id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18023 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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(2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/szhang3/Library/CloudStorage/OneDrive- > Moderna/RSV/MAbs/fitting.cxs Opened 101F_SiteIV_purple.mrc as #1, grid size 208,208,208, pixel 2, shown at level 0.15, step 1, values float32 Opened A14_V_Orange.mrc as #2, grid size 208,208,208, pixel 2, shown at level 0.15, step 1, values float32 Opened ADI-14442_SiteV-II_orange-yellow.mrc as #3, grid size 208,208,208, pixel 2, shown at level 0.15, step 1, values float32 Opened D25_Site0_red.mrc as #4, grid size 208,208,208, pixel 2, shown at level 0.15, step 1, values float32 Opened Motavizumab_SiteII_yellow.mrc as #5, grid size 208,208,208, pixel 2, shown at level 0.15, step 1, values float32 Opened MPE8_SiteIII_green.mrc as #6, grid size 208,208,208, pixel 2, shown at level 0.15, step 1, values float32 Opened preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc as #8, grid size 208,208,208, pixel 2, shown at level 0.108, step 1, values float32 Opened RSB1_SiteV_orange.mrc as #9, grid size 208,208,208, pixel 2, shown at level 0.15, step 1, values float32 Opened Medi8897_Site0_red.mrc as #10, grid size 208,208,208, pixel 2, shown at level 0.0929, step 1, values float32 Opened RSV monomer.mrc as #11, grid size 208,208,208, pixel 2, shown at level 0.1, step 1, values float32 Opened P141_J33_zflip_101_RSVA-mono_MEDI_Mota.mrc as #16, grid size 208,208,208, pixel 2, shown at level 1.16, step 1, values float32 Opened cryosparc_P141_J36_001_volume_map.mrc as #15, grid size 208,208,208, pixel 2, shown at level 1.04, step 1, values float32 Log from Tue Jun 17 10:45:24 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/szhang3/Library/CloudStorage/OneDrive- > Moderna/RSV/EMPEM/EMPEMcomposition/EMPEMcomposition.cxs Opened 101F_SiteIV_purple.mrc as #1, grid size 208,208,208, pixel 2, shown at level 0.15, step 1, values float32 Opened A14_V_Orange.mrc as #2, grid size 208,208,208, pixel 2, shown at level 0.15, step 1, values float32 Opened ADI-14442_SiteV-II_orange-yellow.mrc as #3, grid size 208,208,208, pixel 2, shown at level 0.15, step 1, values float32 Opened D25_Site0_red.mrc as #4, grid size 208,208,208, pixel 2, shown at level 0.15, step 1, values float32 Opened Motavizumab_SiteII_yellow.mrc as #5, grid size 208,208,208, pixel 2, shown at level 0.15, step 1, values float32 Opened MPE8_SiteIII_green.mrc as #6, grid size 208,208,208, pixel 2, shown at level 0.15, step 1, values float32 Opened preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc as #8, grid size 208,208,208, pixel 2, shown at level 0.15, step 1, values float32 Opened RSB1_SiteV_orange.mrc as #9, grid size 208,208,208, pixel 2, shown at level 0.15, step 1, values float32 Opened Medi8897_Site0_red.mrc as #10, grid size 208,208,208, pixel 2, shown at level 0.03, step 1, values float32 Opened RSV monomer.mrc as #11, grid size 208,208,208, pixel 2, shown at level 0.026, step 1, values float32 Log from Mon Jun 16 08:40:41 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/szhang3/Library/CloudStorage/OneDrive- > Moderna/RSV/EMPEM/EMPEMcomposition/EMPEMcomposition.cxs Opened 101F_SiteIV_purple.mrc as #1, grid size 208,208,208, pixel 2, shown at level 0.15, step 1, values float32 Opened A14_V_Orange.mrc as #2, grid size 208,208,208, pixel 2, shown at level 0.15, step 1, values float32 Opened ADI-14442_SiteV-II_orange-yellow.mrc as #3, grid size 208,208,208, pixel 2, shown at level 0.15, step 1, values float32 Opened D25_Site0_red.mrc as #4, grid size 208,208,208, pixel 2, shown at level 0.15, step 1, values float32 Opened Motavizumab_SiteII_yellow.mrc as #5, grid size 208,208,208, pixel 2, shown at level 0.15, step 1, values float32 Opened MPE8_SiteIII_green.mrc as #6, grid size 208,208,208, pixel 2, shown at level 0.15, step 1, values float32 Opened preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc as #8, grid size 208,208,208, pixel 2, shown at level 0.15, step 1, values float32 Opened RSB1_SiteV_orange.mrc as #9, grid size 208,208,208, pixel 2, shown at level 0.15, step 1, values float32 Log from Thu May 8 15:20:48 2025 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/szhang3/Library/CloudStorage/OneDrive- > Moderna/RSV/EMPEM/EMPEMcomposition/101F_SiteIV_purple.mrc Opened 101F_SiteIV_purple.mrc as #1, grid size 208,208,208, pixel 2, shown at level 1.84e-05, step 1, values float32 > open /Users/szhang3/Library/CloudStorage/OneDrive- > Moderna/RSV/EMPEM/EMPEMcomposition/A14_V_Orange.mrc Opened A14_V_Orange.mrc as #2, grid size 208,208,208, pixel 2, shown at level 1.84e-05, step 1, values float32 > open /Users/szhang3/Library/CloudStorage/OneDrive- > Moderna/RSV/EMPEM/EMPEMcomposition/ADI-14442_SiteV-II_orange-yellow.mrc Opened ADI-14442_SiteV-II_orange-yellow.mrc as #3, grid size 208,208,208, pixel 2, shown at level 1.83e-05, step 1, values float32 > open /Users/szhang3/Library/CloudStorage/OneDrive- > Moderna/RSV/EMPEM/EMPEMcomposition/D25_Site0_red.mrc Opened D25_Site0_red.mrc as #4, grid size 208,208,208, pixel 2, shown at level 1.84e-05, step 1, values float32 > open /Users/szhang3/Library/CloudStorage/OneDrive- > Moderna/RSV/EMPEM/EMPEMcomposition/Motavizumab_SiteII_yellow.mrc Opened Motavizumab_SiteII_yellow.mrc as #5, grid size 208,208,208, pixel 2, shown at level 1.84e-05, step 1, values float32 > open /Users/szhang3/Library/CloudStorage/OneDrive- > Moderna/RSV/EMPEM/EMPEMcomposition/MPE8_SiteIII_green.mrc Opened MPE8_SiteIII_green.mrc as #6, grid size 208,208,208, pixel 2, shown at level 1.84e-05, step 1, values float32 > open /Users/szhang3/Library/CloudStorage/OneDrive- > Moderna/RSV/EMPEM/EMPEMcomposition/MPE8_SiteIII_purple.mrc Opened MPE8_SiteIII_purple.mrc as #7, grid size 208,208,208, pixel 2, shown at level 1.84e-05, step 1, values float32 > open /Users/szhang3/Library/CloudStorage/OneDrive- > Moderna/RSV/EMPEM/EMPEMcomposition/preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc Opened preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc as #8, grid size 208,208,208, pixel 2, shown at level 0.000161, step 1, values float32 > open /Users/szhang3/Library/CloudStorage/OneDrive- > Moderna/RSV/EMPEM/EMPEMcomposition/RSB1_SiteV_orange.mrc Opened RSB1_SiteV_orange.mrc as #9, grid size 208,208,208, pixel 2, shown at level 1.76e-05, step 1, values float32 > lighting soft > select clear > volume all level 0.15 > select #8 2 models selected > color #8.1 gray > set bgColor white > color #8.1 light gray > select #1 2 models selected > color #1.1 purple > select #4 2 models selected > color #4.1 red > select #3 2 models selected > ui tool show ""Color Actions"" > color sel orange No visible atoms or bonds selected [Repeated 13 time(s)] > select #5 2 models selected > color #5.1 yellow > select #2 2 models selected > color #2.1 orange > select #9 2 models selected > color #9.1 orange > select #3 2 models selected > ui tool show ""Color Actions"" > color sel gold > color sel sandy brown > color sel dark orange > color sel gold > select #5 2 models selected > ui tool show ""Color Actions"" > color sel gold > color sel yellow [Repeated 1 time(s)] > select clear > select #6 2 models selected > color #6.1 forest green > select clear > select #6 2 models selected > color #6.1 forest green > ui tool show ""Color Actions"" > color sel forest green > color sel green > color sel dodger blue > color sel turquoise > volume #7 color #5eaf88 > volume #7 color #00f900 > color sel forest green [Repeated 1 time(s)] > color #6.1 forest green > close #7 > ui mousemode right zoom > select clear > save ""/Users/szhang3/OneDrive - > Moderna/RSV/EMPEM/EMPEMcomposition/front.png"" width 936 height 671 > supersample 3 transparentBackground true > hide #!4 models > show #!4 models > graphics silhouettes true > save ""/Users/szhang3/OneDrive - > Moderna/RSV/EMPEM/EMPEMcomposition/TopView.png"" width 936 height 671 > supersample 3 transparentBackground true > hide #!3 models > show #!3 models > hide #!5 models > hide #!6 models > show #!6 models > show #!5 models > save ""/Users/szhang3/OneDrive - > Moderna/RSV/EMPEM/EMPEMcomposition/front.png"" width 936 height 671 > supersample 3 transparentBackground true > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > save ""/Users/szhang3/OneDrive - > Moderna/RSV/EMPEM/EMPEMcomposition/SideView.png"" width 936 height 671 > supersample 3 transparentBackground true > hide #!9 models > show #!9 models > hide #!8 models > show #!8 models > hide #!6 models > show #!6 models > hide #!5 models > show #!5 models > hide #!5 models > hide #!3 models > show #!3 models > hide #!2 models > show #!5 models > hide #!3 models > save ""/Users/szhang3/OneDrive - > Moderna/RSV/EMPEM/EMPEMcomposition/front.png"" width 936 height 671 > supersample 3 transparentBackground true > save ""/Users/szhang3/OneDrive - > Moderna/RSV/EMPEM/EMPEMcomposition/SideView.png"" width 936 height 671 > supersample 3 transparentBackground true > hide #!4 models > show #!4 models > save ""/Users/szhang3/OneDrive - > Moderna/RSV/EMPEM/EMPEMcomposition/TopView.png"" width 936 height 671 > supersample 3 transparentBackground true > save ""/Users/szhang3/OneDrive - > Moderna/RSV/EMPEM/EMPEMcomposition/EMPEMcomposition.cxs"" includeMaps true ——— End of log from Thu May 8 15:20:48 2025 ——— opened ChimeraX session > show #!2 models > open /Users/szhang3/Downloads/5udc.pdb 5udc.pdb title: Crystal structure of RSV F A2 bound to MEDI8897 [more info...] Chain information for 5udc.pdb #7 --- Chain | Description | UniProt A D F | protein F | FUS_HRSVA 1-513 B E H | MEDI8897 fab heavy chain | C G L | MEDI8897 fab light chain | Non-standard residues in 5udc.pdb #7 --- BMA — β-D-mannopyranose (β-D-mannose; D-mannose; mannose) CL — chloride ion MAN — α-D-mannopyranose (α-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine; 2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine) > hide atoms > hide cartoons > show cartoons > select add #7 20324 atoms, 20737 bonds, 6 pseudobonds, 2648 residues, 2 models selected > select subtract #7 Nothing selected > select add #7 20324 atoms, 20737 bonds, 6 pseudobonds, 2648 residues, 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.88918,0.059463,0.45368,10.939,0.43217,-0.43489,-0.79,43.97,0.15033,0.89852,-0.41239,-85.347 > ui mousemode right ""translate selected models"" > view matrix models > #7,0.88918,0.059463,0.45368,122.68,0.43217,-0.43489,-0.79,296.84,0.15033,0.89852,-0.41239,5.384 > view matrix models > #7,0.88918,0.059463,0.45368,171.33,0.43217,-0.43489,-0.79,179.17,0.15033,0.89852,-0.41239,201.23 > view matrix models > #7,0.88918,0.059463,0.45368,240.03,0.43217,-0.43489,-0.79,163.15,0.15033,0.89852,-0.41239,168.21 > ui tool show ""Fit in Map"" > fitmap #7 inMap #8 Fit molecule 5udc.pdb (#7) to map preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc (#8) using 20324 atoms average map value = 0.1316, steps = 112 shifted from previous position = 8.08 rotated from previous position = 18.1 degrees atoms outside contour = 10579, contour level = 0.15 Position of 5udc.pdb (#7) relative to preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates: Matrix rotation and translation 0.82604493 0.02497455 0.56305066 249.73640605 0.55945921 -0.15727372 -0.81379996 158.97442632 0.06822879 0.98723920 -0.14388740 179.75571678 Axis 0.92705817 0.25470221 0.27511804 Axis point 0.00000000 6.52392129 85.45899564 Rotation angle (degrees) 103.74246189 Shift along axis 321.46535400 > select clear > hide #!9 models > hide #!8 models > hide #!1 models > hide #!2 models > hide #!4 models > hide #!6 models > hide #!5 models Drag select of 470 residues > select up 4639 atoms, 4727 bonds, 603 residues, 1 model selected > select up 10429 atoms, 10603 bonds, 1345 residues, 1 model selected > delete atoms sel > delete bonds sel > show #!8 models > show #!4 models Drag select of 72 residues > select up 773 atoms, 780 bonds, 106 residues, 1 model selected > select up 1618 atoms, 1659 bonds, 217 residues, 1 model selected > select add /L:126 1627 atoms, 1667 bonds, 218 residues, 1 model selected Drag select of 110 residues > select up 3121 atoms, 3182 bonds, 416 residues, 1 model selected > select up 6517 atoms, 6670 bonds, 861 residues, 1 model selected > delete atoms sel > delete bonds sel > hide #!4 models Drag select of 287 residues, 1 pseudobonds > select up 2458 atoms, 2510 bonds, 1 pseudobond, 326 residues, 2 models selected > select up 3249 atoms, 3326 bonds, 1 pseudobond, 429 residues, 2 models selected > select up 3378 atoms, 3463 bonds, 1 pseudobond, 442 residues, 2 models selected > select up 3378 atoms, 3463 bonds, 1 pseudobond, 442 residues, 2 models selected > vop gaussian #7 sd 3 > molmap #7 20 onGrid #8 Opened 5udc.pdb map 20 as #10, grid size 208,208,208, pixel 2, shown at level 0.0257, step 1, values float32 > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > select #10 2 models selected > select clear Drag select of 10 5udc.pdb map 20 > select clear > select #10 2 models selected > select clear > hide #!10 models > select add #7 3378 atoms, 3463 bonds, 1 pseudobond, 442 residues, 2 models selected > show sel atoms Drag select of 76 atoms, 84 bonds > select up 82 atoms, 87 bonds, 8 residues, 1 model selected > select up 88 atoms, 94 bonds, 8 residues, 1 model selected > select up 127 atoms, 137 bonds, 11 residues, 1 model selected > select up 3378 atoms, 3463 bonds, 442 residues, 1 model selected > select down 127 atoms, 137 bonds, 11 residues, 1 model selected > hide #!8 models > select clear Drag select of 1 atoms Drag select of 6 atoms, 6 bonds Drag select of 1 atoms > select up 12 atoms, 7 bonds, 5 residues, 1 model selected > select up 38 atoms, 37 bonds, 5 residues, 1 model selected > select up 129 atoms, 137 bonds, 13 residues, 1 model selected > delete atoms sel > delete bonds sel > show #!8 models > hide atoms > show cartoons > molmap #7 20 onGrid #8 Opened 5udc.pdb map 20 as #10, grid size 208,208,208, pixel 2, shown at level 0.03, step 1, values float32 > show #!4 models > color #10 #ff2600ff models > hide #!8 models > show #!8 models > hide #!7 models > close #7 > save ""/Users/szhang3/OneDrive - > Moderna/RSV/EMPEM/EMPEMcomposition/Medi8897_Site0_red.mrc"" models #10 > save ""/Users/szhang3/OneDrive - > Moderna/RSV/EMPEM/EMPEMcomposition/EMPEMcomposition.cxs"" includeMaps true > show #!1 models > show #!2 models > show #!3 models > show #!5 models > hide #!3 models > hide #!4 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!2 models > ui mousemode right zoom > rock axis y > movie record > movie encode /Users/szhang3/Desktop/movie2.mp4 Movie saved to /Users/szhang3/Desktop/movie2.mp4 > stop > save ""/Users/szhang3/OneDrive - > Moderna/RSV/EMPEM/EMPEMcomposition/EMPEMcomposition.cxs"" includeMaps true > save ""/Users/szhang3/OneDrive - > Moderna/RSV/EMPEM/EMPEMcomposition/RSV_MEDI_Mota.png"" width 936 height 665 > supersample 3 transparentBackground true > open /Users/szhang3/Downloads/5udc.pdb 5udc.pdb title: Crystal structure of RSV F A2 bound to MEDI8897 [more info...] Chain information for 5udc.pdb #7 --- Chain | Description | UniProt A D F | protein F | FUS_HRSVA 1-513 B E H | MEDI8897 fab heavy chain | C G L | MEDI8897 fab light chain | Non-standard residues in 5udc.pdb #7 --- BMA — β-D-mannopyranose (β-D-mannose; D-mannose; mannose) CL — chloride ion MAN — α-D-mannopyranose (α-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine; 2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine) > hide atoms > show cartoons > select add #7 20324 atoms, 20737 bonds, 6 pseudobonds, 2648 residues, 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.45186,0.83609,0.31109,-39.974,0.59179,-0.019992,-0.80585,30.737,-0.66754,0.54823,-0.50382,-98.435 > ui mousemode right ""translate selected models"" > view matrix models > #7,0.45186,0.83609,0.31109,10.706,0.59179,-0.019992,-0.80585,229.92,-0.66754,0.54823,-0.50382,-81.952 > view matrix models > #7,0.45186,0.83609,0.31109,179.34,0.59179,-0.019992,-0.80585,158.03,-0.66754,0.54823,-0.50382,186.41 > view matrix models > #7,0.45186,0.83609,0.31109,204.92,0.59179,-0.019992,-0.80585,146.3,-0.66754,0.54823,-0.50382,186.25 > view matrix models > #7,0.45186,0.83609,0.31109,199.52,0.59179,-0.019992,-0.80585,144.61,-0.66754,0.54823,-0.50382,185.8 > view matrix models > #7,0.45186,0.83609,0.31109,191.86,0.59179,-0.019992,-0.80585,143.65,-0.66754,0.54823,-0.50382,176.83 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.45386,0.75421,0.47453,201.39,0.72149,0.0014847,-0.69242,150.81,-0.52294,0.65663,-0.54348,175.14 > fitmap #7 inMap #8 Fit molecule 5udc.pdb (#7) to map preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc (#8) using 20324 atoms average map value = 0.1316, steps = 236 shifted from previous position = 23.1 rotated from previous position = 48.8 degrees atoms outside contour = 10580, contour level = 0.15 Position of 5udc.pdb (#7) relative to preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates: Matrix rotation and translation 0.82584349 0.02466872 0.56335955 249.77298201 0.55968844 -0.15772236 -0.81355547 159.01791335 0.06878502 0.98717532 -0.14406078 179.73879837 Axis 0.92699562 0.25460131 0.27542203 Axis point 0.00000000 6.62206876 85.41492505 