id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15651 Crash waking Mac from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.5-arm64-arm-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. 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""rolloutId"" : ""60da5e84ab0ca017dace9abf"", ""factorPackIds"" : { }, ""deploymentId"" : 240000008 }, { ""rolloutId"" : ""645197bf528fbf3c3af54105"", ""factorPackIds"" : { ""SIRI_VALUE_INFERENCE_PERVASIVE_ENTITY_RESOLUTION"" : ""663e65b4a1526e1ca0e288a1"" }, ""deploymentId"" : 240000002 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr bundle with that from OME-Zarr bundle Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle > isolde shorthand isolde is provided by the uninstalled bundle ISOLDE versions 1.7rc1 – 1.7.1 UCSF ChimeraX version: 1.8.dev202312020323 (2023-12-02) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/udalwadi/Downloads/cryosparc_P518_J12_004_volume_map.mrc Opened cryosparc_P518_J12_004_volume_map.mrc as #1, grid size 300,300,300, pixel 1.86, shown at level 0.185, step 2, values float32 > set bgColor white > volume #1 level 0.1956 > volume #1 step 1 > volume #1 level 0.224 > volume #1 level 0.205 > volume #1 level 0.2366 > open 6fyy 6fyy title: Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model C2) [more info...] Chain information for 6fyy #2 --- Chain | Description | UniProt 1 | tRNAi | 2 | 18S ribosomal RNA | 3 | mRNA (31-MER) | A | 40S ribosomal protein S0 | RSSA_KLULA 1-254 B | 40S ribosomal protein S1 | RS3A_KLULA 1-255 C | KLLA0F09812p | Q6CKL3_KLULA 1-259 D | KLLA0D08305p | Q6CRK7_KLULA 1-237 E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 1-261 F | KLLA0D10659p | Q6CRA3_KLULA 1-227 G | 40S ribosomal protein S6 | RS6_KLULA 1-236 H | 40S ribosomal protein S7 | Q6CTD6_KLULA 1-190 I | 40S ribosomal protein S8 | Q6CMG3_KLULA 1-201 J | KLLA0E23673p | Q6CM18_KLULA 1-188 K | KLLA0B08173p | Q6CVZ5_KLULA 1-106 L | KLLA0A10483p | Q6CX80_KLULA 1-156 M | 40S ribosomal protein S12 | Q6CLU4_KLULA 1-134 N | KLLA0F18040p | Q6CJK0_KLULA 1-151 O | 40S ribosomal protein S14 | RS14_KLULA 1-137 P | KLLA0F07843p | Q6CKV4_KLULA 1-142 Q | 40S ribosomal protein S16 | RS16_KLULA 1-143 R | KLLA0B01474p | Q6CWU3_KLULA 1-136 S | KLLA0B01562p | Q6CWT9_KLULA 1-146 T | KLLA0A07194p | Q6CXM0_KLULA 1-144 U | KLLA0F25542p | Q6CIM1_KLULA 4-120 V | 40S ribosomal protein S21 | RS21_KLULA 1-87 W | 40S ribosomal protein S22 | RS22_KLULA 1-130 X | KLLA0B11231p | F2Z602_KLULA 1-145 Y | 40S ribosomal protein S24 | Q6CU44_KLULA 1-135 Z | KLLA0B06182p | Q6CW78_KLULA 1-108 a | 40S ribosomal protein S26 | Q6CS01_KLULA 1-119 b | 40S ribosomal protein S27 | Q6CNL2_KLULA 1-82 c | 40S ribosomal protein S28 | RS28_KLULA 1-67 d | 40S ribosomal protein S29 | RS29_KLULA 1-56 e | 40S ribosomal protein S30 | Q6CUH5_KLULA 1-63 f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 1-150 g | KLLA0E12277p | Q6CNI7_KLULA 1-326 h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25 i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 1-153 j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST 1-304 k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST 1-527 l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST 1-285 m | Eukaryotic translation initiation factor 5 | IF5_YEAST 1-405 o | Eukaryotic translation initiation factor 3 subunit A | EIF3A_YEAST 1-964 p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 1-763 q | eIF3c,Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 251-812 r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAS7 1-274 s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAS7 1-347 Non-standard residues in 6fyy #2 --- C4J — (5S)-5-{3-[(3S)-3-amino-3-carboxypropyl]-1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl}-2,5-anhydro-1-O-phosphono- L-arabinitol GCP — phosphomethylphosphonic acid guanylate ester MET — methionine MG — magnesium ion ZN — zinc ion > select add #2 104236 atoms, 109977 bonds, 1818 pseudobonds, 10152 residues, 4 models selected > style sel stick Changed 104236 atom styles > show sel cartoons > hide sel atoms > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.78224,-0.01675,0.62275,-90.091,0.275,0.90625,-0.32106,36.661,-0.55899,0.4224,0.71352,81.081 > view matrix models > #2,0.84912,0.10524,0.51762,-105.35,-0.46641,-0.31058,0.82826,181.18,0.24793,-0.9447,-0.21463,412.2 > view matrix models > #2,0.84912,0.10524,0.51762,-94.658,-0.46641,-0.31058,0.82826,283.34,0.24793,-0.9447,-0.21463,442.69 > view matrix models > #2,0.87294,0.031115,0.48683,-77.144,-0.45742,-0.29458,0.83904,275.97,0.16952,-0.95512,-0.24292,465.94 > view matrix models > #2,0.87294,0.031115,0.48683,-2.923,-0.45742,-0.29458,0.83904,259.15,0.16952,-0.95512,-0.24292,486.28 > fitmap #2 inMap #1 Fit molecule 6fyy (#2) to map cryosparc_P518_J12_004_volume_map.mrc (#1) using 104236 atoms average map value = 0.2546, steps = 172 shifted from previous position = 12.8 rotated from previous position = 16.4 degrees atoms outside contour = 53818, contour level = 0.23659 Position of 6fyy (#2) relative to cryosparc_P518_J12_004_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.86714589 -0.13640791 0.47901032 25.22552842 -0.49053445 -0.06741437 0.86881025 221.62236506 -0.08622041 -0.98835630 -0.12537087 513.02877013 Axis -0.94114202 0.28643764 -0.17945799 Axis point 0.00000000 341.68179699 147.44910347 Rotation angle (degrees) 99.37059838 Shift along axis -52.32693034 > select clear > volume #1 color #b2b2b256 > volume #1 color #b2b2b257 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > volume #1 level 0.2871 > hide #!2 models > volume #1 level 0.2461 > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > volume #1 level 0.3092 > volume #1 level 0.2145 > volume #1 level 0.3502 > hide #!2 models > volume #1 level 0.2587 > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > volume #1 level 0.2745 > show #!2 models > volume #1 level 0.2082 > clipper clipper is provided by the uninstalled bundle Clipper versions 0.22.2 – 0.22.4 > volume #1 level 0.2997 > volume #1 level 0.205 > open /Users/udalwadi/Downloads/cryosparc_P518_J19_005_volume_map.mrc Opened cryosparc_P518_J19_005_volume_map.mrc as #3, grid size 300,300,300, pixel 1.86, shown at level 0.181, step 2, values float32 > hide #!2 models > hide #!1 models > show #!1 models > hide #!1 models > volume #3 step 1 > show #!1 models > select add #3 2 models selected > view matrix models > #3,0.97234,0.18771,-0.139,-4.7768,-0.20876,0.96532,-0.15676,111.91,0.10475,0.18144,0.97781,-72.876 > view matrix models > #3,-0.052871,0.94097,-0.33435,129.27,-0.99582,-0.024701,0.087955,534.92,0.074504,0.3376,0.93834,-96.259 > fitmap #2 inMap #1 Fit molecule 6fyy (#2) to map cryosparc_P518_J12_004_volume_map.mrc (#1) using 104236 atoms average map value = 0.2546, steps = 44 shifted from previous position = 0.013 rotated from previous position = 0.00396 degrees atoms outside contour = 48416, contour level = 0.20503 Position of 6fyy (#2) relative to cryosparc_P518_J12_004_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.86713420 -0.13641596 0.47902918 25.23170761 -0.49054849 -0.06734700 0.86880755 221.60211602 -0.08625804 -0.98835978 -0.12531753 513.02033075 Axis -0.94113384 0.28646365 -0.17945938 Axis point 0.00000000 341.68345278 147.44524405 Rotation angle (degrees) 99.36743284 Shift along axis -52.33177573 > fitmap #3 inMap #1 Fit map cryosparc_P518_J19_005_volume_map.mrc in map cryosparc_P518_J12_004_volume_map.mrc using 268989 points correlation = 0.6636, correlation about mean = 0.2429, overlap = 1.452e+04 steps = 624, shift = 19, angle = 46.1 degrees Position of cryosparc_P518_J19_005_volume_map.mrc (#3) relative to cryosparc_P518_J12_004_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.61664722 0.78705497 -0.01704920 -120.32074964 -0.77298198 0.60944022 0.17629939 279.96449098 0.14914777 -0.09553581 0.98418893 -25.18812524 Axis -0.17072491 -0.10437929 -0.97977445 Axis point 231.81062517 262.31299932 0.00000000 Rotation angle (degrees) 52.76121374 Shift along axis 15.99793752 > select subtract #3 Nothing selected > hide #!1 models > show #!1 models > volume #3 level 0.2763 > volume #1 level 0.3155 > select add #3 2 models selected > view matrix models > #3,0.99663,0.07994,0.018634,-45.02,-0.081676,0.98837,0.12827,-13.036,-0.0081635,-0.12936,0.99156,27.955 > view matrix models > #3,-0.10824,-0.97273,0.20515,515.96,0.9678,-0.055932,0.24543,-62.639,-0.22727,0.22511,0.94746,6.0559 > view matrix models > #3,0.054024,0.98309,0.17496,-65.639,-0.90591,-0.025447,0.42271,424.46,0.42002,-0.18134,0.88921,-53.172 > view matrix models > #3,0.79558,0.51515,-0.31886,-10.665,-0.29534,0.7893,0.53832,-12.794,0.52899,-0.3341,0.78009,-11.315 > view matrix models > #3,0.79558,0.51515,-0.31886,-16.029,-0.29534,0.7893,0.53832,-17.736,0.52899,-0.3341,0.78009,-7.9427 > view matrix models > #3,0.79558,0.51515,-0.31886,-24.434,-0.29534,0.7893,0.53832,-1.9838,0.52899,-0.3341,0.78009,-16.696 > view matrix models > #3,0.71543,0.67586,-0.17711,-86.231,-0.65096,0.73687,0.18238,218.08,0.25378,-0.015191,0.96714,-78.501 > view matrix models > #3,0.71543,0.67586,-0.17711,-75.856,-0.65096,0.73687,0.18238,209.45,0.25378,-0.015191,0.96714,-68.841 > fitmap #3 inMap #1 Fit map cryosparc_P518_J19_005_volume_map.mrc in map cryosparc_P518_J12_004_volume_map.mrc using 128476 points correlation = 0.6984, correlation about mean = 0.1228, overlap = 1.108e+04 steps = 308, shift = 5.19, angle = 13.2 degrees Position of cryosparc_P518_J19_005_volume_map.mrc (#3) relative to cryosparc_P518_J12_004_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.60302962 0.79744337 -0.02096046 -118.71145804 -0.78372257 0.59714515 0.17087016 287.76489358 0.14877571 -0.08661258 0.98507058 -27.80449051 Axis -0.15983182 -0.10536334 -0.98150515 Axis point 234.45024067 262.37958373 0.00000000 Rotation angle (degrees) 53.65665708 Shift along axis 15.94424839 > select clear > hide #!3 models > hide #!1 models > show #!3 models > select add #3 2 models selected > view matrix models > #3,0.76775,0.61318,-0.18592,-68.39,-0.44504,0.30155,-0.84321,561.2,-0.46097,0.73012,0.5044,60.762 > view matrix models > #3,0.5237,-0.84014,0.1411,312.64,0.85071,0.50698,-0.1388,-75.135,0.045076,0.19272,0.98022,-73.724 > volume flip #3 Opened cryosparc_P518_J19_005_volume_map.mrc z flip as #4, grid size 300,300,300, pixel 1.86, shown at step 1, values float32 > view matrix models > #3,0.5237,-0.84014,0.1411,312.64,0.85071,0.50698,-0.1388,-75.135,0.045076,0.19272,0.98022,-73.724 > select add #4 4 models selected > select subtract #3 2 models selected > view matrix models > #4,0.33397,-0.72622,0.60089,212.56,-0.81441,-0.54327,-0.20394,719.42,0.47455,-0.42126,-0.77288,443.45 > view matrix models > #4,0.04466,-0.72775,0.68438,274.85,-0.97116,0.12899,0.20054,469.61,-0.23422,-0.6736,-0.701,700.79 > show #!1 models > hide #!4 models > show #!4 models > view matrix models > #4,0.85531,-0.33523,0.39505,7.4308,-0.28215,-0.94087,-0.18752,670.19,0.43455,0.048927,-0.89932,358.63 > view matrix models > #4,0.85531,-0.33523,0.39505,1.7707,-0.28215,-0.94087,-0.18752,677.58,0.43455,0.048927,-0.89932,367.39 > view matrix models > #4,0.85499,-0.33665,0.39455,23.884,-0.28176,-0.94016,-0.19163,676.72,0.43545,0.052674,-0.89867,376.6 > fitmap #4 inMap #1 Fit map cryosparc_P518_J19_005_volume_map.mrc z flip in map cryosparc_P518_J12_004_volume_map.mrc using 128476 points correlation = 0.9733, correlation about mean = 0.7822, overlap = 2.336e+04 steps = 296, shift = 8.76, angle = 26.4 degrees Position of cryosparc_P518_J19_005_volume_map.mrc z flip (#4) relative to cryosparc_P518_J12_004_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.78415642 -0.61576631 0.07701012 198.51495110 -0.60614425 -0.78661150 -0.11760741 704.50793065 0.13299573 0.04554336 -0.99006966 487.90344886 Axis 0.94439194 -0.32407052 0.05569697 Axis point 0.00000000 375.11959207 254.13605469 Rotation angle (degrees) 175.04468750 Shift along axis -13.65958849 > hide #!1 models > show #!2 models > select subtract #4 Nothing selected > color #4 #ffffb251 models > color #4 #ffffb252 models > volume #4 level 0.1852 > open /Users/udalwadi/Downloads/cryosparc_P518_J11_class_00_final_volume.mrc Opened cryosparc_P518_J11_class_00_final_volume.mrc as #5, grid size 192,192,192, pixel 2.9, shown at level 0.24, step 1, values float32 > hide #!2 models > hide #!4 models > show #!4 models > fitmap #5 inMap #4 Fit map cryosparc_P518_J11_class_00_final_volume.mrc in map cryosparc_P518_J19_005_volume_map.mrc z flip using 70746 points correlation = 0.9196, correlation about mean = 0.627, overlap = 1.04e+04 steps = 40, shift = 0.131, angle = 0.112 degrees Position of cryosparc_P518_J11_class_00_final_volume.mrc (#5) relative to cryosparc_P518_J19_005_volume_map.mrc z flip (#4) coordinates: Matrix rotation and translation 0.78484613 -0.60494750 0.13436915 205.69770887 -0.61473622 -0.78741217 0.04562296 654.15367311 0.07820441 -0.11840858 -0.98988054 550.51935908 Axis -0.94457373 0.32342400 -0.05636821 Axis point 0.00000000 374.94996492 253.95819583 Rotation angle (degrees) 175.01883020 Shift along axis -13.75944376 > hide #!4 models > show #!2 models > volume #5 level 0.1659 > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > volume #5 level 0.1582 > hide #!5 models > show #!4 models > volume #4 level 0.2999 > hide #!4 models > show #!1 models > volume #1 level 0.2083 > volume #1 level 0.1888 > hide #!1 models > show #!1 models > hide #!1 models > select /l:230 8 atoms, 7 bonds, 1 residue, 1 model selected > select add /1:50 28 atoms, 28 bonds, 2 residues, 1 