGWYKNIIGITPPLLIIFKTSPMHKDEKEAIEAVLGKDIKWVFIHAQYNTPVRIFGNKEDDYKVNRGTVIIKKRKRWNPNNGDYLHSEIVITATGKYRKPSTKNPSETEERYISGTPRPITLNVYSSFDVNPIGVAELTLSQIKADWEHPDIRKRKITVLKYANRMAKIIQYINNLSSVPSVDVRDVL Running AlphaFold prediction > fitmap #3 inMap #1 Fit molecule best_model.pdb (#3) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms average map value = 0.1282, steps = 52 shifted from previous position = 4.63 rotated from previous position = 0.0825 degrees atoms outside contour = 1023, contour level = 0.13014 Position of best_model.pdb (#3) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.02999734 0.12485251 -0.99172185 96.32022999 -0.55635644 0.82218410 0.12033714 92.30100403 0.83040222 0.55536056 0.04479916 66.53693205 Axis 0.21823782 -0.91410339 -0.34174150 Axis point 40.46881965 0.00000000 74.03854111 Rotation angle (degrees) 94.67519542 Shift along axis -86.09037444 > fitmap #3 inMap #1 Fit molecule best_model.pdb (#3) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms average map value = 0.1282, steps = 44 shifted from previous position = 0.0497 rotated from previous position = 0.0411 degrees atoms outside contour = 1018, contour level = 0.13014 Position of best_model.pdb (#3) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.03065665 0.12486176 -0.99170052 96.29089340 -0.55611173 0.82229303 0.12072342 92.32755120 0.83054205 0.55519719 0.04422834 66.56456703 Axis 0.21797214 -0.91420503 -0.34163914 Axis point 40.44870314 0.00000000 73.99649405 Rotation angle (degrees) 94.70742345 Shift along axis -86.15864207 > fitmap #3 inMap #1 Fit molecule best_model.pdb (#3) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms average map value = 0.1282, steps = 44 shifted from previous position = 0.0158 rotated from previous position = 0.0635 degrees atoms outside contour = 1019, contour level = 0.13014 Position of best_model.pdb (#3) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.03120173 0.12421953 -0.99176417 96.30190722 -0.55552386 0.82271957 0.12052376 92.31567692 0.83091509 0.55470913 0.04333664 66.57240819 Axis 0.21783657 -0.91446240 -0.34103629 Axis point 40.42514889 0.00000000 73.99028073 Rotation angle (degrees) 94.73646323 Shift along axis -86.14474540 > fitmap #2 inMap #1 Fit molecule SisAgo.pdb (#2) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms average map value = 0.1314, steps = 56 shifted from previous position = 4.21 rotated from previous position = 0.0674 degrees atoms outside contour = 1931, contour level = 0.13014 Position of SisAgo.pdb (#2) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.28462104 0.60554971 -0.74316930 93.46345205 0.80434960 -0.27091387 -0.52879827 93.53980628 -0.52154844 -0.74827494 -0.40996582 97.96979467 Axis -0.59338134 -0.59917838 0.53747917 Axis point -9.67301333 0.00000000 95.49541560 Rotation angle (degrees) 169.34252404 Shift along axis -58.84977390 > fitmap #2 inMap #1 Fit molecule SisAgo.pdb (#2) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms average map value = 0.1314, steps = 44 shifted from previous position = 0.006 rotated from previous position = 0.0179 degrees atoms outside contour = 1930, contour level = 0.13014 Position of SisAgo.pdb (#2) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.28441427 0.60573168 -0.74310015 93.46649937 0.80430371 -0.27106123 -0.52879255 93.53320929 -0.52173198 -0.74807426 -0.41009850 97.97042134 Axis -0.59347929 -0.59912624 0.53742914 Axis point -9.67006527 0.00000000 95.48750788 Rotation angle (degrees) 169.35387973 Shift along axis -58.85647249 > fitmap #2 inMap #1 Fit molecule SisAgo.pdb (#2) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms average map value = 0.1314, steps = 48 shifted from previous position = 0.0166 rotated from previous position = 0.04 degrees atoms outside contour = 1932, contour level = 0.13014 Position of SisAgo.pdb (#2) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.28484492 0.60525531 -0.74332333 93.45754588 0.80435946 -0.27088059 -0.52880031 93.54981671 -0.52141099 -0.74852514 -0.40968382 97.97089944 Axis -0.59327360 -0.59918006 