Rotation angle (degrees) 103.76674887 Shift along axis 321.52865406 > select clear > ui mousemode right zoom > hide #!8 models > select /A:225 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 218 atoms, 219 bonds, 26 residues, 1 model selected > select up 3474 atoms, 3532 bonds, 448 residues, 1 model selected > select ~sel & ##selected 16850 atoms, 17205 bonds, 5 pseudobonds, 2200 residues, 2 models selected > delete atoms (#!7 & sel) > delete bonds (#!7 & sel) > vop gaussian #7 sd 3 > molmap #7 20 onGrid #8 Opened 5udc.pdb map 20 as #11, grid size 208,208,208, pixel 2, shown at level 0.026, step 1, values float32 > save ""/Users/szhang3/OneDrive - Moderna/RSV/EMPEM/EMPEMcomposition/RSV > monomer.mrc"" models #11 > color #11 #ebebebff models > color #11 silver models > color #11 #d6d6d6ff models > color #11 silver models > color #11 darkgrey models > color #11 #d6d6d6ff models > color #11 silver models > save ""/Users/szhang3/OneDrive - > Moderna/RSV/EMPEM/EMPEMcomposition/EMPEMcomposition.cxs"" includeMaps true ——— End of log from Mon Jun 16 08:40:41 2025 ——— opened ChimeraX session > open /Users/szhang3/Downloads/cryosparc_P141_J26_002_volume_map_sharp.mrc Opened cryosparc_P141_J26_002_volume_map_sharp.mrc as #12, grid size 208,208,208, pixel 2, shown at level 0.127, step 1, values float32 > volume #12 level 0.5003 > color #12 #8671ffff models > color #12 #7974d0ff models > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > select add #12 2 models selected > view matrix models #12,1,0,0,-20.113,0,1,0,6.1289,0,0,1,-81.251 > volume #12 level 0.7243 > view matrix models #12,1,0,0,-72.319,0,1,0,-7.8902,0,0,1,-117.41 > ui mousemode right ""rotate selected models"" > view matrix models > #12,0.85671,0.51448,0.036776,-161.49,-0.23388,0.32393,0.91672,11.617,0.45972,-0.79397,0.39784,75.407 > view matrix models > #12,-0.23839,-0.95776,0.16081,360.59,0.22332,0.10708,0.96884,-45.696,-0.94514,0.26687,0.18837,175.29 > view matrix models > #12,-0.20038,-0.513,-0.83467,446.85,-0.31028,0.84133,-0.4426,175.42,0.92929,0.1703,-0.32776,-91.96 > view matrix models > #12,0.55647,0.37463,-0.74162,79.981,-0.76613,-0.11406,-0.63248,513.39,-0.32154,0.92013,0.22354,-102.08 > view matrix models > #12,0.45813,0.27593,-0.84497,141.52,0.063477,0.93802,0.34073,-72.806,0.88662,-0.20974,0.41222,-142.37 > view matrix models > #12,0.28731,0.74605,-0.60072,27.923,-0.46436,0.65702,0.59388,48.721,0.83775,0.10832,0.5352,-224.9 > view matrix models > #12,0.44323,0.7968,-0.41067,-51.703,-0.25285,0.55065,0.79552,-10.483,0.86001,-0.24876,0.44554,-134.78 > ui mousemode right ""translate selected models"" > view matrix models > #12,0.44323,0.7968,-0.41067,-150.03,-0.25285,0.55065,0.79552,-15.976,0.86001,-0.24876,0.44554,-117.73 > view matrix models > #12,0.44323,0.7968,-0.41067,-158.11,-0.25285,0.55065,0.79552,-12.325,0.86001,-0.24876,0.44554,-115.58 > view matrix models > #12,0.44323,0.7968,-0.41067,-144.76,-0.25285,0.55065,0.79552,-9.0075,0.86001,-0.24876,0.44554,-117.02 > view matrix models > #12,0.44323,0.7968,-0.41067,-140.49,-0.25285,0.55065,0.79552,-11.642,0.86001,-0.24876,0.44554,-118.23 > ui mousemode right ""rotate selected models"" > view matrix models > #12,0.24134,0.81643,-0.5246,-81.23,-0.76619,0.49206,0.41331,180.3,0.59557,0.3022,0.74429,-240.48 > volume flip #12 Opened cryosparc_P141_J26_002_volume_map_sharp.mrc z flip as #13, grid size 208,208,208, pixel 2, shown at step 1, values float32 > view matrix models > #12,0.24134,0.81643,-0.5246,-81.23,-0.76619,0.49206,0.41331,180.3,0.59557,0.3022,0.74429,-240.48 > select subtract #12 Nothing selected > select add #13 2 models selected > view matrix models > #13,0.88137,0.42106,0.21422,-291.9,0.24243,-0.013906,-0.97007,389.62,-0.40548,0.90692,-0.11433,25.925 > view matrix models > #13,0.9139,0.36932,0.16849,-277.21,0.18036,0.0024284,-0.9836,401.9,-0.36368,0.9293,-0.064391,1.324 > ui mousemode right ""translate selected models"" > view matrix models > #13,0.9139,0.36932,0.16849,-103.5,0.18036,0.0024284,-0.9836,361.38,-0.36368,0.9293,-0.064391,155.05 > ui mousemode right ""rotate selected models"" > view matrix models > #13,0.4012,0.89607,0.18997,-116.79,0.23152,0.10146,-0.96752,325.73,-0.88625,0.43216,-0.16676,393.69 > ui mousemode right ""translate selected models"" > view matrix models > #13,0.4012,0.89607,0.18997,-80.842,0.23152,0.10146,-0.96752,334.88,-0.88625,0.43216,-0.16676,370.81 > view matrix models > #13,0.4012,0.89607,0.18997,-77.197,0.23152,0.10146,-0.96752,339.63,-0.88625,0.43216,-0.16676,370.62 > view matrix models > #13,0.4012,0.89607,0.18997,-72.508,0.23152,0.10146,-0.96752,338.25,-0.88625,0.43216,-0.16676,369.84 > view matrix models > #13,0.4012,0.89607,0.18997,-75.103,0.23152,0.10146,-0.96752,341.42,-0.88625,0.43216,-0.16676,364.46 > view matrix models > #13,0.4012,0.89607,0.18997,-73.383,0.23152,0.10146,-0.96752,335.6,-0.88625,0.43216,-0.16676,361.95 > ui mousemode right ""rotate selected models"" > view matrix models > #13,0.37548,0.87546,0.30426,-89.02,0.062866,0.30347,-0.95077,322.83,-0.92469,0.37613,0.058911,331.85 > ui mousemode right ""translate selected models"" > view matrix models > #13,0.37548,0.87546,0.30426,-86.58,0.062866,0.30347,-0.95077,332.72,-0.92469,0.37613,0.058911,323.22 > view matrix models > #13,0.37548,0.87546,0.30426,-90.558,0.062866,0.30347,-0.95077,327.08,-0.92469,0.37613,0.058911,329.22 > hide #!11 models > show #!11 models > hide #!11 models > hide #!5 models > hide #!10 models > hide #!7 models > show #!7 models > select subtract #13 Nothing selected > hide #!13 models > close #7 > open /Users/szhang3/Library/CloudStorage/OneDrive- > Moderna/RSV/EMPEM/EMPEMcomposition/5udc.pdb 5udc.pdb title: Crystal structure of RSV F A2 bound to MEDI8897 [more info...] Chain information for 5udc.pdb #7 --- Chain | Description | UniProt A D F | protein F | FUS_HRSVA 1-513 B E H | MEDI8897 fab heavy chain | C G L | MEDI8897 fab light chain | Non-standard residues in 5udc.pdb #7 --- BMA — β-D-mannopyranose (β-D-mannose; D-mannose; mannose) CL — chloride ion MAN — α-D-mannopyranose (α-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine; 2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine) > show #!12 models > select add #7 20324 atoms, 20737 bonds, 6 pseudobonds, 2648 residues, 2 models selected > view matrix models #7,1,0,0,-0.48937,0,1,0,0.39238,0,0,1,-0.16138 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.33025,-0.94288,-0.043795,17.219,0.75655,0.29216,-0.58504,32.068,0.56442,0.16008,0.80982,3.4109 > ui mousemode right ""translate selected models"" > view matrix models > #7,0.33025,-0.94288,-0.043795,70.064,0.75655,0.29216,-0.58504,196.92,0.56442,0.16008,0.80982,116.9 > hide #!12 models > show #!12 models > ui mousemode right ""rotate selected models"" > view matrix models > #7,-0.58369,0.038922,-0.81105,-28.025,0.59983,0.6939,-0.39838,181.97,0.54728,-0.71902,-0.42837,107.88 > view matrix models > #7,-0.81759,0.15848,-0.55357,-30.782,0.38013,0.87067,-0.31216,170.9,0.4325,-0.46564,-0.77209,80.908 > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.81759,0.15848,-0.55357,-41.559,0.38013,0.87067,-0.31216,158.57,0.4325,-0.46564,-0.77209,64.634 > view matrix models > #7,-0.81759,0.15848,-0.55357,-39.222,0.38013,0.87067,-0.31216,174.81,0.4325,-0.46564,-0.77209,55.488 > volume #12 level 1.602 > volume #13 level 1.565 > view matrix models > #7,-0.81759,0.15848,-0.55357,-53.214,0.38013,0.87067,-0.31216,183.83,0.4325,-0.46564,-0.77209,47.115 > view matrix models > #7,-0.81759,0.15848,-0.55357,-46.239,0.38013,0.87067,-0.31216,184.8,0.4325,-0.46564,-0.77209,49.871 > ui mousemode right ""rotate selected models"" > view matrix models > #7,-0.5328,-0.64649,-0.54605,-3.0846,0.1861,0.53996,-0.82086,174.05,0.82552,-0.53898,-0.16738,87.422 > view matrix models > #7,-0.49607,-0.72907,-0.47156,4.2976,0.14473,0.46607,-0.87283,173.98,0.85614,-0.50123,-0.12568,88.305 > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.49607,-0.72907,-0.47156,2.3478,0.14473,0.46607,-0.87283,152.19,0.85614,-0.50123,-0.12568,103.79 > view matrix models > #7,-0.49607,-0.72907,-0.47156,6.4068,0.14473,0.46607,-0.87283,153.02,0.85614,-0.50123,-0.12568,103.74 > select add #13 20324 atoms, 20737 bonds, 6 pseudobonds, 2648 residues, 4 models selected > select subtract #13 20324 atoms, 20737 bonds, 6 pseudobonds, 2648 residues, 2 models selected > select add #13 20324 atoms, 20737 bonds, 6 pseudobonds, 2648 residues, 4 models selected > view matrix models > #13,0.37548,0.87546,0.30426,-154.4,0.062866,0.30347,-0.95077,275.45,-0.92469,0.37613,0.058911,339.16,#7,-0.49607,-0.72907,-0.47156,-57.439,0.14473,0.46607,-0.87283,101.39,0.85614,-0.50123,-0.12568,113.68 > undo > select subtract #7 2 models selected > view matrix models > #13,0.37548,0.87546,0.30426,-191.16,0.062866,0.30347,-0.95077,228.01,-0.92469,0.37613,0.058911,330.85 > ui mousemode right ""rotate selected models"" > view matrix models > #13,0.33423,0.89314,0.301,-185.77,0.067552,0.29584,-0.95285,229.16,-0.94007,0.3388,0.038545,346.64 > view matrix models > #13,0.12428,0.5826,0.8032,-186.54,0.51428,0.65444,-0.55427,-29.345,-0.84857,0.48196,-0.21828,353.71 > ui mousemode right ""translate selected models"" > view matrix models > #13,0.12428,0.5826,0.8032,-344.99,0.51428,0.65444,-0.55427,21.857,-0.84857,0.48196,-0.21828,235.47 > view matrix models > #13,0.12428,0.5826,0.8032,-273.8,0.51428,0.65444,-0.55427,86.696,-0.84857,0.48196,-0.21828,229.83 > view matrix models > #13,0.12428,0.5826,0.8032,-295.86,0.51428,0.65444,-0.55427,103.05,-0.84857,0.48196,-0.21828,196.19 > color #13 #73fcd6ff models > color #13 #db8976ff models > view matrix models > #13,0.12428,0.5826,0.8032,-304.83,0.51428,0.65444,-0.55427,105.98,-0.84857,0.48196,-0.21828,188.31 > ui mousemode right ""rotate selected models"" > view matrix models > #13,0.72756,0.46178,0.50736,-337.33,0.48255,0.1812,-0.85692,282.49,-0.48764,0.86829,-0.090993,1.7161 > view matrix models > #13,0.73719,0.45306,0.50129,-336.07,0.47587,0.17858,-0.8612,285.39,-0.47969,0.87341,-0.083949,-2.6001 > ui mousemode right ""translate selected models"" > view matrix models > #13,0.73719,0.45306,0.50129,-339.81,0.47587,0.17858,-0.8612,276.72,-0.47969,0.87341,-0.083949,7.9467 > ui mousemode right ""rotate selected models"" > view matrix models > #13,0.59842,0.5518,0.58087,-350.3,0.54223,0.2548,-0.80066,233.04,-0.58981,0.7941,-0.14673,61.822 > ui mousemode right ""translate selected models"" > view matrix models > #13,0.59842,0.5518,0.58087,-347.08,0.54223,0.2548,-0.80066,226.03,-0.58981,0.7941,-0.14673,60.999 > hide atoms > show cartoons > volume #12 level 1.975 > volume #13 level 1.733 > volume #13 level 1.817 > hide #!13 models > hide #!12 models > select subtract #13 Nothing selected > show #!13 models > show #!12 models Drag select of 162 residues > select up 1754 atoms, 1781 bonds, 237 residues, 1 model selected > select up 3249 atoms, 3326 bonds, 429 residues, 1 model selected Drag select of 316 residues, 1 pseudobonds > select up 6093 atoms, 6231 bonds, 1 pseudobond, 803 residues, 2 models selected > select up 6529 atoms, 6683 bonds, 1 pseudobond, 862 residues, 2 models selected > hide #!12 models > hide #!13 models > view matrix models > #7,-0.49607,-0.72907,-0.47156,6.7596,0.14473,0.46607,-0.87283,155.05,0.85614,-0.50123,-0.12568,105.98 > select add /A:209 6538 atoms, 6691 bonds, 1 pseudobond, 863 residues, 2 models selected > select add /D:206 6546 atoms, 6698 bonds, 1 pseudobond, 864 residues, 2 models selected > select up 6659 atoms, 6813 bonds, 1 pseudobond, 878 residues, 2 models selected > select up 13476 atoms, 13746 bonds, 1 pseudobond, 1758 residues, 2 models selected > hide sel cartoons > show sel cartoons > delete atoms (#!7 & sel) > delete bonds (#!7 & sel) > show #!12 models > hide #!12 models > show #!13 models > open /Users/szhang3/Library/CloudStorage/OneDrive- > Moderna/RSV/EMPEM/EMPEMcomposition/4zyp_Mota_AM14.pdb 4zyp_Mota_AM14.pdb title: Crystal structure of motavizumab and quaternary-specific RSV- neutralizing human antibody AM14 In complex with prefusion RSV F glycoprotein [more info...] Chain information for 4zyp_Mota_AM14.pdb #14 --- Chain | Description | UniProt A B C | protein F | FUS_HRSVA 26-513, D9IEJ2_BPT4 518-544 D F H | AM14 antibody fab heavy chain | E G I | AM14 antibody light chain | J K N | motavizumab antibody fab heavy chain | L M O | motavizumab antibody light chain | > hide atoms > show cartoons Drag select of 102 residues, 1 pseudobonds > select up 2138 atoms, 2158 bonds, 1 pseudobond, 266 residues, 2 models selected > select up 10446 atoms, 10621 bonds, 1 pseudobond, 1347 residues, 2 models selected > select add #7/F:313 10452 atoms, 10626 bonds, 1 pseudobond, 1348 residues, 3 models selected > select up 10537 atoms, 10715 bonds, 1 pseudobond, 1358 residues, 3 models selected > select up 13928 atoms, 14161 bonds, 1 pseudobond, 1796 residues, 3 models selected > ui tool show Matchmaker > matchmaker #!14 & sel to #7 & sel Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 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 5udc.pdb, chain F (#7) with 4zyp_Mota_AM14.pdb, chain C (#14), sequence alignment score = 2359 RMSD between 436 pruned atom pairs is 0.589 angstroms; (across all 448 pairs: 1.048) > select clear > hide #!13 models > hide #!7 models > show #!7 models > show #!2 models > show #!11 models > hide #!11 models > show #!8 models > select add #8 2 models selected > select subtract #8 Nothing selected > select add #7 6848 atoms, 6991 bonds, 2 pseudobonds, 890 residues, 2 models selected > select add #14 36838 atoms, 37648 bonds, 11 pseudobonds, 4796 residues, 4 models selected > select add #13 36838 atoms, 37648 bonds, 11 pseudobonds, 4796 residues, 6 models selected > select add #12 36838 atoms, 37648 bonds, 11 pseudobonds, 4796 residues, 8 models selected > show #!11 models > hide #!11 models > view matrix models > #12,0.24134,0.81643,-0.5246,91.851,-0.76619,0.49206,0.41331,243.17,0.59557,0.3022,0.74429,-211.07,#13,0.59842,0.5518,0.58087,-174,0.54223,0.2548,-0.80066,288.89,-0.58981,0.7941,-0.14673,90.411,#7,-0.49607,-0.72907,-0.47156,179.84,0.14473,0.46607,-0.87283,217.92,0.85614,-0.50123,-0.12568,135.39,#14,-0.26307,-0.89838,0.35173,183.77,-0.96224,0.21793,-0.16307,336.3,0.069848,-0.38135,-0.92179,126.27 > view matrix models > #12,0.24134,0.81643,-0.5246,45.145,-0.76619,0.49206,0.41331,175.54,0.59557,0.3022,0.74429,-132.99,#13,0.59842,0.5518,0.58087,-220.71,0.54223,0.2548,-0.80066,221.27,-0.58981,0.7941,-0.14673,168.49,#7,-0.49607,-0.72907,-0.47156,133.13,0.14473,0.46607,-0.87283,150.29,0.85614,-0.50123,-0.12568,213.47,#14,-0.26307,-0.89838,0.35173,137.06,-0.96224,0.21793,-0.16307,268.67,0.069848,-0.38135,-0.92179,204.34 > ui mousemode right ""rotate selected models"" > view matrix models > #12,0.22885,0.90859,-0.34943,-5.3538,-0.47921,0.4176,0.77199,64.106,0.84734,-0.0092161,0.53097,-77.574,#13,0.56675,0.69313,0.44538,-214.7,0.13098,0.4579,-0.8793,277.89,-0.81341,0.55668,0.16873,194.7,#7,-0.33879,-0.73097,-0.59237,129.93,0.57383,0.33842,-0.74579,169.69,0.74562,-0.59258,0.3048,237.02,#14,-0.36988,-0.91046,0.18505,147.48,-0.78177,0.19737,-0.59151,270.76,0.50203,-0.36346,-0.78477,177.09 > show #!10 models > view matrix models > #12,0.50691,0.81558,-0.27904,-53.924,-0.41972,0.51628,0.74651,38.813,0.75291,-0.2613,0.60403,-25.435,#13,0.30281,0.76015,0.57488,-204.36,0.16439,0.5525,-0.81714,237.42,-0.93877,0.34194,0.042342,293.29,#7,-0.18677,-0.89987,-0.39415,148.93,0.55865,0.23274,-0.79608,170.16,0.8081,-0.36888,0.45924,239.17,#14,-0.12353,-0.99184,0.031387,137.36,-0.79976,0.080783,-0.59487,270.34,0.58748,-0.098587,-0.80321,176.37 > ui mousemode right ""translate selected models"" > view matrix models > #12,0.50691,0.81558,-0.27904,-5.7365,-0.41972,0.51628,0.74651,41.253,0.75291,-0.2613,0.60403,-31.317,#13,0.30281,0.76015,0.57488,-156.17,0.16439,0.5525,-0.81714,239.85,-0.93877,0.34194,0.042342,287.41,#7,-0.18677,-0.89987,-0.39415,197.12,0.55865,0.23274,-0.79608,172.6,0.8081,-0.36888,0.45924,233.29,#14,-0.12353,-0.99184,0.031387,185.55,-0.79976,0.080783,-0.59487,272.78,0.58748,-0.098587,-0.80321,170.49 > view matrix models > #12,0.50691,0.81558,-0.27904,9.9167,-0.41972,0.51628,0.74651,33.521,0.75291,-0.2613,0.60403,16.781,#13,0.30281,0.76015,0.57488,-140.52,0.16439,0.5525,-0.81714,232.12,-0.93877,0.34194,0.042342,335.51,#7,-0.18677,-0.89987,-0.39415,212.77,0.55865,0.23274,-0.79608,164.87,0.8081,-0.36888,0.45924,281.39,#14,-0.12353,-0.99184,0.031387,201.2,-0.79976,0.080783,-0.59487,265.04,0.58748,-0.098587,-0.80321,218.59 > view matrix models > #12,0.50691,0.81558,-0.27904,8.0977,-0.41972,0.51628,0.74651,18.777,0.75291,-0.2613,0.60403,10.752,#13,0.30281,0.76015,0.57488,-142.34,0.16439,0.5525,-0.81714,217.38,-0.93877,0.34194,0.042342,329.48,#7,-0.18677,-0.89987,-0.39415,210.95,0.55865,0.23274,-0.79608,150.12,0.8081,-0.36888,0.45924,275.36,#14,-0.12353,-0.99184,0.031387,199.38,-0.79976,0.080783,-0.59487,250.3,0.58748,-0.098587,-0.80321,212.56 > ui tool show ""Fit in Map"" > fitmap #7 inMap #8 Fit molecule 5udc.pdb (#7) to map preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc (#8) using 6848 atoms average map value = 0.173, steps = 260 shifted from previous position = 48.5 rotated from previous position = 29.3 degrees atoms outside contour = 2636, contour level = 0.15 Position of 5udc.pdb (#7) relative to preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates: Matrix rotation and translation 0.04300397 -0.84679709 -0.53017484 198.19738925 0.86630357 0.29594287 -0.40241266 225.13680889 0.49766333 -0.44198701 0.74631005 288.74020833 Axis -0.01980517 -0.51438666 0.85732964 Axis point -74.60302156 321.35625507 0.00000000 Rotation angle (degrees) 87.55682955 Shift along axis 127.81283363 > undo [deleted to fit within ticket limits] 5 atoms, 4 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > select clear > show #!16 models > hide #!16 models Drag select of 31 residues > view sel > ui tool show ""Side View"" > select clear > lighting simple > lighting soft > show #!16 models > select clear > movie record > turn y 2 180 > wait 180 > movie encode /Users/szhang3/Desktop/movie7.mp4 Movie saved to /Users/szhang3/Desktop/movie7.mp4 > rock axis y > stop > rock axis y > stop > show #!12 models > hide #!12 models > rock axis y > movie record > movie encode /Users/szhang3/Desktop/movie8.mp4 Movie saved to /Users/szhang3/Desktop/movie8.mp4 > stop > show #!12 models > hide #!16 models > hide #17 models > show #17 models > hide #!14 models > show #!14 models > hide #!14 models > show #!14 models > hide #!14 models > show #!14 models > hide #!14 models > show #!14 models > hide #17 models > show #17 models > hide #!14 models > show #!14 models > combine #14,17 Remapping chain ID 'B' in ranked_0.pdb #17 to 'F' > rename #18 RSVA-mono_MEDI_Mota_101Fab > hide #17 models > hide #!14 models > hide #!18 models > show #!18 models > hide #!18 models > hide #!12 models > show #!18 models > hide #!18 models > show #!18 models > combine #14,17 Remapping chain ID 'B' in ranked_0.pdb #17 to 'F' > hide #!18 models > hide #!19 models > show #!19 models > select #19/C:111 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 48 atoms, 47 bonds, 7 residues, 1 model selected > select up 817 atoms, 833 bonds, 106 residues, 1 model selected > select up 15037 atoms, 15330 bonds, 1738 residues, 1 model selected > select down 817 atoms, 833 bonds, 106 residues, 1 model selected > select up 15037 atoms, 15330 bonds, 1738 residues, 1 model selected > select down 817 atoms, 833 bonds, 106 residues, 1 model selected > select clear Drag select of 108 residues, 1 pseudobonds > select up 1154 atoms, 1174 bonds, 1 pseudobond, 154 residues, 2 models selected > select up 1491 atoms, 1525 bonds, 1 pseudobond, 198 residues, 2 models selected > delete atoms (#!19 & sel) > delete bonds (#!19 & sel) > rename #19 RSVA-mono_MEDI_Mota_101Fv > show #!16 models > save ""/Users/szhang3/OneDrive - Moderna/RSV/MAbs/101/RSVA- > mono_MEDI_Mota_101Fab.pdb"" models #18 relModel #16 > save ""/Users/szhang3/OneDrive - Moderna/RSV/MAbs/101/RSVA- > mono_MEDI_Mota_101Fv.pdb"" models #19 relModel #16 > close #17 > close #14 > show #!18 models > hide #!19 models > hide #!16 models > show #!12 models > hide #!18 models > select #12/B:179 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 34 atoms, 33 bonds, 5 residues, 1 model selected > select up 3482 atoms, 3540 bonds, 449 residues, 1 model selected > show #!18 models > hide #!18 models > color sel hot pink > select #12/C:433 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 36 atoms, 35 bonds, 5 residues, 1 model selected > select up 3482 atoms, 3541 bonds, 449 residues, 1 model selected > color sel light gray > select clear > show #!18 models > undo > select clear > show #!18 models > rock axis y > show #!16 models > stop > hide #18.1 models > select clear > movie record > turn y 2 180 > wait 180 > movie encode /Users/szhang3/Desktop/movie7.mp4 Movie saved to /Users/szhang3/Desktop/movie7.mp4 > hide #!12 models > show #!12 models > rock axis y > stop > movie record > turn y 2 180 > wait 180 > movie encode /Users/szhang3/Desktop/movie8.mp4 Movie saved to /Users/szhang3/Desktop/movie8.mp4 > show #!1 models > hide #!1 models > show #!6 models > hide #!6 models > show #!7 models > hide #!7 models > show #!8 models > hide #!8 models > show #!9 models > hide #!9 models > show #!10 models > hide #!10 models > show #!1 models > hide #!1 models > hide #!12 models > hide #!16 models > movie record > turn y 2 180 > wait 180 > movie encode /Users/szhang3/Desktop/movie9.mp4 Movie saved to /Users/szhang3/Desktop/movie9.mp4 Drag select of 23 residues > view sel > ui tool show ""Side View"" > select clear > movie record > turn y 2 180 > wait 180 > movie encode /Users/szhang3/Desktop/movie10.mp4 Movie saved to /Users/szhang3/Desktop/movie10.mp4 > open /Users/szhang3/Downloads/cryosparc_P141_J34_002_volume_map_sharp.mrc Opened cryosparc_P141_J34_002_volume_map_sharp.mrc as #14, grid size 208,208,208, pixel 2, shown at level 0.135, step 1, values float32 > close #14 > show #!15 models > hide #!18 models > show #!16 models > hide #!16 models > show #!13 models Drag select of 263 residues, 15 cryosparc_P141_J36_001_volume_map.mrc > hide #!15 models > select up 2371 atoms, 2420 bonds, 311 residues, 3 models selected > select up 3237 atoms, 3321 bonds, 424 residues, 3 models selected > select subtract #15 3237 atoms, 3321 bonds, 424 residues, 1 model selected > ui tool show ""Color Actions"" > color sel #8671ffff > color sel #b146ffff > select clear Drag select of 306 residues, 1 pseudobonds Drag select of 301 residues Drag select of 135 residues > select up 7076 atoms, 7228 bonds, 1 pseudobond, 939 residues, 2 models selected > select up 9711 atoms, 9963 bonds, 1 pseudobond, 1272 residues, 2 models selected > select up 20544 atoms, 20995 bonds, 6 pseudobonds, 2658 residues, 2 models selected > select down 9711 atoms, 9963 bonds, 1 pseudobond, 1272 residues, 2 models selected > color (#!13 & sel) #8671ffff > select clear > hide #13.1 models > select clear Cell requested for row 13 is out of bounds for table with 18 rows! Resizing table model. > show #!15 models > rename #15 cryosparc_P141_J36_001_volume_map_102.mrc > hide #!13 models > show #!13 models > hide #!15 models > open /Users/szhang3/Library/CloudStorage/OneDrive- > Moderna/RSV/MAbs/102/AF2_102/102mab/ranked_0.pdb Chain information for ranked_0.pdb #14 --- Chain | Description A | No description available B | No description available Computing secondary structure > select add #14 3303 atoms, 3347 bonds, 222 residues, 1 model selected Drag select of 197 residues > select up 5234 atoms, 5317 bonds, 480 residues, 2 models selected > select up 6540 atoms, 6668 bonds, 646 residues, 2 models selected > open /Users/szhang3/Library/CloudStorage/OneDrive- > Moderna/RSV/MAbs/102/AF2_102/102mab/ranked_0.pdb Chain information for ranked_0.pdb #17 --- Chain | Description A | No description available B | No description available Computing secondary structure > open /Users/szhang3/Library/CloudStorage/OneDrive- > Moderna/RSV/MAbs/102/AF2_102/102mab/ranked_0.pdb Chain information for ranked_0.pdb #20 --- Chain | Description A | No description available B | No description available Computing secondary structure > select add #17 9843 atoms, 10015 bonds, 868 residues, 3 models selected > select add #20 13146 atoms, 13362 bonds, 1090 residues, 4 models selected > ui tool show Matchmaker > matchmaker #14 to #13 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 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 102_RSVA-PreF-trimer.pdb, chain D (#13) with ranked_0.pdb, chain A (#14), sequence alignment score = 258.8 RMSD between 100 pruned atom pairs is 0.927 angstroms; (across all 114 pairs: 2.093) > hide #17 models > select subtract #17 9843 atoms, 10015 bonds, 868 residues, 3 models selected > select add #17 13146 atoms, 13362 bonds, 1090 residues, 4 models selected > show #17 models > hide #14 models > select subtract #14 9843 atoms, 10015 bonds, 868 residues, 3 models selected > select clear Drag select of 92 residues > select up 1440 atoms, 1467 bonds, 190 residues, 1 model selected > select up 3237 atoms, 3321 bonds, 424 residues, 1 model selected > select add #17 6540 atoms, 6668 bonds, 646 residues, 2 models selected > ui tool show Matchmaker > matchmaker #17 & sel to #13 & sel Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 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 102_RSVA-PreF-trimer.pdb, chain M (#13) with ranked_0.pdb, chain A (#17), sequence alignment score = 258.8 RMSD between 100 pruned atom pairs is 0.927 angstroms; (across all 114 pairs: 2.093) > select clear Drag select of 145 residues > select up 1654 atoms, 1692 bonds, 216 residues, 1 model selected > select up 3237 atoms, 3321 bonds, 424 residues, 1 model selected > select add #20 6540 atoms, 6668 bonds, 646 residues, 2 models selected > matchmaker #20 & sel to #13 & sel Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 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 102_RSVA-PreF-trimer.pdb, chain G (#13) with ranked_0.pdb, chain A (#20), sequence alignment score = 258.8 RMSD between 100 pruned atom pairs is 0.927 angstroms; (across all 114 pairs: 2.093) > show #14 models > select clear > hide #17 models > hide #20 models > hide #14 models Drag select of 124 residues Drag select of 167 residues Drag select of 184 residues > select up 2061 atoms, 2106 bonds, 273 residues, 1 model selected > select up 3237 atoms, 3321 bonds, 424 residues, 1 model selected Drag select of 269 residues Drag select of 138 residues > select up 7055 atoms, 7219 bonds, 934 residues, 1 model selected > select up 9711 atoms, 9963 bonds, 1272 residues, 1 model selected > select up 20544 atoms, 20995 bonds, 2658 residues, 1 model selected > select down 9711 atoms, 9963 bonds, 1272 residues, 1 model selected > select up 20544 atoms, 20995 bonds, 2658 residues, 1 model selected > select down 9711 atoms, 9963 bonds, 1272 residues, 1 model selected > ui tool show ""Color Actions"" > color sel #9193cfff > select clear Drag select of 145 residues > select add #13/R:108 1118 atoms, 10 bonds, 146 residues, 1 model selected > select add #13/D:113 1124 atoms, 15 bonds, 147 residues, 1 model selected > select add #13/R:109 1131 atoms, 21 bonds, 148 residues, 1 model selected Drag select of 40 residues > delete atoms sel > delete bonds sel > select #13/D:59 12 atoms, 12 bonds, 1 residue, 1 model selected > select up 31 atoms, 32 bonds, 3 residues, 1 model selected > select up 120 atoms, 126 bonds, 13 residues, 1 model selected > select up 129 atoms, 134 bonds, 14 residues, 1 model selected > select add #13/D:35 135 atoms, 139 bonds, 15 residues, 1 model selected > select add #13/D:95 143 atoms, 146 bonds, 16 residues, 1 model selected > select add #13/R:54 151 atoms, 153 bonds, 17 residues, 1 model selected > select up 182 atoms, 184 bonds, 21 residues, 1 model selected > select up 233 atoms, 236 bonds, 29 residues, 1 model selected > select add #13/D:72 241 atoms, 243 bonds, 30 residues, 1 model selected > select up 264 atoms, 266 bonds, 33 residues, 1 model selected > select up 294 atoms, 296 bonds, 37 residues, 1 model selected > select up 1795 atoms, 1831 bonds, 236 residues, 1 model selected > select down 294 atoms, 296 bonds, 37 residues, 1 model selected > delete atoms sel > delete bonds sel Drag select of 179 residues > select up 1653 atoms, 1691 bonds, 218 residues, 1 model selected > select add #13/G:58 1663 atoms, 1701 bonds, 219 residues, 1 model selected > select up 1684 atoms, 1724 bonds, 221 residues, 1 model selected > select up 2653 atoms, 2722 bonds, 345 residues, 1 model selected > select down 1684 atoms, 1724 bonds, 221 residues, 1 model selected Drag select of 19 residues Drag select of 36 residues > select subtract #13/G:141 1805 atoms, 1724 bonds, 237 residues, 1 model selected > select subtract #13/G:121 1798 atoms, 1724 bonds, 236 residues, 1 model selected > select subtract #13/G:208 1790 atoms, 1724 bonds, 235 residues, 1 model selected > select subtract #13/G:196 1784 atoms, 1724 bonds, 234 residues, 1 model selected > select subtract #13/G:155 1776 atoms, 1724 bonds, 233 residues, 1 model selected > select add #13/G:141 1784 atoms, 1731 bonds, 234 residues, 1 model selected > select subtract #13/G:142 1777 atoms, 1731 bonds, 233 residues, 1 model selected > select subtract #13/G:141 1769 atoms, 1724 bonds, 232 residues, 1 model selected > select subtract #13/G:143 1760 atoms, 1724 bonds, 231 residues, 1 model selected > select subtract #13/G:152 1753 atoms, 1724 bonds, 230 residues, 1 model selected > select subtract #13/G:150 1746 atoms, 1724 bonds, 229 residues, 1 model selected > select clear Drag select of 170 residues > delete atoms sel > delete bonds sel Drag select of 17 residues > delete atoms sel > delete bonds sel > select #13/G:58 10 atoms, 10 bonds, 1 residue, 1 model selected > select add #13/E:1 18 atoms, 17 bonds, 2 residues, 1 model selected > select add #13/E:94 30 atoms, 29 bonds, 3 residues, 1 model selected > select add #13/E:29 41 atoms, 39 bonds, 4 residues, 1 model selected > select add #13/G:64 50 atoms, 47 bonds, 5 residues, 1 model selected > select up 193 atoms, 192 bonds, 26 residues, 1 model selected > select up 1079 atoms, 1100 bonds, 138 residues, 1 model selected > select down 193 atoms, 192 bonds, 26 residues, 1 model selected > select down 50 atoms, 47 bonds, 5 residues, 1 model selected > select add #13/G:51 58 atoms, 54 bonds, 6 residues, 1 model selected > select add #13/G:69 66 atoms, 61 bonds, 7 residues, 1 model selected > select up 244 atoms, 243 bonds, 32 residues, 1 model selected > select down 66 atoms, 61 bonds, 7 residues, 1 model selected > delete atoms sel > delete bonds sel Drag select of 7 residues > select add #13/G:60 63 atoms, 7 bonds, 8 residues, 1 model selected > select add #13/E:26 69 atoms, 12 bonds, 9 residues, 1 model selected > select add #13/E:27 75 atoms, 17 bonds, 10 residues, 1 model selected > select add #13/G:59 87 atoms, 29 bonds, 11 residues, 1 model selected > select add #13/G:57 96 atoms, 37 bonds, 12 residues, 1 model selected > select add #13/G:53 110 atoms, 52 bonds, 13 residues, 1 model selected > select add #13/G:31 117 atoms, 58 bonds, 14 residues, 1 model selected > select up 252 atoms, 246 bonds, 35 residues, 1 model selected > select down 117 atoms, 58 bonds, 14 residues, 1 model selected > select add #13/G:52 131 atoms, 73 bonds, 15 residues, 1 model selected > select add #13/G:55 139 atoms, 80 bonds, 16 residues, 1 model selected > select add #13/G:56 148 atoms, 88 bonds, 17 residues, 1 model selected > select add #13/G:97 156 atoms, 95 bonds, 18 residues, 1 model selected > select add #13/G:32 161 atoms, 99 bonds, 19 residues, 1 model selected > select add #13/G:33 165 atoms, 102 bonds, 20 residues, 1 model selected > select add #13/G:54 173 atoms, 109 bonds, 21 residues, 1 model selected > select add #13/G:30 179 atoms, 114 bonds, 22 residues, 1 model selected > delete atoms sel > delete bonds sel > select #13/E:31 4 atoms, 3 bonds, 1 residue, 1 model selected > select add #13/E:30 11 atoms, 9 bonds, 2 residues, 1 model selected > select add #13/E:69 18 atoms, 15 bonds, 3 residues, 1 model selected > select add #13/E:68 22 atoms, 18 bonds, 4 residues, 1 model selected > select add #13/G:99 30 atoms, 25 bonds, 5 residues, 1 model selected > select add #13/G:98 41 atoms, 36 bonds, 6 residues, 1 model selected > delete atoms sel > delete bonds sel > select clear > select #13/E:93 4 atoms, 3 bonds, 1 residue, 1 model selected > select #13/E:92 6 atoms, 5 bonds, 1 residue, 1 model selected > select add #13/E:93 10 atoms, 8 bonds, 2 residues, 1 model selected > delete atoms sel > delete bonds sel Drag select of 111 residues > select clear Drag select of 143 residues > select clear Drag select of 163 residues > select clear Drag select of 200 residues > select up 1698 atoms, 1737 bonds, 221 residues, 1 model selected > select down 1542 atoms, 200 residues, 1 model selected > select add #13/L:67 1548 atoms, 5 bonds, 201 residues, 1 model selected > select add #13/L:69 1555 atoms, 11 bonds, 202 residues, 1 model selected > select add #13/L:68 1559 atoms, 14 bonds, 203 residues, 1 model selected > select add #13/L:32 1571 atoms, 26 bonds, 204 residues, 1 model selected > select add #13/L:31 1575 atoms, 29 bonds, 205 residues, 1 model selected > select add #13/M:98 1586 atoms, 40 bonds, 206 residues, 1 model selected > select add #13/L:92 1592 atoms, 45 bonds, 207 residues, 1 model selected > select add #13/L:27 1598 atoms, 50 bonds, 208 residues, 1 model selected > select add #13/L:29 1609 atoms, 60 bonds, 209 residues, 1 model selected > select add #13/L:30 1616 atoms, 66 bonds, 210 residues, 1 model selected > select add #13/M:99 1624 atoms, 73 bonds, 211 residues, 1 model selected > select add #13/M:97 1632 atoms, 80 bonds, 212 residues, 1 model selected > select add #13/L:93 1636 atoms, 83 bonds, 213 residues, 1 model selected > select add #13/L:94 1648 atoms, 95 bonds, 214 residues, 1 model selected > select add #13/L:1 1656 atoms, 102 bonds, 215 residues, 1 model selected > select add #13/L:2 1664 atoms, 109 bonds, 216 residues, 1 model selected > select add #13/M:53 1678 atoms, 124 bonds, 217 residues, 1 model selected > select add #13/M:54 1686 atoms, 131 bonds, 218 residues, 1 model selected > select add #13/M:55 1694 atoms, 138 bonds, 219 residues, 1 model selected > select add #13/M:57 1703 atoms, 146 bonds, 220 residues, 1 model selected > select add #13/M:56 1712 atoms, 154 bonds, 221 residues, 1 