id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17134 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.3.2-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. 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Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/u0159610/SwitchLab Dropbox/brajabandhu > pradhan/Heterotypic_Abeta_medin_manuscript/Data/Morphology_1_maps/Morpholgy_1_Processed_Job101.mrc"" Opened Morpholgy_1_Processed_Job101.mrc as #1, grid size 400,400,400, pixel 0.71, shown at level 0.0164, step 2, values float32 > volume #1 step 1 > volume #1 level 0.133 > set bgColor white > volume #1 level 0.1089 > lighting soft > save /Users/u0159610/Desktop/image18.png supersample 3 > color #1 #73fdffff models > color #1 #7a81ffff models > color #1 #0433ffff models > color #1 #7a81ffff models > color #1 #ff8ad8ff models > color #1 #d783ffff models > color #1 #7a81ffff models > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > color #1 #945200ff models > color #1 #009051ff models > color #1 #8efa00ff models > color #1 #00f900ff models > color #1 #ff7e79ff models > color #1 #ff85ffff models > color #1 #7a81ffff models > color #1 #ff7e79ff models > color #1 #ff85ffff models > color #1 #d783ffff models > color #1 #ff7e79ff models > color #1 #7a81ffff models > color #1 #0433ffff models > color #1 #7a81ffff models > color #1 #6c72e2ff models > color #1 #6e75e6ff models > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > color #1 #d0e6b1ff models > color #1 #cce6d4ff models > color #1 #ac82e6ff models > color #1 #3d2e51ff models > color #1 #00f900ff models > color #1 #fffc79ff models > color #1 #ff7e79ff models > color #1 #ff2600ff models > color #1 #941100ff models > color #1 #ff7e79ff models > color #1 #d783ffff models > color #1 #7a81ffff models > color #1 #0433ffff models > color #1 #7a81ffff models > color #1 #d783ffff models > color #1 #7a81ffff models > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > color #1 #d783ffff models > color #1 #7a81ffff models > ui tool show ""Map Statistics"" > measure mapstats Map Morpholgy_1_Processed_Job101.mrc #1, minimum -0.001785, maximum 2.237, mean 0.003323, SD 0.04851, RMS 0.04862 > ui tool show Toolbar > ui tool show ""Scale Bar"" > set bgColor black > set bgColor white > scalebar > scalebar 50 > scalebar ypos 0.9 > scalebar xpos 0.9 > scalebar xpos 0.1 > scalebar xpos 0.2 > scalebar ypos 0.1 > save /Users/u0159610/Desktop/PopulationA.png supersample 20 > transparentBackground true > volume #1 level 0.04265 > volume #1 color #7a81ff28 > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > ui tool show ""Side View"" > open ""/Users/u0159610/SwitchLab Dropbox/brajabandhu > pradhan/Heterotypic_Abeta_medin_manuscript/Data/Morphology_1_Models/morphology1_extradenisty_8layersMerged.pdb"" Chain information for morphology1_extradenisty_8layersMerged.pdb #3 --- Chain | Description A B C D E F G H I J K L M N O P | No description available q r s t u v w x | No description available > style stick Changed 3352 atom styles > color #3 #7a81ffff > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > color #3 #4f54a5ff > color #3 #6338a5ff > color #3 #4765a5ff > color #3 #5173bbff > color #3 #89bb3aff > color #3 #bb5b46ff > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > preset ""molecular surfaces"" ""atomic coloring (transparent)"" Using preset: Molecular Surfaces / Atomic Coloring (Transparent) Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color fromatoms targ s trans 70 > preset ""molecular surfaces"" ""chain id coloring (opaque)"" Using preset: Molecular Surfaces / Chain ID Coloring (Opaque) Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color bychain targ s trans 0 > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > preset ""initial styles"" ""original look"" Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""initial styles"" sticks Using preset: Initial Styles / Sticks Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""initial styles"" cartoon Using preset: Initial Styles / Cartoon Preset implemented in Python; no expansion to individual ChimeraX commands available. Computing secondary structure > preset ""initial styles"" cartoon Using preset: Initial Styles / Cartoon Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""initial styles"" sticks Using preset: Initial Styles / Sticks Preset implemented in Python; no expansion to individual ChimeraX commands available. > scalebar off > scalebar 50 xpos 0.2 > scalebar 1 > scalebar 10 > scalebar off > volume #1 level 0.291 > color #1#!3 byelement > hide #!1 models > select /E 185 atoms, 186 bonds, 26 residues, 1 model selected > hide sel atoms > select /M 185 atoms, 186 bonds, 26 residues, 1 model selected > hide sel atoms > select /M/K 370 atoms, 372 bonds, 52 residues, 1 model selected > hide sel atoms > select /M/K/s/C 604 atoms, 606 bonds, 88 residues, 1 model selected > hide sel atoms > show #!1 models > stereo Unknown command: stereo > mono Unknown command: mono > camera stereo Could not switch graphics mode. Graphics driver did not create OpenGL context. > camera mono > camera ortho > volume #1 level 0.2868 > volume #1 level 0.1668 > hide #!1 models > hide /t > show #!1 models > lighting soft > lighting simple > lighting soft > lighting full > lighting simple > lighting soft > lighting simple > lighting full > hide /tu > hide /t/u > save /Users/u0159610/Desktop/PopulationA_topview.png supersample 20 > transparentBackground true > volume #1 level 0.4731 Unsupported scale factor (0.000000) detected on Display1 > volume #1 level 0.2399 > hide #!1 models > hide /r > hide /r/q > show #!1 models > volume #1 level 0.07913 > hide #!3 models > open ""/Users/u0159610/SwitchLab Dropbox/brajabandhu > pradhan/Heterotypic_Abeta_medin_manuscript/Data/Morphology_1_Models/morphology1UNit_corrrectedt-0.pdb"" Chain information for morphology1UNit_corrrectedt-0.pdb #5 --- Chain | Description M | No description available Computing secondary structure > dssp #5 Computing secondary structure > style #5 stick Changed 185 atom styles > style #5 stick Changed 185 atom styles > select add #5 789 atoms, 792 bonds, 114 residues, 6 models selected > style sel & #5 stick Changed 185 atom styles > style sel & #5 stick Changed 185 atom styles > show sel & #5 atoms > select subtract #5 604 atoms, 606 bonds, 88 residues, 5 models selected > color #5 #eb27fdff > color #5 #aefd4dff > color #5 #426ffdff > select add #5 789 atoms, 792 bonds, 114 residues, 6 models selected > color (#5 & sel) byelement > select clear > color #5 byatom > ui tool show ""Color Actions"" > color byelement > color byhetero > color light gray > color white > color magenta > color purple > color cornflower blue > color yellow > color red > color byelement > color byhetero > color light sea green > color medium blue > color cornflower blue > color byhetero > color byelement > color byhetero > color bynucleotide > color bychain > color bypolymer > color byhetero > color byelement > color byelement target a > color byhetero target a Cannot color background by het > color byelement target a > color byhetero target a > color forest green target a > color byelement target a > color light sea green target a > hide #5 cartoons > show #5 cartoons > hide #5 cartoons > color byelement target a > color magenta target a > color byelement target a > select add #5 185 atoms, 186 bonds, 26 