Changes between Initial Version and Version 1 of Ticket #18023


Ignore:
Timestamp:
Jun 18, 2025, 11:55:14 AM (6 months ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #18023

    • Property Component Unassigned → Window Toolkit
    • Property Owner set to Tom Goddard
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → Crash on Mac waking from sleep

  • Ticket #18023 – Description

    initial v1  
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    1622     "name" : "_frame.cpython-311-darwin.so"
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    1631     "name" : "_serialize.cpython-311-darwin.so"
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    1639     "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/msgpack\/_cmsgpack.cpython-311-darwin.so",
    1640     "name" : "_cmsgpack.cpython-311-darwin.so"
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    1649     "name" : "QtOpenGL.abi3.so"
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    1658     "name" : "QtOpenGLWidgets.abi3.so"
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    1667     "name" : "QtOpenGLWidgets"
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    1669   {
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    1675     "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic\/_ribbons.cpython-311-darwin.so",
    1676     "name" : "_ribbons.cpython-311-darwin.so"
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    1678   {
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    1684     "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/graphics\/_graphics.cpython-311-darwin.so",
    1685     "name" : "_graphics.cpython-311-darwin.so"
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    1687   {
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    1703     "name" : "_mmcif.cpython-311-darwin.so"
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    1705   {
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    1759   {
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    1775     "name" : "libalign_algs.dylib"
    1776   },
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    1783     "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/dssp\/_dssp.cpython-311-darwin.so",
    1784     "name" : "_dssp.cpython-311-darwin.so"
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     70[deleted to fit within ticket limits]
     71
    192272],
    192373  "sharedCache" : {
    … …  
    33211471> undo
    33221472
    3323 > fitmap #14 inMap #8
    3324 
    3325 Fit molecule 4zyp_Mota_AM14.pdb (#14) to map preF_DS-
    3326 Cav1_20A_7mpg_Box208_0-045.mrc (#8) using 29990 atoms 
    3327 average map value = 0.08896, steps = 100 
    3328 shifted from previous position = 20.1 
    3329 rotated from previous position = 10 degrees 
    3330 atoms outside contour = 20375, contour level = 0.15 
    3331  
    3332 Position of 4zyp_Mota_AM14.pdb (#14) relative to preF_DS-
    3333 Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates: 
    3334 Matrix rotation and translation 
    3335 -0.17692084 -0.98261169 0.05633196 201.63862391 
    3336 -0.69014872 0.08304951 -0.71888631 243.27619117 
    3337 0.70170775 -0.16606341 -0.69284138 205.86393215 
    3338 Axis 0.61513774 -0.71812328 0.32542973 
    3339 Axis point 171.87387039 0.00000000 189.71400218 
    3340 Rotation angle (degrees) 153.29808359 
    3341 Shift along axis 16.32747378 
    3342  
    3343 
    3344 > select subtract #14
    3345 
    3346 6848 atoms, 6991 bonds, 2 pseudobonds, 890 residues, 6 models selected 
    3347 
    3348 > view matrix models
    3349 > #12,0.50691,0.81558,-0.27904,12.765,-0.41972,0.51628,0.74651,11.36,0.75291,-0.2613,0.60403,18.138,#13,0.30281,0.76015,0.57488,-137.67,0.16439,0.5525,-0.81714,209.96,-0.93877,0.34194,0.042342,336.86,#7,-0.18677,-0.89987,-0.39415,215.62,0.55865,0.23274,-0.79608,142.71,0.8081,-0.36888,0.45924,282.74
    3350 
    3351 > view matrix models
    3352 > #12,0.50691,0.81558,-0.27904,20.376,-0.41972,0.51628,0.74651,11.812,0.75291,-0.2613,0.60403,7.1867,#13,0.30281,0.76015,0.57488,-130.06,0.16439,0.5525,-0.81714,210.41,-0.93877,0.34194,0.042342,325.91,#7,-0.18677,-0.89987,-0.39415,223.23,0.55865,0.23274,-0.79608,143.16,0.8081,-0.36888,0.45924,271.79
    3353 
    3354 > fitmap #7 inMap #8
    3355 
    3356 Fit molecule 5udc.pdb (#7) to map preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc (#8)
    3357 using 6848 atoms 
    3358 average map value = 0.173, steps = 284 
    3359 shifted from previous position = 59.9 
    3360 rotated from previous position = 29.3 degrees 
    3361 atoms outside contour = 2636, contour level = 0.15 
    3362  
    3363 Position of 5udc.pdb (#7) relative to preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc
    3364 (#8) coordinates: 
    3365 Matrix rotation and translation 
    3366 0.04241308 -0.84625872 -0.53108127 198.12554067 
    3367 0.86642041 0.29584870 -0.40223031 225.15960097 
    3368 0.49751061 -0.44307982 0.74576368 288.72808585 
    3369 Axis -0.02044280 -0.51475043 0.85709631 
    3370 Axis point -74.41913812 321.40895395 0.00000000 
    3371 Rotation angle (degrees) 87.59213926 
    3372 Shift along axis 127.51653607 
    3373  
    3374 
    3375 > view matrix models
    3376 > #12,0.50691,0.81558,-0.27904,25.841,-0.41972,0.51628,0.74651,-41.303,0.75291,-0.2613,0.60403,13.675,#13,0.30281,0.76015,0.57488,-124.6,0.16439,0.5525,-0.81714,157.3,-0.93877,0.34194,0.042342,332.4,#7,0.042413,-0.84626,-0.53108,203.59,0.86642,0.29585,-0.40223,172.04,0.49751,-0.44308,0.74576,295.22
    3377 
    3378 > ui mousemode right "rotate selected models"
    3379 
    3380 > view matrix models
    3381 > #12,0.47771,0.64673,-0.59459,142.06,-0.32213,0.75862,0.56633,-64.377,0.81733,-0.079004,0.57073,-26.896,#13,0.3904,0.482,0.78439,-114.03,0.33881,0.71699,-0.60921,48.031,-0.85604,0.50359,0.11661,265.41,#7,-0.31314,-0.80892,-0.49759,194.68,0.78631,0.073003,-0.61351,163.3,0.5326,-0.58337,0.61319,292.12
    3382 
    3383 > ui mousemode right "translate selected models"
    3384 
    3385 > view matrix models
    3386 > #12,0.47771,0.64673,-0.59459,150.75,-0.32213,0.75862,0.56633,-63.598,0.81733,-0.079004,0.57073,-27.684,#13,0.3904,0.482,0.78439,-105.35,0.33881,0.71699,-0.60921,48.81,-0.85604,0.50359,0.11661,264.62,#7,-0.31314,-0.80892,-0.49759,203.37,0.78631,0.073003,-0.61351,164.08,0.5326,-0.58337,0.61319,291.33
    3387 
    3388 > ui mousemode right "rotate selected models"
    3389 
    3390 > view matrix models
    3391 > #12,0.41314,0.61482,-0.6718,186.89,-0.39034,0.78605,0.47933,-36.78,0.82277,0.064202,0.56473,-56.837,#13,0.453,0.39802,0.79773,-100.64,0.44309,0.67595,-0.58887,34.012,-0.7736,0.62022,0.12985,218.79,#7,-0.39869,-0.75282,-0.52374,198.4,0.71237,0.10545,-0.69384,157.05,0.57757,-0.64973,0.49424,287.66
    3392 
    3393 > fitmap #7 inMap #8
    3394 
    3395 Fit molecule 5udc.pdb (#7) to map preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc (#8)
    3396 using 6848 atoms 
    3397 average map value = 0.173, steps = 240 
    3398 shifted from previous position = 54.9 
    3399 rotated from previous position = 27.8 degrees 
    3400 atoms outside contour = 2637, contour level = 0.15 
    3401  
    3402 Position of 5udc.pdb (#7) relative to preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc
    3403 (#8) coordinates: 
    3404 Matrix rotation and translation 
    3405 0.04211163 -0.84599024 -0.53153282 198.08913708 
    3406 0.86645607 0.29581680 -0.40217695 225.16757438 
    3407 0.49747411 -0.44361351 0.74547070 288.72456108 
    3408 Axis -0.02073631 -0.51495137 0.85696855 
    3409 Axis point -74.33279639 321.43732765 0.00000000 
    3410 Rotation angle (degrees) 87.61009779 
    3411 Shift along axis 127.36987785 
    3412  
    3413 
    3414 > undo
    3415 
    3416 > select clear
    3417 
    3418 > hide #!8 models
    3419 
    3420 > show #!8 models
    3421 
    3422 > hide #!8 models
    3423 
    3424 > hide #!10 models
    3425 
    3426 > select #7/F:75
    3427 
    3428 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3429 
    3430 > select add #14/C:198
    3431 
    3432 21 atoms, 20 bonds, 2 residues, 2 models selected 
    3433 
    3434 > select up
    3435 
    3436 292 atoms, 292 bonds, 35 residues, 2 models selected 
    3437 
    3438 > select up
    3439 
    3440 6964 atoms, 7081 bonds, 898 residues, 2 models selected 
    3441 
    3442 > ui tool show Matchmaker
    3443 
    3444 > matchmaker #!7 & sel to #14 & sel
    3445 
    3446 Computing secondary structure 
    3447 [Repeated 1 time(s)]  Parameters 
    3448 --- 
    3449 Chain pairing | bb 
    3450 Alignment algorithm | Needleman-Wunsch 
    3451 Similarity matrix | BLOSUM-62 
    3452 SS fraction | 0.3 
    3453 Gap open (HH/SS/other) | 18/18/6 
    3454 Gap extend | 1 
    3455 SS matrix |  |  | H | S | O 
    3456 ---|---|---|--- 
    3457 H | 6 | -9 | -6 
    3458 S |  | 6 | -6 
    3459 O |  |  | 4 
    3460 Iteration cutoff | 2 
    3461  
    3462 Matchmaker 4zyp_Mota_AM14.pdb, chain C (#14) with 5udc.pdb, chain F (#7),
    3463 sequence alignment score = 2359 
    3464 RMSD between 436 pruned atom pairs is 0.589 angstroms; (across all 448 pairs:
    3465 1.048) 
    3466  
    3467 
    3468 > show #!8 models
    3469 
    3470 > hide #!2 models
    3471 
    3472 > show #!2 models
    3473 
    3474 Drag select of 172 residues, 1 pseudobonds 
    3475 
    3476 > select clear
    3477 
    3478 Drag select of 252 residues, 1 pseudobonds 
    3479 Drag select of 215 residues 
    3480 Drag select of 198 residues 
    3481 
    3482 > select up
    3483 
    3484 6378 atoms, 6495 bonds, 1 pseudobond, 848 residues, 2 models selected 
    3485 
    3486 > select up
    3487 
    3488 9793 atoms, 10037 bonds, 1 pseudobond, 1282 residues, 2 models selected 
    3489 
    3490 > select up
    3491 
    3492 29990 atoms, 30657 bonds, 9 pseudobonds, 3906 residues, 2 models selected 
    3493 
    3494 > select down
    3495 
    3496 9793 atoms, 10037 bonds, 1 pseudobond, 1282 residues, 2 models selected 
    3497 
    3498 > delete atoms (#!14 & sel)
    3499 
    3500 > delete bonds (#!14 & sel)
    3501 
    3502 Drag select of 77 residues 
    3503 
    3504 > select up
    3505 
    3506 926 atoms, 934 bonds, 125 residues, 1 model selected 
    3507 
    3508 > select up
    3509 
    3510 3237 atoms, 3321 bonds, 424 residues, 1 model selected 
    3511 
    3512 > select up
    3513 
    3514 20197 atoms, 20620 bonds, 2624 residues, 1 model selected 
    3515 
    3516 > select down
    3517 
    3518 3237 atoms, 3321 bonds, 424 residues, 1 model selected 
    3519 
    3520 > delete atoms sel
    3521 
    3522 > delete bonds sel
    3523 
    3524 > hide #!14 models
    3525 
    3526 > show #!14 models
    3527 
    3528 > hide #!8 models
    3529 
    3530 > hide #!2 models
    3531 
    3532 Drag select of 7 residues 
    3533 Drag select of 257 residues 
    3534 
    3535 > select up
    3536 
    3537 2341 atoms, 2396 bonds, 305 residues, 1 model selected 
    3538 
    3539 > select up
    3540 
    3541 3237 atoms, 3321 bonds, 424 residues, 1 model selected 
    3542 
    3543 > color sel yellow
    3544 
    3545 Drag select of 276 residues, 1 pseudobonds 
    3546 
    3547 > select up
    3548 
    3549 2310 atoms, 2356 bonds, 1 pseudobond, 305 residues, 2 models selected 
    3550 
    3551 > select up
    3552 
    3553 3237 atoms, 3313 bonds, 1 pseudobond, 428 residues, 2 models selected 
    3554 
    3555 > color (#!7 & sel) red
    3556 
    3557 Drag select of 137 residues 
    3558 
    3559 > select up
    3560 
    3561 1687 atoms, 1709 bonds, 226 residues, 1 model selected 
    3562 
    3563 > select up
    3564 
    3565 3277 atoms, 3357 bonds, 429 residues, 1 model selected 
    3566 
    3567 > color sel orange
    3568 
    3569 > select clear
    3570 
    3571 > show #!8 models
    3572 
    3573 > show #!13 models
    3574 
    3575 > hide #!13 models
    3576 
    3577 > show #!12 models
    3578 
    3579 > volume #12 level 1.39
    3580 
    3581 > select add #12
    3582 
    3583 2 models selected 
    3584 
    3585 > view matrix models
    3586 > #12,0.48571,0.75293,-0.44405,97.149,-0.36186,0.63562,0.68194,-50.875,0.7957,-0.17054,0.58118,-5.3488
    3587 
    3588 > ui mousemode right "translate selected models"
    3589 
    3590 > view matrix models
    3591 > #12,0.48571,0.75293,-0.44405,-81.762,-0.36186,0.63562,0.68194,1.008,0.7957,-0.17054,0.58118,-25.456
    3592 
    3593 > hide #!12 models
    3594 
    3595 > select subtract #12
    3596 
    3597 Nothing selected 
    3598 
    3599 > select add #13
    3600 
    3601 2 models selected 
    3602 
    3603 > show #!13 models
    3604 
    3605 > view matrix models
    3606 > #13,0.3904,0.482,0.78439,-223.13,0.33881,0.71699,-0.60921,114.17,-0.85604,0.50359,0.11661,225.52
    3607 
    3608 > volume #13 level 1.469
    3609 
    3610 > ui mousemode right "rotate selected models"
    3611 
    3612 > view matrix models
    3613 > #13,0.65346,0.09534,0.75093,-186,0.11602,0.9677,-0.22383,20.088,-0.74802,0.23339,0.62129,149.82
    3614 
    3615 > view matrix models
    3616 > #13,0.88612,-0.40747,0.22084,-7.0707,-0.10495,-0.64052,-0.76074,534.11,0.45143,0.65092,-0.61034,85.324
    3617 
    3618 > view matrix models
    3619 > #13,0.72742,-0.62402,-0.28542,185.12,-0.61847,-0.7764,0.12122,473.65,-0.29724,0.088351,-0.95071,437.48
    3620 
    3621 > view matrix models
    3622 > #13,0.53954,-0.8382,-0.079465,224.63,-0.84196,-0.53749,-0.047096,505.24,-0.0032355,0.092316,-0.99572,385.98
    3623 
    3624 > view matrix models
    3625 > #13,0.62703,-0.76632,-0.13998,204.42,-0.76603,-0.6392,0.067919,486.13,-0.14152,0.064639,-0.98782,418.75
    3626 
    3627 > view matrix models
    3628 > #13,0.88145,0.46504,0.082382,-164.81,-0.26402,0.62983,-0.73048,284.36,-0.39159,0.62213,0.67794,-20.681
    3629 
    3630 > view matrix models
    3631 > #13,0.88329,0.34827,0.31386,-191.25,0.049695,0.59614,-0.80134,242.71,-0.46619,0.72341,0.50925,10.179
    3632 
    3633 > ui mousemode right "translate selected models"
    3634 
    3635 > view matrix models
    3636 > #13,0.88329,0.34827,0.31386,-106.61,0.049695,0.59614,-0.80134,222.09,-0.46619,0.72341,0.50925,62.54
    3637 
    3638 > view matrix models
    3639 > #13,0.88329,0.34827,0.31386,-109.94,0.049695,0.59614,-0.80134,225.85,-0.46619,0.72341,0.50925,62.945
    3640 
    3641 > ui mousemode right "rotate selected models"
    3642 
    3643 > view matrix models
    3644 > #13,0.91159,0.36755,0.18416,-91.158,0.089086,0.2607,-0.9613,326.09,-0.40133,0.89272,0.20491,80.4
    3645 
    3646 > ui mousemode right "translate selected models"
    3647 
    3648 > view matrix models
    3649 > #13,0.91159,0.36755,0.18416,-83.932,0.089086,0.2607,-0.9613,327,-0.40133,0.89272,0.20491,77.579
    3650 
    3651 > view matrix models
    3652 > #13,0.91159,0.36755,0.18416,-84.949,0.089086,0.2607,-0.9613,324.38,-0.40133,0.89272,0.20491,83.436
    3653 
    3654 > ui mousemode right "rotate selected models"
    3655 
    3656 > view matrix models
    3657 > #13,0.94374,-0.28303,-0.171,128.56,-0.069424,0.33602,-0.93929,335.83,0.32331,0.89832,0.29746,-87.788
    3658 
    3659 > hide #!8 models
    3660 
    3661 > show #!11 models
    3662 
    3663 > hide #!14 models
    3664 
    3665 > show #!14 models
    3666 
    3667 > hide #!14 models
    3668 
    3669 > view matrix models
    3670 > #13,0.38876,0.90043,0.19519,-95.278,-0.21732,0.2955,-0.9303,373.13,-0.89534,0.31924,0.31056,286.38
    3671 
    3672 > fitmap #13 inMap #8
    3673 
    3674 Fit map cryosparc_P141_J26_002_volume_map_sharp.mrc z flip in map preF_DS-
    3675 Cav1_20A_7mpg_Box208_0-045.mrc using 42381 points 
    3676 correlation = 0.7094, correlation about mean = 0.3006, overlap = 1.028e+04 
    3677 steps = 372, shift = 25.6, angle = 83.5 degrees 
    3678  
    3679 Position of cryosparc_P141_J26_002_volume_map_sharp.mrc z flip (#13) relative
    3680 to preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates: 
    3681 Matrix rotation and translation 
    3682 0.96410970 0.08725491 -0.25075700 37.64089028 
    3683 -0.14247136 -0.62694205 -0.76592793 515.19639114 
    3684 -0.22404107 0.77416423 -0.59200958 222.90910283 
    3685 Axis 0.98891178 -0.01715462 -0.14751001 
    3686 Axis point 0.00000000 204.15894680 238.87951769 
    3687 Rotation angle (degrees) 128.86010122 
    3688 Shift along axis -4.49580151 
    3689  
    3690 
    3691 > undo
    3692 
    3693 > show #!5 models
    3694 
    3695 > hide #!5 models
    3696 
    3697 > view matrix models
    3698 > #13,0.94727,-0.023846,-0.31954,104.55,-0.27009,0.47716,-0.83629,323.69,0.17241,0.87849,0.44556,-85.252
    3699 
    3700 > show #!14 models
    3701 
    3702 > view matrix models
    3703 > #13,0.77584,-0.41115,-0.47858,259.32,-0.41688,0.23531,-0.87798,415.74,0.47359,0.88067,0.011164,-51.364
    3704 
    3705 > view matrix models
    3706 > #13,0.77801,-0.41578,-0.47098,258.19,-0.3914,0.26563,-0.88105,404.58,0.49143,0.86981,0.04392,-59.959
    3707 
    3708 > select subtract #13
    3709 
    3710 Nothing selected 
    3711 
    3712 > hide #!13 models
    3713 
    3714 > hide #!11 models
    3715 
    3716 > show #!11 models
    3717 
    3718 > hide #!11 models
    3719 
    3720 > show #!11 models
    3721 
    3722 > hide #!11 models
    3723 
    3724 > show #!11 models
    3725 
    3726 > show #!13 models
    3727 
    3728 > select add #13
    3729 
    3730 2 models selected 
    3731 
    3732 > view matrix models
    3733 > #13,0.75183,-0.46605,-0.46641,273.49,-0.24747,0.45621,-0.85477,327.68,0.61115,0.75807,0.22766,-101.19
    3734 
    3735 > view matrix models
    3736 > #13,0.94999,-0.16376,-0.2659,122.45,-0.20483,0.31595,-0.9264,365.25,0.23572,0.93453,0.26661,-70.734
    3737 
    3738 > view matrix models
    3739 > #13,0.96805,-0.21197,-0.13395,99.892,-0.10011,0.16304,-0.98153,389.1,0.2299,0.96358,0.13661,-46.967
    3740 
    3741 > vop resample #13 onGrid #11
    3742 
    3743 Opened cryosparc_P141_J26_002_volume_map_sharp.mrc z flip resampled as #15,
    3744 grid size 208,208,208, pixel 2, shown at step 1, values float32 
    3745 
    3746 > close #15
    3747 
    3748 > hide #!14 models
    3749 
    3750 > select subtract #13
    3751 
    3752 Nothing selected 
    3753 
    3754 > show #!8 models
    3755 
    3756 > volume #11 level 0.08821
    3757 
    3758 > volume #11 level 0.1004
    3759 
    3760 > vop resample #13 onGrid #11