model selected > select add /j:201 36 atoms, 35 bonds, 3 residues, 1 model selected > select add /k:191 47 atoms, 46 bonds, 4 residues, 1 model selected > select up 1959 atoms, 2151 bonds, 114 residues, 1 model selected > select up 3668 atoms, 3887 bonds, 338 residues, 1 model selected > select up 3767 atoms, 3982 bonds, 350 residues, 1 model selected > select up 5597 atoms, 5842 bonds, 588 residues, 1 model selected > select up 5716 atoms, 5960 bonds, 602 residues, 1 model selected > select up 6295 atoms, 6549 bonds, 676 residues, 1 model selected > select up 7757 atoms, 8035 bonds, 852 residues, 1 model selected > select up 104236 atoms, 109977 bonds, 10152 residues, 1 model selected > select up 104236 atoms, 109977 bonds, 10152 residues, 9 models selected > select down 104236 atoms, 109977 bonds, 10152 residues, 1 model selected > select down 7757 atoms, 8035 bonds, 852 residues, 1 model selected > delete atoms sel > delete bonds sel > select /m:90 8 atoms, 7 bonds, 1 residue, 1 model selected > show #!1 models > view matrix models > #2,0.88483,-0.11954,0.45031,24.973,-0.46269,-0.112,0.87942,223.86,-0.054688,-0.98649,-0.15441,513.62 > fitmap #2 inMap #1 Fit molecule 6fyy (#2) to map cryosparc_P518_J12_004_volume_map.mrc (#1) using 96479 atoms average map value = 0.268, steps = 80 shifted from previous position = 1.29 rotated from previous position = 3.17 degrees atoms outside contour = 38826, contour level = 0.18877 Position of 6fyy (#2) relative to cryosparc_P518_J12_004_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.86702557 -0.13551646 0.47948091 24.91942481 -0.49089805 -0.06747493 0.86860016 221.74999991 -0.08535668 -0.98847479 -0.12502726 512.81061903 Axis -0.94108280 0.28623451 -0.18009154 Axis point 0.00000000 341.61616755 147.29169267 Rotation angle (degrees) 99.36587360 Shift along axis -52.33159577 > select add #2 96479 atoms, 101942 bonds, 1728 pseudobonds, 9300 residues, 4 models selected > select subtract #2 Nothing selected > select /i:78 8 atoms, 7 bonds, 1 residue, 1 model selected > select add /m:83 13 atoms, 11 bonds, 2 residues, 1 model selected > select up 181 atoms, 182 bonds, 23 residues, 1 model selected > select up 2098 atoms, 2133 bonds, 268 residues, 1 model selected > select up 2099 atoms, 2133 bonds, 269 residues, 1 model selected > select up 96479 atoms, 101942 bonds, 9300 residues, 1 model selected > select down 2099 atoms, 2133 bonds, 269 residues, 1 model selected > delete atoms sel > delete bonds sel > volume #1 level 0.296 > open /Users/udalwadi/Downloads/cryosparc_P518_J21_004_volume_map.mrc Opened cryosparc_P518_J21_004_volume_map.mrc as #6, grid size 300,300,300, pixel 1.86, shown at level 0.165, step 2, values float32 > hide #!1 models > volume #6 level 0.1645 > volume #6 level 0.2142 > volume #6 step 1 > volume #6 level 0.1554 > movie record > turn y 2 180 > wait 180 > movie encode /Users/udalwadi/Desktop/movie2.mp4 Movie saved to /Users/udalwadi/Desktop/movie2.mp4 > hide #!6 models > show #!6 models > open 6fyy 6fyy title: Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model C2) [more info...] Chain information for 6fyy #7 --- Chain | Description | UniProt 1 | tRNAi | 2 | 18S ribosomal RNA | 3 | mRNA (31-MER) | A | 40S ribosomal protein S0 | RSSA_KLULA 1-254 B | 40S ribosomal protein S1 | RS3A_KLULA 1-255 C | KLLA0F09812p | Q6CKL3_KLULA 1-259 D | KLLA0D08305p | Q6CRK7_KLULA 1-237 E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 1-261 F | KLLA0D10659p | Q6CRA3_KLULA 1-227 G | 40S ribosomal protein S6 | RS6_KLULA 1-236 H | 40S ribosomal protein S7 | Q6CTD6_KLULA 1-190 I | 40S ribosomal protein S8 | Q6CMG3_KLULA 1-201 J | KLLA0E23673p | Q6CM18_KLULA 1-188 K | KLLA0B08173p | Q6CVZ5_KLULA 1-106 L | KLLA0A10483p | Q6CX80_KLULA 1-156 M | 40S ribosomal protein S12 | Q6CLU4_KLULA 1-134 N | KLLA0F18040p | Q6CJK0_KLULA 1-151 O | 40S ribosomal protein S14 | RS14_KLULA 1-137 P | KLLA0F07843p | Q6CKV4_KLULA 1-142 Q | 40S ribosomal protein S16 | RS16_KLULA 1-143 R | KLLA0B01474p | Q6CWU3_KLULA 1-136 S | KLLA0B01562p | Q6CWT9_KLULA 1-146 T | KLLA0A07194p | Q6CXM0_KLULA 1-144 U | KLLA0F25542p | Q6CIM1_KLULA 4-120 V | 40S ribosomal protein S21 | RS21_KLULA 1-87 W | 40S ribosomal protein S22 | RS22_KLULA 1-130 X | KLLA0B11231p | F2Z602_KLULA 1-145 Y | 40S ribosomal protein S24 | Q6CU44_KLULA 1-135 Z | KLLA0B06182p | Q6CW78_KLULA 1-108 a | 40S ribosomal protein S26 | Q6CS01_KLULA 1-119 b | 40S ribosomal protein S27 | Q6CNL2_KLULA 1-82 c | 40S ribosomal protein S28 | RS28_KLULA 1-67 d | 40S ribosomal