residues, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.66404,-0.71791,-0.20895,375.27,-0.70605,0.69403,-0.14074,166.66,0.24606,0.054072,-0.96775,229.78 > view matrix models > #5,0.70752,0.65113,0.27469,-88.788,0.66238,-0.74649,0.063393,144.79,0.24633,0.13709,-0.95944,216.68 > view matrix models > #5,0.64818,0.71358,0.26583,-87.838,0.72173,-0.68701,0.084345,124.67,0.24282,0.13719,-0.96032,217.31 > view matrix models > #5,0.68496,0.65314,0.32286,-92.475,0.67043,-0.73851,0.071643,141.32,0.28523,0.16738,-0.94373,204.47 > view matrix models > #5,0.98614,0.019482,0.16477,-23.67,-0.040699,0.99114,0.12639,-10.348,-0.16085,-0.13135,0.9782,45.381 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.98614,0.019482,0.16477,-34.026,-0.040699,0.99114,0.12639,-18.512,-0.16085,-0.13135,0.9782,46 > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.99592,0.030301,0.085001,265.29,-0.035085,-0.99785,-0.055357,291.14,0.083141,-0.058114,0.99484,-2.486 > view matrix models > #5,-0.99724,0.030601,0.067692,267.84,-0.03645,-0.99555,-0.08693,295.4,0.06473,-0.089157,0.99391,4.7864 > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.99724,0.030601,0.067692,269.92,-0.03645,-0.99555,-0.08693,297.85,0.06473,-0.089157,0.99391,4.9295 > ui tool show ""Fit in Map"" > fitmap #5 inMap #1 Fit molecule morphology1UNit_corrrectedt-0.pdb (#5) to map Morpholgy_1_Processed_Job101.mrc (#1) using 185 atoms average map value = 0.3618, steps = 76 shifted from previous position = 1.06 rotated from previous position = 2.13 degrees atoms outside contour = 67, contour level = 0.07913 Position of morphology1UNit_corrrectedt-0.pdb (#5) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99817084 -0.00414635 0.06031350 276.34192556 -0.00191319 -0.99497910 -0.10006447 295.44684437 0.06042557 -0.09999683 0.99315123 6.73438554 Axis 0.03023637 -0.05009989 0.99828641 Axis point 137.98621669 147.96980980 0.00000000 Rotation angle (degrees) 179.93591497 Shift along axis 0.27656870 [deleted to fit within ticket limits] > fitmap #7 inMap #1 resolution 5 Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map Morpholgy_1_Processed_Job101.mrc using 935 points correlation = 0.7656, correlation about mean = 0.7479, overlap = 66.33 steps = 28, shift = 0.0164, angle = 0.0274 degrees Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation 0.99982707 -0.01858489 -0.00065507 2.71805464 0.01858140 0.99981496 -0.00497766 -1.95402146 0.00074745 0.00496463 0.99998740 -5.64894959 Axis 0.25824996 -0.03643035 0.96539100 Axis point 116.42950310 210.20378158 0.00000000 Rotation angle (degrees) 1.10297434 Shift along axis -4.68032191 Average map value = 0.5722 for 185 atoms, 29 outside contour > fitmap #7 inMap #1 resolution 5 Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map Morpholgy_1_Processed_Job101.mrc using 935 points correlation = 0.7655, correlation about mean = 0.7478, overlap = 66.31 steps = 60, shift = 0.00128, angle = 0.0155 degrees Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation 0.99982763 -0.01856229 -0.00039408 2.68299887 0.01856007 0.99981503 -0.00504214 -1.94343366 0.00048760 0.00503395 0.99998721 -5.62116856 Axis 0.26188233 -0.02291522 0.96482772 Axis point 112.57159427 209.46947180 0.00000000 Rotation angle (degrees) 1.10231393 Shift along axis -4.67629504 Average map value = 0.5721 for 185 atoms, 29 outside contour > fitmap #7 inMap #1 resolution 5 Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map Morpholgy_1_Processed_Job101.mrc using 935 points correlation = 0.7653, correlation about mean = 0.7473, overlap = 66.28 steps = 44, shift = 0.00145, angle = 0.0167 degrees Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation 0.99982806 -0.01854265 -0.00012217 2.64830006 0.01854178 0.99981484 -0.00514577 -1.92883525 0.00021757 0.00514262 0.99998675 -5.59909258 Axis 0.26732349 -0.00882742 0.96356641 Axis point 108.33830056 209.14511033 0.00000000 Rotation angle (degrees) 1.10262896 Shift along axis -4.67011807 Average map value = 0.5718 for 185 atoms, 29 outside contour > fitmap #7 inMap #1 resolution 5 Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map Morpholgy_1_Processed_Job101.mrc using 935 points correlation = 0.7652, correlation about mean = 0.7473, overlap = 66.3 steps = 44, shift = 0.00261, angle = 0.00977 degrees Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation 0.99982729 -0.01858401 -0.00015909 2.65722322 0.01858299 0.99981490 -0.00498444 -1.95362071 0.00025169 0.00498062 0.99998756 -5.58402025 Axis 0.25895432 -0.01067469 0.96583058 Axis point 109.88455156 207.23484921 0.00000000 Rotation angle (degrees) 1.10249353 Shift along axis -4.68426380 Average map value = 0.5717 for 185 atoms, 29 outside contour > fitmap #7 inMap #1 resolution 5 Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map Morpholgy_1_Processed_Job101.mrc using 935 points correlation = 0.7667, correlation about mean = 0.7495, overlap = 66.24 steps = 48, shift = 0.0165, angle = 0.0264 degrees Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation 0.99982658 -0.01862024 -0.00032098 2.68258555 0.01861823 0.99981200 -0.00541480 -1.90644765 0.00042175 0.00540788 0.99998529 -5.64902585 Axis 0.27903269 -0.01914924 0.96009066 Axis point 109.31400094 212.56079530 0.00000000 Rotation angle (degrees) 1.11121832 Shift along axis -4.63854085 Average map value = 0.5732 for 185 atoms, 29 outside contour > fitmap #7 inMap #1 resolution 5 Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map Morpholgy_1_Processed_Job101.mrc using 935 points correlation = 0.7656, correlation about mean = 0.7479, overlap = 66.3 steps = 28, shift = 0.0126, angle = 0.0225 degrees Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation 0.99982697 -0.01858935 -0.00068137 2.72226990 0.01858551 0.99981343 -0.00526171 -1.92054237 0.00077906 0.00524814 0.99998592 -5.68933931 Axis 0.27185655 -0.03777672 0.96159604 Axis point 114.94689108 213.49590113 0.00000000 Rotation angle (degrees) 1.10758338 Shift along axis -4.65822744 Average map value = 0.5722 for 185 atoms, 29 outside contour > style sel stick Changed 185 atom styles > style sel stick Changed 185 atom styles > hide sel atoms > show sel atoms > hide sel cartoons > fitmap #7 inMap #1 resolution 5 Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map Morpholgy_1_Processed_Job101.mrc using 935 points correlation = 0.765, correlation about mean = 0.7469, overlap = 66.27 steps = 48, shift = 0.00362, angle = 0.026 degrees Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation 0.99983086 -0.01838953 -0.00027530 2.64511899 0.01838782 0.99981697 -0.00528301 -1.89053085 0.00037240 0.00527706 0.99998601 -5.64061933 Axis 0.27594394 -0.01692499 0.96102471 Axis point 109.22013791 212.74245256 0.00000000 Rotation angle (degrees) 1.09638976 Shift along axis -4.65887275 Average map value = 0.5716 for 185 atoms, 29 outside contour > fitmap #7 inMap #1 resolution 5 Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map Morpholgy_1_Processed_Job101.mrc using 935 points correlation = 0.7655, correlation about mean = 0.7477, overlap = 66.3 steps = 40, shift = 0.00266, angle = 0.0137 degrees Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation 0.99982934 -0.01847239 -0.00024099 2.65229082 0.01847094 0.99981659 -0.00506060 -1.92924987 0.00033443 0.00505529 0.99998717 -5.60265192 Axis 0.26407005 -0.01502100 0.96438653 Axis point 110.32768940 209.37519060 0.00000000 Rotation angle (degrees) 1.09749883 