    3761 
    3762 Opened cryosparc_P141_J26_002_volume_map_sharp.mrc z flip resampled as #15,
    3763 grid size 208,208,208, pixel 2, shown at step 1, values float32 
    3764 
    3765 > hide #!8 models
    3766 
    3767 > volume #12 level 1.598
    3768 
    3769 > volume #15 level 1.696
    3770 
    3771 > close #12
    3772 
    3773 > close #13
    3774 
    3775 > volume #15 level 1.487
    3776 
    3777 > ui tool show "Segment Map"
    3778 
    3779 Segmenting cryosparc_P141_J26_002_volume_map_sharp.mrc z flip resampled,
    3780 density threshold 1.486514 
    3781 Showing 8 region surfaces 
    3782 213 watershed regions, grouped to 8 regions 
    3783 Showing cryosparc_P141_J26_002_volume_map_sharp z flip resampled.seg - 8
    3784 regions, 8 surfaces 
    3785 Ungrouped to 2 regions 
    3786 Ungrouped to 25 regions 
    3787 
    3788 > select #12.21
    3789 
    3790 1 model selected 
    3791 Ungrouped to 18 regions 
    3792 
    3793 > select #12.43
    3794 
    3795 1 model selected 
    3796 Ungrouped to 0 regions 
    3797 
    3798 > select #12.26
    3799 
    3800 1 model selected 
    3801 
    3802 > select add #12.25
    3803 
    3804 2 models selected 
    3805 
    3806 > select add #12.32
    3807 
    3808 3 models selected 
    3809 
    3810 > select add #12.31
    3811 
    3812 4 models selected 
    3813 
    3814 > select add #12.30
    3815 
    3816 5 models selected 
    3817 
    3818 > select add #12.9
    3819 
    3820 6 models selected 
    3821 
    3822 > select add #12.29
    3823 
    3824 7 models selected 
    3825 
    3826 > select subtract #12.31
    3827 
    3828 6 models selected 
    3829 
    3830 > select add #12.31
    3831 
    3832 7 models selected 
    3833 Grouped 7 regions 
    3834 
    3835 > select #12.34
    3836 
    3837 1 model selected 
    3838 
    3839 > select add #12.20
    3840 
    3841 2 models selected 
    3842 
    3843 > select add #12.33
    3844 
    3845 3 models selected 
    3846 
    3847 > select add #12.18
    3848 
    3849 4 models selected 
    3850 
    3851 > select add #12.19
    3852 
    3853 5 models selected 
    3854 Grouped 5 regions 
    3855 
    3856 > select #12.22
    3857 
    3858 1 model selected 
    3859 
    3860 > select add #12.1
    3861 
    3862 2 models selected 
    3863 
    3864 > hide #!11 models
    3865 
    3866 > hide #!15 models
    3867 
    3868 > show #!15 models
    3869 
    3870 > hide #!7 models
    3871 
    3872 > select #12.22
    3873 
    3874 1 model selected 
    3875 
    3876 > select #12.2
    3877 
    3878 1 model selected 
    3879 
    3880 > select add #12.41
    3881 
    3882 2 models selected 
    3883 
    3884 > select add #12.22
    3885 
    3886 3 models selected 
    3887 
    3888 > select add #12.16
    3889 
    3890 4 models selected 
    3891 
    3892 > select add #12.17
    3893 
    3894 5 models selected 
    3895 
    3896 > select subtract #12.16
    3897 
    3898 4 models selected 
    3899 
    3900 > select add #12.15
    3901 
    3902 5 models selected 
    3903 
    3904 > select add #12.23
    3905 
    3906 6 models selected 
    3907 
    3908 > select add #12.24
    3909 
    3910 7 models selected 
    3911 Grouped 7 regions 
    3912 
    3913 > select add #12.16
    3914 
    3915 2 models selected 
    3916 
    3917 > select add #12.10
    3918 
    3919 3 models selected 
    3920 
    3921 > select add #12.4
    3922 
    3923 4 models selected 
    3924 
    3925 > select add #12.6
    3926 
    3927 5 models selected 
    3928 
    3929 > select add #12.7
    3930 
    3931 6 models selected 
    3932 
    3933 > select add #12.1
    3934 
    3935 7 models selected 
    3936 
    3937 > select subtract #12.7
    3938 
    3939 6 models selected 
    3940 Grouped 6 regions 
    3941 
    3942 > select add #12.43
    3943 
    3944 2 models selected 
    3945 
    3946 > select add #12.37
    3947 
    3948 3 models selected 
    3949 
    3950 > select subtract #12.37
    3951 
    3952 2 models selected 
    3953 
    3954 > select add #12.7
    3955 
    3956 3 models selected 
    3957 Grouped 3 regions 
    3958 
    3959 > select add #12.39
    3960 
    3961 2 models selected 
    3962 
    3963 > select add #12.37
    3964 
    3965 3 models selected 
    3966 Grouped 3 regions 
    3967 
    3968 > select add #12.40
    3969 
    3970 2 models selected 
    3971 
    3972 > select add #12.36
    3973 
    3974 3 models selected 
    3975 Grouped 3 regions 
    3976 
    3977 > select #12.3
    3978 
    3979 1 model selected 
    3980 
    3981 > select add #12.8
    3982 
    3983 2 models selected 
    3984 
    3985 > select add #12.1
    3986 
    3987 3 models selected 
    3988 Grouped 3 regions 
    3989 
    3990 > select add #12.42
    3991 
    3992 2 models selected 
    3993 
    3994 > select add #12.44
    3995 
    3996 3 models selected 
    3997 
    3998 > select add #12.35
    3999 
    4000 4 models selected 
    4001 Grouped 4 regions 
    4002 
    4003 > view matrix models
    4004 > #12.1,0.46306,0.74641,-0.47795,121.51,-0.27886,0.63456,0.72081,-42.248,0.84131,-0.2005,0.50198,-54.824
    4005 
    4006 > undo
    4007 
    4008 > select clear
    4009 
    4010 > select #12.27
    4011 
    4012 1 model selected 
    4013 
    4014 > select add #12.28
    4015 
    4016 2 models selected 
    4017 Drag select of 233, 193 of 6492 triangles, 226, 673 of 5104 triangles, 215,
    4018 1541 of 7516 triangles, 248, 1005 of 17444 triangles, 15
    4019 cryosparc_P141_J26_002_volume_map_sharp.mrc z flip resampled 
    4020 
    4021 > select #12.12
    4022 
    4023 1 model selected 
    4024 
    4025 > select add #12.5
    4026 
    4027 2 models selected 
    4028 
    4029 > select add #12.11
    4030 
    4031 3 models selected 
    4032 
    4033 > select add #12.14
    4034 
    4035 4 models selected 
    4036 
    4037 > select add #12.13
    4038 
    4039 5 models selected 
    4040 
    4041 > select add #12.28
    4042 
    4043 6 models selected 
    4044 
    4045 > select add #12.27
    4046 
    4047 7 models selected 
    4048 Grouped 7 regions 
    4049 
    4050 > hide #12.1 models
    4051 
    4052 > show #12.1 models
    4053 
    4054 > hide #!15 models
    4055 
    4056 > hide #12.1 models
    4057 
    4058 > show #12.1 models
    4059 
    4060 > select clear
    4061 
    4062 Drag select of 80, 240 of 360 triangles, 256, 10893 of 17716 triangles 
    4063 Grouped 2 regions 
    4064 
    4065 > hide #12.1 models
    4066 
    4067 > show #12.1 models
    4068 
    4069 > hide #12.2 models
    4070 
    4071 > show #12.2 models
    4072 
    4073 > hide #12.9 models
    4074 
    4075 > show #12.9 models
    4076 
    4077 > hide #12.18 models
    4078 
    4079 > hide #12.9 models
    4080 
    4081 > hide #12.1 models
    4082 
    4083 > color #12.2 darkgrey
    4084 
    4085 > show #!15 models
    4086 
    4087 > hide #!15 models
    4088 
    4089 > show #!11 models
    4090 
    4091 > select subtract #12.1
    4092 
    4093 Nothing selected 
    4094 
    4095 > select add #12
    4096 
    4097 5 models selected 
    4098 
    4099 > color #11 #945200ff models
    4100 
    4101 > color #11 #941100ff models
    4102 
    4103 > undo
    4104 
    4105 > color #11 #d6d6d6ff models
    4106 
    4107 > color #11 silver models
    4108 
    4109 > color #12.2 #ff9300ff
    4110 
    4111 > color #12.2 #8671ffff
    4112 
    4113 > ui mousemode right "translate selected models"
    4114 
    4115 > view matrix models #12,1,0,0,-57.407,0,1,0,-24.9,0,0,1,35.728
    4116 
    4117 > volume #15 level 1.469
    4118 
    4119 > hide #12.2 models
    4120 
    4121 > show #12.2 models
    4122 
    4123 > undo
    4124 
    4125 > show #12.2 models
    4126 
    4127 > undo
    4128 
    4129 [Repeated 2 time(s)]
    4130 
    4131 > show #12.1 models
    4132 
    4133 > show #12.9 models
    4134 
    4135 > show #12.18 models
    4136 
    4137 > show #!14 models
    4138 
    4139 > show #!10 models
    4140 
    4141 > show #!5 models
    4142 
    4143 > hide #!5 models
    4144 
    4145 > show #!5 models
    4146 
    4147 > hide #!5 models
    4148 
    4149 > show #!5 models
    4150 
    4151 > hide #!5 models
    4152 
    4153 > show #!5 models
    4154 
    4155 > hide #!5 models
    4156 
    4157 > show #!5 models
    4158 
    4159 > hide #!5 models
    4160 
    4161 > show #!5 models
    4162 
    4163 > hide #!5 models
    4164 
    4165 > show #!5 models
    4166 
    4167 > hide #12.9 models
    4168 
    4169 > show #12.9 models
    4170 
    4171 > hide #12.9 models
    4172 
    4173 > show #12.9 models
    4174 
    4175 > hide #12.9 models
    4176 
    4177 > show #12.9 models
    4178 
    4179 > hide #!5 models
    4180 
    4181 > color #12.9 #ffd479ff
    4182 
    4183 > color #12.9 #fffc79ff
    4184 
    4185 > select #12.18
    4186 
    4187 1 model selected 
    4188 
    4189 > color #12.9 #8671ffff
    4190 
    4191 > color #12.9 #c1607eff
    4192 
    4193 > color #12.9 #f2ad93ff
    4194 
    4195 > color #12.9 #cd9f9bff
    4196 
    4197 > color #12.9 #00f900ff
    4198 
    4199 > color #12.9 #009051ff
    4200 
    4201 > color #12.9 #008f00ff
    4202 
    4203 > color #12.9 #009051ff
    4204 
    4205 > color #12.9 #409191ff
    4206 
    4207 > color #12.9 #5eaf88ff
    4208 
    4209 > color #12.9 #a6ca8cff
    4210 
    4211 > color #12.9 #8b9e70ff
    4212 
    4213 > color #12.9 #9ea946ff
    4214 
    4215 > color #12.9 #f8dd71ff
    4216 
    4217 > color #12.9 #7974d0ff
    4218 
    4219 > color #12.9 #e97d4dff
    4220 
    4221 > color #12.9 #8ec9a4ff
    4222 
    4223 > color #12.9 #3f8e97ff
    4224 
    4225 > color #12.9 #008f00ff
    4226 
    4227 > select clear
    4228 
    4229 > fitmap #14 inMap #8
    4230 
    4231 Fit molecule 4zyp_Mota_AM14.pdb (#14) to map preF_DS-
    4232 Cav1_20A_7mpg_Box208_0-045.mrc (#8) using 16960 atoms 
    4233 average map value = 0.1544, steps = 144 
    4234 shifted from previous position = 0.528 
    4235 rotated from previous position = 0.283 degrees 
    4236 atoms outside contour = 7361, contour level = 0.15 
    4237  
    4238 Position of 4zyp_Mota_AM14.pdb (#14) relative to preF_DS-
    4239 Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates: 
    4240 Matrix rotation and translation 
    4241 -0.18010596 -0.98182955 0.05977107 201.36259741 
    4242 -0.68922031 0.08260889 -0.71982716 242.93107209 
    4243 0.70180995 -0.17084060 -0.69157522 205.54116766 
    4244 Axis 0.61408494 -0.71817134 0.32730661 
    4245 Axis point 171.66462494 0.00000000 189.54450963 
    4246 Rotation angle (degrees) 153.44891129 
    4247 Shift along axis 16.46258878 
    4248  
    4249 
    4250 > show #!8 models
    4251 
    4252 > hide #!12 models
    4253 
    4254 > hide #!14 models
    4255 
    4256 > show #!14 models
    4257 
    4258 > hide #!10 models
    4259 
    4260 > hide #!11 models
    4261 
    4262 > show #!11 models
    4263 
    4264 > hide #!11 models
    4265 
    4266 Segmenting cryosparc_P141_J26_002_volume_map_sharp.mrc z flip resampled,
    4267 density threshold 1.468559 
    4268 Showing 8 region surfaces 
    4269 213 watershed regions, grouped to 8 regions 
    4270 Showing cryosparc_P141_J26_002_volume_map_sharp z flip resampled.seg - 8
    4271 regions, 8 surfaces 
    4272 
    4273 > hide #!12 models
    4274 
    4275 > show #!12 models
    4276 
    4277 > close #12
    4278 
    4279 > volume #8 level 0.1022
    4280 
    4281 > volume #8 level 0.108
    4282 
    4283 > show #!11 models
    4284 
    4285 > hide #!11 models
    4286 
    4287 > show #!11 models
    4288 
    4289 > hide #!8 models
    4290 
    4291 > show #!10 models
    4292 
    4293 > show #!5 models
    4294 
    4295 > hide #!5 models
    4296 
    4297 > show #!15 models
    4298 
    4299 > hide #!15 models
    4300 
    4301 Segmenting cryosparc_P141_J26_002_volume_map_sharp.mrc z flip resampled,
    4302 density threshold 1.468559 
    4303 Showing 8 region surfaces 
    4304 213 watershed regions, grouped to 8 regions 
    4305 Showing cryosparc_P141_J26_002_volume_map_sharp z flip resampled.seg - 8
    4306 regions, 8 surfaces 
    4307 Closing all segmentations. 
    4308 
    4309 > volume #10 level 0.09286
    4310 
    4311 > fitmap #15 inMap #8
    4312 
    4313 Fit map cryosparc_P141_J26_002_volume_map_sharp.mrc z flip resampled in map
    4314 preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc using 42051 points 
    4315 correlation = 0.7109, correlation about mean = 0.3055, overlap = 1.021e+04 
    4316 steps = 312, shift = 33.6, angle = 52.2 degrees 
    4317  
    4318 Position of cryosparc_P141_J26_002_volume_map_sharp.mrc z flip resampled (#15)
    4319 relative to preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates: 
    4320 Matrix rotation and translation 
    4321 0.94840554 0.16123937 0.27299962 -107.90053249 
    4322 0.10051708 0.66371404 -0.74120172 211.54231643 
    4323 -0.30070458 0.73040094 0.61326276 -2.34692398 
    4324 Axis 0.93101412 0.36295580 -0.03841615 
    4325 Axis point 0.00000000 130.36856314 237.80566180 
    4326 Rotation angle (degrees) 52.21565226 
    4327 Shift along axis -23.58624890 
    4328  
    4329 
    4330 > undo
    4331 
    4332 [Repeated 1 time(s)]
    4333 
    4334 > show #!15 models
    4335 
    4336 > undo
    4337 
    4338 [Repeated 7 time(s)]
    4339 
    4340 > show #!15 models
    4341 
    4342 > select add #15
    4343 
    4344 2 models selected 
    4345 
    4346 > view matrix models
    4347 > #15,0.94841,0.16124,0.273,-117.07,0.10052,0.66371,-0.7412,115.39,-0.3007,0.7304,0.61326,-43.209
    4348 
    4349 > show #!11 models
    4350 
    4351 > hide #!8 models
    4352 
    4353 > view matrix models
    4354 > #15,0.94841,0.16124,0.273,-117.21,0.10052,0.66371,-0.7412,114.64,-0.3007,0.7304,0.61326,-43.651
    4355 
    4356 > ui mousemode right "rotate selected models"
    4357 
    4358 > view matrix models
    4359 > #15,0.95075,-0.061444,0.30381,-85.526,0.054946,0.99804,0.0299,-121.28,-0.30506,-0.011734,0.95226,7.4806
    4360 
    4361 > show #!10 models
    4362 
    4363 > view matrix models
    4364 > #15,0.95082,-0.063522,0.30317,-85.015,0.055902,0.99787,0.033756,-122.4,-0.30467,-0.015148,0.95234,7.9806
    4365 
    4366 > view matrix models
    4367 > #15,0.92703,-0.16943,0.33453,-68.221,0.16804,0.98522,0.03331,-146.05,-0.33522,0.025336,0.9418,10.406
    4368 
    4369 > ui mousemode right "translate selected models"
    4370 
    4371 > view matrix models
    4372 > #15,0.92703,-0.16943,0.33453,-39.098,0.16804,0.98522,0.03331,-48.065,-0.33522,0.025336,0.9418,85.943
    4373 
    4374 > view matrix models
    4375 > #15,0.92703,-0.16943,0.33453,-33.43,0.16804,0.98522,0.03331,-40.38,-0.33522,0.025336,0.9418,80.326
    4376 
    4377 > ui mousemode right "rotate selected models"
    4378 
    4379 > view matrix models
    4380 > #15,0.89395,-0.39322,0.215,43.102,0.37568,0.91909,0.11893,-97.498,-0.24437,-0.025547,0.96935,61.648
    4381 
    4382 > ui mousemode right "translate selected models"
    4383 
    4384 > view matrix models
    4385 > #15,0.89395,-0.39322,0.215,42.194,0.37568,0.91909,0.11893,-95.573,-0.24437,-0.025547,0.96935,68.382
    4386 
    4387 > view matrix models
    4388 > #15,0.89395,-0.39322,0.215,32.807,0.37568,0.91909,0.11893,-106.51,-0.24437,-0.025547,0.96935,69.1
    4389 
    4390 > ui mousemode right "rotate selected models"
    4391 
    4392 > view matrix models
    4393 > #15,0.95561,-0.18569,0.22875,-21.817,0.18447,0.98247,0.026898,-51.155,-0.22973,0.016495,0.97311,57.299
    4394 
    4395 > ui mousemode right "translate selected models"
    4396 
    4397 > view matrix models
    4398 > #15,0.95561,-0.18569,0.22875,-7.2447,0.18447,0.98247,0.026898,-42.602,-0.22973,0.016495,0.97311,61.164
    4399 
    4400 > view matrix models
    4401 > #15,0.95561,-0.18569,0.22875,-11.006,0.18447,0.98247,0.026898,-43.599,-0.22973,0.016495,0.97311,62.893
    4402 
    4403 > view matrix models
    4404 > #15,0.95561,-0.18569,0.22875,-14.643,0.18447,0.98247,0.026898,-44.671,-0.22973,0.016495,0.97311,66.237
    4405 
    4406 > view matrix models
    4407 > #15,0.95561,-0.18569,0.22875,-25.201,0.18447,0.98247,0.026898,-48.132,-0.22973,0.016495,0.97311,67.734
    4408 
    4409 > view matrix models
    4410 > #15,0.95561,-0.18569,0.22875,-15.536,0.18447,0.98247,0.026898,-48.418,-0.22973,0.016495,0.97311,60.254
    4411 
    4412 > view matrix models
    4413 > #15,0.95561,-0.18569,0.22875,-13.424,0.18447,0.98247,0.026898,-46.58,-0.22973,0.016495,0.97311,58.127
    4414 
    4415 > ui mousemode right "rotate selected models"
    4416 
    4417 > view matrix models
    4418 > #15,0.97217,-0.09067,0.21604,-31.121,0.055836,0.98518,0.16221,-50.024,-0.22754,-0.14563,0.96282,89.014
    4419 
    4420 > ui mousemode right "translate selected models"
    4421 
    4422 > view matrix models
    4423 > #15,0.97217,-0.09067,0.21604,-34.718,0.055836,0.98518,0.16221,-50.066,-0.22754,-0.14563,0.96282,91.458
    4424 
    4425 > ui mousemode right "rotate selected models"
    4426 
    4427 > view matrix models
    4428 > #15,0.98619,-0.084722,0.1423,-21.158,0.081732,0.9963,0.026738,-25.221,-0.14403,-0.014739,0.98946,42.301
    4429 
    4430 > view matrix models
    4431 > #15,0.96344,-0.15336,0.21968,-22.402,0.20645,0.94757,-0.24391,20.138,-0.17075,0.28035,0.94459,6.7746
    4432 
    4433 > view matrix models
    4434 > #15,0.93922,0.0051213,-0.34328,91.407,-0.031005,0.99707,-0.069955,24.223,0.34191,0.076347,0.93663,-73.828
    4435 
    4436 > view matrix models
    4437 > #15,0.98223,0.010431,-0.18738,42.701,-0.014758,0.99966,-0.021709,8.3002,0.18708,0.024089,0.98205,-39.615
    4438 
    4439 > ui mousemode right "translate selected models"
    4440 
    4441 > view matrix models
    4442 > #15,0.98223,0.010431,-0.18738,42.474,-0.014758,0.99966,-0.021709,12.727,0.18708,0.024089,0.98205,-37.476
    4443 
    4444 > hide #!14 models
    4445 
    4446 > show #!14 models
    4447 
    4448 > select clear
    4449 
    4450 > open /Users/szhang3/Library/CloudStorage/OneDrive-
    4451 > Moderna/RSV/EMPEM/EMPEMcomposition/4zyp_Mota_AM14.pdb
    4452 
    4453 4zyp_Mota_AM14.pdb title: 
    4454 Crystal structure of motavizumab and quaternary-specific RSV- neutralizing
    4455 human antibody AM14 In complex with prefusion RSV F glycoprotein [more
    4456 info...] 