0.53759622 Axis point -9.68563318 0.00000000 95.51648504 Rotation angle (degrees) 169.32837268 Shift along axis -58.83029407 > fitmap #2 inMap #1 Fit molecule SisAgo.pdb (#2) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms average map value = 0.1314, steps = 64 shifted from previous position = 3.89 rotated from previous position = 0.0328 degrees atoms outside contour = 1932, contour level = 0.13014 Position of SisAgo.pdb (#2) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.28490365 0.60495022 -0.74354915 93.45571001 0.80418220 -0.27129206 -0.52885897 93.54474974 -0.52165226 -0.74862275 -0.40919805 97.97041634 Axis -0.59324649 -0.59900475 0.53782145 Axis point -9.69984169 0.00000000 95.54826664 Rotation angle (degrees) 169.32596530 Shift along axis -58.78543018 > fitmap #2 inMap #1 Fit molecule SisAgo.pdb (#2) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms average map value = 0.1314, steps = 48 shifted from previous position = 0.0432 rotated from previous position = 0.0759 degrees atoms outside contour = 1922, contour level = 0.13014 Position of SisAgo.pdb (#2) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.28393956 0.60567639 -0.74332673 93.47725637 0.80405390 -0.27194232 -0.52872006 93.50154394 -0.52237519 -0.74779920 -0.40978123 97.97497605 Axis -0.59369322 -0.59876731 0.53759285 Axis point -9.68557439 0.00000000 95.51219970 Rotation angle (degrees) 169.36770614 Shift along axis -58.81183499 > fitmap #2 inMap #1 Fit molecule SisAgo.pdb (#2) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms average map value = 0.1314, steps = 48 shifted from previous position = 0.0424 rotated from previous position = 0.0702 degrees atoms outside contour = 1930, contour level = 0.13014 Position of SisAgo.pdb (#2) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.28466918 0.60547632 -0.74321065 93.46030719 0.80438443 -0.27086696 -0.52876931 93.54678443 -0.52146844 -0.74835131 -0.40992820 97.96825119 Axis -0.59335587 -0.59919321 0.53749075 Axis point -9.67999822 0.00000000 95.49977496 Rotation angle (degrees) 169.33688696 Shift along axis -58.85079137 > fitmap #3 inMap #1 Fit molecule best_model.pdb (#3) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms average map value = 0.1282, steps = 72 shifted from previous position = 7.58 rotated from previous position = 0.0094 degrees atoms outside contour = 1020, contour level = 0.13014 Position of best_model.pdb (#3) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.03129680 0.12430634 -0.99175030 96.30305046 -0.55560351 0.82264811 0.12064427 92.31435583 0.83085825 0.55479566 0.04331878 66.56932244 Axis 0.21782119 -0.91443394 -0.34112242 Axis point 40.43192855 0.00000000 73.98066354 Rotation angle (degrees) 94.74176381 Shift along axis -86.14682309 > fitmap #3 inMap #1 Fit molecule best_model.pdb (#3) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms average map value = 0.1282, steps = 44 shifted from previous position = 0.00405 rotated from previous position = 0.0211 degrees atoms outside contour = 1021, contour level = 0.13014 Position of best_model.pdb (#3) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.03093041 0.12427036 -0.99176630 96.30250714 -0.55561038 0.82267763 0.12041113 92.31590775 0.83086738 0.55475994 0.04360014 66.57323445 Axis 0.21791411 -0.91442083 -0.34109822 Axis point 40.42549180 0.00000000 74.00666615 Rotation angle (degrees) 94.72229457 Shift along axis -86.13792513 > fitmap #3 inMap #1 Fit molecule best_model.pdb (#3) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms average map value = 0.1282, steps = 44 shifted from previous position = 0.00377 rotated from previous position = 0.00865 degrees atoms outside contour = 1018, contour level = 0.13014 Position of best_model.pdb (#3) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.03090068 0.12437903 -0.99175361 96.30201984 -0.55569100 0.82261301 0.12048056 92.31619056 0.83081456 0.55483141 0.04369701 66.57708386 Axis 0.21791457 -0.91438561 -0.34119231 Axis point 40.42736468 0.00000000 74.00744858 Rotation angle (degrees) 94.72051328 