protein S29 | RS29_KLULA 1-56 e | 40S ribosomal protein S30 | Q6CUH5_KLULA 1-63 f | Ubiquitin-40S ribosomal protein S27a | RS27A_KLULA 1-150 g | KLLA0E12277p | Q6CNI7_KLULA 1-326 h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25 i | Eukaryotic translation initiation factor 1A | IF1A_YEAST 1-153 j | Eukaryotic translation initiation factor 2 subunit alpha | IF2A_YEAST 1-304 k | Eukaryotic translation initiation factor 2 subunit gamma | IF2G_YEAST 1-527 l | Eukaryotic translation initiation factor 2 subunit beta | IF2B_YEAST 1-285 m | Eukaryotic translation initiation factor 5 | IF5_YEAST 1-405 o | Eukaryotic translation initiation factor 3 subunit A | EIF3A_YEAST 1-964 p | Eukaryotic translation initiation factor 3 subunit B | EIF3B_YEAST 1-763 q | eIF3c,Eukaryotic translation initiation factor 3 subunit C | EIF3C_YEAST 251-812 r | Eukaryotic translation initiation factor 3 subunit G | EIF3G_YEAS7 1-274 s | Eukaryotic translation initiation factor 3 subunit I | EIF3I_YEAS7 1-347 Non-standard residues in 6fyy #7 --- C4J — (5S)-5-{3-[(3S)-3-amino-3-carboxypropyl]-1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl}-2,5-anhydro-1-O-phosphono- L-arabinitol GCP — phosphomethylphosphonic acid guanylate ester MET — methionine MG — magnesium ion ZN — zinc ion > log metadata #7 Metadata for 6fyy #7 --- Title | Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model C2) Citation | Llacer, J.L., Hussain, T., Saini, A.K., Nanda, J.D., Kaur, S., Gordiyenko, Y., Kumar, R., Hinnebusch, A.G., Lorsch, J.R., Ramakrishnan, V. (2018). Translational initiation factor eIF5 replaces eIF1 on the 40S ribosomal subunit to promote start-codon recognition. Elife, 7. PMID: 30475211. DOI: 10.7554/eLife.39273 Non-standard residues | C4J — (5S)-5-{3-[(3S)-3-amino-3-carboxypropyl]-1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl}-2,5-anhydro-1-O-phosphono-L-arabinitol GCP — phosphomethylphosphonic acid guanylate ester MET — methionine MG — magnesium ion ZN — zinc ion Sources (natural) | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) Saccharomyces cerevisiae Gene source | Saccharomyces cerevisiae (baker's yeast) CryoEM Map | EMDB 4328 — open map Experimental method | Electron microscopy Resolution | 3.05Å > open 4328 fromDatabase emdb Opened emdb 4328 as #8, grid size 300,300,300, pixel 1.34, shown at level 0.12, step 2, values float32, fit PDB 6fyy > hide #!6 models > hide #!2 models > hide #!7 models > volume #8 step 1 > show #!1 models > select add #8 2 models selected > view matrix models > #8,0.99605,-0.081682,-0.034732,24.38,0.022516,-0.14598,0.98903,30.648,-0.085856,-0.98591,-0.14356,447.06 > view matrix models > #8,0.99605,-0.081682,-0.034732,23.472,0.022516,-0.14598,0.98903,115.51,-0.085856,-0.98591,-0.14356,498.82 > view matrix models > #8,0.99605,-0.081682,-0.034732,59.43,0.022516,-0.14598,0.98903,77.305,-0.085856,-0.98591,-0.14356,518.78 > fitmap #8 inMap #1 Fit map emdb 4328 in map cryosparc_P518_J12_004_volume_map.mrc using 184474 points correlation = 0.84, correlation about mean = 0.3476, overlap = 1.813e+04 steps = 340, shift = 46.6, angle = 31 degrees Position of emdb 4328 (#8) relative to cryosparc_P518_J12_004_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.86664036 -0.13636673 0.47993603 25.05515592 -0.49145159 -0.06735569 0.86829634 221.78389403 -0.08608031 -0.98836599 -0.12539081 513.12993252 Axis -0.94092326 0.28684696 -0.17995066 Axis point 0.00000000 341.77788682 147.43124861 Rotation angle (degrees) 99.38415200 Shift along axis -52.29501193 > select clear > show #!2 models > hide #!1 models > volume #8 level 0.09335 > hide #!8 models > hide #!2 models > show #!6 models > open /Users/udalwadi/Downloads/cryosparc_P522_J14_005_volume_map.mrc Opened cryosparc_P522_J14_005_volume_map.mrc as #9, grid size 300,300,300, pixel 1.86, shown at level 0.084, step 2, values float32 > hide #!6 models > volume #9 step 1 > volume #9 level 0.07942 > show #!8 models > select add #9 2 models selected > volume #8 level 0.17 > volume #9 level 0.1939 > volume #8 level 0.1333 > view matrix models > #9,-0.97852,-0.023591,-0.20478,662.38,-0.019694,-0.97819,0.20679,510.82,-0.2052,0.20638,0.95671,15.461 > view matrix models > #9,-0.97852,-0.023591,-0.20478,661.31,-0.019694,-0.97819,0.20679,487.89,-0.2052,0.20638,0.95671,1.6739 > view matrix models > #9,-0.94467,-0.29821,-0.13665,710.21,0.26117,-0.93581,0.23674,382.53,-0.19847,0.18795,0.96192,3.4341 > view matrix models > #9,-0.94467,-0.29821,-0.13665,688.68,0.26117,-0.93581,0.23674,416.32,-0.19847,0.18795,0.96192,1.5888 > fitmap #9 in#8 Expected a keyword > fitmap #9 inMap #8 Fit map cryosparc_P522_J14_005_volume_map.mrc in map emdb 4328 using 80564 points correlation = 0.3048, correlation about mean = 0.04287, overlap = 1051 steps = 284, shift = 32, angle = 15.7 degrees Position of cryosparc_P522_J14_005_volume_map.mrc (#9) relative to emdb 4328 (#8) coordinates: Matrix rotation and translation -0.87885797 0.42189630 -0.22273794 391.06478629 0.25562097 0.02221745 -0.96652176 396.97206304 -0.40282328 -0.90637183 -0.12737153 610.63519457 Axis 0.23832973 0.71354523 -0.65882634 Axis point 155.58678717 0.00000000 470.94979247 Rotation angle (degrees) 172.75048594 Shift along axis -25.84266693 > view matrix models > #9,-0.99123,-0.058498,-0.11849,598.29,0.051564,-0.99682,0.060773,538.28,-0.12166,0.054131,0.99109,9.2531 > view matrix models > #9,-0.57447,-0.80209,0.16321,605.34,0.76363,-0.59698,-0.24593,294.19,0.29469,-0.016652,0.95545,-86.763 > volume flip #9 Opened cryosparc_P522_J14_005_volume_map.mrc z flip as #10, grid size 300,300,300, pixel 1.86, shown at step 1, values float32 > select subtract #9 Nothing selected > select add #10 2 models selected > view matrix models > #10,0.13439,-0.97982,0.14794,445.54,-0.97954,-0.10879,0.16932,567.68,-0.1498,-0.16767,-0.97439,626.97 > fitmap #10 inMap #8 Fit map cryosparc_P522_J14_005_volume_map.mrc z flip in map emdb 4328 using 80564 points correlation = 0.6866, correlation about mean = 0.3968, overlap = 3531 steps = 652, shift = 30.4, angle = 48.3 degrees Position of cryosparc_P522_J14_005_volume_map.mrc z flip (#10) relative to emdb 4328 (#8) coordinates: Matrix rotation and translation 0.96390445 -0.15899215 0.21356430 -82.90372039 -0.19967534 0.09891465 0.97485674 -31.78417685 -0.17611921 -0.98231227 0.06359746 506.50499095 Axis -0.98054524 0.19523215 -0.02038235 Axis point 0.00000000 251.72436521 278.24898633 Rotation angle (degrees) 86.37601637 Shift along axis 64.76179304 > select clear > hide #!8 models > show #!7 models > hide #!7 models > show #!2 models > close #9 > volume #10 level 0.1 > volume #10 level 0.084 > hide #!10 models > show #!8 models > volume #8 level 0.08336 > close #7 > open 6zmw 6zmw title: Structure of a human 48S translational initiation complex [more info...] Chain information for 6zmw #7 --- Chain | Description | UniProt 1 | Eukaryotic translation initiation factor 3 subunit B | EIF3B_HUMAN 1-814 2 | Eukaryotic translation initiation factor 3 subunit I | EIF3I_HUMAN 1-325 3 | Eukaryotic translation initiation factor 3 subunit K | EIF3K_HUMAN 1-218 4 | Eukaryotic translation initiation factor 3 subunit F | EIF3F_HUMAN 1-357 5 | Eukaryotic translation initiation factor 3 subunit L | EIF3L_HUMAN 1-564 6 | Eukaryotic translation initiation factor 3 subunit M | EIF3M_HUMAN 1-374 7 | mRNA | 8 | Eukaryotic translation initiation factor 3 subunit H | EIF3H_HUMAN 1-352 9 | 60S ribosomal protein L41 | RL41_HUMAN 1-25 A | 18S rRNA | B | 40S ribosomal protein S11 | RS11_HUMAN 1-158 C | 40S ribosomal protein S4, X isoform | RS4X_HUMAN 1-263 D | 40S ribosomal protein S9 | RS9_HUMAN 1-194 E | 40S ribosomal protein S23 | RS23_HUMAN 1-143 F | 40S ribosomal protein S30 | RS30_HUMAN 75-133 G | 40S ribosomal protein S7 | RS7_HUMAN 1-194 H | 40S ribosomal protein S27 | RS27_HUMAN 1-84 I | 40S ribosomal protein S13 | RS13_HUMAN 1-151 J | 40S ribosomal protein S15a | RS15A_HUMAN 1-130 K | 40S ribosomal protein S21 | RS21_HUMAN 1-83 L | 40S ribosomal protein S2 | RS2_HUMAN 1-293 M | 40S ribosomal protein S17 | RS17_HUMAN 1-135 N | 40S ribosomal protein SA | RSSA_HUMAN 1-295 O | 40S ribosomal protein S3a | RS3A_HUMAN 1-264 P | 40S ribosomal protein S14 | RS14_HUMAN 1-151 Q | 40S ribosomal protein S26 | RS26_HUMAN 1-115 R | 40S ribosomal protein S8 | RS8_HUMAN 1-208 S | 40S ribosomal protein S6 | RS6_HUMAN 1-249 T | 40S ribosomal protein S24 | RS24_HUMAN 1-133 V | 40S ribosomal protein S5 | RS5_HUMAN 1-204 Y | 40S ribosomal protein S16 | RS16_HUMAN 1-146 Z | 40S ribosomal protein S3 | RS3_HUMAN 1-243 a | 40S ribosomal protein S10 | RS10_HUMAN 1-165 b | 40S ribosomal protein S15 | RS15_HUMAN 1-145 c | Receptor of activated protein C kinase 1 | RACK1_HUMAN 1-317 d | 40S ribosomal protein S19 | RS19_HUMAN 1-145 e | 40S ribosomal protein S25 | RS25_HUMAN 1-125 f | 40S ribosomal protein S18 | RS18_HUMAN 1-152 g | Eukaryotic translation initiation factor 4 gamma 1 | IF4G1_HUMAN 290-1599 h | 40S ribosomal protein S20 | RS20_HUMAN 1-119 i | 40S ribosomal protein S29 | RS29_HUMAN 1-56 j | Eukaryotic