Shift along axis -4.67375221 Average map value = 0.572 for 185 atoms, 29 outside contour > fitmap #7 inMap #1 resolution 5 Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map Morpholgy_1_Processed_Job101.mrc using 935 points correlation = 0.7669, correlation about mean = 0.75, overlap = 66.3 steps = 44, shift = 0.0132, angle = 0.0119 degrees Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation 0.99982584 -0.01866038 -0.00028300 2.68147870 0.01865874 0.99981350 -0.00498194 -1.96540373 0.00037591 0.00497579 0.99998755 -5.58465357 Axis 0.25776923 -0.01705693 0.96605594 Axis point 111.67442851 207.17186729 0.00000000 Rotation angle (degrees) 1.10674778 Shift along axis -4.67036131 Average map value = 0.5735 for 185 atoms, 29 outside contour > fitmap #7 inMap #1 resolution 5 Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map Morpholgy_1_Processed_Job101.mrc using 935 points correlation = 0.7655, correlation about mean = 0.7477, overlap = 66.31 steps = 28, shift = 0.0139, angle = 0.0106 degrees Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation 0.99982717 -0.01858597 -0.00042657 2.69068456 0.01858357 0.99981445 -0.00507061 -1.94353852 0.00052073 0.00506181 0.99998705 -5.63007317 Axis 0.26292380 -0.02458120 0.96450342 Axis point 112.86277359 209.85444386 0.00000000 Rotation angle (degrees) 1.10408631 Shift along axis -4.67500527 Average map value = 0.5721 for 185 atoms, 29 outside contour > fitmap #7 inMap #1 resolution 5 Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map Morpholgy_1_Processed_Job101.mrc using 935 points correlation = 0.7661, correlation about mean = 0.7487, overlap = 66.26 steps = 44, shift = 0.00877, angle = 0.0176 degrees Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation 0.99982643 -0.01862921 -0.00026377 2.67726022 0.01862754 0.99981229 -0.00532837 -1.91847052 0.00036298 0.00532253 0.99998577 -5.63487308 Axis 0.27483104 -0.01617233 0.96135652 Axis point 109.15767797 211.30045601 0.00000000 Rotation angle (degrees) 1.11029996 Shift along axis -4.65030159 Average map value = 0.5727 for 185 atoms, 29 outside contour > fitmap #7 inMap #1 resolution 5 Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map Morpholgy_1_Processed_Job101.mrc using 935 points correlation = 0.7652, correlation about mean = 0.7473, overlap = 66.31 steps = 44, shift = 0.0122, angle = 0.0229 degrees Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation 0.99982777 -0.01854992 -0.00057764 2.70364492 0.01854674 0.99981502 -0.00509451 -1.93526352 0.00067203 0.00508292 0.99998686 -5.65725892 Axis 0.26443311 -0.03246937 0.96385729 Axis point 114.63744033 211.32869188 0.00000000 Rotation angle (degrees) 1.10265991 Shift along axis -4.67502019 Average map value = 0.5717 for 185 atoms, 29 outside contour > fitmap #7 inMap #1 resolution 5 Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map Morpholgy_1_Processed_Job101.mrc using 935 points correlation = 0.7664, correlation about mean = 0.7491, overlap = 66.25 steps = 40, shift = 0.0148, angle = 0.0211 degrees Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation 0.99982662 -0.01861706 -0.00037946 2.68926053 0.01861474 0.99981216 -0.00539782 -1.90790437 0.00047988 0.00538982 0.99998536 -5.65751373 Axis 0.27822794 -0.02216343 0.96025934 Axis point 110.16878053 212.80157414 0.00000000 Rotation angle (degrees) 1.11082426 Shift along axis -4.64216727 Average map value = 0.573 for 185 atoms, 29 outside contour > fitmap #7 inMap #1 resolution 5 Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map Morpholgy_1_Processed_Job101.mrc using 935 points correlation = 0.7666, correlation about mean = 0.7493, overlap = 66.26 steps = 36, shift = 0.00127, angle = 0.0112 degrees Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation 0.99982668 -0.01860872 -0.00057440 2.71289734 0.01860534 0.99981227 -0.00540926 -1.90515226 0.00067495 0.00539764 0.99998520 -5.68476450 Axis 0.27873237 -0.03222332 0.95982807 Axis point 112.59380150 214.22088613 0.00000000 Rotation angle (degrees) 1.11079366 Shift along axis -4.63883389 Average map value = 0.5731 for 185 atoms, 29 outside contour > fitmap #7 inMap #1 resolution 5 Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map Morpholgy_1_Processed_Job101.mrc using 935 points correlation = 0.7666, correlation about mean = 0.7494, overlap = 66.26 steps = 40, shift = 0.00139, angle = 0.027 degrees Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation 0.99982695 -0.01860224 -0.00015237 2.65918117 0.01860119 0.99981345 -0.00520126 -1.93001873 0.00024910 0.00519753 0.99998646 -5.59832625 Axis 0.26917924 -0.01039218 0.96303403 Axis point 108.45783392 209.30725652 0.00000000 Rotation angle (degrees) 1.10677930 Shift along axis -4.65552522 Average map value = 0.5731 for 185 atoms, 29 outside contour > fitmap #7 inMap #1 resolution 5 Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map Morpholgy_1_Processed_Job101.mrc using 935 points correlation = 0.7657, correlation about mean = 0.748, overlap = 66.3 steps = 28, shift = 0.0108, angle = 0.0272 degrees Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation 0.99982757 -0.01855924 -0.00062269 2.70969491 0.01855579 0.99981457 -0.00514900 -1.92999004 0.00071814 0.00513656 0.99998655 -5.66568244 Axis 0.26689941 -0.03479303 0.96309613 Axis point 114.87849569 212.03997166 0.00000000 Rotation angle (degrees) 1.10407783 Shift along axis -4.66623063 Average map value = 0.5723 for 185 atoms, 29 outside contour > fitmap #7 inMap #1 resolution 5 Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map Morpholgy_1_Processed_Job101.mrc using 935 points correlation = 0.7655, correlation about mean = 0.7476, overlap = 66.27 steps = 44, shift = 0.000448, angle = 0.0168 degrees Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation 0.99982884 -0.01849497 -0.00047971 2.68359563 0.01849211 0.99981444 -0.00539764 -1.89095318 0.00057945 0.00538784 0.99998532 -5.68024092 Axis 0.27983652 -0.02748087 0.95965427 Axis point 111.31624296 214.39673735 0.00000000 Rotation angle (degrees) 1.10421772 Shift along axis -4.64813439 Average map value = 0.572 for 185 atoms, 29 outside contour > fitmap #7 inMap #1 resolution 5 Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map Morpholgy_1_Processed_Job101.mrc using 935 points correlation = 0.7654, correlation about mean = 0.7476, overlap = 66.31 steps = 48, shift = 0.00279, angle = 0.0239 degrees Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation 0.99982733 -0.01857958 -0.00034519 2.67959664 0.01857762 0.99981486 -0.00501251 -1.94963781 0.00043826 0.00500523 0.99998738 -5.61155085 Axis 0.26025595 -0.02035365 0.96532511 Axis point 112.15308101 208.73478575 0.00000000 Rotation angle (degrees) 1.10277975 Shift along axis -4.67990770 Average map value = 0.572 for 185 atoms, 29 outside contour > fitmap #7 inMap #1 resolution 5 Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map Morpholgy_1_Processed_Job101.mrc using 935 points correlation = 0.7662, correlation about mean = 0.7488, overlap = 66.27 steps = 40, shift = 0.00871, angle = 0.0142 degrees Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation 0.99982825 -0.01852843 -0.00041020 2.68030961 0.01852602 0.99981461 -0.00524654 -1.91401148 0.00050733 0.00523804 0.99998615 -5.64395581 Axis 0.27218466 -0.02381960 0.96195017 Axis point 111.42009132 211.99539254 0.00000000 Rotation angle (degrees) 1.10358866 Shift along axis -4.65407414 