    4457  
    4458 Chain information for 4zyp_Mota_AM14.pdb #12 
    4459 --- 
    4460 Chain | Description | UniProt 
    4461 A B C | protein F | FUS_HRSVA 26-513, D9IEJ2_BPT4 518-544 
    4462 D F H | AM14 antibody fab heavy chain |   
    4463 E G I | AM14 antibody light chain |   
    4464 J K N | motavizumab antibody fab heavy chain |   
    4465 L M O | motavizumab antibody light chain |   
    4466  
    4467 
    4468 > hide #!15 models
    4469 
    4470 > hide #!11 models
    4471 
    4472 > hide #!10 models
    4473 
    4474 > color #14 #ff2600ff
    4475 
    4476 > select clear
    4477 
    4478 > show #!15 models
    4479 
    4480 > hide #!12 models
    4481 
    4482 > show #!12 models
    4483 
    4484 > hide #!14 models
    4485 
    4486 > show #!14 models
    4487 
    4488 > hide #!14 models
    4489 
    4490 > ui mousemode right zoom
    4491 
    4492 > hide #!12 atoms
    4493 
    4494 > show #!12 cartoons
    4495 
    4496 > hide #!15 models
    4497 
    4498 > show #!14 models
    4499 
    4500 Drag select of 1904 residues, 4 pseudobonds 
    4501 
    4502 > select up
    4503 
    4504 15527 atoms, 15817 bonds, 4 pseudobonds, 2013 residues, 2 models selected 
    4505 
    4506 > select up
    4507 
    4508 16960 atoms, 17299 bonds, 4 pseudobonds, 2200 residues, 2 models selected 
    4509 
    4510 > select #12/A:343
    4511 
    4512 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4513 Drag select of 1454 residues, 3 pseudobonds 
    4514 
    4515 > select up
    4516 
    4517 12478 atoms, 12694 bonds, 3 pseudobonds, 1610 residues, 3 models selected 
    4518 
    4519 > select up
    4520 
    4521 20449 atoms, 20840 bonds, 3 pseudobonds, 2646 residues, 3 models selected 
    4522 
    4523 > ui tool show Matchmaker
    4524 
    4525 > matchmaker #!12 & sel to #14 & sel
    4526 
    4527 Computing secondary structure 
    4528 [Repeated 1 time(s)]  Parameters 
    4529 --- 
    4530 Chain pairing | bb 
    4531 Alignment algorithm | Needleman-Wunsch 
    4532 Similarity matrix | BLOSUM-62 
    4533 SS fraction | 0.3 
    4534 Gap open (HH/SS/other) | 18/18/6 
    4535 Gap extend | 1 
    4536 SS matrix |  |  | H | S | O 
    4537 ---|---|---|--- 
    4538 H | 6 | -9 | -6 
    4539 S |  | 6 | -6 
    4540 O |  |  | 4 
    4541 Iteration cutoff | 2 
    4542  
    4543 Matchmaker 4zyp_Mota_AM14.pdb, chain A (#14) with 4zyp_Mota_AM14.pdb, chain A
    4544 (#12), sequence alignment score = 2489.2 
    4545 RMSD between 449 pruned atom pairs is 0.000 angstroms; (across all 449 pairs:
    4546 0.000) 
    4547  
    4548 
    4549 > show #!15 models
    4550 
    4551 > select clear
    4552 
    4553 > hide #!15 models
    4554 
    4555 > hide #!12 models
    4556 
    4557 > show #!12 models
    4558 
    4559 > hide #!12 models
    4560 
    4561 > show #!12 models
    4562 
    4563 Drag select of 155 residues, 1 pseudobonds 
    4564 Drag select of 144 residues 
    4565 Drag select of 112 residues 
    4566 Drag select of 246 residues, 1 pseudobonds 
    4567 
    4568 > select up
    4569 
    4570 6977 atoms, 7116 bonds, 2 pseudobonds, 920 residues, 2 models selected 
    4571 
    4572 > select up
    4573 
    4574 13030 atoms, 13358 bonds, 2 pseudobonds, 1706 residues, 2 models selected 
    4575 
    4576 > delete atoms (#!12 & sel)
    4577 
    4578 > delete bonds (#!12 & sel)
    4579 
    4580 > color #12 #0433ffff
    4581 
    4582 > color #12 #7a81ffff
    4583 
    4584 > select clear
    4585 
    4586 > hide #!14 models
    4587 
    4588 > hide #!12 models
    4589 
    4590 > show #!14 models
    4591 
    4592 > show #!15 models
    4593 
    4594 > color #14 #c1607eff
    4595 
    4596 > select clear
    4597 
    4598 > show #!12 models
    4599 
    4600 > hide #!14 models
    4601 
    4602 Drag select of 80 residues 
    4603 
    4604 > select up
    4605 
    4606 1091 atoms, 1107 bonds, 144 residues, 1 model selected 
    4607 
    4608 > select up
    4609 
    4610 3277 atoms, 3357 bonds, 429 residues, 1 model selected 
    4611 
    4612 > delete atoms sel
    4613 
    4614 > delete bonds sel
    4615 
    4616 > hide #!15 models
    4617 
    4618 > select #12/C:206
    4619 
    4620 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4621 
    4622 > select add #12/A:173
    4623 
    4624 14 atoms, 12 bonds, 2 residues, 1 model selected 
    4625 
    4626 > select up
    4627 
    4628 141 atoms, 140 bonds, 19 residues, 1 model selected 
    4629 
    4630 > select up
    4631 
    4632 6964 atoms, 7081 bonds, 898 residues, 1 model selected 
    4633 
    4634 > select clear
    4635 
    4636 > select add #12/C:206
    4637 
    4638 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4639 
    4640 > select add #12/A:218
    4641 
    4642 17 atoms, 15 bonds, 2 residues, 1 model selected 
    4643 
    4644 > select up
    4645 
    4646 252 atoms, 253 bonds, 30 residues, 1 model selected 
    4647 
    4648 > select up
    4649 
    4650 6964 atoms, 7081 bonds, 898 residues, 1 model selected 
    4651 
    4652 > delete atoms sel
    4653 
    4654 > delete bonds sel
    4655 
    4656 > select clear
    4657 
    4658 > show #!10 models
    4659 
    4660 > hide #!10 models
    4661 
    4662 > show #!7 models
    4663 
    4664 > select #7/F:46
    4665 
    4666 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4667 
    4668 > select add #12/B:224
    4669 
    4670 15 atoms, 13 bonds, 2 residues, 2 models selected 
    4671 
    4672 > select up
    4673 
    4674 292 atoms, 293 bonds, 36 residues, 2 models selected 
    4675 
    4676 > select up
    4677 
    4678 6964 atoms, 7080 bonds, 898 residues, 2 models selected 
    4679 
    4680 > select up
    4681 
    4682 6965 atoms, 7080 bonds, 899 residues, 2 models selected 
    4683 
    4684 > ui tool show Matchmaker
    4685 
    4686 > matchmaker #!7 & sel to #12 & sel
    4687 
    4688 Computing secondary structure 
    4689 [Repeated 1 time(s)]  Parameters 
    4690 --- 
    4691 Chain pairing | bb 
    4692 Alignment algorithm | Needleman-Wunsch 
    4693 Similarity matrix | BLOSUM-62 
    4694 SS fraction | 0.3 
    4695 Gap open (HH/SS/other) | 18/18/6 
    4696 Gap extend | 1 
    4697 SS matrix |  |  | H | S | O 
    4698 ---|---|---|--- 
    4699 H | 6 | -9 | -6 
    4700 S |  | 6 | -6 
    4701 O |  |  | 4 
    4702 Iteration cutoff | 2 
    4703  
    4704 Matchmaker 4zyp_Mota_AM14.pdb, chain B (#12) with 5udc.pdb, chain F (#7),
    4705 sequence alignment score = 2356 
    4706 RMSD between 433 pruned atom pairs is 0.628 angstroms; (across all 448 pairs:
    4707 0.827) 
    4708  
    4709 
    4710 > select clear
    4711 
    4712 > show #!15 models
    4713 
    4714 > show #!14 models
    4715 
    4716 > hide #!15 models
    4717 
    4718 > hide #!14 models
    4719 
    4720 > show #!15 models
    4721 
    4722 > select add #15
    4723 
    4724 2 models selected 
    4725 
    4726 > ui mousemode right "rotate selected models"
    4727 
    4728 > view matrix models
    4729 > #15,0.88629,0.30254,0.35066,-117.74,-0.38278,0.90474,0.18687,64.443,-0.26072,-0.29984,0.91767,139.72
    4730 
    4731 > ui mousemode right "translate selected models"
    4732 
    4733 > view matrix models
    4734 > #15,0.88629,0.30254,0.35066,-131.83,-0.38278,0.90474,0.18687,61.754,-0.26072,-0.29984,0.91767,147.47
    4735 
    4736 > ui mousemode right "rotate selected models"
    4737 
    4738 > view matrix models
    4739 > #15,0.7604,0.46961,0.44861,-156.15,-0.62785,0.70823,0.32283,120.67,-0.16612,-0.52714,0.83338,186.47
    4740 
    4741 > view matrix models
    4742 > #15,0.85017,0.31753,0.41999,-142.92,-0.4089,0.9007,0.14675,78.257,-0.33169,-0.29649,0.89559,168.68
    4743 
    4744 > view matrix models
    4745 > #15,0.86333,0.34985,0.36368,-138.09,-0.39526,0.91684,0.056318,94.133,-0.31374,-0.19237,0.92982,137.66
    4746 
    4747 > ui mousemode right "translate selected models"
    4748 
    4749 > view matrix models
    4750 > #15,0.86333,0.34985,0.36368,-139.16,-0.39526,0.91684,0.056318,91.132,-0.31374,-0.19237,0.92982,142.75
    4751 
    4752 > view matrix models
    4753 > #15,0.86333,0.34985,0.36368,-139.82,-0.39526,0.91684,0.056318,91.396,-0.31374,-0.19237,0.92982,141.6
    4754 
    4755 > hide #!15 models
    4756 
    4757 > show #!15 models
    4758 
    4759 > volume flip #15
    4760 
    4761 Opened cryosparc_P141_J26_002_volume_map_sharp.mrc z flip resampled z flip as
    4762 #13, grid size 208,208,208, pixel 2, shown at step 1, values float32 
    4763 
    4764 > hide #!12 models
    4765 
    4766 > show #!12 models
    4767 
    4768 > hide #!7 models
    4769 
    4770 > show #!7 models
    4771 
    4772 > hide #!13 models
    4773 
    4774 > hide #!12 models
    4775 
    4776 Drag select of 591 residues, 1 pseudobonds 
    4777 
    4778 > select up
    4779 
    4780 4996 atoms, 5086 bonds, 1 pseudobond, 647 residues, 4 models selected 
    4781 
    4782 > select up
    4783 
    4784 6719 atoms, 6853 bonds, 1 pseudobond, 877 residues, 4 models selected 
    4785 
    4786 > show #!12 models
    4787 
    4788 Drag select of 185 residues 
    4789 
    4790 > select up
    4791 
    4792 8797 atoms, 8974 bonds, 1 pseudobond, 1146 residues, 5 models selected 
    4793 
    4794 > select up
    4795 
    4796 9956 atoms, 10174 bonds, 1 pseudobond, 1301 residues, 5 models selected 
    4797 
    4798 > combine #7,12
    4799 
    4800 Remapping chain ID 'L' in 4zyp_Mota_AM14.pdb #12 to 'M' 
    4801 
    4802 > hide #!12 models
    4803 
    4804 > select add #12
    4805 
    4806 13438 atoms, 13714 bonds, 3 pseudobonds, 1750 residues, 6 models selected 
    4807 
    4808 > select subtract #12
    4809 
    4810 6719 atoms, 6853 bonds, 1 pseudobond, 877 residues, 4 models selected 
    4811 
    4812 > hide #!7 models
    4813 
    4814 > select add #7
    4815 
    4816 6848 atoms, 6991 bonds, 2 pseudobonds, 890 residues, 4 models selected 
    4817 
    4818 > select subtract #7
    4819 
    4820 2 models selected 
    4821 
    4822 > select #16/B:52
    4823 
    4824 14 atoms, 15 bonds, 1 residue, 1 model selected 
    4825 
    4826 > select up
    4827 
    4828 82 atoms, 84 bonds, 10 residues, 1 model selected 
    4829 
    4830 > select up
    4831 
    4832 3482 atoms, 3540 bonds, 449 residues, 1 model selected 
    4833 
    4834 > delete atoms sel
    4835 
    4836 > delete bonds sel
    4837 
    4838 > save "/Users/szhang3/OneDrive - Moderna/RSV/RSVAmono_MEDI_Mota_model.pdb"
    4839 > models #16 relModel #11
    4840 
    4841 > ui mousemode right zoom
    4842 
    4843 > show #!15 models
    4844 
    4845 > show #!13 models
    4846 
    4847 > hide #!15 models
    4848 
    4849 > ui mousemode right "translate selected models"
    4850 
    4851 > ui mousemode right "rotate selected models"
    4852 
    4853 > select add #13
    4854 
    4855 2 models selected 
    4856 
    4857 > view matrix models
    4858 > #13,-0.58926,0.23529,-0.77293,412.56,0.60259,0.76525,-0.22644,-64.47,0.53821,-0.59918,-0.59272,277.85
    4859 
    4860 > ui mousemode right "translate selected models"
    4861 
    4862 > view matrix models
    4863 > #13,-0.58926,0.23529,-0.77293,450.96,0.60259,0.76525,-0.22644,-70.226,0.53821,-0.59918,-0.59272,329.99
    4864 
    4865 > ui mousemode right "rotate selected models"
    4866 
    4867 > view matrix models
    4868 > #13,-0.69746,-0.20934,-0.68536,540.28,0.2257,0.84353,-0.48735,48.007,0.68015,-0.4946,-0.54108,269.57
    4869 
    4870 > ui mousemode right "translate selected models"
    4871 
    4872 > view matrix models
    4873 > #13,-0.69746,-0.20934,-0.68536,509.91,0.2257,0.84353,-0.48735,57.162,0.68015,-0.4946,-0.54108,275.59
    4874 
    4875 > ui mousemode right zoom
    4876 
    4877 > ui mousemode right "rotate selected models"
    4878 
    4879 > view matrix models
    4880 > #13,-0.71657,0.34654,-0.60534,401.53,0.54335,0.82151,-0.1729,-66.549,0.43737,-0.45281,-0.77696,364.93
    4881 
    4882 > open /Users/szhang3/Downloads/cryosparc_P141_J33_003_volume_map_sharp.mrc
    4883 
    4884 Opened cryosparc_P141_J33_003_volume_map_sharp.mrc as #17, grid size
    4885 208,208,208, pixel 2, shown at level 0.146, step 1, values float32 
    4886 
    4887 > volume #17 level 1.218
    4888 
    4889 > hide #!13 models
    4890 
    4891 > select subtract #13
    4892 
    4893 Nothing selected 
    4894 
    4895 > volume #17 level 1.153
    4896 
    4897 > volume #17 level 1.244
    4898 
    4899 > open /Users/szhang3/Downloads/cryosparc_P141_J33_003_volume_map.mrc
    4900 
    4901 Opened cryosparc_P141_J33_003_volume_map.mrc as #18, grid size 208,208,208,
    4902 pixel 2, shown at level 0.0925, step 1, values float32 
    4903 
    4904 > volume #18 level 1.008
    4905 
    4906 > volume #18 level 1.352
    4907 
    4908 > volume #18 level 1.264
    4909 
    4910 > select add #18
    4911 
    4912 2 models selected 
    4913 
    4914 > view matrix models
    4915 > #18,-0.98508,0.15839,-0.067283,388.97,0.075864,0.75064,0.65634,-87.645,0.15446,0.64145,-0.75146,165.29
    4916 
    4917 > view matrix models
    4918 > #18,-0.90282,0.38096,-0.19947,348.98,0.016118,0.4935,0.8696,-60.385,0.42972,0.78187,-0.45168,20.226
    4919 
    4920 > ui mousemode right "translate selected models"
    4921 
    4922 > view matrix models
    4923 > #18,-0.90282,0.38096,-0.19947,371.3,0.016118,0.4935,0.8696,-109.55,0.42972,0.78187,-0.45168,71.611
    4924 
    4925 > ui mousemode right "rotate selected models"
    4926 
    4927 > view matrix models
    4928 > #18,-0.90158,0.35858,-0.24201,384.09,0.016012,0.5867,0.80964,-118.26,0.43232,0.72608,-0.5347,99.16
    4929 
    4930 > view matrix models
    4931 > #18,-0.82464,0.49676,0.27056,239.61,0.47175,0.34004,0.81353,-159.62,0.31212,0.7985,-0.51476,104.44
    4932 
    4933 > view matrix models
    4934 > #18,-0.85261,0.51254,0.10174,274.41,0.33842,0.39326,0.85488,-151.57,0.39815,0.76332,-0.50875,93.143
    4935 
    4936 > ui mousemode right "translate selected models"
    4937 
    4938 > view matrix models
    4939 > #18,-0.85261,0.51254,0.10174,248.3,0.33842,0.39326,0.85488,-142.61,0.39815,0.76332,-0.50875,120.5
    4940 
    4941 > select up
    4942 
    4943 40612 atoms, 41463 bonds, 5277 residues, 32 models selected 
    4944 
    4945 > select up
    4946 
    4947 40612 atoms, 41463 bonds, 5277 residues, 32 models selected 
    4948 
    4949 > volume flip #18
    4950 
    4951 Opened cryosparc_P141_J33_003_volume_map.mrc z flip as #19, grid size
    4952 208,208,208, pixel 2, shown at step 1, values float32 
    4953 
    4954 > view matrix models
    4955 > #1,1,0,0,-0.078501,0,1,0,0.061263,0,0,1,-0.1085,#2,1,0,0,-0.078501,0,1,0,0.061263,0,0,1,-0.1085,#3,1,0,0,-0.078501,0,1,0,0.061263,0,0,1,-0.1085,#4,1,0,0,-0.078501,0,1,0,0.061263,0,0,1,-0.1085,#5,1,0,0,-0.078501,0,1,0,0.061263,0,0,1,-0.1085,#6,1,0,0,-0.078501,0,1,0,0.061263,0,0,1,-0.1085,#8,1,0,0,-0.078501,0,1,0,0.061263,0,0,1,-0.1085,#9,1,0,0,-0.078501,0,1,0,0.061263,0,0,1,-0.1085,#10,1,0,0,-0.078501,0,1,0,0.061263,0,0,1,-0.1085,#11,1,0,0,-0.078501,0,1,0,0.061263,0,0,1,-0.1085,#7,-0.20511,0.82965,-0.51924,138.92,0.82206,-0.14189,-0.55144,177.56,-0.53118,-0.53995,-0.65292,196.49,#14,-0.18011,-0.98183,0.059771,201.28,-0.68922,0.082609,-0.71983,242.99,0.70181,-0.17084,-0.69158,205.43,#15,0.86333,0.34985,0.36368,-139.9,-0.39526,0.91684,0.056318,91.458,-0.31374,-0.19237,0.92982,141.49,#12,-0.18011,-0.98183,0.059771,201.28,-0.68922,0.082609,-0.71983,242.99,0.70181,-0.17084,-0.69158,205.43,#13,-0.71657,0.34654,-0.60534,401.45,0.54335,0.82151,-0.1729,-66.488,0.43737,-0.45281,-0.77696,364.82,#16,-0.20511,0.82965,-0.51924,138.92,0.82206,-0.14189,-0.55144,177.56,-0.53118,-0.53995,-0.65292,196.49,#17,1,0,0,-0.078501,0,1,0,0.061263,0,0,1,-0.1085,#18,-0.85261,0.51254,0.10174,248.23,0.33842,0.39326,0.85488,-142.54,0.39815,0.76332,-0.50875,120.39
    4956 
    4957 > view matrix models
    4958 > #1,1,0,0,-0.21688,0,1,0,-0.62888,0,0,1,0.035002,#2,1,0,0,-0.21688,0,1,0,-0.62888,0,0,1,0.035002,#3,1,0,0,-0.21688,0,1,0,-0.62888,0,0,1,0.035002,#4,1,0,0,-0.21688,0,1,0,-0.62888,0,0,1,0.035002,#5,1,0,0,-0.21688,0,1,0,-0.62888,0,0,1,0.035002,#6,1,0,0,-0.21688,0,1,0,-0.62888,0,0,1,0.035002,#8,1,0,0,-0.21688,0,1,0,-0.62888,0,0,1,0.035002,#9,1,0,0,-0.21688,0,1,0,-0.62888,0,0,1,0.035002,#10,1,0,0,-0.21688,0,1,0,-0.62888,0,0,1,0.035002,#11,1,0,0,-0.21688,0,1,0,-0.62888,0,0,1,0.035002,#7,-0.20511,0.82965,-0.51924,138.78,0.82206,-0.14189,-0.55144,176.87,-0.53118,-0.53995,-0.65292,196.63,#14,-0.18011,-0.98183,0.059771,201.15,-0.68922,0.082609,-0.71983,242.3,0.70181,-0.17084,-0.69158,205.58,#15,0.86333,0.34985,0.36368,-140.04,-0.39526,0.91684,0.056318,90.767,-0.31374,-0.19237,0.92982,141.63,#12,-0.18011,-0.98183,0.059771,201.15,-0.68922,0.082609,-0.71983,242.3,0.70181,-0.17084,-0.69158,205.58,#13,-0.71657,0.34654,-0.60534,401.31,0.54335,0.82151,-0.1729,-67.178,0.43737,-0.45281,-0.77696,364.96,#16,-0.20511,0.82965,-0.51924,138.78,0.82206,-0.14189,-0.55144,176.87,-0.53118,-0.53995,-0.65292,196.63,#17,1,0,0,-0.21688,0,1,0,-0.62888,0,0,1,0.035002,#18,-0.85261,0.51254,0.10174,248.09,0.33842,0.39326,0.85488,-143.23,0.39815,0.76332,-0.50875,120.54
    4959 
    4960 > select subtract #18
    4961 
    4962 40612 atoms, 41463 bonds, 5277 residues, 30 models selected 
    4963 
    4964 > select subtract #17
    4965 
    4966 40612 atoms, 41463 bonds, 5277 residues, 28 models selected 
    4967 
    4968 > select subtract #15
    4969 
    4970 40612 atoms, 41463 bonds, 5277 residues, 26 models selected 
    4971 
    4972 > select add #14
    4973 
    4974 40612 atoms, 41463 bonds, 5 pseudobonds, 5277 residues, 27 models selected 
    4975 
    4976 > select subtract #13
    4977 
    4978 40612 atoms, 41463 bonds, 5 pseudobonds, 5277 residues, 25 models selected 
    4979 
    4980 > select subtract #14
    4981 
    4982 23652 atoms, 24164 bonds, 3077 residues, 23 models selected 
    4983 
    4984 > select add #13
    4985 
    4986 23652 atoms, 24164 bonds, 3077 residues, 25 models selected 
    4987 
    4988 > select add #12
    4989 
    4990 23652 atoms, 24164 bonds, 2 pseudobonds, 3077 residues, 26 models selected 
    4991 
    4992 > select subtract #11
    4993 
    4994 23652 atoms, 24164 bonds, 2 pseudobonds, 3077 residues, 24 models selected 
    4995 
    4996 > select subtract #12
    4997 
    4998 16933 atoms, 17303 bonds, 2204 residues, 22 models selected 
    4999 
    5000 > select subtract #13
    5001 
    5002 16933 atoms, 17303 bonds, 2204 residues, 20 models selected 
    5003 
    5004 > select add #16
    5005 
    5006 16933 atoms, 17303 bonds, 3 pseudobonds, 2204 residues, 22 models selected 
    5007 
    5008 > select subtract #16
    5009 
    5010 6848 atoms, 6991 bonds, 890 residues, 19 models selected 
    5011 
    5012 > select subtract #1
    5013 
    5014 6848 atoms, 6991 bonds, 890 residues, 17 models selected 
    5015 
    5016 > select subtract #2
    5017 
    5018 6848 atoms, 6991 bonds, 890 residues, 15 models selected 
    5019 
    5020 > select subtract #4
    5021 
    5022 6848 atoms, 6991 bonds, 890 residues, 13 models selected 
    5023 
    5024 > select subtract #3
    5025 
    5026 6848 atoms, 6991 bonds, 890 residues, 11 models selected 
    5027 
    5028 > select subtract #5
    5029 
    5030 6848 atoms, 6991 bonds, 890 residues, 9 models selected 
    5031 
    5032 > select subtract #6
    5033 
    5034 6848 atoms, 6991 bonds, 890 residues, 7 models selected 
    5035 
    5036 > select subtract #8
    5037 
    5038 6848 atoms, 6991 bonds, 890 residues, 5 models selected 
    5039 
    5040 > select add #7
    5041 
    5042 6848 atoms, 6991 bonds, 2 pseudobonds, 890 residues, 6 models selected 
    5043 
    5044 > select subtract #9
    5045 
    5046 6848 atoms, 6991 bonds, 2 pseudobonds, 890 residues, 4 models selected 
    5047 
    5048 > select subtract #7
    5049 
    5050 2 models selected 
    5051 
    5052 > select subtract #10
    5053 
    5054 Nothing selected 
    5055 
    5056 > select add #19
    5057 
    5058 2 models selected 
    5059 
    5060 > view matrix models
    5061 > #19,-0.85261,0.51254,0.10174,236.5,0.33842,0.39326,0.85488,-144.07,0.39815,0.76332,-0.50875,98.202
    5062 
    5063 > ui mousemode right "rotate selected models"
    5064 
    5065 > view matrix models
    5066 > #19,-0.91805,0.052648,0.39295,285.43,-0.31286,-0.70499,-0.63648,560.09,0.24351,-0.70726,0.66369,189.86
    5067 
    5068 > view matrix models
    5069 > #19,0.89378,0.43488,-0.10971,-60.834,-0.34247,0.5038,-0.79303,338.15,-0.2896,0.74637,0.59922,-1.6195
    5070 
    5071 > view matrix models
    5072 > #19,0.92863,0.10557,-0.35568,58.1,-0.33168,0.66578,-0.66837,273.06,0.16625,0.73864,0.65327,-106.19
    5073 
    5074 > ui mousemode right "translate selected models"
    5075 
    5076 > view matrix models
    5077 > #19,0.92863,0.10557,-0.35568,69.057,-0.33168,0.66578,-0.66837,246.3,0.16625,0.73864,0.65327,-95.497
    5078 
    5079 > view matrix models
    5080 > #19,0.92863,0.10557,-0.35568,68.853,-0.33168,0.66578,-0.66837,237.97,0.16625,0.73864,0.65327,-96.946
    5081 
    5082 > ui mousemode right "rotate selected models"
    5083 
    5084 > view matrix models
    5085 > #19,0.9149,-0.22501,-0.33517,139.01,-0.20446,0.45762,-0.86532,300.59,0.34808,0.86021,0.37267,-98.742
    5086 
    5087 > view matrix models
    5088 > #19,0.81984,0.27041,-0.50471,88.562,-0.57248,0.40365,-0.71367,354.79,0.010746,0.87404,0.48574,-57.071
    5089 
    5090 > view matrix models
    5091 > #19,0.83637,0.35676,-0.41619,46.74,-0.53801,0.67975,-0.49849,239.92,0.10506,0.64083,0.76046,-86.8
    5092 
    5093 > ui mousemode right "translate selected models"
    5094 
    5095 > view matrix models
    5096 > #19,0.83637,0.35676,-0.41619,60.477,-0.53801,0.67975,-0.49849,259.66,0.10506,0.64083,0.76046,-80.504
    5097 
    5098 > view matrix models
    5099 > #19,0.83637,0.35676,-0.41619,80.111,-0.53801,0.67975,-0.49849,253.2,0.10506,0.64083,0.76046,-77.294
    5100 
    5101 > view matrix models
    5102 > #19,0.83637,0.35676,-0.41619,78.412,-0.53801,0.67975,-0.49849,252.55,0.10506,0.64083,0.76046,-81.818
    5103 
    5104 > ui mousemode right "rotate selected models"
    5105 
    5106 > view matrix models
    5107 > #19,0.70058,-0.15608,-0.69629,280.1,-0.26867,0.84628,-0.46004,152.13,0.66106,0.50937,0.55095,-121.74
    5108 
    5109 > ui mousemode right "translate selected models"
    5110 
    5111 > view matrix models
    5112 > #19,0.70058,-0.15608,-0.69629,234.18,-0.26867,0.84628,-0.46004,164.89,0.66106,0.50937,0.55095,-118.4
    5113 
    5114 > view matrix models
    5115 > #19,0.70058,-0.15608,-0.69629,236.24,-0.26867,0.84628,-0.46004,169.88,0.66106,0.50937,0.55095,-122.69
    5116 
    5117 > view matrix models
    5118 > #19,0.70058,-0.15608,-0.69629,235.87,-0.26867,0.84628,-0.46004,169.88,0.66106,0.50937,0.55095,-118.48
    5119 
    5120 > view matrix models
    5121 > #19,0.70058,-0.15608,-0.69629,234.52,-0.26867,0.84628,-0.46004,171.08,0.66106,0.50937,0.55095,-119.1
    5122 
    5123 > ui mousemode right "rotate selected models"
    5124 
    5125 > view matrix models
    5126 > #19,0.61078,-0.38767,-0.6904,302.13,-0.079273,0.83762,-0.54047,151.64,0.78782,0.38484,0.48087,-102.7
    5127 
    5128 > open /Users/szhang3/Downloads/6oe5.cif
    5129 
    5130 6oe5.cif title: 
    5131 Splayed open prefusion RSV F captured by CR9501 and motavizumab Fabs [more
    5132 info...] 