initiation factor 4A-I | IF4A1_HUMAN 1-406 k | Ubiquitin-40S ribosomal protein S27a | RS27A_HUMAN 1-156 m | 40S ribosomal protein S12 | RS12_HUMAN 1-132 n | 40S ribosomal protein S28 | RS28_HUMAN 1-69 o | Eukaryotic translation initiation factor 3 subunit G | EIF3G_HUMAN 1-320 p | Eukaryotic translation initiation factor 1 | EIF1_HUMAN 1-113 q | Eukaryotic translation initiation factor 1A, X-chromosomal | IF1AX_HUMAN 1-144 r | Eukaryotic translation initiation factor 2 subunit 1 | IF2A_HUMAN 1-315 s | Eukaryotic translation initiation factor 2 subunit 2 | IF2B_HUMAN 1-333 t | Eukaryotic translation initiation factor 2 subunit 3 | IF2G_HUMAN 1-472 u | Eukaryotic translation initiation factor 3 subunit A | EIF3A_HUMAN 1-1382 v | Eukaryotic translation initiation factor 3 subunit E | EIF3E_HUMAN 1-445 w | Initiator Met-tRNA-i | x | Eukaryotic translation initiation factor 3 subunit D | EIF3D_HUMAN 1-548 y | Eukaryotic translation initiation factor 3 subunit C | EIF3C_HUMAN 1-913 z | Eukaryotic translation initiation factor 3 subunit J | EIF3J_HUMAN 1-258 Non-standard residues in 6zmw #7 --- MG — magnesium ion ZN — zinc ion > log metadata #7 Metadata for 6zmw #7 --- Title | Structure of a human 48S translational initiation complex Citation | Brito Querido, J., Sokabe, M., Kraatz, S., Gordiyenko, Y., Skehel, J.M., Fraser, C.S., Ramakrishnan, V. (2020). Structure of a human 48Stranslational initiation complex. Science, 369, 1220-1227. PMID: 32883864. DOI: 10.1126/science.aba4904 Non-standard residues | MG — magnesium ion ZN — zinc ion Source (natural) | Homo sapiens (human) Gene source | Homo sapiens (human) CryoEM Map | EMDB 11302 — open map Experimental method | Electron microscopy Resolution | 3.7Å > open 11302 fromDatabase emdb Summary of feedback from opening 11302 fetched from emdb --- notes | Fetching compressed map 11302 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-11302/map/emd_11302.map.gz Fetching map header 11302 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-11302/header/emd-11302.xml Opened emdb 11302 as #9, grid size 500,500,500, pixel 1.07, shown at level 0.025, step 2, values float32, fit PDB 6zmw > hide #!8 models > select add #9 2 models selected > select subtract #9 Nothing selected > select add #7 118147 atoms, 123656 bonds, 1743 pseudobonds, 13029 residues, 4 models selected > style sel stick Changed 118147 atom styles > show sel cartoons > hide sel atoms > select clear > volume #9 step 1 > volume #9 level 0.04347 > hide #!7 models > hide #!2 models > show #!1 models > volume #1 color #b2b2b2 > select add #9 2 models selected > view matrix models > #9,-0.86848,-0.12223,-0.48043,667.75,-0.22672,-0.7639,0.6042,334.6,-0.44085,0.63365,0.63572,61.502 > view matrix models > #9,-0.86848,-0.12223,-0.48043,716.68,-0.22672,-0.7639,0.6042,136.45,-0.44085,0.63365,0.63572,36.051 > view matrix models > #9,-0.86848,-0.12223,-0.48043,714.86,-0.22672,-0.7639,0.6042,151.31,-0.44085,0.63365,0.63572,47.239 > view matrix models > #9,-0.52261,0.66108,-0.53838,440.56,0.84881,0.46272,-0.25576,-200.77,0.080044,-0.59065,-0.80295,630.01 > view matrix models > #9,0.47221,-0.10693,0.87497,-35.173,-0.34339,-0.93652,0.07087,378.86,0.81185,-0.33392,-0.47895,276.68 > view matrix models > #9,0.92031,0.18658,0.34382,-77.267,0.01028,-0.89016,0.45554,162.52,0.39105,-0.4157,-0.82114,507.78 > view matrix models > #9,0.92031,0.18658,0.34382,-43.949,0.01028,-0.89016,0.45554,419.97,0.39105,-0.4157,-0.82114,546.51 > view matrix models > #9,0.92031,0.18658,0.34382,-139.75,0.01028,-0.89016,0.45554,472.35,0.39105,-0.4157,-0.82114,512.83 > fitmap #9 inMap #1 Fit map emdb 11302 in map cryosparc_P518_J12_004_volume_map.mrc using 509527 points correlation = 0.8987, correlation about mean = 0.571, overlap = 1.528e+04 steps = 360, shift = 56.8, angle = 39.6 degrees Position of emdb 11302 (#9) relative to cryosparc_P518_J12_004_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.70376914 -0.40454511 0.58399679 27.60471357 -0.53568100 -0.84212742 0.06218737 662.91111969 0.46664212 -0.35660153 -0.80937042 458.66096395 Axis -0.92191290 0.25834206 -0.28867973 Axis point 0.00000000 364.18873862 183.85386638 Rotation angle (degrees) 166.87181460 Shift along axis 13.40255730 > hide #!1 models > select subtract #9 Nothing selected > show #!7 models > hide #!7 models > hide #!9 models > show #!2 models > hide #!2 models > show #!2 models > mmaker #7/A to #2/2 Using Nucleic matrix instead of BLOSUM-62 for matching Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 