Average map value = 0.5728 for 185 atoms, 29 outside contour > fitmap #7 inMap #1 resolution 5 Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map Morpholgy_1_Processed_Job101.mrc using 935 points correlation = 0.7667, correlation about mean = 0.7496, overlap = 66.23 steps = 48, shift = 0.00681, angle = 0.0128 degrees Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation 0.99982652 -0.01862274 -0.00033732 2.68512474 0.01862063 0.99981185 -0.00543533 -1.90439842 0.00043848 0.00542811 0.99998517 -5.65345130 Axis 0.27996280 -0.01999304 0.95980264 Axis point 109.40258500 212.86674545 0.00000000 Rotation angle (degrees) 1.11169837 Shift along axis -4.63638774 Average map value = 0.5732 for 185 atoms, 29 outside contour > fitmap #7 inMap #1 resolution 5 Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map Morpholgy_1_Processed_Job101.mrc using 935 points correlation = 0.7657, correlation about mean = 0.748, overlap = 66.29 steps = 28, shift = 0.0126, angle = 0.0215 degrees Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation 0.99982715 -0.01858013 -0.00067373 2.71962956 0.01857633 0.99981354 -0.00527354 -1.91799975 0.00077159 0.00526011 0.99998587 -5.68934090 Axis 0.27255524 -0.03739716 0.96141307 Axis point 114.76883287 213.61711452 0.00000000 Rotation angle (degrees) 1.10724573 Shift along axis -4.65682968 Average map value = 0.5723 for 185 atoms, 29 outside contour > fitmap #7 inMap #1 resolution 5 Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map Morpholgy_1_Processed_Job101.mrc using 935 points correlation = 0.7661, correlation about mean = 0.7486, overlap = 66.27 steps = 40, shift = 0.00469, angle = 0.00571 degrees Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation 0.99982693 -0.01859407 -0.00060457 2.71353216 0.01859058 0.99981290 -0.00534398 -1.91139375 0.00070382 0.00533181 0.99998554 -5.68502395 Axis 0.27579649 -0.03380058 0.96062158 Axis point 113.41825141 213.82359027 0.00000000 Rotation angle (degrees) 1.10899903 Shift along axis -4.64816780 Average map value = 0.5727 for 185 atoms, 29 outside contour > fitmap #7 inMap #1 resolution 5 Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map Morpholgy_1_Processed_Job101.mrc using 935 points correlation = 0.7651, correlation about mean = 0.747, overlap = 66.27 steps = 40, shift = 0.00819, angle = 0.0117 degrees Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation 0.99982880 -0.01849851 -0.00042818 2.67910523 0.01849594 0.99981446 -0.00538003 -1.89345310 0.00052762 0.00537119 0.99998544 -5.67416129 Axis 0.27898522 -0.02480210 0.95997505 Axis point 110.75670628 213.97223656 0.00000000 Rotation angle (degrees) 1.10406865 Shift along axis -4.65266091 Average map value = 0.5716 for 185 atoms, 29 outside contour > fitmap #7 inMap #1 resolution 5 Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map Morpholgy_1_Processed_Job101.mrc using 935 points correlation = 0.7665, correlation about mean = 0.7492, overlap = 66.25 steps = 36, shift = 0.0131, angle = 0.0127 degrees Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation 0.99982636 -0.01863277 -0.00026188 2.67733643 0.01863111 0.99981226 -0.00532304 -1.91922242 0.00036102 0.00531724 0.99998580 -5.63076750 Axis 0.27452962 -0.01607150 0.96144433 Axis point 109.14875392 211.15207095 0.00000000 Rotation angle (degrees) 1.11041087 Shift along axis -4.64781653 Average map value = 0.573 for 185 atoms, 29 outside contour > save ""/Users/u0159610/SwitchLab Dropbox/brajabandhu > pradhan/Heterotypic_Abeta_medin_manuscript/Data/Morphology_1_Models/morphology1UNit_corrrectedt-18.pdb"" > models #7 relModel #1 > close #2-9#10-11 > open ""/Users/u0159610/SwitchLab Dropbox/brajabandhu > pradhan/Heterotypic_Abeta_medin_manuscript/Data/Morphology_1_Models/morphology1_protofibril_1.pdb"" Chain information for morphology1_protofibril_1.pdb #2 --- Chain | Description A B C D E F G M | No description available > show atoms > style stick Changed 1480 atom styles > select add #2 1480 atoms, 1488 bonds, 208 residues, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.99712,0.011368,-0.075002,284.09,-0.012056,-0.99989,0.0087208,277.74,-0.074895,0.0095999,0.99715,9.3875 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.99712,0.011368,-0.075002,290.59,-0.012056,-0.99989,0.0087208,283.16,-0.074895,0.0095999,0.99715,9.6066 Opened morphology1_protofibril_1.pdb map 5 as #3, grid size 41,59,42, pixel 1.67, shown at level 0.0872, step 1, values float32 Opened morphology1_protofibril_1.pdb map 5 as #4, grid size 41,59,42, pixel 1.67, shown at level 0.0872, step 1, values float32 > fitmap #2 inMap #1 resolution 5 Fit map morphology1_protofibril_1.pdb map 5 in map Morpholgy_1_Processed_Job101.mrc using 5811 points correlation = 0.7421, correlation about mean = 0.7363, overlap = 541.4 steps = 80, shift = 2.55, angle = 4.2 degrees Position of morphology1_protofibril_1.pdb map 5 (#4) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99995626 -0.00781806 -0.00513678 286.10152571 0.00782294 -0.99996898 -0.00093033 280.91408265 -0.00512935 -0.00097048 0.99998640 3.37116897 Axis -0.00256655 -0.00047517 0.99999659 Axis point 142.50585215 141.01723168 0.00000000 Rotation angle (degrees) 179.55191207 Shift along axis 2.50338328 Average map value = 0.578 for 1480 atoms, 249 outside contour > fitmap #2 inMap #1 resolution 5 Fit map morphology1_protofibril_1.pdb map 5 in map Morpholgy_1_Processed_Job101.mrc using 5811 points correlation = 0.7421, correlation about mean = 0.7362, overlap = 540.6 steps = 40, shift = 0.0117, angle = 0.00481 degrees Position of morphology1_protofibril_1.pdb map 5 (#3) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99995625 -0.00780104 -0.00516443 286.10308444 0.00780634 -0.99996904 -0.00100774 280.92597963 -0.00515641 -0.00104801 0.99998618 3.39716076 Axis -0.00258023 -0.00051390 0.99999654 Axis point 142.50784539 141.02205278 0.00000000 Rotation angle (degrees) 179.55287534 Shift along axis 2.51456918 Average map value = 0.5775 for 1480 atoms, 248 outside contour > fitmap #2 inMap #1 resolution 5 Fit map morphology1_protofibril_1.pdb map 5 in map Morpholgy_1_Processed_Job101.mrc using 5811 points correlation = 0.7421, correlation about mean = 0.7363, overlap = 540.4 steps = 36, shift = 0.00142, angle = 0.0142 degrees Position of morphology1_protofibril_1.pdb map 5 (#3) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99995674 -0.00781719 -0.00504326 286.09077048 0.00782345 -0.99996866 -0.00122230 280.94919131 -0.00503354 -0.00126170 0.99998656 3.40790841 Axis -0.00251922 -0.00062097 0.99999663 Axis point 142.50038467 141.03500871 0.00000000 Rotation angle (degrees) 179.55192266 Shift along axis 2.51271210 Average map value = 0.5775 for 1480 atoms, 247 outside contour > fitmap #2 inMap #1 resolution 5 Fit map morphology1_protofibril_1.pdb map 5 in map Morpholgy_1_Processed_Job101.mrc using 5811 points correlation = 0.7421, correlation about mean = 0.7362, overlap = 540.2 steps = 40, shift = 0.0036, angle = 0.00163 degrees Position of morphology1_protofibril_1.pdb map 5 (#3) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99995676 -0.00780803 -0.00505321 286.09110371 0.00781418 -0.99996877 -0.00119724 280.94764772 -0.00504370 -0.00123667 0.99998654 3.40947031 Axis -0.00252424 -0.00060844 0.99999663 Axis point 142.50121213 141.03355766 0.00000000 Rotation angle (degrees) 179.55245063 Shift along axis 2.51635444 Average map