    5133  
    5134 Chain information for 6oe5.cif #20 
    5135 --- 
    5136 Chain | Description | UniProt 
    5137 A | Fusion glycoprotein F0,Fibritin | FUS_HRSVA 1-513, WAC_BPT4 518-544 
    5138 B | Motavizumab Fab Heavy Chain |   
    5139 C | Motavizumab Fab Light Chain |   
    5140 H | CR9501 Fab Heavy Chain |   
    5141 L | CR9501 Fab Light Chain |   
    5142  
    5143 
    5144 > hide #!16,20 atoms
    5145 
    5146 > show #!16,20 cartoons
    5147 
    5148 > select add #20
    5149 
    5150 8527 atoms, 8716 bonds, 8 pseudobonds, 1113 residues, 4 models selected 
    5151 
    5152 > select subtract #19
    5153 
    5154 8527 atoms, 8716 bonds, 8 pseudobonds, 1113 residues, 2 models selected 
    5155 
    5156 > ui mousemode right "translate selected models"
    5157 
    5158 > view matrix models #20,1,0,0,63.799,0,1,0,9.3042,0,0,1,25.952
    5159 
    5160 > view matrix models #20,1,0,0,97.251,0,1,0,69.114,0,0,1,172.29
    5161 
    5162 > view matrix models #20,1,0,0,94.477,0,1,0,77.895,0,0,1,190.66
    5163 
    5164 > view matrix models #20,1,0,0,84.039,0,1,0,100.28,0,0,1,213.23
    5165 
    5166 > hide #!19 models
    5167 
    5168 > select clear
    5169 
    5170 > select add #20/A:55
    5171 
    5172 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5173 
    5174 > select add #16/F:303
    5175 
    5176 14 atoms, 12 bonds, 2 residues, 2 models selected 
    5177 
    5178 > select up
    5179 
    5180 191 atoms, 194 bonds, 24 residues, 2 models selected 
    5181 
    5182 > select up
    5183 
    5184 3692 atoms, 3753 bonds, 475 residues, 2 models selected 
    5185 
    5186 > select up
    5187 
    5188 3706 atoms, 3766 bonds, 477 residues, 2 models selected 
    5189 
    5190 > select up
    5191 
    5192 3910 atoms, 3971 bonds, 502 residues, 2 models selected 
    5193 
    5194 > select up
    5195 
    5196 3921 atoms, 3981 bonds, 504 residues, 2 models selected 
    5197 
    5198 > select up
    5199 
    5200 4372 atoms, 4435 bonds, 565 residues, 2 models selected 
    5201 
    5202 > select up
    5203 
    5204 5458 atoms, 5535 bonds, 702 residues, 2 models selected 
    5205 
    5206 > ui tool show Matchmaker
    5207 
    5208 > matchmaker #!20 & sel to #16 & sel
    5209 
    5210 Computing secondary structure 
    5211 [Repeated 1 time(s)]  Parameters 
    5212 --- 
    5213 Chain pairing | bb 
    5214 Alignment algorithm | Needleman-Wunsch 
    5215 Similarity matrix | BLOSUM-62 
    5216 SS fraction | 0.3 
    5217 Gap open (HH/SS/other) | 18/18/6 
    5218 Gap extend | 1 
    5219 SS matrix |  |  | H | S | O 
    5220 ---|---|---|--- 
    5221 H | 6 | -9 | -6 
    5222 S |  | 6 | -6 
    5223 O |  |  | 4 
    5224 Iteration cutoff | 2 
    5225  
    5226 Matchmaker combination, chain F (#16) with 6oe5.cif, chain A (#20), sequence
    5227 alignment score = 2210 
    5228 RMSD between 231 pruned atom pairs is 0.920 angstroms; (across all 250 pairs:
    5229 1.163) 
    5230  
    5231 
    5232 > hide #!20 models
    5233 
    5234 > show #!20 models
    5235 
    5236 > show #!19 models
    5237 
    5238 > select add #20
    5239 
    5240 12010 atoms, 12256 bonds, 8 pseudobonds, 1563 residues, 3 models selected 
    5241 
    5242 > select subtract #20
    5243 
    5244 3483 atoms, 3540 bonds, 450 residues, 1 model selected 
    5245 
    5246 > select add #16
    5247 
    5248 10085 atoms, 10312 bonds, 3 pseudobonds, 1314 residues, 3 models selected 
    5249 
    5250 > select subtract #16
    5251 
    5252 Nothing selected 
    5253 
    5254 > select add #19
    5255 
    5256 2 models selected 
    5257 
    5258 > view matrix models
    5259 > #19,0.61078,-0.38767,-0.6904,308.55,-0.079273,0.83762,-0.54047,151.76,0.78782,0.38484,0.48087,-97.761
    5260 
    5261 > ui mousemode right "rotate selected models"
    5262 
    5263 > view matrix models
    5264 > #19,-0.80076,-0.53579,-0.26777,538.89,0.10987,0.30807,-0.945,317.49,0.58882,-0.78614,-0.18782,346.25
    5265 
    5266 > ui mousemode right "translate selected models"
    5267 
    5268 > view matrix models
    5269 > #19,-0.80076,-0.53579,-0.26777,509.71,0.10987,0.30807,-0.945,315.5,0.58882,-0.78614,-0.18782,324.22
    5270 
    5271 > view matrix models
    5272 > #19,-0.80076,-0.53579,-0.26777,508.19,0.10987,0.30807,-0.945,315.78,0.58882,-0.78614,-0.18782,322.46
    5273 
    5274 > view matrix models
    5275 > #19,-0.80076,-0.53579,-0.26777,512.36,0.10987,0.30807,-0.945,317.67,0.58882,-0.78614,-0.18782,324.84
    5276 
    5277 > view matrix models
    5278 > #19,-0.80076,-0.53579,-0.26777,516.86,0.10987,0.30807,-0.945,315.66,0.58882,-0.78614,-0.18782,321.47
    5279 
    5280 > select subtract #19
    5281 
    5282 Nothing selected 
    5283 
    5284 > hide #!19 models
    5285 
    5286 > show #!19 models
    5287 
    5288 > hide #!19 models
    5289 
    5290 > hide #!20 models
    5291 
    5292 > show #!20 models
    5293 
    5294 > show #!18 models
    5295 
    5296 > ui mousemode right "rotate selected models"
    5297 
    5298 > select add #18
    5299 
    5300 2 models selected 
    5301 
    5302 > view matrix models
    5303 > #18,-0.97509,0.11284,0.19099,343.15,0.2208,0.5765,0.7867,-145.64,-0.021337,0.80927,-0.58705,212.34
    5304 
    5305 > view matrix models
    5306 > #18,0.57224,-0.33586,0.74816,13.639,-0.62888,0.40582,0.66319,90.899,-0.52635,-0.85001,0.021009,560.59
    5307 
    5308 > view matrix models
    5309 > #18,0.16891,-0.57784,0.79848,139.97,-0.5889,0.59045,0.55187,63.893,-0.79036,-0.56344,-0.24056,603.17
    5310 
    5311 > ui mousemode right "translate selected models"
    5312 
    5313 > view matrix models
    5314 > #18,0.16891,-0.57784,0.79848,114.93,-0.5889,0.59045,0.55187,89.792,-0.79036,-0.56344,-0.24056,571.87
    5315 
    5316 > view matrix models
    5317 > #18,0.16891,-0.57784,0.79848,114.64,-0.5889,0.59045,0.55187,74.173,-0.79036,-0.56344,-0.24056,574.35
    5318 
    5319 > ui mousemode right "rotate selected models"
    5320 
    5321 > view matrix models
    5322 > #18,0.16911,-0.54739,0.81962,103.91,-0.56567,0.62708,0.53552,64.549,-0.8071,-0.5542,-0.20359,568.7
    5323 
    5324 > view matrix models
    5325 > #18,0.55936,-0.49561,0.66445,41.794,-0.51538,0.41988,0.74705,58.531,-0.64924,-0.76031,-0.020565,545.68
    5326 
    5327 > ui mousemode right "translate selected models"
    5328 
    5329 > view matrix models
    5330 > #18,0.55936,-0.49561,0.66445,58.699,-0.51538,0.41988,0.74705,54.872,-0.64924,-0.76031,-0.020565,530.41
    5331 
    5332 > view matrix models
    5333 > #18,0.55936,-0.49561,0.66445,51.512,-0.51538,0.41988,0.74705,55.959,-0.64924,-0.76031,-0.020565,521.99
    5334 
    5335 > ui mousemode right "rotate selected models"
    5336 
    5337 > view matrix models
    5338 > #18,0.13793,-0.70247,0.69822,177.13,-0.43583,0.58999,0.67968,15.48,-0.8894,-0.39805,-0.22478,532.15
    5339 
    5340 > view matrix models
    5341 > #18,0.1326,-0.7026,0.69913,178.09,-0.43325,0.59332,0.67843,14.463,-0.89147,-0.39285,-0.22572,531.63
    5342 
    5343 > ui mousemode right "translate selected models"
    5344 
    5345 > view matrix models
    5346 > #18,0.1326,-0.7026,0.69913,176.88,-0.43325,0.59332,0.67843,17.209,-0.89147,-0.39285,-0.22572,537.57
    5347 
    5348 > hide #!18 models
    5349 
    5350 > select subtract #18
    5351 
    5352 Nothing selected 
    5353 
    5354 > show #!19 models
    5355 
    5356 > transparency #18,20 50
    5357 
    5358 > transparency #18,19 50
    5359 
    5360 > hide #!19 models
    5361 
    5362 > hide #!20 models
    5363 
    5364 > show #!20 models
    5365 
    5366 Drag select of 286 residues, 1 pseudobonds 
    5367 
    5368 > select up
    5369 
    5370 2678 atoms, 2744 bonds, 1 pseudobond, 354 residues, 2 models selected 
    5371 
    5372 > select up
    5373 
    5374 3237 atoms, 3321 bonds, 1 pseudobond, 424 residues, 2 models selected 
    5375 
    5376 > color (#!20 & sel) yellow
    5377 
    5378 > hide #!20 models
    5379 
    5380 > show #!20 models
    5381 
    5382 > hide #!20 models
    5383 
    5384 > show #!20 models
    5385 
    5386 Drag select of 244 residues 
    5387 
    5388 > select up
    5389 
    5390 6025 atoms, 6163 bonds, 1 pseudobond, 791 residues, 3 models selected 
    5391 
    5392 > select up
    5393 
    5394 8148 atoms, 8362 bonds, 1 pseudobond, 1073 residues, 3 models selected 
    5395 
    5396 > select up
    5397 
    5398 18612 atoms, 19028 bonds, 8 pseudobonds, 2427 residues, 3 models selected 
    5399 
    5400 > select down
    5401 
    5402 8148 atoms, 8362 bonds, 1 pseudobond, 1073 residues, 3 models selected 
    5403 
    5404 > select add #20/L:185
    5405 
    5406 8156 atoms, 8369 bonds, 1 pseudobond, 1074 residues, 3 models selected 
    5407 
    5408 > select up
    5409 
    5410 8191 atoms, 8405 bonds, 1 pseudobond, 1078 residues, 3 models selected 
    5411 
    5412 > select up
    5413 
    5414 9789 atoms, 10042 bonds, 1 pseudobond, 1285 residues, 3 models selected 
    5415 
    5416 > delete atoms (#!16,20 & sel)
    5417 
    5418 > delete bonds (#!16,20 & sel)
    5419 
    5420 > undo
    5421 
    5422 Undo failed, probably because structures have been modified. 
    5423 
    5424 > hide #!20 models
    5425 
    5426 > show #!20 models
    5427 
    5428 > close #20
    5429 
    5430 > open /Users/szhang3/Downloads/6oe5.cif
    5431 
    5432 6oe5.cif title: 
    5433 Splayed open prefusion RSV F captured by CR9501 and motavizumab Fabs [more
    5434 info...] 
    5435  
    5436 Chain information for 6oe5.cif #20 
    5437 --- 
    5438 Chain | Description | UniProt 
    5439 A | Fusion glycoprotein F0,Fibritin | FUS_HRSVA 1-513, WAC_BPT4 518-544 
    5440 B | Motavizumab Fab Heavy Chain |   
    5441 C | Motavizumab Fab Light Chain |   
    5442 H | CR9501 Fab Heavy Chain |   
    5443 L | CR9501 Fab Light Chain |   
    5444  
    5445 
    5446 > select #20/A:88@ND2
    5447 
    5448 1 atom, 1 residue, 1 model selected 
    5449 
    5450 > select add #16/F:169
    5451 
    5452 7 atoms, 5 bonds, 2 residues, 2 models selected 
    5453 
    5454 > select up
    5455 
    5456 14 atoms, 12 bonds, 2 residues, 2 models selected 
    5457 
    5458 > select up
    5459 
    5460 264 atoms, 263 bonds, 33 residues, 2 models selected 
    5461 
    5462 > select up
    5463 
    5464 3700 atoms, 3758 bonds, 476 residues, 2 models selected 
    5465 
    5466 > select up
    5467 
    5468 3782 atoms, 3838 bonds, 487 residues, 2 models selected 
    5469 
    5470 > select up
    5471 
    5472 4372 atoms, 4435 bonds, 565 residues, 2 models selected 
    5473 
    5474 > select up
    5475 
    5476 5458 atoms, 5535 bonds, 702 residues, 2 models selected 
    5477 
    5478 > ui tool show Matchmaker
    5479 
    5480 > matchmaker #!20 & sel to #16 & sel
    5481 
    5482 Computing secondary structure 
    5483 [Repeated 1 time(s)]  Parameters 
    5484 --- 
    5485 Chain pairing | bb 
    5486 Alignment algorithm | Needleman-Wunsch 
    5487 Similarity matrix | BLOSUM-62 
    5488 SS fraction | 0.3 
    5489 Gap open (HH/SS/other) | 18/18/6 
    5490 Gap extend | 1 
    5491 SS matrix |  |  | H | S | O 
    5492 ---|---|---|--- 
    5493 H | 6 | -9 | -6 
    5494 S |  | 6 | -6 
    5495 O |  |  | 4 
    5496 Iteration cutoff | 2 
    5497  
    5498 Matchmaker combination, chain F (#16) with 6oe5.cif, chain A (#20), sequence
    5499 alignment score = 2210 
    5500 RMSD between 231 pruned atom pairs is 0.920 angstroms; (across all 250 pairs:
    5501 1.163) 
    5502  
    5503 
    5504 > matchmaker #!20 & sel to #16 & sel
    5505 
    5506 Computing secondary structure 
    5507 [Repeated 1 time(s)]  Parameters 
    5508 --- 
    5509 Chain pairing | bb 
    5510 Alignment algorithm | Needleman-Wunsch 
    5511 Similarity matrix | BLOSUM-62 
    5512 SS fraction | 0.3 
    5513 Gap open (HH/SS/other) | 18/18/6 
    5514 Gap extend | 1 
    5515 SS matrix |  |  | H | S | O 
    5516 ---|---|---|--- 
    5517 H | 6 | -9 | -6 
    5518 S |  | 6 | -6 
    5519 O |  |  | 4 
    5520 Iteration cutoff | 2 
    5521  
    5522 Matchmaker combination, chain F (#16) with 6oe5.cif, chain A (#20), sequence
    5523 alignment score = 2210 
    5524 RMSD between 231 pruned atom pairs is 0.920 angstroms; (across all 250 pairs:
    5525 1.163) 
    5526  
    5527 
    5528 > select clear
    5529 
    5530 > select #20/L:5@CB
    5531 
    5532 1 atom, 1 residue, 1 model selected 
    5533 
    5534 > select add #20/H:85@CB
    5535 
    5536 2 atoms, 2 residues, 1 model selected 
    5537 
    5538 > select up
    5539 
    5540 12 atoms, 10 bonds, 2 residues, 1 model selected 
    5541 
    5542 > select up
    5543 
    5544 53 atoms, 51 bonds, 8 residues, 1 model selected 
    5545 
    5546 > select up
    5547 
    5548 3315 atoms, 3400 bonds, 437 residues, 1 model selected 
    5549 
    5550 > delete atoms sel
    5551 
    5552 > delete bonds sel
    5553 
    5554 > hide #!16,20 atoms
    5555 
    5556 > show #!16,20 cartoons
    5557 
    5558 > hide #!20 models
    5559 
    5560 > show #!20 models
    5561 
    5562 > hide #!20 models
    5563 
    5564 Drag select of 327 residues, 1 pseudobonds 
    5565 
    5566 > select up
    5567 
    5568 2939 atoms, 2989 bonds, 1 pseudobond, 381 residues, 2 models selected 
    5569 
    5570 > select up
    5571 
    5572 3482 atoms, 3540 bonds, 1 pseudobond, 449 residues, 2 models selected 
    5573 
    5574 > delete atoms (#!16 & sel)
    5575 
    5576 > delete bonds (#!16 & sel)
    5577 
    5578 > show #!20 models
    5579 
    5580 > undo
    5581 
    5582 [Repeated 1 time(s)]Undo failed, probably because structures have been
    5583 modified. 
    5584 
    5585 > show #!14 models
    5586 
    5587 > select clear
    5588 
    5589 > select add #14/A:81
    5590 
    5591 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5592 Drag select of 8 residues 
    5593 Drag select of 17 residues 
    5594 Drag select of 114 residues 
    5595 Drag select of 80 residues 
    5596 
    5597 > select up
    5598 
    5599 3258 atoms, 3300 bonds, 431 residues, 1 model selected 
    5600 
    5601 > select up
    5602 
    5603 13478 atoms, 13759 bonds, 1751 residues, 1 model selected 
    5604 
    5605 > delete atoms sel
    5606 
    5607 > delete bonds sel
    5608 
    5609 > hide #!14 models
    5610 
    5611 > show #!14 models
    5612 
    5613 > hide #!16 models
    5614 
    5615 > show #!16 models
    5616 
    5617 > show #!20 models
    5618 
    5619 > hide #!16 models
    5620 
    5621 > hide #!14 models
    5622 
    5623 Drag select of 174 residues, 1 pseudobonds 
    5624 Drag select of 46 residues, 4 pseudobonds 
    5625 
    5626 > select up
    5627 
    5628 561 atoms, 571 bonds, 4 pseudobonds, 70 residues, 2 models selected 
    5629 
    5630 > select up
    5631 
    5632 1295 atoms, 1313 bonds, 4 pseudobonds, 162 residues, 2 models selected 
    5633 
    5634 > select up
    5635 
    5636 1309 atoms, 1326 bonds, 4 pseudobonds, 164 residues, 2 models selected 
    5637 
    5638 > select up
    5639 
    5640 1513 atoms, 1531 bonds, 4 pseudobonds, 189 residues, 2 models selected 
    5641 
    5642 > select up
    5643 
    5644 1524 atoms, 1541 bonds, 4 pseudobonds, 191 residues, 2 models selected 
    5645 
    5646 > select up
    5647 
    5648 1975 atoms, 1995 bonds, 4 pseudobonds, 252 residues, 2 models selected 
    5649 
    5650 > select up
    5651 
    5652 5212 atoms, 5316 bonds, 8 pseudobonds, 676 residues, 2 models selected 
    5653 
    5654 > select down
    5655 
    5656 1975 atoms, 1995 bonds, 4 pseudobonds, 252 residues, 2 models selected 
    5657 
    5658 > delete atoms (#!20 & sel)
    5659 
    5660 > delete bonds (#!20 & sel)
    5661 
    5662 > show #!16 models
    5663 
    5664 > show #!14 models
    5665 
    5666 > combine #14,16,20
    5667 
    5668 Remapping chain ID 'B' in 6oe5.cif #20 to 'D' 
    5669 
    5670 > hide #!20 models
    5671 
    5672 > hide #!16 models
    5673 
    5674 > hide #!14 models
    5675 
    5676 > save "/Users/szhang3/OneDrive - Moderna/RSV/RSVAmono_MEDI_Mota_model.pdb"
    5677 > models #21 relModel #11
    5678 
    5679 Drag select of 283 residues, 1 pseudobonds 
    5680 
    5681 > select up
    5682 
    5683 2523 atoms, 2571 bonds, 1 pseudobond, 326 residues, 2 models selected 
    5684 
    5685 > select up
    5686 
    5687 3482 atoms, 3540 bonds, 1 pseudobond, 449 residues, 2 models selected 
    5688 
    5689 > color (#!21 & sel) gray
    5690 
    5691 > select clear
    5692 
    5693 Drag select of 157 residues, 1 pseudobonds 
    5694 
    5695 > select up
    5696 
    5697 1661 atoms, 1689 bonds, 1 pseudobond, 225 residues, 2 models selected 
    5698 
    5699 > select up
    5700 
    5701 3237 atoms, 3321 bonds, 1 pseudobond, 424 residues, 2 models selected 
    5702 
    5703 > color (#!21 & sel) yellow
    5704 
    5705 > select clear
    5706 
    5707 Drag select of 275 residues, 1 pseudobonds 
    5708 
    5709 > select up
    5710 
    5711 2564 atoms, 2612 bonds, 1 pseudobond, 342 residues, 2 models selected 
    5712 
    5713 > select up
    5714 
    5715 3237 atoms, 3313 bonds, 1 pseudobond, 428 residues, 2 models selected 
    5716 
    5717 > color (#!21 & sel) red
    5718 
    5719 > select clear
    5720 
    5721 > show #!19 models
    5722 
    5723 > show #!18 models
    5724 
    5725 > hide #!18 models
    5726 
    5727 > show #!18 models
    5728 
    5729 > show #!17 models
    5730 
    5731 > hide #!17 models
    5732 
    5733 > close #17
    5734 
    5735 > hide #!19 models
    5736 
    5737 > hide #!18 models
    5738 
    5739 > show #!19 models
    5740 
    5741 > select add #19
    5742 
    5743 2 models selected 
    5744 
    5745 > view matrix models
    5746 > #19,-0.80076,-0.53579,-0.26777,518.3,0.10987,0.30807,-0.945,314.19,0.58882,-0.78614,-0.18782,317.2
    5747 
    5748 > hide #!19 models
    5749 
    5750 > select subtract #19
    5751 
    5752 Nothing selected 
    5753 
    5754 > select add #18
    5755 
    5756 2 models selected 
    5757 
    5758 > show #!18 models
    5759 
    5760 > view matrix models
    5761 > #18,0.1326,-0.7026,0.69913,176.64,-0.43325,0.59332,0.67843,16.803,-0.89147,-0.39285,-0.22572,538.2
    5762 
    5763 > ui mousemode right "rotate selected models"
    5764 
    5765 > view matrix models
    5766 > #18,-0.33468,-0.78412,0.52262,324.92,-0.40325,0.62044,0.67264,5.8168,-0.85169,0.014377,-0.52385,498.75
    5767 
    5768 > view matrix models
    5769 > #18,-0.36878,-0.74911,0.55031,319.03,-0.46103,0.6615,0.5915,24.437,-0.80713,-0.035575,-0.58931,512.98
    5770 
    5771 > ui mousemode right "translate selected models"
    5772 
    5773 > view matrix models
    5774 > #18,-0.36878,-0.74911,0.55031,317.62,-0.46103,0.6615,0.5915,27.356,-0.80713,-0.035575,-0.58931,516.04
    5775 
    5776 > view matrix models
    5777 > #18,-0.36878,-0.74911,0.55031,312.99,-0.46103,0.6615,0.5915,29.075,-0.80713,-0.035575,-0.58931,516.96
    5778 
    5779 > view matrix models
    5780 > #18,-0.36878,-0.74911,0.55031,315.43,-0.46103,0.6615,0.5915,28.326,-0.80713,-0.035575,-0.58931,513.05
    5781 
    5782 > view matrix models
    5783 > #18,-0.36878,-0.74911,0.55031,317.05,-0.46103,0.6615,0.5915,27.767,-0.80713,-0.035575,-0.58931,510.95
    5784 
    5785 > ui mousemode right "rotate selected models"
    5786 
    5787 > view matrix models
    5788 > #18,-0.41005,-0.69265,0.59338,305.04,-0.52738,0.71086,0.46535,55.007,-0.74413,-0.12212,-0.65678,529.71
    5789 
    5790 > ui mousemode right "translate selected models"
    5791 
    5792 > view matrix models
    5793 > #18,-0.41005,-0.69265,0.59338,299.33,-0.52738,0.71086,0.46535,55.582,-0.74413,-0.12212,-0.65678,529.95
    5794 
    5795 > show #!19 models
    5796 
    5797 > select add #19
    5798 
    5799 4 models selected 
    5800 
    5801 > select subtract #18
    5802 
    5803 2 models selected 
    5804 
    5805 > hide #!18 models
    5806 
    5807 > show #!12 models
    5808 
    5809 > hide #!12 models
    5810 
    5811 > show #!14 models
    5812 
    5813 > hide #!14 models
    5814 
    5815 > show #!14 models
    5816 
    5817 > hide #!14 models
    5818 
    5819 > show #!12 models
    5820 
    5821 > close #12
    5822 
    5823 > open /Users/szhang3/Library/CloudStorage/OneDrive-
    5824 > Moderna/RSV/EMPEM/EMPEMcomposition/4zyp_Mota_AM14.pdb
    5825 
    5826 4zyp_Mota_AM14.pdb title: 
    5827 Crystal structure of motavizumab and quaternary-specific RSV- neutralizing
    5828 human antibody AM14 In complex with prefusion RSV F glycoprotein [more
    5829 info...] 