Shift along axis -86.14257185 > fitmap #3 inMap #1 Fit molecule best_model.pdb (#3) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms average map value = 0.1282, steps = 48 shifted from previous position = 0.0497 rotated from previous position = 0.063 degrees atoms outside contour = 1022, contour level = 0.13014 Position of best_model.pdb (#3) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.03026295 0.12491332 -0.99170612 96.32005642 -0.55628371 0.82220378 0.12053873 92.30171986 0.83044131 0.55531774 0.04460493 66.53564920 Axis 0.21811915 -0.91413163 -0.34174170 Axis point 40.47032821 0.00000000 74.01997921 Rotation angle (degrees) 94.68784685 Shift along axis -86.10467886 > view > cofr frontCenter > ui tool show ""Side View"" > view orient > fitmap #3 inMap #1 Fit molecule best_model.pdb (#3) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms average map value = 0.1282, steps = 56 shifted from previous position = 3.89 rotated from previous position = 0.00933 degrees atoms outside contour = 1019, contour level = 0.13014 Position of best_model.pdb (#3) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.03028762 0.12488642 -0.99170875 96.32425006 -0.55615220 0.82229298 0.12053715 92.29707511 0.83052849 0.55519172 0.04455056 66.52131139 Axis 0.21805663 -0.91417631 -0.34166208 Axis point 40.47186834 0.00000000 74.01482981 Rotation angle (degrees) 94.68755530 Shift along axis -86.09946863 > fitmap #3 inMap #1 Fit molecule best_model.pdb (#3) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms average map value = 0.1282, steps = 44 shifted from previous position = 0.0602 rotated from previous position = 0.0983 degrees atoms outside contour = 1020, contour level = 0.13014 Position of best_model.pdb (#3) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.03148495 0.12412770 -0.99176672 96.30144748 -0.55534912 0.82282438 0.12061348 92.31542625 0.83102120 0.55457420 0.04302762 66.56969721 Axis 0.21772828 -0.91453547 -0.34090947 Axis point 40.42181780 -0.00000000 73.97382706 Rotation angle (degrees) 94.75047463 Shift along axis -86.15242362 > fitmap #3 inMap #1 Fit molecule best_model.pdb (#3) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms average map value = 0.1282, steps = 44 shifted from previous position = 0.0469 rotated from previous position = 0.0928 degrees atoms outside contour = 1023, contour level = 0.13014 Position of best_model.pdb (#3) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.03045822 0.12487696 -0.99170472 96.32335142 -0.55617924 0.82226218 0.12062243 92.28825311 0.83050414 0.55523945 0.04440932 66.54516815 Axis 0.21804087 -0.91417497 -0.34167572 Axis point 40.46180126 -0.00000000 74.01692293 Rotation angle (degrees) 94.69740388 Shift along axis -86.10205246 > fitmap #2 inMap #1 Fit molecule SisAgo.pdb (#2) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms average map value = 0.1314, steps = 52 shifted from previous position = 2.67 rotated from previous position = 0.0802 degrees atoms outside contour = 1923, contour level = 0.13014 Position of SisAgo.pdb (#2) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.28375365 0.60596235 -0.74316464 93.48662197 0.80405927 -0.27192048 -0.52872312 93.48252375 -0.52246793 -0.74757544 -0.41007116 97.97279847 Axis -0.59378347 -0.59878761 0.53747054 Axis point -9.66444175 0.00000000 95.48545371 Rotation angle (degrees) 169.38047536 Shift along axis -58.82949460 > fitmap #2 inMap #1 Fit molecule SisAgo.pdb (#2) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms average map value = 0.1314, steps = 40 shifted from previous position = 0.0702 rotated from previous position = 0.0891 degrees atoms outside contour = 1933, contour level = 0.13014 Position of SisAgo.pdb (#2) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.28485856 0.60520610 -0.74335817 93.45590405 0.80429469 -0.27099463 -0.52884040 93.55276831 -0.52150344 -0.74852365 -0.40956886 97.97077379 Axis -0.59326955 -0.59913377 0.53765227 Axis point -9.68993821 0.00000000 95.52519175 Rotation angle (degrees) 169.33034215 Shift along axis -58.82095699 > fitmap #2 inMap #1 Fit molecule SisAgo.pdb (#2) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms average map value = 0.1314, steps = 44 shifted from previous position = 0.00203 rotated from previous position = 0.0234 degrees atoms outside contour = 1931, contour level = 0.13014 Position of SisAgo.pdb (#2) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.28502403 0.60494137 -0.74351021 93.45252992 0.80418867 -0.27116617 -0.52891369 93.55198686 -0.52157652 -0.74867551 -0.40919807 97.96997164 Axis -0.59319456 -0.59905701 0.53782052 Axis point -9.69692559 0.00000000 95.54738419 Rotation angle (degrees) 169.32511613 Shift along axis -58.78824441 > fitmap #2 inMap #1 Fit molecule SisAgo.pdb (#2) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms average map value = 0.1314, steps = 48 shifted from previous position = 0.0681 rotated from previous position = 0.064 degrees atoms outside contour = 1923, contour level = 0.13014 Position of SisAgo.pdb (#2) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.28450875 0.60568569 -0.74310148 93.48619046 0.80445389 -0.27078212 -0.52870709 93.49309098 -0.52144884 -0.74821257 -0.41020628 97.97449346 Axis -0.59342857 -0.59923334 0.53736574 Axis point -9.63755371 0.00000000 95.46532436 Rotation angle (degrees) 169.34196696 Shift along axis -58.85341701 > ui tool show ""Side View"" > view > fitmap #2 inMap #1 Fit molecule SisAgo.pdb (#2) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms average map value = 0.1314, steps = 80 shifted from previous position = 15.6 rotated from previous position = 0.0171 degrees atoms outside contour = 1930, contour level = 0.13014 Position of SisAgo.pdb (#2) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.28442666 0.60578749 -0.74304992 93.46694182 0.80432022 -0.27098520 -0.52880640 93.53321029 -0.52169977 -0.74805662 -0.41017167 97.97023743 Axis -0.59347534 -0.59915953 0.53739640 Axis point -9.66509813 0.00000000 95.48140432 Rotation angle (degrees) 169.35535483 Shift along axis -58.86278610 > fitmap #2 inMap #1 Fit molecule SisAgo.pdb (#2) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms average map value = 0.1314, steps = 48 shifted from previous position = 0.0118 rotated from previous position = 0.0538 degrees atoms outside contour = 1930, contour level = 0.13014 Position of SisAgo.pdb (#2) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.28503772 0.60516525 -0.74332275 93.45926243 0.80415768 -0.27103737 -0.52902682 93.54324145 -0.52161682 -0.74854120 -0.40939235 97.96802855 Axis -0.59319965 -0.59912191 0.53774261 Axis point -9.67192833 0.00000000 95.52594396 Rotation angle (degrees) 169.33736835 Shift along axis -58.80222300 > fitmap #2 inMap #1 Fit molecule SisAgo.pdb (#2) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 3722 atoms average map value = 0.1314, steps = 48 shifted from previous position = 0.00535 rotated from previous position = 0.0751 degrees atoms outside contour = 1934, contour level = 0.13014 Position of SisAgo.pdb (#2) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.28400058 0.60569414 -0.74328896 93.46313390 0.80403423 -0.27189572 -0.52877394 93.53401577 -0.52237229 -0.74780178 -0.40978022 97.97373349 Axis -0.59366914 -0.59878875 0.53759556 Axis point -9.70323338 0.00000000 95.52230007 Rotation angle (degrees) 169.36978891 Shift along axis -58.82305128 > fitmap #3 inMap #1 Fit molecule best_model.pdb (#3) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms average map value = 0.1282, steps = 96 shifted from previous position = 15.7 rotated from previous position = 0.0765 degrees atoms outside contour = 1019, contour level = 0.13014 Position of best_model.pdb (#3) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.03125010 0.12419508 -0.99176571 96.30208056 -0.55549429 0.82273835 0.12053180 92.31537729 0.83093303 0.55468675 0.04327900 66.57108185 Axis 0.21782209 -0.91447549 -0.34101042 Axis point 40.42496810 0.00000000 73.98732537 Rotation angle (degrees) 94.73897069 Shift along axis -86.14486199 > fitmap #3 inMap #1 Fit molecule best_model.pdb (#3) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms average map value = 0.1282, steps = 44 shifted from previous position = 0.002 rotated from previous position = 0.0193 degrees atoms outside contour = 1021, contour level = 0.13014 Position of best_model.pdb (#3) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.03092915 0.12423425 -0.99177086 96.30313189 -0.55557791 0.82270380 0.12038219 92.31537346 0.83088914 0.55472922 0.04357628 66.57054592 Axis 0.21791319 -0.91443390 -0.34106376 Axis point 40.42519409 -0.00000000 74.00667820 Rotation angle (degrees) 94.72219238 Shift along axis -86.13538519 > fitmap #3 inMap #1 Fit molecule best_model.pdb (#3) to map cryosparc_P3_J291_class_00_00063_volume.mrc (#1) using 2047 atoms average map value = 0.1282, steps = 44 shifted from previous position = 0.00425 rotated from previous position = 0.00651 degrees atoms outside contour = 1020, contour level = 0.13014 Position of best_model.pdb (#3) relative to cryosparc_P3_J291_class_00_00063_volume.mrc (#1) coordinates: Matrix rotation and translation -0.03091175 0.12431226 -0.99176163 96.30229822 -0.55564285 0.82265237 0.12043385 92.31612211 0.83084635 0.55478801 0.04364359 66.57477090 Axis 0.21791646 -0.91440654 -0.34113501 Axis point 40.42617267 0.00000000 74.00742776 Rotation angle (degrees) 94.72123576 Shift along axis -86.13959472 > cofr frontCenter ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show AlphaFold OpenGL version: 4.1 INTEL-20.2.50 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine OpenGL vendor: Intel Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 512 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1916.80.2.0.0 (iBridge: 20.16.3045.0.0,0) OS Loader Version: 564.40.4~66 Software: System Software Overview: System Version: macOS 13.2.1 (22D68) Kernel Version: Darwin 22.3.0 Time since boot: 1 day, 20 hours, 43 minutes Graphics/Displays: Intel Iris Plus Graphics: Chipset Model: Intel Iris Plus Graphics Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x8a53 Revision ID: 0x0007 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Sceptre F27: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Mirror: Off Online: Yes Rotation: Supported Connection Type: DVI or HDMI Adapter Firmware Version: 7.55 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.1.0 Babel: 2.11.0 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.4 ChimeraX-AddH: 2.2.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.6 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.41.5 ChimeraX-AtomicLibrary: 8.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.4 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.5 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 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-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.8 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.8 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 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 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.7.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.24.3 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.4 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.2.0 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.7.31 imagesize: 1.4.1 importlib-metadata: 5.1.0 ipykernel: 6.15.3 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 5.1.0 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.4 numpy: 1.23.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.2.0 pip: 22.2.2 pkginfo: 1.8.3 platformdirs: 2.5.4 prompt-toolkit: 3.0.33 psutil: 5.9.1 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2022.6 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.3.0 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.0 setuptools: 65.1.1 setuptools-scm: 7.0.5 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 typing-extensions: 4.4.0 urllib3: 1.26.13 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 zipp: 3.11.0 }}} " defect closed normal Graphics nonchimerax all ChimeraX