6fyy, chain 2 (#2) with 6zmw, chain A (#7), sequence alignment score = 4965.1 RMSD between 729 pruned atom pairs is 1.410 angstroms; (across all 1685 pairs: 6.015) > show #!7 models > hide #!2 models > show #!2 models > hide #!2 models > show #!9 models > hide #!7 models > show #!10 models > hide #!10 models > show #!1 models > volume #1 level 0.1368 > hide #!9 models > ui tool show ""Hide Dust"" > surface dust #1 size 11.14 > surface dust #1 size 10.94 > surface dust #1 size 7.2 > surface dust #1 size 5.89 > surface dust #1 size 5.79 > surface dust #1 size 4.74 > surface dust #1 size 3.12 > surface dust #1 size 5.6 > surface dust #1 size 3.51 > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > surface dust #1 size 2 > surface dust #1 size 2.8 > surface undust #1 > hide #!9 models > show #!9 models > hide #!9 models > show #!7 models > hide #!1 models > hide #!7 models > show #!10 models > show #!7 models > hide #!10 models > show #!9 models > hide #!9 models > show #!1 models > hide #!1 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > open /Users/udalwadi/Downloads/cryosparc_P522_J24_009_volume_map.mrc Opened cryosparc_P522_J24_009_volume_map.mrc as #11, grid size 600,600,600, pixel 0.929, shown at level 0.0184, step 4, values float32 > hide #!7 models > volume #11 level 0.02321 > volume #11 step 1 > volume flip #11 Opened cryosparc_P522_J24_009_volume_map.mrc z flip as #12, grid size 600,600,600, pixel 0.929, shown at step 1, values float32 > show #!1 models > volume #1 level 0.205 > select add #12 2 models selected > close #11 > volume #12 level 0.04107 > view matrix models > #12,0.26368,0.91802,-0.29618,90.255,0.946,-0.30613,-0.10667,72.032,-0.18859,-0.25206,-0.94916,745.95 > view matrix models > #12,0.26368,0.91802,-0.29618,32.903,0.946,-0.30613,-0.10667,-61.206,-0.18859,-0.25206,-0.94916,669.5 > view matrix models > #12,0.98316,-0.079926,-0.16432,20.979,-0.096213,-0.99094,-0.093662,441,-0.15535,0.1079,-0.98195,576.52 > view matrix models > #12,0.65867,-0.64684,0.38438,95.05,-0.71786,-0.69329,0.063429,510.66,0.22546,-0.31771,-0.92099,546.54 > view matrix models > #12,0.65867,-0.64684,0.38438,169.77,-0.71786,-0.69329,0.063429,649.63,0.22546,-0.31771,-0.92099,553.09 > view matrix models > #12,0.46094,-0.82235,0.33358,293.8,-0.88227,-0.46513,0.072468,639.84,0.09556,-0.32771,-0.93993,602.79 > view matrix models > #12,0.46094,-0.82235,0.33358,280.58,-0.88227,-0.46513,0.072468,647.89,0.09556,-0.32771,-0.93993,593.15 > view matrix models > #12,0.74555,-0.6521,0.13754,209.11,-0.66204,-0.74838,0.040502,661.55,0.076518,-0.12125,-0.98967,561.73 > fitmap #12 inMap #1 Fit map cryosparc_P522_J24_009_volume_map.mrc z flip in map cryosparc_P518_J12_004_volume_map.mrc using 389275 points correlation = 0.9422, correlation about mean = 0.4606, overlap = 1.255e+04 steps = 136, shift = 14.1, angle = 10.1 degrees Position of cryosparc_P522_J24_009_volume_map.mrc z flip (#12) relative to cryosparc_P518_J12_004_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.77795427 -0.62348598 0.07779704 202.39827122 -0.61442819 -0.78079224 -0.11332017 704.21779790 0.13139686 0.04035721 -0.99050803 490.37003502 Axis 0.94275773 -0.32881642 0.05556637 Axis point 0.00000000 376.77290131 254.37001596 Rotation angle (degrees) 175.32496911 Shift along axis -13.49775526 > hide #!1 models > volume #12 level 0.03477 > select subtract #12 Nothing selected > show #!7 models > volume #12 level 0.02373 > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > volume #12 level 0.02688 > volume #12 step 8 > volume #12 level 0.01427 > volume #12 step 2 > hide #!7 models > ui tool show ""Hide Dust"" > surface dust #12 size 2 > surface dust #12 size 2.7 > volume #12 step 1 > volume #12 level 0.01738 > surface undust #12 > surface dust #12 size 3.8 > show #!7 models ===== Log before crash end ===== Log: still updating bundle list from toolshed > isolde shorthand isolde is provided by the uninstalled bundle ISOLDE versions 1.7rc1 – 1.8.dev0 UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Model Number: MKGR3LL/A Chip: Apple M1 Pro Total Number of Cores: 8 (6 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 10151.121.1 OS Loader Version: 10151.121.1 Software: System Software Overview: System Version: macOS 14.5 (23F79) Kernel Version: Darwin 23.5.0 Time since boot: 28 days, 32 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 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sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Window Toolkit duplicate all ChimeraX