    5830  
    5831 Chain information for 4zyp_Mota_AM14.pdb #12 
    5832 --- 
    5833 Chain | Description | UniProt 
    5834 A B C | protein F | FUS_HRSVA 26-513, D9IEJ2_BPT4 518-544 
    5835 D F H | AM14 antibody fab heavy chain |   
    5836 E G I | AM14 antibody light chain |   
    5837 J K N | motavizumab antibody fab heavy chain |   
    5838 L M O | motavizumab antibody light chain |   
    5839  
    5840 
    5841 > view matrix models
    5842 > #19,-0.80076,-0.53579,-0.26777,513.82,0.10987,0.30807,-0.945,301.58,0.58882,-0.78614,-0.18782,317.77
    5843 
    5844 > undo
    5845 
    5846 > hide #!12,21 atoms
    5847 
    5848 > show #!12,21 cartoons
    5849 
    5850 > ui mousemode right zoom
    5851 
    5852 > hide #!19 models
    5853 
    5854 > select subtract #19
    5855 
    5856 Nothing selected 
    5857 
    5858 > select #21/B:82
    5859 
    5860 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5861 
    5862 > select down
    5863 
    5864 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5865 
    5866 > select up
    5867 
    5868 204 atoms, 204 bonds, 25 residues, 1 model selected 
    5869 
    5870 > select up
    5871 
    5872 3482 atoms, 3540 bonds, 449 residues, 1 model selected 
    5873 
    5874 > select add #12/A:493
    5875 
    5876 3488 atoms, 3545 bonds, 450 residues, 2 models selected 
    5877 
    5878 > select up
    5879 
    5880 3658 atoms, 3716 bonds, 471 residues, 2 models selected 
    5881 
    5882 > select up
    5883 
    5884 6964 atoms, 7080 bonds, 898 residues, 2 models selected 
    5885 
    5886 > select up
    5887 
    5888 40075 atoms, 40968 bonds, 5220 residues, 2 models selected 
    5889 
    5890 > select down
    5891 
    5892 6964 atoms, 7080 bonds, 898 residues, 2 models selected 
    5893 
    5894 > ui tool show Matchmaker
    5895 
    5896 > matchmaker #!12 & sel to #21 & sel
    5897 
    5898 Computing secondary structure 
    5899 [Repeated 1 time(s)]  Parameters 
    5900 --- 
    5901 Chain pairing | bb 
    5902 Alignment algorithm | Needleman-Wunsch 
    5903 Similarity matrix | BLOSUM-62 
    5904 SS fraction | 0.3 
    5905 Gap open (HH/SS/other) | 18/18/6 
    5906 Gap extend | 1 
    5907 SS matrix |  |  | H | S | O 
    5908 ---|---|---|--- 
    5909 H | 6 | -9 | -6 
    5910 S |  | 6 | -6 
    5911 O |  |  | 4 
    5912 Iteration cutoff | 2 
    5913  
    5914 Matchmaker combination, chain B (#21) with 4zyp_Mota_AM14.pdb, chain A (#12),
    5915 sequence alignment score = 2468.2 
    5916 RMSD between 449 pruned atom pairs is 0.308 angstroms; (across all 449 pairs:
    5917 0.308) 
    5918  
    5919 
    5920 > select clear
    5921 
    5922 > hide #!21 models
    5923 
    5924 > show #!21 models
    5925 
    5926 > hide #!21 models
    5927 
    5928 Drag select of 168 residues 
    5929 Drag select of 156 residues 
    5930 Drag select of 168 residues, 1 pseudobonds 
    5931 Drag select of 141 residues, 1 pseudobonds 
    5932 Drag select of 255 residues, 1 pseudobonds 
    5933 Drag select of 130 residues 
    5934 
    5935 > select up
    5936 
    5937 10139 atoms, 10311 bonds, 3 pseudobonds, 1356 residues, 2 models selected 
    5938 
    5939 > select up
    5940 
    5941 19544 atoms, 20036 bonds, 3 pseudobonds, 2559 residues, 2 models selected 
    5942 
    5943 > delete atoms (#!12 & sel)
    5944 
    5945 > delete bonds (#!12 & sel)
    5946 
    5947 > show #!21 models
    5948 
    5949 > show #!18 models
    5950 
    5951 > hide #!18 models
    5952 
    5953 > show #!19 models
    5954 
    5955 > fitmap #21 inMap #19
    5956 
    5957 Fit molecule combination (#21) to map cryosparc_P141_J33_003_volume_map.mrc z
    5958 flip (#19) using 10085 atoms 
    5959 average map value = 1.638, steps = 60 
    5960 shifted from previous position = 1.21 
    5961 rotated from previous position = 4.44 degrees 
    5962 atoms outside contour = 1422, contour level = 1.264 
    5963  
    5964 Position of combination (#21) relative to
    5965 cryosparc_P141_J33_003_volume_map.mrc z flip (#19) coordinates: 
    5966 Matrix rotation and translation 
    5967 0.46228095 0.72823210 -0.50593906 179.40738253 
    5968 -0.65307841 0.66556354 0.36126688 232.06673071 
    5969 0.59982073 0.16341108 0.78327001 172.74635996 
    5970 Axis -0.11112916 -0.62106927 -0.77583714 
    5971 Axis point 126.78666523 -107.25329339 0.00000000 
    5972 Rotation angle (degrees) 62.89920534 
    5973 Shift along axis -298.08994989 
    5974  
    5975 
    5976 > hide #!19 models
    5977 
    5978 Drag select of 27 residues 
    5979 
    5980 > select up
    5981 
    5982 544 atoms, 544 bonds, 68 residues, 2 models selected 
    5983 
    5984 > select up
    5985 
    5986 10446 atoms, 10620 bonds, 1347 residues, 2 models selected 
    5987 
    5988 > ui tool show Matchmaker
    5989 
    5990 > matchmaker #!12 & sel to #21 & sel
    5991 
    5992 Computing secondary structure 
    5993 [Repeated 1 time(s)]  Parameters 
    5994 --- 
    5995 Chain pairing | bb 
    5996 Alignment algorithm | Needleman-Wunsch 
    5997 Similarity matrix | BLOSUM-62 
    5998 SS fraction | 0.3 
    5999 Gap open (HH/SS/other) | 18/18/6 
    6000 Gap extend | 1 
    6001 SS matrix |  |  | H | S | O 
    6002 ---|---|---|--- 
    6003 H | 6 | -9 | -6 
    6004 S |  | 6 | -6 
    6005 O |  |  | 4 
    6006 Iteration cutoff | 2 
    6007  
    6008 Matchmaker combination, chain B (#21) with 4zyp_Mota_AM14.pdb, chain B (#12),
    6009 sequence alignment score = 2486.8 
    6010 RMSD between 449 pruned atom pairs is 0.000 angstroms; (across all 449 pairs:
    6011 0.000) 
    6012  
    6013 
    6014 > select clear
    6015 
    6016 > show #!19 models
    6017 
    6018 > volume #19 level 1.817
    6019 
    6020 > volume #19 level 1.701
    6021 
    6022 > save "/Users/szhang3/OneDrive - Moderna/RSV/MAbs/fitting.cxs" includeMaps
    6023 > true
    6024 
    6025 > rename #21 mono_MEDI_Mota
    6026 
    6027 > show #!16 models
    6028 
    6029 > hide #!16 models
    6030 
    6031 > close #16
    6032 
    6033 > close #15
    6034 
    6035 > close #13
    6036 
    6037 > show #!18 models
    6038 
    6039 > hide #!18 models
    6040 
    6041 > show #!11 models
    6042 
    6043 > volume #19 level 1.162
    6044 
    6045 > select add #11
    6046 
    6047 2 models selected 
    6048 
    6049 > ui mousemode right "rotate selected models"
    6050 
    6051 > view matrix models
    6052 > #11,-0.32797,0.67647,-0.65941,292.11,0.1516,0.72666,0.67006,-130.35,0.93245,0.11979,-0.34088,86.988
    6053 
    6054 > view matrix models
    6055 > #11,-0.39571,0.49844,-0.77134,369.49,0.056922,0.8516,0.5211,-101.99,0.91661,0.1623,-0.36536,87.116
    6056 
    6057 > fitmap #11 inMap #8
    6058 
    6059 Fit map RSV monomer.mrc in map preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc using
    6060 10770 points 
    6061 correlation = 0.9671, correlation about mean = 0.6097, overlap = 584.8 
    6062 steps = 80, shift = 7.11, angle = 5.6 degrees 
    6063  
    6064 Position of RSV monomer.mrc (#11) relative to preF_DS-
    6065 Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates: 
    6066 Matrix rotation and translation 
    6067 -0.48067845 0.45566289 -0.74921263 384.77138142 
    6068 0.04115820 0.86517263 0.49978228 -93.74623885 
    6069 0.87593050 0.20939832 -0.43462410 100.84505324 
    6070 Axis -0.17060091 -0.95477347 -0.24352198 
    6071 Axis point 171.33930350 0.00000000 174.78961288 
    6072 Rotation angle (degrees) 121.67261641 
    6073 Shift along axis -0.69391379 
    6074  
    6075 
    6076 > ui mousemode right zoom
    6077 
    6078 > hide #!11 models
    6079 
    6080 > select subtract #11
    6081 
    6082 Nothing selected 
    6083 Segmenting cryosparc_P141_J33_003_volume_map.mrc z flip, density threshold
    6084 1.161735 
    6085 Showing 8 region surfaces 
    6086 30 watershed regions, grouped to 8 regions 
    6087 Showing cryosparc_P141_J33_003_volume_map z flip.seg - 8 regions, 8 surfaces 
    6088 Closing all segmentations. 
    6089 
    6090 > show #!11 models
    6091 
    6092 > hide #!11 models
    6093 
    6094 > vop resample #18,19 onGrid #11
    6095 
    6096 Opened cryosparc_P141_J33_003_volume_map.mrc resampled as #13, grid size
    6097 208,208,208, pixel 2, shown at step 1, values float32 
    6098 Opened cryosparc_P141_J33_003_volume_map.mrc z flip resampled as #15, grid
    6099 size 208,208,208, pixel 2, shown at step 1, values float32 
    6100 
    6101 > close #18
    6102 
    6103 > close #19
    6104 
    6105 > hide #!13 models
    6106 
    6107 Segmenting cryosparc_P141_J33_003_volume_map.mrc z flip resampled, density
    6108 threshold 1.161735 
    6109 Showing 8 region surfaces 
    6110 24 watershed regions, grouped to 8 regions 
    6111 Showing cryosparc_P141_J33_003_volume_map z flip resampled.seg - 8 regions, 8
    6112 surfaces 
    6113 Closing all segmentations. 
    6114 
    6115 > show #!8 models
    6116 
    6117 > hide #!8 models
    6118 
    6119 > show #!11 models
    6120 
    6121 > hide #!15 models
    6122 
    6123 > show #!15 models
    6124 
    6125 > hide #!15 models
    6126 
    6127 > show #!15 models
    6128 
    6129 Segmenting cryosparc_P141_J33_003_volume_map.mrc z flip resampled, density
    6130 threshold 1.161735 
    6131 Showing 8 region surfaces 
    6132 24 watershed regions, grouped to 8 regions 
    6133 Showing cryosparc_P141_J33_003_volume_map z flip resampled.seg - 8 regions, 8
    6134 surfaces 
    6135 Closing all segmentations. 
    6136 
    6137 > vop resample #113,15 onGrid #8
    6138 
    6139 Opened cryosparc_P141_J33_003_volume_map.mrc z flip resampled resampled as
    6140 #16, grid size 208,208,208, pixel 2, shown at step 1, values float32 
    6141 
    6142 > close #13
    6143 
    6144 > close #15
    6145 
    6146 > hide #!16 models
    6147 
    6148 > show #!16 models
    6149 
    6150 > color #16 #5eaf88ff models
    6151 
    6152 > color #16 #8ec9a4ff models
    6153 
    6154 > transparency #16 50
    6155 
    6156 > hide #!11 models
    6157 
    6158 Segmenting cryosparc_P141_J33_003_volume_map.mrc z flip resampled resampled,
    6159 density threshold 1.161735 
    6160 Showing 8 region surfaces 
    6161 25 watershed regions, grouped to 8 regions 
    6162 Showing cryosparc_P141_J33_003_volume_map z flip resampled resampled.seg - 8
    6163 regions, 8 surfaces 
    6164 
    6165 > select #13.4
    6166 
    6167 1 model selected 
    6168 
    6169 > select add #13.2
    6170 
    6171 2 models selected 
    6172 Grouped 2 regions 
    6173 
    6174 > select #13.8
    6175 
    6176 1 model selected 
    6177 
    6178 > select add #13.1
    6179 
    6180 2 models selected 
    6181 
    6182 > select #13.1
    6183 
    6184 1 model selected 
    6185 Ungrouped to 2 regions 
    6186 
    6187 > select #13.8
    6188 
    6189 1 model selected 
    6190 
    6191 > select add #13.5
    6192 
    6193 2 models selected 
    6194 
    6195 > select add #13.9
    6196 
    6197 3 models selected 
    6198 Grouped 3 regions 
    6199 
    6200 > select #13.6
    6201 
    6202 1 model selected 
    6203 
    6204 > select add #13.4
    6205 
    6206 2 models selected 
    6207 Grouped 2 regions 
    6208 
    6209 > select #13.3
    6210 
    6211 1 model selected 
    6212 
    6213 > select add #13.7
    6214 
    6215 2 models selected 
    6216 Grouped 2 regions 
    6217 
    6218 > select #13.3
    6219 
    6220 1 model selected 
    6221 
    6222 > hide #13.1 models
    6223 
    6224 > show #13.1 models
    6225 
    6226 > color #13.1 #f8dd71ff
    6227 
    6228 > color #13.1 #fbe9a8ff
    6229 
    6230 > color #13.3 #ff7e79ff
    6231 
    6232 > select clear
    6233 
    6234 > select #13.4
    6235 
    6236 1 model selected 
    6237 
    6238 > color #13.3 #d6d6d6ff
    6239 
    6240 > color #13.3 #ff7e79ff
    6241 
    6242 > select #13.4
    6243 
    6244 1 model selected 
    6245 
    6246 > hide #13.3 models
    6247 
    6248 > show #13.3 models
    6249 
    6250 > hide #13.4 models
    6251 
    6252 > show #13.4 models
    6253 
    6254 > color #13.4 silver
    6255 
    6256 > color #13.4 #d6d6d6ff
    6257 
    6258 > select clear
    6259 
    6260 > hide #13.4 models
    6261 
    6262 > hide #!16 models
    6263 
    6264 > hide #!12 models
    6265 
    6266 > hide #!13 models
    6267 
    6268 > hide #13.1 models
    6269 
    6270 > hide #13.2 models
    6271 
    6272 > hide #13.3 models
    6273 
    6274 > show #!16 models
    6275 
    6276 > hide #!16 models
    6277 
    6278 > show #13.4 models
    6279 
    6280 > hide #13.4 models
    6281 
    6282 > show #13.3 models
    6283 
    6284 > hide #13.3 models
    6285 
    6286 > show #13.2 models
    6287 
    6288 > hide #!21 models
    6289 
    6290 > show #!21 models
    6291 
    6292 > hide #13.2 models
    6293 
    6294 > show #13.2 models
    6295 
    6296 > hide #13.2 models
    6297 
    6298 > show #13.2 models
    6299 
    6300 > save "/Users/szhang3/OneDrive - Moderna/RSV/MAbs/fitting.cxs" includeMaps
    6301 > true
    6302 
    6303 > show #!16 models
    6304 
    6305 > hide #13.2 models
    6306 
    6307 Cell requested for row 14 is out of bounds for table with 21 rows! Resizing
    6308 table model. 
    6309 
    6310 > open /Users/szhang3/Downloads/cryosparc_P141_J34_002_volume_map_sharp.mrc
    6311 
    6312 Opened cryosparc_P141_J34_002_volume_map_sharp.mrc as #15, grid size
    6313 208,208,208, pixel 2, shown at level 0.135, step 1, values float32 
    6314 
    6315 > volume #15 level 0.8685
    6316 
    6317 > volume #15 level 1.453
    6318 
    6319 > open /Users/szhang3/Downloads/cryosparc_P141_J36_001_volume_map.mrc
    6320 
    6321 Opened cryosparc_P141_J36_001_volume_map.mrc as #17, grid size 256,256,256,
    6322 pixel 2, shown at level 0.0693, step 1, values float32 
    6323 
    6324 > volume #17 level 0.8811
    6325 
    6326 > select add #15
    6327 
    6328 2 models selected 
    6329 
    6330 > ui mousemode right "translate selected models"
    6331 
    6332 > ui mousemode right "rotate selected models"
    6333 
    6334 > view matrix models
    6335 > #15,-0.67099,-0.72968,0.13169,473.62,0.71538,-0.68378,-0.14376,225.89,0.19495,-0.0022474,0.98081,-36.493
    6336 
    6337 > ui mousemode right "translate selected models"
    6338 
    6339 > view matrix models
    6340 > #15,-0.67099,-0.72968,0.13169,487.59,0.71538,-0.68378,-0.14376,233.9,0.19495,-0.0022474,0.98081,-42.898
    6341 
    6342 > view matrix models
    6343 > #15,-0.67099,-0.72968,0.13169,330.26,0.71538,-0.68378,-0.14376,144.25,0.19495,-0.0022474,0.98081,-13.741
    6344 
    6345 > close #15
    6346 
    6347 > select add #17
    6348 
    6349 2 models selected 
    6350 
    6351 > view matrix models #17,1,0,0,-161.53,0,1,0,-11.067,0,0,1,-72.622
    6352 
    6353 > ui mousemode right "rotate selected models"
    6354 
    6355 > view matrix models
    6356 > #17,0.99923,0.018727,0.034358,-174.46,-0.019852,0.99927,0.032701,-14.052,-0.033721,-0.033358,0.99887,-55.745
    6357 
    6358 > view matrix models
    6359 > #17,0.75605,0.60226,0.25627,-305.59,-0.23619,-0.1141,0.96498,68.361,0.61041,-0.79011,0.055978,195.39
    6360 
    6361 > view matrix models
    6362 > #17,-0.087447,0.95716,0.27604,-176.32,0.15033,-0.26125,0.95349,6.0868,0.98476,0.12488,-0.12105,-72.494
    6363 
    6364 > volume #17 level 1.058
    6365 
    6366 > ui mousemode right "translate selected models"
    6367 
    6368 > view matrix models
    6369 > #17,-0.087447,0.95716,0.27604,-67.343,0.15033,-0.26125,0.95349,12.984,0.98476,0.12488,-0.12105,-54.225
    6370 
    6371 > view matrix models
    6372 > #17,-0.087447,0.95716,0.27604,-78.242,0.15033,-0.26125,0.95349,23.618,0.98476,0.12488,-0.12105,-28.93
    6373 
    6374 > view matrix models
    6375 > #17,-0.087447,0.95716,0.27604,-78.441,0.15033,-0.26125,0.95349,24.409,0.98476,0.12488,-0.12105,-32.037
    6376 
    6377 > show #!8 models
    6378 
    6379 > ui tool show "Fit in Map"
    6380 
    6381 > fitmap #17 inMap #8
    6382 
    6383 Fit map cryosparc_P141_J36_001_volume_map.mrc in map preF_DS-
    6384 Cav1_20A_7mpg_Box208_0-045.mrc using 73461 points 
    6385 correlation = 0.8309, correlation about mean = 0.792, overlap = 2.017e+04 
    6386 steps = 260, shift = 12.3, angle = 56 degrees 
    6387  
    6388 Position of cryosparc_P141_J36_001_volume_map.mrc (#17) relative to preF_DS-
    6389 Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates: 
    6390 Matrix rotation and translation 
    6391 0.70324932 0.68336034 0.19610977 -193.58828243 
    6392 -0.22024758 -0.05286234 0.97401056 49.89143717 
    6393 0.67596701 -0.72816497 0.11333305 212.37654719 
    6394 Axis -0.85709001 -0.24162070 -0.45499028 
    6395 Axis point 0.00000000 175.75273055 124.55920872 
    6396 Rotation angle (degrees) 96.78476794 
    6397 Shift along axis 57.23851454 
    6398  
    6399 
    6400 > transparency #17 50
    6401 
    6402 > ui mousemode right "rotate selected models"
    6403 
    6404 > view matrix models
    6405 > #17,0.9628,0.038849,0.2674,-126.46,-0.2702,0.13329,0.95353,23.314,0.0014013,-0.99031,0.13883,442.49
    6406 
    6407 > fitmap #17 inMap #8
    6408 
    6409 Fit map cryosparc_P141_J36_001_volume_map.mrc in map preF_DS-
    6410 Cav1_20A_7mpg_Box208_0-045.mrc using 73461 points 
    6411 correlation = 0.8309, correlation about mean = 0.792, overlap = 2.017e+04 
    6412 steps = 204, shift = 15.3, angle = 42.5 degrees 
    6413  
    6414 Position of cryosparc_P141_J36_001_volume_map.mrc (#17) relative to preF_DS-
    6415 Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates: 
    6416 Matrix rotation and translation 
    6417 0.70318709 0.68336267 0.19632468 -193.61262830 
    6418 -0.22050568 -0.05290549 0.97394982 49.97965908 
    6419 0.67594760 -0.72815964 0.11348290 212.35349781 
    6420 Axis -0.85705446 -0.24150208 -0.45512020 
    6421 Axis point 0.00000000 175.78346196 124.52896371 
    6422 Rotation angle (degrees) 96.78348511 
    6423 Shift along axis 57.22000862 
    6424  
    6425 
    6426 > view matrix models
    6427 > #17,0.68912,0.63077,0.35672,-217.8,-0.40196,-0.076857,0.91242,117.31,0.60295,-0.77216,0.20058,219.93
    6428 
    6429 > ui mousemode right "translate selected models"
    6430 
    6431 > view matrix models
    6432 > #17,0.68912,0.63077,0.35672,-190.71,-0.40196,-0.076857,0.91242,116.87,0.60295,-0.77216,0.20058,145.6
    6433 
    6434 > view matrix models
    6435 > #17,0.68912,0.63077,0.35672,-190.77,-0.40196,-0.076857,0.91242,115.14,0.60295,-0.77216,0.20058,150.93
    6436 
    6437 > ui mousemode right "rotate selected models"
    6438 
    6439 > view matrix models
    6440 > #17,0.92014,0.31176,0.23695,-145.26,-0.22946,-0.061074,0.9714,52.068,0.31731,-0.9482,0.015339,312.65
    6441 
    6442 > ui mousemode right "translate selected models"
    6443 
    6444 > view matrix models
    6445 > #17,0.92014,0.31176,0.23695,-167.69,-0.22946,-0.061074,0.9714,55.779,0.31731,-0.9482,0.015339,389.3
    6446 
    6447 > fitmap #17 inMap #8
    6448 
    6449 Fit map cryosparc_P141_J36_001_volume_map.mrc in map preF_DS-
    6450 Cav1_20A_7mpg_Box208_0-045.mrc using 73461 points 
    6451 correlation = 0.8309, correlation about mean = 0.792, overlap = 2.017e+04 
    6452 steps = 136, shift = 6.81, angle = 25 degrees 
    6453  
    6454 Position of cryosparc_P141_J36_001_volume_map.mrc (#17) relative to preF_DS-
    6455 Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates: 
    6456 Matrix rotation and translation 
    6457 0.70317534 0.68336839 0.19634684 -193.61854025 
    6458 -0.22051976 -0.05292473 0.97394559 49.98975812 
    6459 0.67595523 -0.72815288 0.11348086 212.34915105 
    6460 Axis -0.85705062 -0.24149523 -0.45513107 
    6461 Axis point 0.00000000 175.78569670 124.52495634 
    6462 Rotation angle (degrees) 96.78443776 
    6463 Shift along axis 57.22190560 
    6464  
    6465 
    6466 > hide #!13 models
    6467 
    6468 > hide #!16 models
    6469 
    6470 > hide #!21 models
    6471 
    6472 > view matrix models
    6473 > #17,0.70318,0.68337,0.19635,-194.4,-0.22052,-0.052925,0.97395,49.39,0.67596,-0.72815,0.11348,212.42
    6474 
    6475 > ui mousemode right zoom
    6476 
    6477 > ui mousemode right "translate selected models"
    6478 
    6479 > view matrix models
    6480 > #17,0.70318,0.68337,0.19635,-155.24,-0.22052,-0.052925,0.97395,42.132,0.67596,-0.72815,0.11348,202.16
    6481 
    6482 > ui mousemode right "rotate selected models"
    6483 
    6484 > view matrix models
    6485 > #17,0.8757,-0.44406,0.18964,68.194,-0.11865,0.18281,0.97596,-40.42,-0.46805,-0.87715,0.10739,534.82
    6486 
    6487 > ui mousemode right "translate selected models"
    6488 
    6489 > view matrix models
    6490 > #17,0.8757,-0.44406,0.18964,50.163,-0.11865,0.18281,0.97596,-35.908,-0.46805,-0.87715,0.10739,539.61