model selected > select add #13/M:52 1726 atoms, 169 bonds, 222 residues, 1 model selected > select add #13/M:32 1731 atoms, 173 bonds, 223 residues, 1 model selected > select add #13/M:33 1735 atoms, 176 bonds, 224 residues, 1 model selected > select add #13/M:31 1742 atoms, 182 bonds, 225 residues, 1 model selected > delete atoms sel > delete bonds sel > show #14 models > show #17 models > show #20 models > color #14 #8671ffff > color #17 #8671ffff > color #20 #8671ffff > show #!15 models > select add #14 3303 atoms, 3347 bonds, 222 residues, 1 model selected > select add #17 6606 atoms, 6694 bonds, 444 residues, 2 models selected > select add #20 9909 atoms, 10041 bonds, 666 residues, 3 models selected > hide #!13 models > show #!13 models > fitmap #14 inMap #15 Fit molecule ranked_0.pdb (#14) to map cryosparc_P141_J36_001_volume_map_102.mrc (#15) using 3303 atoms average map value = 2.79, steps = 224 shifted from previous position = 52.8 rotated from previous position = 56.5 degrees atoms outside contour = 0, contour level = 1.0438 Position of ranked_0.pdb (#14) relative to cryosparc_P141_J36_001_volume_map_102.mrc (#15) coordinates: Matrix rotation and translation -0.62734549 0.77176533 -0.10399957 217.72604797 0.69329175 0.49268381 -0.52593651 226.86042132 -0.35466065 -0.40204594 -0.84414151 228.48561977 Axis 0.42660575 0.86312836 -0.27021653 Axis point 65.05331663 0.00000000 144.64183947 Rotation angle (degrees) 171.65085044 Shift along axis 226.95225413 > undo > color #20 #8671ffff > select add #14 3303 atoms, 3347 bonds, 222 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models > #14,-0.62735,0.77177,-0.104,177.43,0.69329,0.49268,-0.52594,222.68,-0.35466,-0.40205,-0.84414,254.73 > view matrix models > #14,-0.62735,0.77177,-0.104,181.89,0.69329,0.49268,-0.52594,226.92,-0.35466,-0.40205,-0.84414,256.74 > ui mousemode right ""rotate selected models"" > view matrix models > #14,-0.71871,0.19046,0.66872,185.79,0.59691,0.66225,0.45292,228.69,-0.3566,0.72468,-0.58965,253.42 > view matrix models > #14,-0.44435,-0.76836,0.46062,188.81,0.14195,-0.56806,-0.81065,229.59,0.88453,-0.29483,0.36149,260.14 > view matrix models > #14,-0.55212,-0.79977,0.23565,188.29,0.05904,-0.31943,-0.94577,228.33,0.83167,-0.50827,0.22358,260.52 > show #!15 models > view matrix models > #14,-0.55504,-0.7989,0.23173,188.28,0.058002,-0.31507,-0.9473,228.31,0.8298,-0.51234,0.22121,260.52 > ui mousemode right ""translate selected models"" > view matrix models > #14,-0.55504,-0.7989,0.23173,179.05,0.058002,-0.31507,-0.9473,218.94,0.8298,-0.51234,0.22121,256.5 > view matrix models > #14,-0.55504,-0.7989,0.23173,178.89,0.058002,-0.31507,-0.9473,220.15,0.8298,-0.51234,0.22121,260.29 > ui mousemode right ""rotate selected models"" > view matrix models > #14,-0.63621,-0.77016,0.045735,178.28,0.60285,-0.53324,-0.59349,222.14,0.48147,-0.35001,0.80354,260.94 > view matrix models > #14,-0.52502,-0.69318,-0.49381,176.74,0.56671,0.14815,-0.81049,219.19,0.63498,-0.70537,0.31505,261.07 > hide #!15 models > show #!15 models > view matrix models > #14,-0.46607,-0.69123,-0.55224,176.63,-0.18176,0.68567,-0.70485,217.09,0.86588,-0.22813,-0.44521,257.66 > hide #!15 models > view matrix models > #14,0.63032,-0.46315,-0.62306,176.35,0.43449,-0.45465,0.77751,225.15,-0.64337,-0.76078,-0.08534,259.46 > view matrix models > #14,-0.82198,-0.12488,0.55566,177.16,0.29305,-0.92934,0.22463,225.36,0.48834,0.34748,0.80049,258.49 > delete atoms sel > delete bonds sel > hide #17 models > show #17 models > hide #20 models > show #20 models > combine #13,17,20 Remapping chain ID 'A' in ranked_0.pdb #17 to 'S' Remapping chain ID 'B' in ranked_0.pdb #17 to 'T' Remapping chain ID 'A' in ranked_0.pdb #20 to 'U' Remapping chain ID 'B' in ranked_0.pdb #20 to 'V' > hide #!13 models > hide #17 models > hide #20 models > rename #14 RSVA-trimer_102Fab > show #!15 models > hide #!15 models > show #!15 models > save ""/Users/szhang3/OneDrive - Moderna/RSV/MAbs/102/RSVA-trimer_102Fab.pdb"" > models #14 relModel #15 > open /Users/szhang3/Library/CloudStorage/OneDrive-Moderna/RSV/MAbs/102/RSVA- > trimer_102Fab.pdb Chain information for RSVA-trimer_102Fab.pdb #21 --- Chain | Description A B C | No description available D G M | No description available E L R | No description available S U | No description available T V | No description available > hide #!15 models > hide #!14 models > select #21/K:601@CL 1 atom, 1 residue, 1 model selected > select add #21/P:601@CL 2 atoms, 2 residues, 1 model selected > select add #21/Q:601@CL 3 atoms, 3 residues, 1 model selected Drag select of 105 atoms > select up 130 atoms, 137 bonds, 14 residues, 1 model selected Drag select of 19 atoms > select up 180 atoms, 189 bonds, 18 residues, 1 model selected > select up 257 atoms, 274 bonds, 25 residues, 1 model selected Drag select of 2 atoms > select up 275 atoms, 291 bonds, 27 residues, 1 model selected > select up 299 atoms, 315 bonds, 31 residues, 1 model selected > select down 275 atoms, 291 bonds, 27 residues, 1 model selected > select add #21/D:100B@CD1 276 atoms, 291 bonds, 28 residues, 1 model selected > select up 286 atoms, 302 bonds, 28 residues, 1 model selected > select up 310 atoms, 326 bonds, 32 residues, 1 model selected > select down 286 atoms, 302 bonds, 28 residues, 1 model selected > delete atoms sel > delete bonds sel Drag select of 47 atoms > select up 69 atoms, 73 bonds, 6 residues, 1 model selected > select up 127 atoms, 137 bonds, 11 residues, 1 model selected > delete atoms sel > delete bonds sel > select #21/H:612@CL 1 atom, 1 residue, 1 model selected > select up 21528 atoms, 21889 bonds, 2389 residues, 1 model selected > select down 1 atom, 1 residue, 1 model selected > view matrix models > #21,0.98978,0.13978,0.028083,-32.582,-0.14096,0.98897,0.04541,23.889,-0.021426,-0.048905,0.99857,15.159 > delete atoms sel > delete bonds sel > select clear > hide #!21 atoms > show #!21 cartoons > show #!14 models > hide #!14 models > show #!14 models > select add #21 21527 atoms, 21889 bonds, 12 pseudobonds, 2388 residues, 2 models selected > view matrix models > #21,-0.3201,0.25008,0.91378,44.277,0.46934,0.87971,-0.076349,-63.042,-0.82296,0.40444,-0.39897,403.01 > ui mousemode right ""translate selected models"" > view matrix models > #21,-0.3201,0.25008,0.91378,21.326,0.46934,0.87971,-0.076349,-54.994,-0.82296,0.40444,-0.39897,406.61 > view matrix models > #21,-0.3201,0.25008,0.91378,23.366,0.46934,0.87971,-0.076349,-55.404,-0.82296,0.40444,-0.39897,404.25 > ui mousemode right ""rotate selected models"" > view matrix models > #21,-0.4491,0.29211,0.84439,58.458,0.50475,0.86274,-0.029997,-69.835,-0.73725,0.41274,-0.5349,412.93 > ui mousemode right ""translate selected models"" > view matrix models > #21,-0.4491,0.29211,0.84439,58,0.50475,0.86274,-0.029997,-69.2,-0.73725,0.41274,-0.5349,409.84 > ui tool show Matchmaker > matchmaker #!21 & sel to #14 & sel No 'to' model specified > select clear Drag select of 65 residues > select up 1104 atoms, 1104 bonds, 138 residues, 2 models selected > select up 20870 atoms, 21218 bonds, 2692 residues, 2 models selected > matchmaker #!21 & sel to #14 & sel Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 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 RSVA-trimer_102Fab, chain A (#14) with RSVA-trimer_102Fab.pdb, chain A (#21), sequence alignment score = 2486.8 RMSD between 448 pruned atom pairs is 0.000 angstroms; (across all 448 pairs: 0.000) > select clear > select add #21 21527 atoms, 21889 bonds, 12 pseudobonds, 2388 residues, 2 models selected > view matrix models > #21,1,1.8341e-07,-9.4532e-07,-2.8853,-1.8368e-07,1,2.7799e-07,0.66478,9.4473e-07,-2.7833e-07,1,0.7915 > ui mousemode right ""rotate selected models"" > view matrix models > #21,0.13032,0.21959,0.96685,-64.28,0.59565,0.76223,-0.2534,-27.871,-0.7926,0.60892,-0.03147,275.08 > view matrix models > #21,0.10785,0.24986,0.96226,-64.54,0.53875,0.79877,-0.26779,-19.636,-0.83553,0.5473,-0.048461,301.08 > view matrix models > #21,-0.095715,0.37139,0.92353,-35.936,0.63736,0.73553,-0.22973,-36.773,-0.7646,0.56663,-0.30711,337.37 > ui mousemode right ""translate selected models"" > view matrix models > #21,-0.095715,0.37139,0.92353,-46.259,0.63736,0.73553,-0.22973,-29.312,-0.7646,0.56663,-0.30711,343.36 > select clear > select #14/C:510 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #21/B:507 19 atoms, 17 bonds, 2 residues, 2 models selected > select up 352 atoms, 352 bonds, 44 residues, 2 models selected > select up 6964 atoms, 7081 bonds, 898 residues, 2 models selected > matchmaker #!21 & sel to #14 & sel Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 