value = 0.5774 for 1480 atoms, 247 outside contour > fitmap #2 inMap #1 resolution 5 Fit map morphology1_protofibril_1.pdb map 5 in map Morpholgy_1_Processed_Job101.mrc using 5811 points correlation = 0.7421, correlation about mean = 0.7363, overlap = 540.3 steps = 44, shift = 0.00182, angle = 0.00125 degrees Position of morphology1_protofibril_1.pdb map 5 (#3) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99995677 -0.00781777 -0.00503622 286.09024756 0.00782394 -0.99996868 -0.00120685 280.94737346 -0.00502663 -0.00124620 0.99998661 3.40659334 Axis -0.00251573 -0.00061323 0.99999665 Axis point 142.50008162 141.03412344 0.00000000 Rotation angle (degrees) 179.55189200 Shift along axis 2.51457190 Average map value = 0.5774 for 1480 atoms, 247 outside contour > fitmap #2 inMap #1 resolution 5 Fit map morphology1_protofibril_1.pdb map 5 in map Morpholgy_1_Processed_Job101.mrc using 5811 points correlation = 0.7421, correlation about mean = 0.7362, overlap = 540 steps = 44, shift = 0.00328, angle = 0.00163 degrees Position of morphology1_protofibril_1.pdb map 5 (#3) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99995691 -0.00781010 -0.00502164 286.08770944 0.00781637 -0.99996871 -0.00123003 280.95131065 -0.00501187 -0.00126923 0.99998666 3.41096782 Axis -0.00250839 -0.00062478 0.99999666 Axis point 142.49933303 141.03556307 0.00000000 Rotation angle (degrees) 179.55232859 Shift along axis 2.51780327 Average map value = 0.5773 for 1480 atoms, 247 outside contour > fitmap #2 inMap #1 resolution 5 Fit map morphology1_protofibril_1.pdb map 5 in map Morpholgy_1_Processed_Job101.mrc using 5811 points correlation = 0.7421, correlation about mean = 0.7363, overlap = 540.8 steps = 40, shift = 0.0102, angle = 0.00857 degrees Position of morphology1_protofibril_1.pdb map 5 (#3) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99995670 -0.00776828 -0.00512700 286.09378473 0.00777419 -0.99996915 -0.00113273 280.94529717 -0.00511804 -0.00117254 0.99998624 3.40234733 Axis -0.00256128 -0.00057628 0.99999655 Axis point 142.50541169 141.02947923 0.00000000 Rotation angle (degrees) 179.55473496 Shift along axis 2.50766607 Average map value = 0.5778 for 1480 atoms, 248 outside contour > view matrix models > #2,-0.99996,-0.0077683,-0.005127,294.34,0.0077742,-0.99997,-0.0011327,248.55,-0.005118,-0.0011725,0.99999,0.5517 > undo > ui tool show ""Fit in Map"" > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5792, steps = 48 shifted from previous position = 0.0576 rotated from previous position = 0.123 degrees atoms outside contour = 246, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997007 -0.00573243 -0.00519930 285.82903142 0.00573480 -0.99998347 -0.00044034 281.19550317 -0.00519669 -0.00047014 0.99998641 3.28690324 Axis -0.00259898 -0.00022756 0.99999660 Axis point 142.51571327 141.00784959 0.00000000 Rotation angle (degrees) 179.67148497 Shift along axis 2.48003732 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5792, steps = 44 shifted from previous position = 0.00322 rotated from previous position = 0.0182 degrees atoms outside contour = 246, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997093 -0.00547606 -0.00530924 285.80734630 0.00547769 -0.99998497 -0.00029148 281.21275085 -0.00530756 -0.00032056 0.99998589 3.28504061 Axis -0.00265418 -0.00015295 0.99999647 Axis point 142.52298469 140.99797428 0.00000000 Rotation angle (degrees) 179.68619539 Shift along axis 2.48343229 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5793, steps = 40 shifted from previous position = 0.00277 rotated from previous position = 0.00923 degrees atoms outside contour = 246, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997034 -0.00555959 -0.00533205 285.82105151 0.00556049 -0.99998454 -0.00015511 281.18426212 -0.00533110 -0.00018475 0.99998580 3.26711551 Axis -0.00266577 -0.00008490 0.99999644 Axis point 142.52402544 140.98957896 0.00000000 Rotation angle (degrees) 179.68143041 Shift along axis 2.48129621 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5787, steps = 40 shifted from previous position = 0.0155 rotated from previous position = 0.0242 degrees atoms outside contour = 247, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997169 -0.00542940 -0.00521320 285.79271700 0.00543229 -0.99998511 -0.00053972 281.25043116 -0.00521020 -0.00056802 0.99998629 3.31748221 Axis -0.00260583 -0.00027687 0.99999657 Axis point 142.51881750 141.01371336 0.00000000 Rotation angle (degrees) 179.68883277 Shift along axis 2.49487162 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5788, steps = 40 shifted from previous position = 0.0043 rotated from previous position = 0.00653 degrees atoms outside contour = 246, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997146 -0.00546598 -0.00521904 285.79706178 0.00546831 -0.99998497 -0.00043172 281.23274521 -0.00521660 -0.00046025 0.99998631 3.29957890 Axis -0.00260889 -0.00022293 0.99999657 Axis point 142.51844379 141.00737829 0.00000000 Rotation angle (degrees) 179.68675309 Shift along axis 2.49125819 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5787, steps = 48 shifted from previous position = 0.00429 rotated from previous position = 0.00899 degrees atoms outside contour = 247, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997210 -0.00535497 -0.00521145 285.78226175 0.00535787 -0.99998551 -0.00054295 281.26070992 -0.00520846 -0.00057086 0.99998630 3.31761272 Axis -0.00260496 -0.00027839 0.99999657 Axis point 142.51880821 141.01352325 0.00000000 Rotation angle (degrees) 179.69309725 Shift along axis 2.49484973 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5791, steps = 44 shifted from previous position = 0.0112 rotated from previous position = 0.0208 degrees atoms outside contour = 246, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997073 -0.00548505 -0.00533790 285.81256237 0.00548634 -0.99998494 -0.00022683 281.20405975 -0.00533658 -0.00025610 0.99998575 3.28157715 Axis -0.00266860 -0.00012067 0.99999643 Axis point 142.52500364 140.99421303 0.00000000 Rotation angle (degrees) 179.68568998 Shift along axis 2.48491184 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5787, steps = 44 shifted from previous position = 0.0101 rotated from previous position = 0.0173 degrees atoms outside contour = 247, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997144 -0.00547308 -0.00521489 285.79852385 0.00547577 -0.99998490 -0.00050197 281.23978161 -0.00521206 -0.00053051 0.99998630 3.31144457 Axis -0.00260672 -0.00025806 0.99999657 Axis point 142.51866518 141.01147807 0.00000000 Rotation angle (degrees) 179.68633605 Shift along axis 2.49385941 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5791, steps = 44 shifted from previous position = 0.0105 rotated from previous position = 0.0186 degrees atoms outside contour = 246, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997071 -0.00549109 -0.00533461 285.81296892 0.00549224 -0.99998491 -0.00020128 281.20008446 -0.00533343 -0.00023058 0.99998577 3.27728030 Axis -0.00266699 -0.00010790 0.99999644 Axis point 142.52478468 140.99263101 0.00000000 Rotation angle (degrees) 179.68534819 Shift along axis 2.48466494 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5787, steps = 44 shifted from previous position = 0.00995 rotated from previous position = 0.0177 degrees atoms outside contour = 247, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997141 -0.00547821 -0.00521466 285.79911132 0.00548082 -0.99998488 -0.00048634 281.23710081 -0.00521192 -0.00051491 0.99998631 3.30880499 Axis -0.00260663 -0.00025025 0.99999657 Axis point 142.51860088 141.01048918 0.00000000 Rotation angle (degrees) 179.68604419 Shift along axis 2.49344132 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5786, steps = 48 shifted from previous position = 0.00283 rotated from previous position = 0.000413 degrees atoms outside contour = 247, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997145 -0.00547507 -0.00521148 285.79912485 0.00547770 -0.99998489 -0.00049201 281.23863067 -0.00520870 -0.00052054 0.99998632 3.31180079 Axis -0.00260503 -0.00025308 0.99999657 Axis point 142.51882696 141.01103544 0.00000000 Rotation angle (degrees) 179.68622360 Shift along axis 2.49609969 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5792, steps = 44 shifted from previous position = 0.0161 rotated from previous position = 0.0188 degrees atoms outside contour = 247, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997065 -0.00550757 -0.00532952 285.81366129 0.00550865 -0.99998482 -0.00018777 281.19565799 -0.00532840 -0.00021712 0.99998580 3.27159509 Axis -0.00266447 -0.00010116 0.99999645 Axis point 142.52396879 140.99158284 0.00000000 Rotation angle (degrees) 179.68440566 Shift along axis 2.48159723 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5793, steps = 44 shifted from previous position = 0.00106 rotated from previous position = 0.000728 degrees atoms outside contour = 247, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997066 -0.00551379 -0.00532000 285.81328805 0.00551484 -0.99998479 -0.00018207 281.19391481 -0.00531892 -0.00021140 0.99998586 3.26845818 Axis -0.00265972 -0.00009831 0.99999646 Axis point 142.52333678 140.99114893 0.00000000 Rotation angle (degrees) 179.68405042 Shift along axis 2.48062122 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5786, steps = 40 shifted from previous position = 0.0183 rotated from previous position = 0.0204 degrees atoms outside contour = 247, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997163 -0.00543685 -0.00521542 285.79451310 0.00543960 -0.99998509 -0.00051407 281.24712352 -0.00521255 -0.00054243 0.99998629 3.31636988 Axis -0.00260697 -0.00026406 0.99999657 Axis point 142.51920162 141.01256790 0.00000000 Rotation angle (degrees) 179.68840992 Shift along axis 2.49703204 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5791, steps = 36 shifted from previous position = 0.0123 rotated from previous position = 0.0125 degrees atoms outside contour = 245, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997091 -0.00549098 -0.00529745 285.80870867 0.00549274 -0.99998488 -0.00031826 281.21417063 -0.00529562 -0.00034735 0.99998594 3.28956553 Axis -0.00264825 -0.00016634 0.99999648 Axis point 142.52260656 140.99977920 0.00000000 Rotation angle (degrees) 179.68533677 Shift along axis 2.48588293 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5791, steps = 44 shifted from previous position = 0.00174 rotated from previous position = 0.00201 degrees atoms outside contour = 246, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997106 -0.00545755 -0.00530357 285.80434808 0.00545927 -0.99998507 -0.00030994 281.21774690 -0.00530180 -0.00033889 0.99998591 3.28761910 Axis -0.00265132 -0.00016215 0.99999647 Axis point 142.52277567 140.99916406 0.00000000 Rotation angle (degrees) 179.68725341 Shift along axis 2.48424927 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5786, steps = 48 shifted from previous position = 0.0129 rotated from previous position = 0.0135 degrees atoms outside contour = 247, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997148 -0.00546826 -0.00521155 285.79810682 0.00547107 -0.99998491 -0.00052608 281.24358372 -0.00520859 -0.00055458 0.99998631 3.31647707 Axis -0.00260502 -0.00027010 0.99999657 Axis point 142.51878980 141.01305910 0.00000000 Rotation angle (degrees) 179.68660874 Shift along axis 2.49599183 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5792, steps = 44 shifted from previous position = 0.0159 rotated from previous position = 0.0203 degrees atoms outside contour = 247, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997066 -0.00550547 -0.00532931 285.81337430 0.00550658 -0.99998483 -0.00019458 281.19679464 -0.00532816 -0.00022392 0.99998580 3.27271288 Axis -0.00266435 -0.00010457 0.99999645 Axis point 142.52397171 140.99200730 0.00000000 Rotation angle (degrees) 179.68452521 Shift along axis 2.48179026 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5792, steps = 40 shifted from previous position = 0.00119 rotated from previous position = 0.00259 degrees atoms outside contour = 246, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997044 -0.00553904 -0.00533541 285.81907960 0.00553999 -0.99998466 -0.00016485 281.18883978 -0.00533442 -0.00019440 0.99998578 3.27064228 Axis -0.00266744 -0.00008975 0.99999644 Axis point 142.52448337 140.99040651 0.00000000 Rotation angle (degrees) 179.68260637 Shift along axis 2.48298781 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5792, steps = 40 shifted from previous position = 0.000196 rotated from previous position = 0.0052 degrees atoms outside contour = 246, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997017 -0.00562184 -0.00529981 285.82618470 0.00562274 -0.99998420 -0.00015448 281.17617465 -0.00529886 -0.00018428 0.99998597 3.26445272 Axis -0.00264965 -0.00008463 0.99999649 Axis point 142.52219741 140.98999022 0.00000000 Rotation angle (degrees) 179.67786361 Shift along axis 2.48330521 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5787, steps = 44 shifted from previous position = 0.0133 rotated from previous position = 0.022 degrees atoms outside contour = 247, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997145 -0.00546953 -0.00521654 285.79857251 0.00547220 -0.99998492 -0.00049855 281.23999553 -0.00521374 -0.00052708 0.99998629 3.31219617 Axis -0.00260755 -0.00025635 0.99999657 Axis point 142.51894163 141.01132826 0.00000000 Rotation angle (degrees) 179.68653980 Shift along axis 2.49485442 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5792, steps = 44 shifted from previous position = 0.0122 rotated from previous position = 0.0182 degrees atoms outside contour = 246, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997070 -0.00549372 -0.00533315 285.81291481 0.00549489 -0.99998490 -0.00020366 281.19991373 -0.00533195 -0.00023295 0.99998578 3.27671658 Axis -0.00266626 -0.00010909 0.99999644 Axis point 142.52457021 140.99273622 0.00000000 Rotation angle (degrees) 179.68519686 Shift along axis 2.48397702 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5786, steps = 44 shifted from previous position = 0.014 rotated from previous position = 0.0194 degrees atoms outside contour = 247, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997149 -0.00545835 -0.00521981 285.79789135 0.00546115 -0.99998497 -0.00052179 281.24465593 -0.00521688 -0.00055028 0.99998626 3.31752343 Axis -0.00260916 -0.00026796 0.99999656 Axis point 142.51938599 141.01288306 0.00000000 Rotation angle (degrees) 179.68717684 Shift along axis 2.49645949 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5786, steps = 40 shifted from previous position = 0.000298 rotated from previous position = 0.00752 degrees atoms outside contour = 247, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997196 -0.00533670 -0.00525548 285.78559855 0.00533969 -0.99998560 -0.00055616 281.26563998 -0.00525244 -0.00058421 0.99998606 3.32739241 Axis -0.00262696 -0.00028503 0.99999651 Axis point 142.52180095 141.01470299 0.00000000 Rotation angle (degrees) 179.69414155 Shift along axis 2.49646357 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5793, steps = 48 shifted from previous position = 0.0186 rotated from previous position = 0.0257 degrees atoms outside contour = 246, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997056 -0.00551274 -0.00534083 285.81528373 0.00551363 -0.99998480 -0.00015148 281.19034734 -0.00533992 -0.00018093 0.99998575 3.26662491 Axis -0.00267017 -0.00008304 0.99999643 Axis point 142.52443350 140.98926237 0.00000000 Rotation angle (degrees) 179.68411504 Shift along axis 2.48008691 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5786, steps = 40 shifted from previous position = 0.0177 rotated from previous position = 0.0245 degrees atoms outside contour = 247, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997174 -0.00541563 -0.00521659 285.79147244 0.00541857 -0.99998518 -0.00054872 281.25358844 -0.00521354 -0.00057697 0.99998627 3.32006684 Axis -0.00260751 -0.00028136 0.99999656 Axis point 142.51916361 141.01431597 0.00000000 Rotation angle (degrees) 179.68962035 Shift along axis 2.49571679 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5791, steps = 44 shifted from previous position = 0.0126 rotated from previous position = 0.0194 degrees atoms outside contour = 247, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997078 -0.00548312 -0.00532925 285.81113129 0.00548445 -0.99998495 -0.00023659 281.20544779 -0.00532788 -0.00026581 0.99998580 3.28140297 Axis -0.00266427 -0.00012554 0.99999644 Axis point 142.52441335 140.99477633 0.00000000 Rotation angle (degrees) 179.68579961 Shift along axis 2.48461185 > save ""/Users/u0159610/SwitchLab Dropbox/brajabandhu > pradhan/Heterotypic_Abeta_medin_manuscript/Data/Morphology_1_Models/morphology1_protofibril_0.pdb"" > relModel #1 Computing secondary structure > dssp Computing secondary structure > close #4 > close #3 > dssp #2 Computing secondary structure > view matrix models > #2,-0.99997,-0.0054831,-0.0053293,284.67,0.0054845,-0.99998,-0.00023659,299.41,-0.0053279,-0.00026581,0.99999,13.64 > undo > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5787, steps = 44 shifted from previous position = 0.0114 rotated from previous position = 0.0153 degrees atoms outside contour = 247, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997218 -0.00526409 -0.00528835 285.77895882 0.00526620 -0.99998607 -0.00038462 281.25430592 -0.00528625 -0.00041246 0.99998597 3.30669901 Axis -0.00264363 -0.00019921 0.99999649 Axis point 142.52363328 141.00366316 0.00000000 Rotation angle (degrees) 179.69832696 Shift along axis 2.49516562 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5787, steps = 44 shifted from previous position = 0.0016 rotated from previous position = 0.0145 degrees atoms outside contour = 247, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997144 -0.00547511 -0.00521306 285.79844310 0.00547780 -0.99998489 -0.00050206 281.23944336 -0.00521023 -0.00053060 0.99998631 3.31075673 Axis -0.00260580 -0.00025811 0.99999657 Axis point 142.51847979 141.01145421 0.00000000 Rotation angle (degrees) 179.68621946 Shift along axis 2.49342098 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5791, steps = 44 shifted from previous position = 0.00967 rotated from previous position = 0.0186 degrees atoms outside contour = 246, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997072 -0.00548976 -0.00533500 285.81293917 0.00549091 -0.99998492 -0.00020210 281.20039404 -0.00533381 -0.00023139 0.99998577 3.27774731 Axis -0.00266719 -0.00010831 0.99999644 Axis point 142.52486366 140.99269157 0.00000000 Rotation angle (degrees) 179.68542427 Shift along axis 2.48496276 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5791, steps = 44 shifted from previous position = 0.000769 rotated from previous position = 0.0132 degrees atoms outside contour = 245, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997071 -0.00556961 -0.00525247 285.81403894 0.00557180 -0.99998441 -0.00040236 281.21376204 -0.00525015 -0.00043162 0.99998615 3.29379557 Axis -0.00262564 -0.00020843 0.99999653 Axis point 142.51969760 141.00528549 0.00000000 Rotation angle (degrees) 179.68081948 Shift along axis 2.48472449 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5786, steps = 48 shifted from previous position = 0.014 rotated from previous position = 0.0103 degrees atoms outside contour = 247, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997157 -0.00545658 -0.00520816 285.79665814 0.00545944 -0.99998497 -0.00053536 281.24671605 -0.00520516 -0.00056378 0.99998632 3.31914774 Axis -0.00260331 -0.00027473 0.99999657 Axis point 142.51888133 141.01379852 0.00000000 Rotation angle (degrees) 179.68727655 Shift along axis 2.49785310 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5787, steps = 40 shifted from previous position = 0.00268 rotated from previous position = 0.00198 degrees atoms outside contour = 247, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997171 -0.00542357 -0.00521439 285.79218066 0.00542648 -0.99998514 -0.00054393 281.25182380 -0.00521137 -0.00057221 0.99998628 3.31863634 Axis -0.00260642 -0.00027897 0.99999656 Axis point 142.51895906 141.01399683 0.00000000 Rotation angle (degrees) 179.68916616 Shift along axis 2.49526842 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5792, steps = 44 shifted from previous position = 0.0149 rotated from previous position = 0.0206 degrees atoms outside contour = 247, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997068 -0.00550090 -0.00532938 285.81281724 0.00550211 -0.99998486 -0.00021141 281.19944342 -0.00532814 -0.00024073 0.99998580 3.27535821 Axis -0.00266437 -0.00011297 0.99999644 Axis point 142.52401103 140.99302163 0.00000000 Rotation angle (degrees) 179.68478436 Shift along axis 2.48206900 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5792, steps = 40 shifted from previous position = 0.000486 rotated from previous position = 0.00463 degrees atoms outside contour = 246, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997037 -0.00555592 -0.00533157 285.82082945 0.00555681 -0.99998456 -0.00015206 281.18493164 -0.00533065 -0.00018169 0.99998580 3.26798775 Axis -0.00266554 -0.00008338 0.99999644 Axis point 142.52417272 140.98964824 0.00000000 Rotation angle (degrees) 179.68164106 Shift along axis 2.48266512 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5792, steps = 40 shifted from previous position = 9.2e-05 rotated from previous position = 0.00792 degrees atoms outside contour = 246, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997006 -0.00567262 -0.00526612 285.82894502 0.00567368 -0.99998390 -0.00018580 281.17274239 -0.00526499 -0.00021568 0.99998614 3.26353546 Axis -0.00263276 -0.00010031 0.99999653 Axis point 142.51997835 140.99193797 0.00000000 Rotation angle (degrees) 179.67494948 Shift along axis 2.48279938 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5787, steps = 44 shifted from previous position = 0.0132 rotated from previous position = 0.0199 degrees atoms outside contour = 247, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997139 -0.00547796 -0.00521995 285.80003455 0.00548049 -0.99998489 -0.00047076 281.23542549 -0.00521729 -0.00049935 0.99998629 3.30834221 Axis -0.00260929 -0.00024247 0.99999657 Axis point 142.51908905 141.00961909 0.00000000 Rotation angle (degrees) 179.68606085 Shift along axis 2.49440448 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5791, steps = 44 shifted from previous position = 0.0102 rotated from previous position = 0.016 degrees atoms outside contour = 246, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997074 -0.00548586 -0.00533437 285.81238437 0.00548709 -0.99998494 -0.00021526 281.20258805 -0.00533311 -0.00024452 0.99998577 3.27979953 Axis -0.00266685 -0.00011488 0.99999644 Axis point 142.52485661 140.99352306 0.00000000 Rotation angle (degrees) 179.68564530 Shift along axis 2.48526278 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.579, steps = 40 shifted from previous position = 0.00345 rotated from previous position = 0.00645 degrees atoms outside contour = 245, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997093 -0.00546794 -0.00531756 285.80813260 0.00546975 -0.99998500 -0.00032513 281.21844890 -0.00531570 -0.00035421 0.99998583 3.29577979 Axis -0.00265830 -0.00016977 0.99999645 Axis point 142.52395589 141.00027885 0.00000000 Rotation angle (degrees) 179.68665575 Shift along axis 2.48826058 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.579, steps = 40 shifted from previous position = 0.00233 rotated from previous position = 0.0121 degrees atoms outside contour = 246, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997110 -0.00554616 -0.00520318 285.80548854 0.00554876 -0.99998450 -0.00048522 281.22643773 -0.00520040 -0.00051407 0.99998637 3.29926127 Axis -0.00260088 -0.00024976 0.99999659 Axis point 142.51700542 141.01001896 0.00000000 Rotation angle (degrees) 179.68215146 Shift along axis 2.48566454 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5792, steps = 48 shifted from previous position = 0.00668 rotated from previous position = 0.00415 degrees atoms outside contour = 244, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997106 -0.00559063 -0.00516336 285.80607510 0.00559342 -0.99998423 -0.00052598 281.22543878 -0.00516034 -0.00055484 0.99998656 3.29261874 Axis -0.00258091 -0.00027014 0.99999663 Axis point 142.51412518 141.01273735 0.00000000 Rotation angle (degrees) 179.67959800 Shift along axis 2.47899662 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5791, steps = 44 shifted from previous position = 0.00546 rotated from previous position = 0.00663 degrees atoms outside contour = 246, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997110 -0.00552146 -0.00522947 285.80502446 0.00552395 -0.99998465 -0.00046120 281.22735829 -0.00522684 -0.00049007 0.99998624 3.29846891 Axis -0.00261406 -0.00023776 0.99999656 Axis point 142.51853309 141.00869013 0.00000000 Rotation angle (degrees) 179.68356964 Shift along axis 2.48448211 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5791, steps = 44 shifted from previous position = 0.000437 rotated from previous position = 0.000214 degrees atoms outside contour = 246, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997111 -0.00551890 -0.00522997 285.80481105 0.00552140 -0.99998466 -0.00046389 281.22798982 -0.00522733 -0.00049275 0.99998624 3.29933099 Axis -0.00261431 -0.00023910 0.99999655 Axis point 142.51860688 141.00882515 0.00000000 Rotation angle (degrees) 179.68371619 Shift along axis 2.48489598 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5788, steps = 44 shifted from previous position = 0.00765 rotated from previous position = 0.00324 degrees atoms outside contour = 246, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997142 -0.00547974 -0.00521147 285.79850374 0.00548242 -0.99998486 -0.00050038 281.23849483 -0.00520865 -0.00052893 0.99998632 3.30919534 Axis -0.00260501 -0.00025727 0.99999657 Axis point 142.51818312 141.01130866 0.00000000 Rotation angle (degrees) 179.68595466 Shift along axis 2.49232183 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5791, steps = 36 shifted from previous position = 0.00665 rotated from previous position = 0.0149 degrees atoms outside contour = 245, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997080 -0.00547980 -0.00532958 285.81115177 0.00548131 -0.99998496 -0.00026831 281.21018507 -0.00532803 -0.00029752 0.99998579 3.28775870 Axis -0.00266439 -0.00014140 0.99999644 Axis point 142.52465288 140.99694057 0.00000000 Rotation angle (degrees) 179.68598475 Shift along axis 2.48647375 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5789, steps = 40 shifted from previous position = 0.00481 rotated from previous position = 0.0087 degrees atoms outside contour = 246, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997126 -0.00548481 -0.00523614 285.80189802 0.00548692 -0.99998489 -0.00038787 281.22418624 -0.00523394 -0.00041659 0.99998624 3.29556460 Axis -0.00261750 -0.00020106 0.99999655 Axis point 142.51956619 141.00440685 0.00000000 Rotation angle (degrees) 179.68568028 Shift along axis 2.49092433 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5792, steps = 44 shifted from previous position = 0.00976 rotated from previous position = 0.0123 degrees atoms outside contour = 247, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997066 -0.00550389 -0.00532995 285.81334422 0.00550500 -0.99998484 -0.00019521 281.19715368 -0.00532879 -0.00022455 0.99998580 3.27318560 Axis -0.00266467 -0.00010488 0.99999644 Axis point 142.52406853 140.99207428 0.00000000 Rotation angle (degrees) 179.68461585 Shift along axis 2.48208404 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5792, steps = 40 shifted from previous position = 0.00159 rotated from previous position = 0.0191 degrees atoms outside contour = 246, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997075 -0.00563902 -0.00517089 285.81360148 0.00564145 -0.99998400 -0.00045534 281.21009017 -0.00516824 -0.00048450 0.99998655 3.28739503 Axis -0.00258477 -0.00023490 0.99999663 Axis point 142.51451992 141.00846014 0.00000000 Rotation angle (degrees) 179.67683553 Shift along axis 2.48256583 > fitmap #2 inMap #1 Fit molecule morphology1_protofibril_1.pdb (#2) to map Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms average map value = 0.5791, steps = 44 shifted from previous position = 0.000887 rotated from previous position = 0.00734 degrees atoms outside contour = 245, contour level = 0.07913 Position of morphology1_protofibril_1.pdb (#2) relative to Morpholgy_1_Processed_Job101.mrc (#1) coordinates: Matrix rotation and translation -0.99997109 -0.00552429 -0.00522768 285.80502118 0.00552674 -0.99998464 -0.00045484 281.22630251 -0.00522509 -0.00048372 0.99998626 3.29599487 Axis -0.00261318 -0.00023458 0.99999656 Axis point 142.51833063 141.00835752 0.00000000 Rotation angle (degrees) 179.68340861 Shift along axis 2.48315396 > select subtract #2 Nothing selected ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,7 Model Number: Z16S000UNFN/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 11881.81.4 OS Loader Version: 11881.81.4 Software: System Software Overview: System Version: macOS 15.3.2 (24D81) Kernel Version: Darwin 24.3.0 Time since boot: 6 hours, 30 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal S24R65x: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect assigned normal Window Toolkit all ChimeraX