    6491 
    6492 > ui mousemode right "rotate selected models"
    6493 
    6494 > view matrix models
    6495 > #17,0.94068,-0.31789,0.11859,21.277,-0.21114,-0.27486,0.93801,105.63,-0.26559,-0.90741,-0.32568,602.49
    6496 
    6497 > view matrix models
    6498 > #17,0.91479,-0.33946,0.21892,8.0263,-0.17628,0.15214,0.97251,-12.894,-0.36344,-0.92824,0.079335,531.62
    6499 
    6500 > ui mousemode right "translate selected models"
    6501 
    6502 > view matrix models
    6503 > #17,0.91479,-0.33946,0.21892,10.097,-0.17628,0.15214,0.97251,-18.102,-0.36344,-0.92824,0.079335,539.07
    6504 
    6505 > fitmap #17 inMap #8
    6506 
    6507 Fit map cryosparc_P141_J36_001_volume_map.mrc in map preF_DS-
    6508 Cav1_20A_7mpg_Box208_0-045.mrc using 73461 points 
    6509 correlation = 0.8309, correlation about mean = 0.792, overlap = 2.017e+04 
    6510 steps = 252, shift = 4.47, angle = 55.9 degrees 
    6511  
    6512 Position of cryosparc_P141_J36_001_volume_map.mrc (#17) relative to preF_DS-
    6513 Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates: 
    6514 Matrix rotation and translation 
    6515 0.24029116 -0.95069509 0.19605868 343.29956128 
    6516 0.06441283 0.21714764 0.97401124 -92.11385375 
    6517 -0.96856138 -0.22141760 0.11341562 503.63433465 
    6518 Axis -0.61196839 0.59619664 0.51965783 
    6519 Axis point 0.00000000 453.19259214 456.80776908 
    6520 Rotation angle (degrees) 102.39046528 
    6521 Shift along axis -3.28892408 
    6522  
    6523 
    6524 > hide #!17 models
    6525 
    6526 > show #!17 models
    6527 
    6528 > hide #!8 models
    6529 
    6530 > show #!12 models
    6531 
    6532 > fitmap #12 inMap #17
    6533 
    6534 Fit molecule 4zyp_Mota_AM14.pdb (#12) to map
    6535 cryosparc_P141_J36_001_volume_map.mrc (#17) using 10446 atoms 
    6536 average map value = 2.45, steps = 56 
    6537 shifted from previous position = 2.1 
    6538 rotated from previous position = 3.55 degrees 
    6539 atoms outside contour = 220, contour level = 1.0576 
    6540  
    6541 Position of 4zyp_Mota_AM14.pdb (#12) relative to
    6542 cryosparc_P141_J36_001_volume_map.mrc (#17) coordinates: 
    6543 Matrix rotation and translation 
    6544 -0.75383878 -0.14056332 0.64184815 274.61567558 
    6545 -0.18599955 0.98254436 -0.00327799 274.55087929 
    6546 -0.63018352 -0.12185454 -0.76682476 264.50115086 
    6547 Axis -0.09275720 0.99505418 -0.03554275 
    6548 Axis point 199.66307778 0.00000000 83.28346891 
    6549 Rotation angle (degrees) 140.26951543 
    6550 Shift along axis 238.31932015 
    6551  
    6552 
    6553 > fitmap #12 inMap #17
    6554 
    6555 Fit molecule 4zyp_Mota_AM14.pdb (#12) to map
    6556 cryosparc_P141_J36_001_volume_map.mrc (#17) using 10446 atoms 
    6557 average map value = 2.45, steps = 28 
    6558 shifted from previous position = 0.00419 
    6559 rotated from previous position = 0.0184 degrees 
    6560 atoms outside contour = 220, contour level = 1.0576 
    6561  
    6562 Position of 4zyp_Mota_AM14.pdb (#12) relative to
    6563 cryosparc_P141_J36_001_volume_map.mrc (#17) coordinates: 
    6564 Matrix rotation and translation 
    6565 -0.75392157 -0.14068518 0.64172419 274.62320626 
    6566 -0.18624007 0.98249835 -0.00340870 274.56071911 
    6567 -0.63001341 -0.12208466 -0.76692793 264.49389002 
    6568 Axis -0.09285523 0.99504143 -0.03564336 
    6569 Axis point 199.67028025 0.00000000 83.30375891 
    6570 Rotation angle (degrees) 140.27991354 
    6571 Shift along axis 238.27163930 
    6572  
    6573 
    6574 > fitmap #12 inMap #17
    6575 
    6576 Fit molecule 4zyp_Mota_AM14.pdb (#12) to map
    6577 cryosparc_P141_J36_001_volume_map.mrc (#17) using 10446 atoms 
    6578 average map value = 2.45, steps = 44 
    6579 shifted from previous position = 0.0467 
    6580 rotated from previous position = 0.0218 degrees 
    6581 atoms outside contour = 219, contour level = 1.0576 
    6582  
    6583 Position of 4zyp_Mota_AM14.pdb (#12) relative to
    6584 cryosparc_P141_J36_001_volume_map.mrc (#17) coordinates: 
    6585 Matrix rotation and translation 
    6586 -0.75416077 -0.14066488 0.64144752 274.61545734 
    6587 -0.18612770 0.98251977 -0.00337391 274.51436054 
    6588 -0.62976028 -0.12193563 -0.76715950 264.48869026 
    6589 Axis -0.09280514 0.99504815 -0.03558639 
    6590 Axis point 199.62614812 0.00000000 83.32625385 
    6591 Rotation angle (degrees) 140.30006211 
    6592 Shift along axis 238.25708308 
    6593  
    6594 
    6595 > select add #12
    6596 
    6597 10446 atoms, 10621 bonds, 3 pseudobonds, 1347 residues, 4 models selected 
    6598 
    6599 > view matrix models
    6600 > #12,-0.12774,-0.99178,0.0069335,230.82,-0.70239,0.085525,-0.70664,232.16,0.70024,-0.095134,-0.70754,200,#17,0.24029,-0.9507,0.19606,373.96,0.064413,0.21715,0.97401,-102.75,-0.96856,-0.22142,0.11342,496.77
    6601 
    6602 > volume #17 level 1.667
    6603 
    6604 > transparency #17 0
    6605 
    6606 > set bgColor black
    6607 
    6608 > set bgColor transparent
    6609 
    6610 > lighting soft
    6611 
    6612 > lighting simple
    6613 
    6614 > ui mousemode right "rotate selected models"
    6615 
    6616 > view matrix models
    6617 > #12,-0.23171,-0.95771,-0.17057,238.69,-0.85195,0.28442,-0.43965,239.85,0.46957,0.04344,-0.88183,216.26,#17,0.20006,-0.89727,0.39355,325.97,0.32049,0.43951,0.83912,-190.75,-0.92589,-0.041744,0.37549,382.67
    6618 
    6619 > select subtract #17
    6620 
    6621 10446 atoms, 10621 bonds, 3 pseudobonds, 1347 residues, 2 models selected 
    6622 
    6623 > view matrix models
    6624 > #12,-0.29588,-0.93972,-0.17143,241.58,-0.81142,0.34195,-0.474,239.48,0.50404,-0.0011431,-0.86368,213.96
    6625 
    6626 > undo
    6627 
    6628 [Repeated 2 time(s)]
    6629 
    6630 > select subtract #17
    6631 
    6632 10446 atoms, 10621 bonds, 3 pseudobonds, 1347 residues, 2 models selected 
    6633 
    6634 > view matrix models
    6635 > #12,-0.56325,-0.80162,0.2004,248.86,-0.42383,0.072085,-0.90287,223.16,0.70931,-0.59348,-0.38035,188.05
    6636 
    6637 > fitmap #12 inMap #17
    6638 
    6639 Fit molecule 4zyp_Mota_AM14.pdb (#12) to map
    6640 cryosparc_P141_J36_001_volume_map.mrc (#17) using 10446 atoms 
    6641 average map value = 2.45, steps = 104 
    6642 shifted from previous position = 2.45 
    6643 rotated from previous position = 35.3 degrees 
    6644 atoms outside contour = 1010, contour level = 1.6665 
    6645  
    6646 Position of 4zyp_Mota_AM14.pdb (#12) relative to
    6647 cryosparc_P141_J36_001_volume_map.mrc (#17) coordinates: 
    6648 Matrix rotation and translation 
    6649 -0.75394829 -0.14065966 0.64169840 274.63622876 
    6650 -0.18631825 0.98248303 -0.00355089 274.55457993 
    6651 -0.62995832 -0.12223731 -0.76694886 264.49003822 
    6652 Axis -0.09286893 0.99503717 -0.03572662 
    6653 Axis point 199.67752190 0.00000000 83.31477226 
    6654 Rotation angle (degrees) 140.28273670 
    6655 Shift along axis 238.23750442 
    6656  
    6657 
    6658 > hide #!17 models
    6659 
    6660 > show #!17 models
    6661 
    6662 > hide #!17 models
    6663 
    6664 > show #!17 models
    6665 
    6666 > hide #!17 models
    6667 
    6668 > show #!17 models
    6669 
    6670 > hide #!17 models
    6671 
    6672 > show #!17 models
    6673 
    6674 > view matrix models
    6675 > #12,-0.52284,-0.81851,0.23806,246.45,-0.53039,0.093748,-0.84255,227.05,0.66732,-0.56679,-0.48315,191.47
    6676 
    6677 > fitmap #12 inMap #17
    6678 
    6679 Fit molecule 4zyp_Mota_AM14.pdb (#12) to map
    6680 cryosparc_P141_J36_001_volume_map.mrc (#17) using 10446 atoms 
    6681 average map value = 2.45, steps = 88 
    6682 shifted from previous position = 2.18 
    6683 rotated from previous position = 30.7 degrees 
    6684 atoms outside contour = 1005, contour level = 1.6665 
    6685  
    6686 Position of 4zyp_Mota_AM14.pdb (#12) relative to
    6687 cryosparc_P141_J36_001_volume_map.mrc (#17) coordinates: 
    6688 Matrix rotation and translation 
    6689 -0.75403314 -0.14065260 0.64160024 274.61373569 
    6690 -0.18621483 0.98250296 -0.00346098 274.56128623 
    6691 -0.62988733 -0.12208518 -0.76703139 264.48802707 
    6692 Axis -0.09283314 0.99504304 -0.03565618 
    6693 Axis point 199.64917664 0.00000000 83.31915691 
    6694 Rotation angle (degrees) 140.28934834 
    6695 Shift along axis 238.27640921 
    6696  
    6697 
    6698 > undo
    6699 
    6700 > fitmap #12 inMap #17
    6701 
    6702 Fit molecule 4zyp_Mota_AM14.pdb (#12) to map
    6703 cryosparc_P141_J36_001_volume_map.mrc (#17) using 10446 atoms 
    6704 average map value = 2.45, steps = 40 
    6705 shifted from previous position = 0.0106 
    6706 rotated from previous position = 0.00925 degrees 
    6707 atoms outside contour = 1008, contour level = 1.6665 
    6708  
    6709 Position of 4zyp_Mota_AM14.pdb (#12) relative to
    6710 cryosparc_P141_J36_001_volume_map.mrc (#17) coordinates: 
    6711 Matrix rotation and translation 
    6712 -0.75385541 -0.14064919 0.64180981 274.62420754 
    6713 -0.18636811 0.98247339 -0.00360001 274.54912593 
    6714 -0.63005472 -0.12232678 -0.76685540 264.49135574 
    6715 Axis -0.09288504 0.99503418 -0.03576788 
    6716 Axis point 199.68627639 0.00000000 83.31105650 
    6717 Rotation angle (degrees) 140.27481543 
    6718 Shift along axis 238.21699160 
    6719  
    6720 
    6721 > transparency #17 50
    6722 
    6723 > volume #17 level 1.113
    6724 
    6725 > hide #!17 models
    6726 
    6727 > select #12/A:166
    6728 
    6729 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6730 
    6731 > select up
    6732 
    6733 94 atoms, 93 bonds, 13 residues, 1 model selected 
    6734 
    6735 > select up
    6736 
    6737 3482 atoms, 3540 bonds, 449 residues, 1 model selected 
    6738 
    6739 > color sel purple
    6740 
    6741 > show #!17 models
    6742 
    6743 > select #17
    6744 
    6745 2 models selected 
    6746 
    6747 > show #!21 models
    6748 
    6749 > show #!8 models
    6750 
    6751 > select add #12
    6752 
    6753 10446 atoms, 10621 bonds, 3 pseudobonds, 1347 residues, 4 models selected 
    6754 
    6755 > ui mousemode right "translate selected models"
    6756 
    6757 > view matrix models
    6758 > #12,-0.12749,-0.99181,0.0072951,207.62,-0.70271,0.085135,-0.70637,237,0.69996,-0.095183,-0.70781,216.33,#17,0.24029,-0.9507,0.19606,350.79,0.064413,0.21715,0.97401,-97.929,-0.96856,-0.22142,0.11342,513.11
    6759 
    6760 > ui mousemode right "rotate selected models"
    6761 
    6762 > view matrix models
    6763 > #12,0.44166,-0.69451,-0.56798,202.21,-0.85766,-0.141,-0.49451,233.52,0.26335,0.70554,-0.65792,255.54,#17,-0.5998,-0.7626,0.24224,512.23,0.349,0.023089,0.93684,-116.45,-0.72003,0.64646,0.2523,209.06
    6764 
    6765 > view matrix models
    6766 > #12,-0.14812,-0.9886,-0.02695,208.45,-0.77331,0.13277,-0.61997,240.44,0.61648,-0.070989,-0.78417,219.67,#17,0.23341,-0.94357,0.23492,341.27,0.16639,0.27679,0.94641,-131.57,-0.95804,-0.18181,0.22161,474.07
    6767 
    6768 > ui mousemode right "translate selected models"
    6769 
    6770 > view matrix models
    6771 > #12,-0.14812,-0.9886,-0.02695,195.41,-0.77331,0.13277,-0.61997,243.95,0.61648,-0.070989,-0.78417,213.98,#17,0.23341,-0.94357,0.23492,328.23,0.16639,0.27679,0.94641,-128.06,-0.95804,-0.18181,0.22161,468.38
    6772 
    6773 > view matrix models
    6774 > #12,-0.14812,-0.9886,-0.02695,200,-0.77331,0.13277,-0.61997,242.57,0.61648,-0.070989,-0.78417,212.13,#17,0.23341,-0.94357,0.23492,332.82,0.16639,0.27679,0.94641,-129.44,-0.95804,-0.18181,0.22161,466.54
    6775 
    6776 > fitmap #17 inMap #8
    6777 
    6778 Fit map cryosparc_P141_J36_001_volume_map.mrc in map preF_DS-
    6779 Cav1_20A_7mpg_Box208_0-045.mrc using 70472 points 
    6780 correlation = 0.8345, correlation about mean = 0.7897, overlap = 2.012e+04 
    6781 steps = 72, shift = 2.54, angle = 6.92 degrees 
    6782  
    6783 Position of cryosparc_P141_J36_001_volume_map.mrc (#17) relative to preF_DS-
    6784 Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates: 
    6785 Matrix rotation and translation 
    6786 0.23853813 -0.95106427 0.19640853 343.75560813 
    6787 0.06546134 0.21753365 0.97385518 -92.36495526 
    6788 -0.96892433 -0.21944443 0.11414801 503.06545376 
    6789 Axis -0.61092202 0.59660416 0.52042075 
    6790 Axis point 0.00000000 453.78241748 457.42033457 
    6791 Rotation angle (degrees) 102.40907999 
    6792 Shift along axis -3.30748718 
    6793  
    6794 
    6795 > fitmap #12 inMap #17
    6796 
    6797 Fit molecule 4zyp_Mota_AM14.pdb (#12) to map
    6798 cryosparc_P141_J36_001_volume_map.mrc (#17) using 10446 atoms 
    6799 average map value = 2.45, steps = 56 
    6800 shifted from previous position = 2.28 
    6801 rotated from previous position = 6.93 degrees 
    6802 atoms outside contour = 242, contour level = 1.1129 
    6803  
    6804 Position of 4zyp_Mota_AM14.pdb (#12) relative to
    6805 cryosparc_P141_J36_001_volume_map.mrc (#17) coordinates: 
    6806 Matrix rotation and translation 
    6807 -0.75396462 -0.14067447 0.64167596 274.62896663 
    6808 -0.18642584 0.98246220 -0.00366406 274.53988973 
    6809 -0.62990694 -0.12238755 -0.76696710 264.48653786 
    6810 Axis -0.09290279 0.99503133 -0.03580108 
    6811 Axis point 199.67717545 0.00000000 83.32700147 
    6812 Rotation angle (degrees) 140.28522076 
    6813 Shift along axis 238.19309194 
    6814  
    6815 
    6816 > select clear
    6817 
    6818 > volume #17 level 0.301
    6819 
    6820 > select add #17
    6821 
    6822 2 models selected 
    6823 
    6824 > select add #12
    6825 
    6826 10446 atoms, 10621 bonds, 3 pseudobonds, 1347 residues, 4 models selected 
    6827 
    6828 > view matrix models
    6829 > #12,-0.12627,-0.99198,0.0059101,199.6,-0.70335,0.085322,-0.70571,243.41,0.69954,-0.093263,-0.70848,207.98,#17,0.23854,-0.95106,0.19641,343.25,0.065461,0.21753,0.97386,-91.856,-0.96892,-0.21944,0.11415,504.13
    6830 
    6831 > ui mousemode right "rotate selected models"
    6832 
    6833 > view matrix models
    6834 > #12,-0.41673,-0.81863,0.39519,213.89,-0.59279,-0.084849,-0.80087,234.48,0.68915,-0.56802,-0.44992,192.33,#17,0.68295,-0.72803,0.059594,210.45,-0.055017,0.030085,0.99803,-22.64,-0.72839,-0.68488,-0.019508,585.55
    6835 
    6836 > ui mousemode right "translate selected models"
    6837 
    6838 > view matrix models
    6839 > #12,-0.41673,-0.81863,0.39519,213.07,-0.59279,-0.084849,-0.80087,237.86,0.68915,-0.56802,-0.44992,195.1,#17,0.68295,-0.72803,0.059594,209.62,-0.055017,0.030085,0.99803,-19.257,-0.72839,-0.68488,-0.019508,588.33
    6840 
    6841 > view matrix models
    6842 > #12,-0.41673,-0.81863,0.39519,212.7,-0.59279,-0.084849,-0.80087,240.04,0.68915,-0.56802,-0.44992,194.06,#17,0.68295,-0.72803,0.059594,209.26,-0.055017,0.030085,0.99803,-17.073,-0.72839,-0.68488,-0.019508,587.29
    6843 
    6844 > view matrix models
    6845 > #12,-0.41673,-0.81863,0.39519,212.96,-0.59279,-0.084849,-0.80087,239.29,0.68915,-0.56802,-0.44992,194.14,#17,0.68295,-0.72803,0.059594,209.52,-0.055017,0.030085,0.99803,-17.827,-0.72839,-0.68488,-0.019508,587.37
    6846 
    6847 > ui mousemode right zoom
    6848 
    6849 > ui mousemode right "rotate selected models"
    6850 
    6851 > ui mousemode right "translate selected models"
    6852 
    6853 > view matrix models
    6854 > #12,-0.41673,-0.81863,0.39519,207.51,-0.59279,-0.084849,-0.80087,241.56,0.68915,-0.56802,-0.44992,193.87,#17,0.68295,-0.72803,0.059594,204.07,-0.055017,0.030085,0.99803,-15.552,-0.72839,-0.68488,-0.019508,587.1
    6855 
    6856 > view matrix models
    6857 > #12,-0.41673,-0.81863,0.39519,208.03,-0.59279,-0.084849,-0.80087,237.84,0.68915,-0.56802,-0.44992,194.9,#17,0.68295,-0.72803,0.059594,204.58,-0.055017,0.030085,0.99803,-19.274,-0.72839,-0.68488,-0.019508,588.13
    6858 
    6859 > view matrix models
    6860 > #12,-0.41673,-0.81863,0.39519,208.14,-0.59279,-0.084849,-0.80087,238.22,0.68915,-0.56802,-0.44992,194.55,#17,0.68295,-0.72803,0.059594,204.69,-0.055017,0.030085,0.99803,-18.892,-0.72839,-0.68488,-0.019508,587.78
    6861 
    6862 > view matrix models
    6863 > #12,-0.41673,-0.81863,0.39519,208.62,-0.59279,-0.084849,-0.80087,238.13,0.68915,-0.56802,-0.44992,193.1,#17,0.68295,-0.72803,0.059594,205.18,-0.055017,0.030085,0.99803,-18.982,-0.72839,-0.68488,-0.019508,586.33
    6864 
    6865 > view matrix models
    6866 > #12,-0.41673,-0.81863,0.39519,209.58,-0.59279,-0.084849,-0.80087,237.17,0.68915,-0.56802,-0.44992,198.86,#17,0.68295,-0.72803,0.059594,206.14,-0.055017,0.030085,0.99803,-19.946,-0.72839,-0.68488,-0.019508,592.09
    6867 
    6868 > ui mousemode right zoom
    6869 
    6870 > ui mousemode right "translate selected models"
    6871 
    6872 > view matrix models
    6873 > #12,-0.41673,-0.81863,0.39519,208.43,-0.59279,-0.084849,-0.80087,240.29,0.68915,-0.56802,-0.44992,198.81,#17,0.68295,-0.72803,0.059594,204.98,-0.055017,0.030085,0.99803,-16.823,-0.72839,-0.68488,-0.019508,592.04
    6874 
    6875 > view matrix models
    6876 > #12,-0.41673,-0.81863,0.39519,207.24,-0.59279,-0.084849,-0.80087,240.66,0.68915,-0.56802,-0.44992,196.58,#17,0.68295,-0.72803,0.059594,203.79,-0.055017,0.030085,0.99803,-16.456,-0.72839,-0.68488,-0.019508,589.81
    6877 
    6878 > view matrix models
    6879 > #12,-0.41673,-0.81863,0.39519,205.84,-0.59279,-0.084849,-0.80087,235.35,0.68915,-0.56802,-0.44992,195.4,#17,0.68295,-0.72803,0.059594,202.39,-0.055017,0.030085,0.99803,-21.763,-0.72839,-0.68488,-0.019508,588.63
    6880 
    6881 > ui mousemode right "rotate selected models"
    6882 
    6883 > view matrix models
    6884 > #12,-0.46523,-0.82013,0.3331,207.05,-0.57607,-0.0052031,-0.81739,237.6,0.67209,-0.57216,-0.47003,195.7,#17,0.67988,-0.72023,0.13795,181.58,-0.089433,0.10528,0.99041,-28.692,-0.72785,-0.6857,0.0071625,581.95
    6885 
    6886 > ui mousemode right "translate selected models"
    6887 
    6888 > view matrix models
    6889 > #12,-0.46523,-0.82013,0.3331,211.47,-0.57607,-0.0052031,-0.81739,234.38,0.67209,-0.57216,-0.47003,197.34,#17,0.67988,-0.72023,0.13795,186,-0.089433,0.10528,0.99041,-31.911,-0.72785,-0.6857,0.0071625,583.58
    6890 
    6891 > view matrix models
    6892 > #12,-0.46523,-0.82013,0.3331,211.51,-0.57607,-0.0052031,-0.81739,234.73,0.67209,-0.57216,-0.47003,198.33,#17,0.67988,-0.72023,0.13795,186.04,-0.089433,0.10528,0.99041,-31.566,-0.72785,-0.6857,0.0071625,584.58
    6893 
    6894 > view matrix models
    6895 > #12,-0.46523,-0.82013,0.3331,211.43,-0.57607,-0.0052031,-0.81739,234.73,0.67209,-0.57216,-0.47003,199.56,#17,0.67988,-0.72023,0.13795,185.97,-0.089433,0.10528,0.99041,-31.558,-0.72785,-0.6857,0.0071625,585.8
    6896 
    6897 > ui mousemode right "rotate selected models"
    6898 
    6899 > view matrix models
    6900 > #12,-0.48108,-0.80208,0.35386,212.51,-0.64197,0.047429,-0.76526,238.39,0.59702,-0.59532,-0.53773,200.73,#17,0.70262,-0.69963,0.1298,177.29,-0.013704,0.16908,0.98551,-64.92,-0.71144,-0.69421,0.10921,557.81
    6901 
    6902 > ui mousemode right "translate selected models"
    6903 
    6904 > view matrix models
    6905 > #12,-0.48108,-0.80208,0.35386,211.69,-0.64197,0.047429,-0.76526,237.5,0.59702,-0.59532,-0.53773,202.7,#17,0.70262,-0.69963,0.1298,176.47,-0.013704,0.16908,0.98551,-65.804,-0.71144,-0.69421,0.10921,559.79
    6906 
    6907 > view matrix models
    6908 > #12,-0.48108,-0.80208,0.35386,212.03,-0.64197,0.047429,-0.76526,236.16,0.59702,-0.59532,-0.53773,201.37,#17,0.70262,-0.69963,0.1298,176.81,-0.013704,0.16908,0.98551,-67.15,-0.71144,-0.69421,0.10921,558.46
    6909 
    6910 > view matrix models
    6911 > #12,-0.48108,-0.80208,0.35386,210.74,-0.64197,0.047429,-0.76526,237.81,0.59702,-0.59532,-0.53773,205.39,#17,0.70262,-0.69963,0.1298,175.53,-0.013704,0.16908,0.98551,-65.5,-0.71144,-0.69421,0.10921,562.47
    6912 
    6913 > fitmap #17 inMap #8
    6914 
    6915 Fit map cryosparc_P141_J36_001_volume_map.mrc in map preF_DS-
    6916 Cav1_20A_7mpg_Box208_0-045.mrc using 133800 points 
    6917 correlation = 0.802, correlation about mean = 0.7912, overlap = 2.048e+04 
    6918 steps = 176, shift = 3.59, angle = 29.8 degrees 
    6919  
    6920 Position of cryosparc_P141_J36_001_volume_map.mrc (#17) relative to preF_DS-
    6921 Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates: 
    6922 Matrix rotation and translation 
    6923 0.26333938 -0.94460316 0.19590110 335.87494626 
    6924 0.05857854 0.21835133 0.97411049 -90.92679362 
    6925 -0.96292311 -0.24504605 0.11283398 508.38801880 
    6926 Axis -0.62250579 0.59169989 0.51222825 
    6927 Axis point 0.00000000 447.45056315 450.88479824 
    6928 Rotation angle (degrees) 101.69709572 
    6929 Shift along axis -2.47476769 
    6930  
    6931 
    6932 > fitmap #17 inMap #8
    6933 
    6934 Fit map cryosparc_P141_J36_001_volume_map.mrc in map preF_DS-