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 RSVA-trimer_102Fab, chain C (#14) with RSVA-trimer_102Fab.pdb, chain B (#21), sequence alignment score = 2483.2 RMSD between 438 pruned atom pairs is 0.403 angstroms; (across all 449 pairs: 0.722) > select clear > select #21/U:4 19 atoms, 18 bonds, 1 residue, 1 model selected > select add #21/V:45 29 atoms, 27 bonds, 2 residues, 1 model selected > select up 130 atoms, 128 bonds, 8 residues, 1 model selected > select up 3303 atoms, 3347 bonds, 222 residues, 1 model selected > select ~sel & ##selected 18224 atoms, 18542 bonds, 12 pseudobonds, 2166 residues, 2 models selected > delete atoms (#!21 & sel) > delete bonds (#!21 & sel) > select clear > select ~sel & ##selected Nothing selected > combine #14,21 Remapping chain ID 'U' in RSVA-trimer_102Fab.pdb #21 to 'W' Remapping chain ID 'V' in RSVA-trimer_102Fab.pdb #21 to 'X' > hide #!21 models > hide #!14 models > close #21 > show #!13 models > hide #!13 models > close #13 > save ""/Users/szhang3/OneDrive - Moderna/RSV/MAbs/102/RSVA-trimer_102Fab.pdb"" > models #22 relModel #15 > open /Users/szhang3/Library/CloudStorage/OneDrive-Moderna/RSV/MAbs/102/RSVA- > trimer_102Fab.pdb Chain information for RSVA-trimer_102Fab.pdb #13 --- Chain | Description A B C | No description available D G M | No description available E L R | No description available S U W | No description available T V X | No description available > hide #!13,22 atoms > show #!13,22 cartoons > show #!13,22 atoms > close #22 Drag select of 76 atoms > select up 99 atoms, 107 bonds, 9 residues, 1 model selected > select up 127 atoms, 137 bonds, 11 residues, 1 model selected > select add #13/Q:601@CL 128 atoms, 137 bonds, 12 residues, 1 model selected > select add #13/P:601@CL 129 atoms, 137 bonds, 13 residues, 1 model selected > select add #13/K:601@CL 130 atoms, 137 bonds, 14 residues, 1 model selected > select add #13/O:4@C4 131 atoms, 137 bonds, 15 residues, 1 model selected > select up 141 atoms, 148 bonds, 15 residues, 1 model selected > select up 257 atoms, 274 bonds, 25 residues, 1 model selected > select add #13/I:3@O2 258 atoms, 274 bonds, 26 residues, 1 model selected > select up 268 atoms, 285 bonds, 26 residues, 1 model selected > select up 384 atoms, 411 bonds, 36 residues, 1 model selected > delete atoms sel > delete bonds sel > save ""/Users/szhang3/OneDrive - Moderna/RSV/MAbs/102/RSVA-trimer_102Fab.pdb"" > models #13 relModel #15 > open /Users/szhang3/Library/CloudStorage/OneDrive-Moderna/RSV/MAbs/102/RSVA- > trimer_102Fab.pdb Chain information for RSVA-trimer_102Fab.pdb #21 --- Chain | Description A B C | No description available D G M | No description available E L R | No description available S U W | No description available T V X | No description available > close #21 > hide #!13 atoms > show #!13 cartoons > hide #13.1 models Drag select of 118 residues > select up 1797 atoms, 1808 bonds, 223 residues, 1 model selected > select up 10435 atoms, 10609 bonds, 1346 residues, 1 model selected > color sel gray > color sel light gray > select clear > select #13/T:18 10 atoms, 9 bonds, 1 residue, 1 model selected Drag select of 54 residues Drag select of 76 residues Drag select of 91 residues > select up 3398 atoms, 3409 bonds, 221 residues, 1 model selected > select up 5862 atoms, 5928 bonds, 390 residues, 1 model selected > select up 9909 atoms, 10041 bonds, 666 residues, 1 model selected > select up 24860 atoms, 25264 bonds, 2614 residues, 1 model selected > select down 9909 atoms, 10041 bonds, 666 residues, 1 model selected > ui tool show ""Color Actions"" > color sel #a392b7ff > color sel #8671ffff > select clear Drag select of 43 residues Drag select of 160 residues Drag select of 52 residues > select up 2665 atoms, 2705 bonds, 357 residues, 1 model selected > select up 4460 atoms, 4563 bonds, 593 residues, 1 model selected > ui tool show ""Color Actions"" > color sel #9193cfff > select clear > show #!15 models > volume #15 level 1.199 > hide #!15 models > transparency 50 > show #!15 models Cell requested for row 14 is out of bounds for table with 21 rows! Resizing table model. > set bgColor white > lighting simple > lighting soft > color #15 #ead0e680 models > select clear > hide #!15 models > show #!15 models > volume #15 level 1.035 > hide #!15 models Drag select of 55 residues > select #13/A:45 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #13/A:52 22 atoms, 22 bonds, 2 residues, 1 model selected > select add #13/B:152 29 atoms, 28 bonds, 3 residues, 1 model selected > view sel > view matrix models #13,1,0,0,-3.4945,0,1,0,-7.729,0,0,1,-1.8359 > view matrix models #13,1,0,0,-10.809,0,1,0,-24.954,0,0,1,-5.549 > ui mousemode right zoom > undo > select add #13/B:153 27 atoms, 26 bonds, 3 residues, 1 model selected > view sel > ui tool show ""Side View"" > select clear > select #13/A:44 12 atoms, 12 bonds, 1 residue, 1 model selected > select up 76 atoms, 76 bonds, 11 residues, 1 model selected > select up 3471 atoms, 3528 bonds, 448 residues, 1 model selected > color sel gray > select clear > show #!15 models > rock axis y > movie record > movie encode /Users/szhang3/Desktop/movie7.mp4 Movie saved to /Users/szhang3/Desktop/movie7.mp4 > stop > hide #!15 models > show #!5 models > show #!15 models > hide #!15 models > hide #!5 models > show #!1 models > select #13/A:205 7 atoms, 7 bonds, 1 residue, 1 model selected > select up 47 atoms, 47 bonds, 6 residues, 1 model selected > select up 3471 atoms, 3528 bonds, 448 residues, 1 model selected > color sel light gray > select #13/B:178 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 34 atoms, 33 bonds, 5 residues, 1 model selected > select up 3482 atoms, 3540 bonds, 449 residues, 1 model selected > color sel gray > select clear Drag select of 81 residues > select up 1225 atoms, 1241 bonds, 146 residues, 1 model selected > select up 3052 atoms, 3106 bonds, 306 residues, 1 model selected > select add #13/U:6 3069 atoms, 3122 bonds, 307 residues, 1 model selected > select add #13/U:29 3089 atoms, 3142 bonds, 308 residues, 1 model selected > select up 3172 atoms, 3225 bonds, 313 residues, 1 model selected > select up 4803 atoms, 4881 bonds, 421 residues, 1 model selected > hide sel target a > hide sel cartoons > select up 4809 atoms, 4886 bonds, 422 residues, 1 model selected > select up 24860 atoms, 25264 bonds, 2614 residues, 1 model selected > select up 99284 atoms, 101033 bonds, 11001 residues, 32 models selected > select up 99284 atoms, 101033 bonds, 11001 residues, 32 models selected > rock axis y > select clear > movie record > movie encode /Users/szhang3/Desktop/movie8.mp4 Movie saved to /Users/szhang3/Desktop/movie8.mp4 > stop ===== 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 Max 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: Mac14,5 Model Number: MPHG3LL/A Chip: Apple M2 Max Total Number of Cores: 12 (8 performance and 4 efficiency) Memory: 32 GB System Firmware Version: 11881.121.1 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: 8 days, 1 hour, 38 minutes Graphics/Displays: Apple M2 Max: Chipset Model: Apple M2 Max Type: GPU Bus: Built-In Total Number of Cores: 30 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: LS34A650U: Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD) UI Looks like: 3440 x 1440 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal 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 autocommand: 2.2.2 babel: 2.16.0 backports.tarfile: 1.2.0 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-Clipper: 0.24.0 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-ISOLDE: 1.9 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 importlib_metadata: 8.0.0 importlib_resources: 6.4.0 inflect: 7.3.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jaraco.context: 5.3.0 jaraco.functools: 4.0.1 jaraco.text: 3.12.1 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: 3.10.1 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 more-itertools: 10.3.0 msgpack: 1.0.8 narwhals: 1.31.0 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: 2.2.4 numpy: 1.26.4 openvr: 1.26.701 ordered-set: 4.1.0 packaging: 23.2 packaging: 24.1 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 platformdirs: 4.2.2 plotly: 6.0.1 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 pyKVFinder: 0.7.3 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 toml: 0.10.2 tomli: 2.0.1 tornado: 6.4.2 traitlets: 5.14.3 typeguard: 4.3.0 typing_extensions: 4.12.2 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: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 zipp: 3.19.2 }}} " defect closed normal Window Toolkit duplicate all ChimeraX