    6935 Cav1_20A_7mpg_Box208_0-045.mrc using 133800 points 
    6936 correlation = 0.802, correlation about mean = 0.7912, overlap = 2.048e+04 
    6937 steps = 24, shift = 0.0114, angle = 0.0459 degrees 
    6938  
    6939 Position of cryosparc_P141_J36_001_volume_map.mrc (#17) relative to preF_DS-
    6940 Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates: 
    6941 Matrix rotation and translation 
    6942 0.26266838 -0.94479741 0.19586519 336.09755618 
    6943 0.05898515 0.21833646 0.97408928 -91.02138639 
    6944 -0.96308154 -0.24430932 0.11307910 508.18910564 
    6945 Axis -0.62214780 0.59179004 0.51255895 
    6946 Axis point 0.00000000 447.61634049 451.12147224 
    6947 Rotation angle (degrees) 101.70999009 
    6948 Shift along axis -2.49103089 
    6949  
    6950 
    6951 > fitmap #17 inMap #8
    6952 
    6953 Fit map cryosparc_P141_J36_001_volume_map.mrc in map preF_DS-
    6954 Cav1_20A_7mpg_Box208_0-045.mrc using 133800 points 
    6955 correlation = 0.802, correlation about mean = 0.7912, overlap = 2.048e+04 
    6956 steps = 24, shift = 0.00519, angle = 0.00771 degrees 
    6957  
    6958 Position of cryosparc_P141_J36_001_volume_map.mrc (#17) relative to preF_DS-
    6959 Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates: 
    6960 Matrix rotation and translation 
    6961 0.26255870 -0.94483912 0.19581103 336.14644425 
    6962 0.05903895 0.21828099 0.97409846 -91.02298534 
    6963 -0.96310816 -0.24419755 0.11309389 508.16796837 
    6964 Axis -0.62210531 0.59178539 0.51261588 
    6965 Axis point 0.00000000 447.63086447 451.15689773 
    6966 Rotation angle (degrees) 101.71438944 
    6967 Shift along axis -2.48959114 
    6968  
    6969 
    6970 > fitmap #17 inMap #8
    6971 
    6972 Fit map cryosparc_P141_J36_001_volume_map.mrc in map preF_DS-
    6973 Cav1_20A_7mpg_Box208_0-045.mrc using 133800 points 
    6974 correlation = 0.802, correlation about mean = 0.7912, overlap = 2.048e+04 
    6975 steps = 24, shift = 0.000512, angle = 0.00128 degrees 
    6976  
    6977 Position of cryosparc_P141_J36_001_volume_map.mrc (#17) relative to preF_DS-
    6978 Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates: 
    6979 Matrix rotation and translation 
    6980 0.26253816 -0.94484341 0.19581785 336.15163822 
    6981 0.05904075 0.21828599 0.97409723 -91.02458096 
    6982 -0.96311365 -0.24417646 0.11309267 508.16428247 
    6983 Axis -0.62209501 0.59179273 0.51261990 
    6984 Axis point 0.00000000 447.63777500 451.16158673 
    6985 Rotation angle (degrees) 101.71487962 
    6986 Shift along axis -2.49081979 
    6987  
    6988 
    6989 > ui mousemode right "rotate selected models"
    6990 
    6991 > ui mousemode right "translate selected models"
    6992 
    6993 > view matrix models
    6994 > #12,-0.48108,-0.80208,0.35386,209.08,-0.64197,0.047429,-0.76526,234.23,0.59702,-0.59532,-0.53773,204.69,#17,0.26254,-0.94484,0.19582,334.28,0.059041,0.21829,0.9741,-95.231,-0.96311,-0.24418,0.11309,507.5
    6995 
    6996 > fitmap #17 inMap #8
    6997 
    6998 Fit map cryosparc_P141_J36_001_volume_map.mrc in map preF_DS-
    6999 Cav1_20A_7mpg_Box208_0-045.mrc using 133800 points 
    7000 correlation = 0.802, correlation about mean = 0.7912, overlap = 2.048e+04 
    7001 steps = 56, shift = 4, angle = 0.0202 degrees 
    7002  
    7003 Position of cryosparc_P141_J36_001_volume_map.mrc (#17) relative to preF_DS-
    7004 Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates: 
    7005 Matrix rotation and translation 
    7006 0.26243896 -0.94484804 0.19592848 336.12597123 
    7007 0.05870710 0.21830347 0.97411347 -90.93814216 
    7008 -0.96316108 -0.24414293 0.11276062 508.21187058 
    7009 Axis -0.62211346 0.59189939 0.51247435 
    7010 Axis point 0.00000000 447.64140705 451.06093433 
    7011 Rotation angle (degrees) 101.72698571 
    7012 Shift along axis -2.48917384 
    7013  
    7014 
    7015 > volume #17 level 0.7131
    7016 
    7017 > volume #17 level 0.9161
    7018 
    7019 > fitmap #17 inMap #8
    7020 
    7021 Fit map cryosparc_P141_J36_001_volume_map.mrc in map preF_DS-
    7022 Cav1_20A_7mpg_Box208_0-045.mrc using 82019 points 
    7023 correlation = 0.8223, correlation about mean = 0.7974, overlap = 2.027e+04 
    7024 steps = 48, shift = 0.136, angle = 1 degrees 
    7025  
    7026 Position of cryosparc_P141_J36_001_volume_map.mrc (#17) relative to preF_DS-
    7027 Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates: 
    7028 Matrix rotation and translation 
    7029 0.24597805 -0.94908637 0.19679903 341.20213079 
    7030 0.06301258 0.21826572 0.97385290 -92.10297104 
    7031 -0.96722500 -0.22714562 0.11349296 504.71777770 
    7032 Axis -0.61434813 0.59543452 0.51772011 
    7033 Axis point 0.00000000 451.89119580 455.38995867 
    7034 Rotation angle (degrees) 102.18867732 
    7035 Shift along axis -3.15563373 
    7036  
    7037 
    7038 > ui mousemode right "rotate selected models"
    7039 
    7040 > view matrix models
    7041 > #12,0.14478,-0.97394,-0.17459,197.38,-0.74565,0.0085955,-0.66629,233.93,0.65042,0.22665,-0.72497,231.5,#17,-0.57574,-0.79053,0.20875,512.98,0.17985,0.12661,0.97551,-101.72,-0.7976,0.59919,0.069283,277.02
    7042 
    7043 > ui mousemode right "translate selected models"
    7044 
    7045 > view matrix models
    7046 > #12,0.14478,-0.97394,-0.17459,188.82,-0.74565,0.0085955,-0.66629,234.68,0.65042,0.22665,-0.72497,213.76,#17,-0.57574,-0.79053,0.20875,504.42,0.17985,0.12661,0.97551,-100.97,-0.7976,0.59919,0.069283,259.29
    7047 
    7048 > fitmap #17 inMap #8
    7049 
    7050 Fit map cryosparc_P141_J36_001_volume_map.mrc in map preF_DS-
    7051 Cav1_20A_7mpg_Box208_0-045.mrc using 82019 points 
    7052 correlation = 0.8223, correlation about mean = 0.7974, overlap = 2.027e+04 
    7053 steps = 244, shift = 3.92, angle = 50.1 degrees 
    7054  
    7055 Position of cryosparc_P141_J36_001_volume_map.mrc (#17) relative to preF_DS-
    7056 Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates: 
    7057 Matrix rotation and translation 
    7058 0.24595697 -0.94915233 0.19650703 341.29093539 
    7059 0.06298376 0.21795680 0.97392396 -92.03239153 
    7060 -0.96723224 -0.22716664 0.11338917 504.74584026 
    7061 Axis -0.61442468 0.59531740 0.51776394 
    7062 Axis point 0.00000000 451.81499078 455.37215285 
    7063 Rotation angle (degrees) 102.20139130 
    7064 Shift along axis -3.14686612 
    7065  
    7066 
    7067 > fitmap #17 inMap #8
    7068 
    7069 Fit map cryosparc_P141_J36_001_volume_map.mrc in map preF_DS-
    7070 Cav1_20A_7mpg_Box208_0-045.mrc using 82019 points 
    7071 correlation = 0.8223, correlation about mean = 0.7974, overlap = 2.027e+04 
    7072 steps = 28, shift = 0.02, angle = 0.00572 degrees 
    7073  
    7074 Position of cryosparc_P141_J36_001_volume_map.mrc (#17) relative to preF_DS-
    7075 Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates: 
    7076 Matrix rotation and translation 
    7077 0.24596145 -0.94915694 0.19647915 341.31667969 
    7078 0.06308318 0.21795208 0.97391858 -92.05723234 
    7079 -0.96722462 -0.22715189 0.11348365 504.72349239 
    7080 Axis -0.61440799 0.59529304 0.51781176 
    7081 Axis point 0.00000000 451.82706073 455.40596199 
    7082 Rotation angle (degrees) 102.19862946 
    7083 Shift along axis -3.15696319 
    7084  
    7085 
    7086 > fitmap #12 inMap #17
    7087 
    7088 Fit molecule 4zyp_Mota_AM14.pdb (#12) to map
    7089 cryosparc_P141_J36_001_volume_map.mrc (#17) using 10446 atoms 
    7090 average map value = 2.45, steps = 76 
    7091 shifted from previous position = 8.36 
    7092 rotated from previous position = 19.6 degrees 
    7093 atoms outside contour = 176, contour level = 0.9161 
    7094  
    7095 Position of 4zyp_Mota_AM14.pdb (#12) relative to
    7096 cryosparc_P141_J36_001_volume_map.mrc (#17) coordinates: 
    7097 Matrix rotation and translation 
    7098 -0.75414553 -0.14067198 0.64146388 274.60252920 
    7099 -0.18620159 0.98250551 -0.00344853 274.54253886 
    7100 -0.62975669 -0.12204229 -0.76714548 264.48668317 
    7101 Axis -0.09282891 0.99504408 -0.03563817 
    7102 Axis point 199.62736777 0.00000000 83.33289175 
    7103 Rotation angle (degrees) 140.29938978 
    7104 Shift along axis 238.26505255 
    7105  
    7106 
    7107 > hide #!8 models
    7108 
    7109 > open /Users/szhang3/Library/CloudStorage/OneDrive-
    7110 > Moderna/RSV/RSVAmono_MEDI_Mota_model.pdb
    7111 
    7112 Chain information for RSVAmono_MEDI_Mota_model.pdb #15 
    7113 --- 
    7114 Chain | Description 
    7115 B | No description available 
    7116 C | No description available 
    7117 D | No description available 
    7118 H | No description available 
    7119 L | No description available 
    7120  
    7121 
    7122 > hide sel atoms
    7123 
    7124 > show sel cartoons
    7125 
    7126 > hide sel atoms
    7127 
    7128 [Repeated 1 time(s)]
    7129 
    7130 > select subtract #17
    7131 
    7132 10446 atoms, 10621 bonds, 3 pseudobonds, 1347 residues, 2 models selected 
    7133 
    7134 > hide sel atoms
    7135 
    7136 [Repeated 1 time(s)]
    7137 
    7138 > show sel cartoons
    7139 
    7140 > select #15/L:199@NE2
    7141 
    7142 1 atom, 1 residue, 1 model selected 
    7143 
    7144 > select up
    7145 
    7146 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7147 
    7148 > select up
    7149 
    7150 50 atoms, 51 bonds, 7 residues, 1 model selected 
    7151 
    7152 > select up
    7153 
    7154 1619 atoms, 1654 bonds, 211 residues, 1 model selected 
    7155 
    7156 > select up
    7157 
    7158 10085 atoms, 10311 bonds, 1314 residues, 1 model selected 
    7159 
    7160 > hide sel atoms
    7161 
    7162 > show sel cartoons
    7163 
    7164 > hide #!17 models
    7165 
    7166 > select add #12/B:506
    7167 
    7168 10093 atoms, 10318 bonds, 1315 residues, 2 models selected 
    7169 Drag select of 492 residues, 2 pseudobonds 
    7170 
    7171 > select up
    7172 
    7173 4059 atoms, 4147 bonds, 2 pseudobonds, 545 residues, 4 models selected 
    7174 
    7175 > select up
    7176 
    7177 6474 atoms, 6642 bonds, 2 pseudobonds, 848 residues, 4 models selected 
    7178 
    7179 > select up
    7180 
    7181 20170 atoms, 20622 bonds, 6 pseudobonds, 2628 residues, 4 models selected 
    7182 
    7183 > ui tool show "Fit in Map"
    7184 
    7185 > ui tool show Matchmaker
    7186 
    7187 > matchmaker #!15 & sel to #21 & sel
    7188 
    7189 Computing secondary structure 
    7190 [Repeated 1 time(s)]  Parameters 
    7191 --- 
    7192 Chain pairing | bb 
    7193 Alignment algorithm | Needleman-Wunsch 
    7194 Similarity matrix | BLOSUM-62 
    7195 SS fraction | 0.3 
    7196 Gap open (HH/SS/other) | 18/18/6 
    7197 Gap extend | 1 
    7198 SS matrix |  |  | H | S | O 
    7199 ---|---|---|--- 
    7200 H | 6 | -9 | -6 
    7201 S |  | 6 | -6 
    7202 O |  |  | 4 
    7203 Iteration cutoff | 2 
    7204  
    7205 Matchmaker mono_MEDI_Mota, chain B (#21) with RSVAmono_MEDI_Mota_model.pdb,
    7206 chain B (#15), sequence alignment score = 2486.8 
    7207 RMSD between 449 pruned atom pairs is 0.000 angstroms; (across all 449 pairs:
    7208 0.000) 
    7209  
    7210 
    7211 > select clear
    7212 
    7213 > hide #!12 models
    7214 
    7215 > show #!12 models
    7216 
    7217 > hide #!15 models
    7218 
    7219 > show #!15 models
    7220 
    7221 > hide #!21 models
    7222 
    7223 > hide #!12 models
    7224 
    7225 Drag select of 320 residues, 1 pseudobonds 
    7226 
    7227 > select up
    7228 
    7229 2829 atoms, 2887 bonds, 1 pseudobond, 375 residues, 2 models selected 
    7230 
    7231 > select up
    7232 
    7233 6719 atoms, 6853 bonds, 1 pseudobond, 877 residues, 2 models selected 
    7234 
    7235 > delete atoms (#!15 & sel)
    7236 
    7237 > delete bonds (#!15 & sel)
    7238 
    7239 > show #!21 models
    7240 
    7241 > hide #!21 models
    7242 
    7243 > show #!21 models
    7244 
    7245 > hide #!21 models
    7246 
    7247 > show #!17 models
    7248 
    7249 > show #!12 models
    7250 
    7251 > select add #15
    7252 
    7253 3366 atoms, 3458 bonds, 1 pseudobond, 437 residues, 2 models selected 
    7254 
    7255 > select subtract #15
    7256 
    7257 Nothing selected 
    7258 
    7259 > select add #15
    7260 
    7261 3366 atoms, 3458 bonds, 1 pseudobond, 437 residues, 2 models selected 
    7262 
    7263 > view matrix models
    7264 > #15,0.99832,0.042098,0.039812,-8.9067,-0.039991,0.99783,-0.052307,33.148,-0.041927,0.050627,0.99784,-1.8934
    7265 
    7266 > ui mousemode right "rotate selected models"
    7267 
    7268 > view matrix models
    7269 > #15,0.51669,0.60051,0.61026,-166.8,-0.25736,0.78875,-0.55824,211.35,-0.81657,0.13138,0.56209,186.36
    7270 
    7271 > ui mousemode right "translate selected models"
    7272 
    7273 > view matrix models
    7274 > #15,0.51669,0.60051,0.61026,-184.23,-0.25736,0.78875,-0.55824,233.93,-0.81657,0.13138,0.56209,217.32
    7275 
    7276 > view matrix models
    7277 > #15,0.51669,0.60051,0.61026,-163.46,-0.25736,0.78875,-0.55824,237.06,-0.81657,0.13138,0.56209,234.95
    7278 
    7279 > ui mousemode right "rotate selected models"
    7280 
    7281 > view matrix models
    7282 > #15,0.45704,0.88924,0.019064,-84.944,0.22467,-0.094679,-0.96982,423.33,-0.86061,0.44753,-0.24306,351.24
    7283 
    7284 > view matrix models
    7285 > #15,0.34695,0.69419,0.63065,-161.22,0.6988,0.25715,-0.6675,223.99,-0.62555,0.67228,-0.39588,306.83
    7286 
    7287 > ui mousemode right "translate selected models"
    7288 
    7289 > view matrix models
    7290 > #15,0.34695,0.69419,0.63065,-155.21,0.6988,0.25715,-0.6675,218.39,-0.62555,0.67228,-0.39588,321.09
    7291 
    7292 > ui mousemode right "rotate selected models"
    7293 
    7294 > view matrix models
    7295 > #15,0.35664,0.91127,0.2059,-108.2,0.33944,0.078942,-0.93731,361.19,-0.8704,0.40417,-0.28117,383.24
    7296 
    7297 > ui mousemode right "translate selected models"
    7298 
    7299 > view matrix models
    7300 > #15,0.35664,0.91127,0.2059,-111.9,0.33944,0.078942,-0.93731,356.36,-0.8704,0.40417,-0.28117,377.47
    7301 
    7302 > fitmap #15 inMap #17
    7303 
    7304 Fit molecule RSVAmono_MEDI_Mota_model.pdb (#15) to map
    7305 cryosparc_P141_J36_001_volume_map.mrc (#17) using 3366 atoms 
    7306 average map value = 2.504, steps = 264 
    7307 shifted from previous position = 70.8 
    7308 rotated from previous position = 19 degrees 
    7309 atoms outside contour = 160, contour level = 0.9161 
    7310  
    7311 Position of RSVAmono_MEDI_Mota_model.pdb (#15) relative to
    7312 cryosparc_P141_J36_001_volume_map.mrc (#17) coordinates: 
    7313 Matrix rotation and translation 
    7314 0.95762749 -0.28800913 -0.00059252 162.69514121 
    7315 -0.24938915 -0.82818387 -0.50191287 549.31419915 
    7316 0.14406477 0.48079333 -0.86491799 288.76390270 
    7317 Axis 0.98859165 -0.14552365 0.03885127 
    7318 Axis point 0.00000000 248.24855247 216.92170178 
    7319 Rotation angle (degrees) 150.19674124 
    7320 Shift along axis 92.11969663 
    7321  
    7322 
    7323 > view matrix models
    7324 > #15,0.50055,0.8097,0.30631,-112.84,0.14636,0.26958,-0.95179,314.72,-0.85324,0.52126,0.01643,309.15
    7325 
    7326 > view matrix models
    7327 > #15,0.50055,0.8097,0.30631,-117.37,0.14636,0.26958,-0.95179,326.66,-0.85324,0.52126,0.01643,316.8
    7328 
    7329 > view matrix models
    7330 > #15,0.50055,0.8097,0.30631,-126.2,0.14636,0.26958,-0.95179,337.95,-0.85324,0.52126,0.01643,293.29
    7331 
    7332 > view matrix models
    7333 > #15,0.50055,0.8097,0.30631,-128.98,0.14636,0.26958,-0.95179,349.02,-0.85324,0.52126,0.01643,294.16
    7334 
    7335 > ui mousemode right "rotate selected models"
    7336 
    7337 > view matrix models
    7338 > #15,0.69146,0.71483,-0.10444,-51.479,0.10539,-0.24283,-0.96433,455.36,-0.71469,0.65579,-0.24324,303.46
    7339 
    7340 > fitmap #15 inMap #17
    7341 
    7342 Fit molecule RSVAmono_MEDI_Mota_model.pdb (#15) to map
    7343 cryosparc_P141_J36_001_volume_map.mrc (#17) using 3366 atoms 
    7344 average map value = 2.547, steps = 832 
    7345 shifted from previous position = 62.9 
    7346 rotated from previous position = 108 degrees 
    7347 atoms outside contour = 47, contour level = 0.9161 
    7348  
    7349 Position of RSVAmono_MEDI_Mota_model.pdb (#15) relative to
    7350 cryosparc_P141_J36_001_volume_map.mrc (#17) coordinates: 
    7351 Matrix rotation and translation 
    7352 0.29462335 -0.71397673 0.63516480 215.41870644 
    7353 0.67519967 -0.31482104 -0.66707805 366.69507471 
    7354 0.67624144 0.62539983 0.38932322 -72.28107957 
    7355 Axis 0.68100675 -0.02164329 0.73195722 
    7356 Axis point -40.28268173 259.62048826 0.00000000 
    7357 Rotation angle (degrees) 108.38721116 
    7358 Shift along axis 85.85844847 
    7359  
    7360 
    7361 > undo
    7362 
    7363 > ui mousemode right zoom
    7364 
    7365 > ui mousemode right "rotate selected models"
    7366 
    7367 > view matrix models
    7368 > #15,0.19483,0.82204,0.53506,-135.71,-0.049845,0.5531,-0.83162,297.73,-0.97957,0.13535,0.14873,358.02
    7369 
    7370 > view matrix models
    7371 > #15,0.57305,0.80444,-0.15651,-40.524,0.3457,-0.41044,-0.84382,427.27,-0.74304,0.42945,-0.5133,407.86
    7372 
    7373 > volume #17 level 0.8361
    7374 
    7375 > view matrix models
    7376 > #15,0.66079,0.69021,-0.2949,-2.0843,0.32345,-0.6164,-0.71793,443.16,-0.6773,0.37902,-0.63056,432.82
    7377 
    7378 > view matrix models
    7379 > #15,0.63533,0.77115,-0.040903,-67.588,0.23026,-0.23973,-0.94314,432.32,-0.73711,0.58979,-0.32988,337.61
    7380 
    7381 > view matrix models
    7382 > #15,0.52932,0.84143,0.10873,-97.387,0.33037,-0.08637,-0.93989,387.95,-0.78146,0.53342,-0.3237,353.45
    7383 
    7384 > view matrix models
    7385 > #15,0.71456,0.69799,-0.047018,-63.735,0.33911,-0.40437,-0.84941,428.25,-0.61189,0.59101,-0.52564,360.76
    7386 
    7387 > view matrix models
    7388 > #15,0.54901,-0.30078,0.77982,-24.158,-0.83521,-0.16191,0.52556,260.2,-0.031821,-0.93985,-0.3401,530.19
    7389 
    7390 > view matrix models
    7391 > #15,0.78148,-0.31664,0.53761,-3.3674,-0.62358,-0.36763,0.68993,234.24,-0.020819,-0.87441,-0.48475,546.71
    7392 
    7393 > fitmap #15 inMap #17
    7394 
    7395 Fit molecule RSVAmono_MEDI_Mota_model.pdb (#15) to map
    7396 cryosparc_P141_J36_001_volume_map.mrc (#17) using 3366 atoms 
    7397 average map value = 2.572, steps = 256 
    7398 shifted from previous position = 69.5 
    7399 rotated from previous position = 12 degrees 
    7400 atoms outside contour = 27, contour level = 0.83613 
    7401  
    7402 Position of RSVAmono_MEDI_Mota_model.pdb (#15) relative to
    7403 cryosparc_P141_J36_001_volume_map.mrc (#17) coordinates: 
    7404 Matrix rotation and translation 
    7405 0.23981198 0.83025195 0.50316192 -49.55829511 
    7406 -0.91635012 0.36474602 -0.16511455 346.76529763 
    7407 -0.32061298 -0.42147603 0.84827194 165.74602048 
    7408 Axis -0.13159822 0.42286896 -0.89658449 
    7409 Axis point 205.19400853 246.84698063 0.00000000 
    7410 Rotation angle (degrees) 76.91390262 
    7411 Shift along axis 4.55275294 
    7412  
    7413 
    7414 > undo
    7415 
    7416 > ui mousemode right "translate selected models"
    7417 
    7418 > view matrix models
    7419 > #15,0.54901,-0.30078,0.77982,-26.134,-0.83521,-0.16191,0.52556,259.46,-0.031821,-0.93985,-0.3401,529.99
    7420 
    7421 > view matrix models
    7422 > #15,0.54901,-0.30078,0.77982,-27.017,-0.83521,-0.16191,0.52556,261.44,-0.031821,-0.93985,-0.3401,526.93
    7423 
    7424 > ui mousemode right "rotate selected models"
    7425 
    7426 > view matrix models
    7427 > #15,0.5036,-0.58422,0.63646,63.936,-0.79588,-0.027129,0.60485,213.29,-0.33609,-0.81114,-0.47863,575.46
    7428 
    7429 > ui mousemode right "translate selected models"
    7430 
    7431 > view matrix models
    7432 > #15,0.5036,-0.58422,0.63646,63.014,-0.79588,-0.027129,0.60485,215.86,-0.33609,-0.81114,-0.47863,574.16
    7433 
    7434 > fitmap #15 inMap #17
    7435 
    7436 Fit molecule RSVAmono_MEDI_Mota_model.pdb (#15) to map
    7437 cryosparc_P141_J36_001_volume_map.mrc (#17) using 3366 atoms 
    7438 average map value = 2.572, steps = 256 
    7439 shifted from previous position = 69.6 
    7440 rotated from previous position = 31.8 degrees 
    7441 atoms outside contour = 27, contour level = 0.83613 
    7442  
    7443 Position of RSVAmono_MEDI_Mota_model.pdb (#15) relative to
    7444 cryosparc_P141_J36_001_volume_map.mrc (#17) coordinates: 
    7445 Matrix rotation and translation 
    7446 0.24068380 0.83093813 0.50161054 -49.46780136 
    7447 -0.91608696 0.36524164 -0.16547881 346.71221958 
    7448 -0.32071170 -0.41969081 0.84911933 165.23344332 
    7449 Axis -0.13052942 0.42223515 -0.89703933 
    7450 Axis point 205.48317396 246.57687629 0.00000000 
    7451 Rotation angle (degrees) 76.84875230 
    7452 Shift along axis 4.63019080 
    7453  
    7454 
    7455 > undo
    7456 
    7457 > view matrix models
    7458 > #15,0.5036,-0.58422,0.63646,63.883,-0.79588,-0.027129,0.60485,213.31,-0.33609,-0.81114,-0.47863,575.5
    7459 
    7460 > ui mousemode right zoom
    7461 
    7462 > select clear
    7463 
    7464 > open /Users/szhang3/Library/CloudStorage/OneDrive-
    7465 > Moderna/RSV/RSVAmono_MEDI_Mota_model.pdb
    7466 
    7467 Chain information for RSVAmono_MEDI_Mota_model.pdb #18 
    7468 --- 
    7469 Chain | Description 
    7470 B | No description available 
    7471 C | No description available 
    7472 D | No description available 
    7473 H | No description available 
    7474 L | No description available 
    7475  
    7476 
    7477 > select #18/L:160@CG
    7478 
    7479 1 atom, 1 residue, 1 model selected 
    7480 
    7481 > select #18/D:66@NH1
    7482 
    7483 1 atom, 1 residue, 1 model selected 
    7484 
    7485 > select up
    7486 
    7487 11 atoms, 10 bonds, 1 residue, 1 model selected 
    7488 
    7489 > select up
    7490 
    7491 19 atoms, 18 bonds, 2 residues, 1 model selected 
    7492 
    7493 > select up
    7494 
    7495 1042 atoms, 1072 bonds, 134 residues, 1 model selected 
    7496 
    7497 > select up
    7498 
    7499 1049 atoms, 1078 bonds, 135 residues, 1 model selected 
    7500 
    7501 > select up
    7502 
    7503 1626 atoms, 1671 bonds, 213 residues, 1 model selected 
    7504 
    7505 > select up
    7506 
    7507 10085 atoms, 10311 bonds, 1314 residues, 1 model selected 
    7508 
    7509 > select up
    7510 
    7511 40701 atoms, 41562 bonds, 5285 residues, 31 models selected 
    7512 
    7513 > select down
    7514 
    7515 10085 atoms, 10311 bonds, 1314 residues, 1 model selected 
    7516 
    7517 > select down
    7518 
    7519 1626 atoms, 1671 bonds, 213 residues, 1 model selected 
    7520 
    7521 > select up
    7522 
    7523 10085 atoms, 10311 bonds, 1314 residues, 1 model selected 
    7524 
    7525 > hide sel atoms
    7526 
    7527 > show sel cartoons
    7528 
    7529 > select clear
    7530 
    7531 > hide #!12 models
    7532 
    7533 > hide #!15 models
    7534 
    7535 > hide #!17 models
    7536 
    7537 Drag select of 412 residues, 2 pseudobonds 
    7538 
    7539 > select up
    7540 
    7541 3879 atoms, 3948 bonds, 2 pseudobonds, 504 residues, 2 models selected 
    7542 
    7543 > select up
    7544 
    7545 6719 atoms, 6853 bonds, 2 pseudobonds, 877 residues, 2 models selected 
    7546 
    7547 > delete atoms (#!18 & sel)
    7548 
    7549 > delete bonds (#!18 & sel)
    7550 
    7551 > open /Users/szhang3/Library/CloudStorage/OneDrive-
    7552 > Moderna/RSV/RSVAmono_MEDI_Mota_model.pdb
    7553 
    7554 Chain information for RSVAmono_MEDI_Mota_model.pdb #19 
    7555 --- 
    7556 Chain | Description 
    7557 B | No description available 
    7558 C | No description available 
    7559 D | No description available 
    7560 H | No description available 
    7561 L | No description available 
    7562  
    7563 
    7564 > hide #!18-19 atoms
    7565 
    7566 > show #!18-19 cartoons
    7567 
    7568 > select clear
    7569 
    7570 Drag select of 357 residues, 1 pseudobonds 
    7571 
    7572 > select up
    7573 
    7574 3498 atoms, 3559 bonds, 1 pseudobond, 451 residues, 2 models selected 
    7575 
    7576 > select up
    7577 
    7578 6719 atoms, 6853 bonds, 1 pseudobond, 877 residues, 2 models selected 
    7579 
    7580 > delete atoms (#!19 & sel)
    7581 
    7582 > delete bonds (#!19 & sel)
    7583 
    7584 > show #!17 models
    7585 
    7586 > show #!15 models
    7587 
    7588 > show #!12 models
    7589 
    7590 > select add #18
    7591 
    7592 3366 atoms, 3458 bonds, 1 pseudobond, 437 residues, 2 models selected 
    7593 
    7594 > ui mousemode right "translate selected models"
    7595 
    7596 > ui mousemode right "rotate selected models"
    7597 
    7598 > view matrix models
    7599 > #18,0.55429,0.10497,-0.82568,218.75,-0.57303,0.7676,-0.28709,187.56,0.60366,0.63227,0.48563,-98.776
    7600 
    7601 > view matrix models
    7602 > #18,0.63305,0.033195,-0.7734,210.06,-0.47624,0.80434,-0.35529,181.04,0.61028,0.59324,0.525,-100.61
    7603 
    7604 > ui mousemode right "translate selected models"
    7605 
    7606 > view matrix models
    7607 > #18,0.63305,0.033195,-0.7734,249.06,-0.47624,0.80434,-0.35529,224.92,0.61028,0.59324,0.525,-155.92
    7608 
    7609 > view matrix models
    7610 > #18,0.63305,0.033195,-0.7734,257.89,-0.47624,0.80434,-0.35529,218.35,0.61028,0.59324,0.525,-152.02
    7611 
    7612 > ui mousemode right "rotate selected models"
    7613 
    7614 > view matrix models
    7615 > #18,-0.33306,0.54093,0.77231,-26.862,-0.60108,-0.75288,0.26811,401.68,0.72648,-0.37492,0.57589,5.265
    7616 
    7617 > view matrix models
    7618 > #18,-0.37042,0.91343,0.16865,35.097,-0.73583,-0.39937,0.54686,294.65,0.56687,0.078465,0.82006,-109.93
    7619 
    7620 > ui mousemode right "translate selected models"
    7621 
    7622 > view matrix models
    7623 > #18,-0.37042,0.91343,0.16865,34.18,-0.73583,-0.39937,0.54686,292.61,0.56687,0.078465,0.82006,-109.39
    7624 
    7625 > view matrix models
    7626 > #18,-0.37042,0.91343,0.16865,34.659,-0.73583,-0.39937,0.54686,291.39,0.56687,0.078465,0.82006,-108.73
    7627 
    7628 > select subtract #18
    7629 
    7630 Nothing selected 
    7631 
    7632 > select add #19
    7633 
    7634 3366 atoms, 3458 bonds, 1 pseudobond, 437 residues, 2 models selected 
    7635 
    7636 > view matrix models #19,1,0,0,0.048033,0,1,0,-0.097133,0,0,1,0.18177
    7637 
    7638 > ui mousemode right "rotate selected models"
    7639 
    7640 > view matrix models
    7641 > #19,0.16657,0.081137,0.98269,-103.31,0.72911,-0.68107,-0.067351,230.04,0.66382,0.72771,-0.1726,13.746
    7642 
    7643 > view matrix models
    7644 > #19,-0.73965,-0.18703,0.64648,149.43,0.38059,-0.90849,0.1726,272.86,0.55504,0.37371,0.74315,-96.714
    7645 
    7646 > view matrix models
    7647 > #19,0.21338,0.96846,0.12869,-98.777,-0.83027,0.11033,0.54634,173.66,0.51491,-0.22343,0.82762,5.1646
    7648 
    7649 > ui mousemode right "translate selected models"
    7650 
    7651 > view matrix models
    7652 > #19,0.21338,0.96846,0.12869,16.157,-0.83027,0.11033,0.54634,172.66,0.51491,-0.22343,0.82762,-8.909
    7653 
    7654 > ui mousemode right "rotate selected models"
    7655 
    7656 > view matrix models
    7657 > #19,-0.74953,-0.64739,-0.13817,519.6,-0.45452,0.35155,0.81843,14.989,-0.48127,0.67623,-0.55775,255.78
    7658 
    7659 > ui mousemode right "translate selected models"
    7660 
    7661 > view matrix models
    7662 > #19,-0.74953,-0.64739,-0.13817,545.74,-0.45452,0.35155,0.81843,29.773,-0.48127,0.67623,-0.55775,294.13
    7663 
    7664 > view matrix models
    7665 > #19,-0.74953,-0.64739,-0.13817,538.74,-0.45452,0.35155,0.81843,16.554,-0.48127,0.67623,-0.55775,297.27
    7666 
    7667 > view matrix models
    7668 > #19,-0.74953,-0.64739,-0.13817,539.4,-0.45452,0.35155,0.81843,20.659,-0.48127,0.67623,-0.55775,302.02
    7669 
    7670 > ui mousemode right "rotate selected models"
    7671 
    7672 > view matrix models
    7673 > #19,-0.46575,-0.80685,-0.36342,576.62,-0.7528,0.14538,0.642,140.26,-0.46516,0.57259,-0.6751,344.3
    7674 
    7675 > view matrix models
    7676 > #19,-0.37055,-0.75396,-0.54243,590.69,-0.82322,-0.0038459,0.56771,194.59,-0.43012,0.65691,-0.61925,311.35
    7677 
    7678 > view matrix models
    7679 > #19,-0.43822,-0.65378,-0.61687,597.05,-0.57456,-0.32404,0.75158,181.02,-0.69126,0.68379,-0.23364,262.25
    7680 
    7681 > view matrix models
    7682 > #19,-0.58763,-0.57197,-0.57231,593.52,-0.52216,-0.27225,0.80823,151.61,-0.6181,0.77377,-0.13868,214.46
    7683 
    7684 > ui mousemode right "translate selected models"
    7685 
    7686 > view matrix models
    7687 > #19,-0.58763,-0.57197,-0.57231,585.56,-0.52216,-0.27225,0.80823,156.28,-0.6181,0.77377,-0.13868,221.39
    7688 
    7689 > view matrix models
    7690 > #19,-0.58763,-0.57197,-0.57231,583.23,-0.52216,-0.27225,0.80823,159.15,-0.6181,0.77377,-0.13868,217.39
    7691 
    7692 > select subtract #19
    7693 
    7694 Nothing selected 
    7695 
    7696 > select add #19
    7697 
    7698 3366 atoms, 3458 bonds, 1 pseudobond, 437 residues, 2 models selected 
    7699 
    7700 > select add #18
    7701 
    7702 6732 atoms, 6916 bonds, 2 pseudobonds, 874 residues, 4 models selected 
    7703 
    7704 > view matrix models
    7705 > #18,-0.37042,0.91343,0.16865,41.333,-0.73583,-0.39937,0.54686,295.03,0.56687,0.078465,0.82006,-107.94,#19,-0.58763,-0.57197,-0.57231,589.91,-0.52216,-0.27225,0.80823,162.78,-0.6181,0.77377,-0.13868,218.18
    7706 
    7707 > undo
    7708 
    7709 > select subtract #19
    7710 
    7711 3366 atoms, 3458 bonds, 1 pseudobond, 437 residues, 2 models selected 
    7712 
    7713 > view matrix models
    7714 > #18,-0.37042,0.91343,0.16865,42.288,-0.73583,-0.39937,0.54686,295.35,0.56687,0.078465,0.82006,-107.51
    7715 
    7716 > view matrix models
    7717 > #18,-0.37042,0.91343,0.16865,41.12,-0.73583,-0.39937,0.54686,294.52,0.56687,0.078465,0.82006,-107.34
    7718 
    7719 > select clear
    7720 
    7721 > color #17 #ebebebff models
    7722 
    7723 > transparency #17 50
    7724 
    7725 > set bgColor white
    7726 
    7727 > set bgColor #ffffff00
    7728 
    7729 > volume #17 level 1.039
    7730 
    7731 > color #15 silver
    7732 
    7733 > color #15 darkgrey
    7734 
    7735 > select clear
    7736 
    7737 > color #15 #fffb00ff
    7738 
    7739 > color #19 #fffb00ff
    7740 
    7741 > color #20 #fffb00ff
    7742 
    7743 > select clear
    7744 
    7745 > color #18 #fffb00ff
    7746 
    7747 > hide #!15 models
    7748 
    7749 > show #!15 models
    7750 
    7751 > hide #!15 models
    7752 
    7753 > hide #!18 models
    7754 
    7755 > hide #!19 models
    7756 
    7757 > show #!19 models
    7758 
    7759 > show #!18 models
    7760 
    7761 > show #!15 models
    7762 
    7763 > combine #15,18,19
    7764 
    7765 Remapping chain ID 'A' in RSVAmono_MEDI_Mota_model.pdb #18 to 'B' 
    7766 Remapping chain ID 'C' in RSVAmono_MEDI_Mota_model.pdb #18 to 'E' 
    7767 Remapping chain ID 'D' in RSVAmono_MEDI_Mota_model.pdb #18 to 'G' 
    7768 Remapping chain ID 'F' in RSVAmono_MEDI_Mota_model.pdb #18 to 'H' 
    7769 Remapping chain ID 'I' in RSVAmono_MEDI_Mota_model.pdb #18 to 'J' 
    7770 Remapping chain ID 'A' in RSVAmono_MEDI_Mota_model.pdb #19 to 'K' 
    7771 Remapping chain ID 'C' in RSVAmono_MEDI_Mota_model.pdb #19 to 'L' 
    7772 Remapping chain ID 'D' in RSVAmono_MEDI_Mota_model.pdb #19 to 'M' 
    7773 Remapping chain ID 'F' in RSVAmono_MEDI_Mota_model.pdb #19 to 'N' 
    7774 Remapping chain ID 'I' in RSVAmono_MEDI_Mota_model.pdb #19 to 'O' 
    7775 
    7776 > close #18-19
    7777 
    7778 > close #15
    7779 
    7780 > hide #!12 models
    7781 
    7782 > show #!12 models
    7783 
    7784 > combine #12,22
    7785 
    7786 Remapping chain ID 'A' in combination #22 to 'P' 
    7787 Remapping chain ID 'B' in combination #22 to 'Q' 
    7788 Remapping chain ID 'C' in combination #22 to 'R' 
    7789 
    7790 > hide #!22 models
    7791 
    7792 > hide #!15 models
    7793 
    7794 > close #15
    7795 
    7796 > show #!22 models
    7797 
    7798 > hide #!12 models
    7799 
    7800 > show #!12 models
    7801 
    7802 > hide #!12 models
    7803 
    7804 > show #!12 models
    7805 
    7806 > hide #!22 models
    7807 
    7808 > show #!22 models
    7809 
    7810 > combine #12,22
    7811 
    7812 Remapping chain ID 'A' in combination #22 to 'P' 
    7813 Remapping chain ID 'B' in combination #22 to 'Q' 
    7814 Remapping chain ID 'C' in combination #22 to 'R' 
    7815 
    7816 > hide #!22 models
    7817 
    7818 > show #!22 models
    7819 
    7820 > hide #!22 models
    7821 
    7822 > hide #!15 models
    7823 
    7824 > hide #!12 models
    7825 
    7826 > show #!12 models
    7827 
    7828 > hide #!12 models
    7829 
    7830 > show #!15 models
    7831 
    7832 > save "/Users/szhang3/OneDrive - Moderna/RSV/MAbs/102_RSVA-PreF-trimer.pdb"
    7833 > models #15 relModel #17
    7834 
    7835 > hide #!17 models
    7836 
    7837 > hide #!15 models
    7838 
    7839 > close #17
    7840 
    7841 > close #15
    7842 
    7843 > show #!22 models
    7844 
    7845 > close #22
    7846 
    7847 > show #!21 models
    7848 
    7849 > show #!20 models
    7850 
    7851 > hide #!20 models
    7852 
    7853 > show #!16 models
    7854 
    7855 > open /Users/szhang3/Library/CloudStorage/OneDrive-
    7856 > Moderna/RSV/RSVAmono_MEDI_Mota_model.pdb
    7857 
    7858 Chain information for RSVAmono_MEDI_Mota_model.pdb #15 
    7859 --- 
    7860 Chain | Description 
    7861 B | No description available 
    7862 C | No description available 
    7863 D | No description available 
    7864 H | No description available 
    7865 L | No description available 
    7866  
    7867 
    7868 > hide #!15,21 atoms
    7869 
    7870 > show #!15,21 cartoons
    7871 
    7872 > hide #!15 models
    7873 
    7874 > show #!15 models
    7875 
    7876 > hide #!21 models
    7877 
    7878 > show #!21 models
    7879 
    7880 > hide #!21 models
    7881 
    7882 > hide #!16 models
    7883 
    7884 Drag select of 200 residues 
    7885 
    7886 > select up
    7887 
    7888 2210 atoms, 2244 bonds, 279 residues, 1 model selected 
    7889 
    7890 > select up
    7891 
    7892 6145 atoms, 6265 bonds, 799 residues, 1 model selected 
    7893 
    7894 > delete atoms sel
    7895 
    7896 > delete bonds sel
    7897 
    7898 Drag select of 78 residues 
    7899 
    7900 > select up
    7901 
    7902 3940 atoms, 4046 bonds, 515 residues, 1 model selected 
    7903 
    7904 > select up
    7905 
    7906 31190 atoms, 31839 bonds, 4049 residues, 28 models selected 
    7907 
    7908 > select down
    7909 
    7910 3940 atoms, 4046 bonds, 515 residues, 1 model selected 
    7911 
    7912 > select down
    7913 
    7914 574 atoms, 78 residues, 1 model selected 
    7915 
    7916 > delete atoms sel
    7917 
    7918 > delete bonds sel
    7919 
    7920 > show #!16 models
    7921 
    7922 > show #!20 models
    7923 
    7924 > hide #!20 models
    7925 
    7926 > show #!21 models
    7927 
    7928 > hide #!15 models
    7929 
    7930 > show #!15 models
    7931 
    7932 > select add #15
    7933 
    7934 3366 atoms, 3458 bonds, 1 pseudobond, 437 residues, 2 models selected 
    7935 
    7936 > view matrix models #15,1,0,0,23.361,0,1,0,53.548,0,0,1,-12.247
    7937 
    7938 > ui mousemode right "rotate selected models"
    7939 
    7940 > view matrix models
    7941 > #15,-0.61272,0.4682,0.63668,31.486,-0.14783,0.7235,-0.67431,270.22,-0.77635,-0.50729,-0.37409,486.94
    7942 
    7943 > view matrix models
    7944 > #15,-0.60749,0.46833,0.64158,29.673,-0.15035,0.7253,-0.67181,269.71,-0.77997,-0.50458,-0.3702,486.12
    7945 
    7946 > view matrix models
    7947 > #15,-0.26951,0.7708,0.57726,-63.103,-0.78375,0.17274,-0.59657,450.43,-0.55956,-0.61321,0.55756,278.91
    7948 
    7949 > view matrix models
    7950 > #15,-0.23628,0.83096,0.50367,-63.802,-0.77933,0.14753,-0.609,457.23,-0.58036,-0.53642,0.61273,255.58
    7951 
    7952 > view matrix models
    7953 > #15,0.48556,0.41166,-0.77121,181.95,-0.80982,-0.12048,-0.57418,505.41,-0.32928,0.90334,0.27487,16.108
    7954 
    7955 > view matrix models
    7956 > #15,0.8129,0.25728,-0.5225,111.7,0.16214,-0.96164,-0.22126,451.4,-0.55938,0.095142,-0.82343,435.77
    7957 
    7958 > view matrix models
    7959 > #15,0.83049,0.32886,-0.44959,80.084,0.32753,-0.94115,-0.083402,394.52,-0.45056,-0.077992,-0.88933,467.09
    7960 
    7961 > view matrix models
    7962 > #15,0.44192,0.70749,-0.55151,85.307,0.23191,-0.68401,-0.69163,487.85,-0.86656,0.17775,-0.46635,388.7
    7963 
    7964 > ui mousemode right "translate selected models"
    7965 
    7966 > view matrix models
    7967 > #15,0.44192,0.70749,-0.55151,88.228,0.23191,-0.68401,-0.69163,489.07,-0.86656,0.17775,-0.46635,457.3
    7968 
    7969 > view matrix models
    7970 > #15,0.44192,0.70749,-0.55151,105.93,0.23191,-0.68401,-0.69163,490.02,-0.86656,0.17775,-0.46635,444.96
    7971 
    7972 > view matrix models
    7973 > #15,0.44192,0.70749,-0.55151,112.31,0.23191,-0.68401,-0.69163,495.87,-0.86656,0.17775,-0.46635,448.4
    7974 
    7975 > fitmap #15 inMap #16
    7976 
    7977 Fit molecule RSVAmono_MEDI_Mota_model.pdb (#15) to map
    7978 cryosparc_P141_J33_003_volume_map.mrc z flip resampled resampled (#16) using
    7979 3366 atoms 
    7980 average map value = 1.865, steps = 140 
    7981 shifted from previous position = 12.4 
    7982 rotated from previous position = 30.1 degrees 
    7983 atoms outside contour = 187, contour level = 1.1617 
    7984  
    7985 Position of RSVAmono_MEDI_Mota_model.pdb (#15) relative to
    7986 cryosparc_P141_J33_003_volume_map.mrc z flip resampled resampled (#16)
    7987 coordinates: 
    7988 Matrix rotation and translation 
    7989 -0.05745200 0.79150272 -0.60845928 185.43737272 
    7990 0.35509446 -0.55341035 -0.75342212 457.08323274 
    7991 -0.93306333 -0.25934613 -0.24926369 501.42714965 
    7992 Axis 0.67239520 0.44175836 -0.59391434 
    7993 Axis point 0.00000000 94.22720794 395.50982080 
    7994 Rotation angle (degrees) 158.44464219 
    7995 Shift along axis 28.80276358 
    7996  
    7997 
    7998 > select clear
    7999 
    8000 > ui mousemode right zoom
    8001 
    8002 > hide #!16 models
    8003 
    8004 > show #!16 models
    8005 
    8006 > hide #!16 models
    8007 
    8008 > color #15 #0433ffff
    8009 
    8010 > color #15 #00f900ff
    8011 
    8012 > color #15 #5eaf88ff
    8013 
    8014 > color #15 #00f900ff
    8015 
    8016 > select add #15
    8017 
    8018 3366 atoms, 3458 bonds, 1 pseudobond, 437 residues, 2 models selected 
    8019 
    8020 > color (#!15 & sel) forest green
    8021 
    8022 > show #!16 models
    8023 
    8024 > select clear
    8025 
    8026 > color #16 #a6ca8cff models
    8027 
    8028 > color #16 #8ec9a4ff models
    8029 
    8030 > color #16 #e6f1f7ff models
    8031 
    8032 > transparency 50
    8033 
    8034 > select clear
    8035 
    8036 > undo
    8037 
    8038 [Repeated 8 time(s)]
    8039 
    8040 > show #!16 models
    8041 
    8042 > transparency 50
    8043 
    8044 > select clear
    8045 
    8046 > combine #15,21
    8047 
    8048 Remapping chain ID 'A' in mono_MEDI_Mota #21 to 'E' 
    8049 Remapping chain ID 'C' in mono_MEDI_Mota #21 to 'G' 
    8050 Remapping chain ID 'D' in mono_MEDI_Mota #21 to 'J' 
    8051 Remapping chain ID 'F' in mono_MEDI_Mota #21 to 'K' 
    8052 Remapping chain ID 'I' in mono_MEDI_Mota #21 to 'M' 
    8053 
    8054 > hide #!17 models
    8055 
    8056 > hide #!15 models
    8057 
    8058 > hide #!21 models
    8059 
    8060 > show #!17 models
    8061 
    8062 > hide #!17 models
    8063 
    8064 > show #!17 models
    8065 
    8066 > hide #!16 models
    8067 
    8068 > show #!16 models
    8069 
    8070 > save "/Users/szhang3/OneDrive - Moderna/RSV/MAbs/101/101_RSVA-
    8071 > mono_MEDI_Mota.pdb" models #17 relModel #16
    8072 
    8073 > hide #!17 models
    8074 
    8075 > show #!17 models
    8076 
    8077 > save "/Users/szhang3/OneDrive -
    8078 > Moderna/RSV/MAbs/101/P141_J33_zflip_101_RSVA-mono_MEDI_Mota.mrc" models #16
    8079 
    8080 > open /Users/szhang3/Library/CloudStorage/OneDrive-
    8081 > Moderna/RSV/MAbs/101/101_RSVA-mono_MEDI_Mota.pdb
    8082 
    8083 Chain information for 101_RSVA-mono_MEDI_Mota.pdb #18 
    8084 --- 
    8085 Chain | Description 
    8086 B | No description available 
    8087 C G | No description available 
    8088 D J | No description available 
    8089 H | No description available 
    8090 L | No description available 
    8091  
    8092 
    8093 > open /Users/szhang3/Library/CloudStorage/OneDrive-
    8094 > Moderna/RSV/MAbs/101/P141_J33_zflip_101_RSVA-mono_MEDI_Mota.mrc
    8095 
    8096 Opened P141_J33_zflip_101_RSVA-mono_MEDI_Mota.mrc as #19, grid size
    8097 208,208,208, pixel 2, shown at level 0.0913, step 1, values float32 
    8098 
    8099 > volume #19 level 0.4148
    8100 
    8101 > hide #!16 models
    8102 
    8103 > hide #!17 models
    8104 
    8105 > hide #!18 models
    8106 
    8107 > show #!18 models
    8108 
    8109 > hide #!18 models
    8110 
    8111 > show #!18 models
    8112 
    8113 > hide #!19 models
    8114 
    8115 Drag select of 128 atoms 
    8116 
    8117 > select up
    8118 
    8119 13451 atoms, 13769 bonds, 1751 residues, 1 model selected 
    8120 
    8121 > select down
    8122 
    8123 128 atoms, 12 residues, 1 model selected 
    8124 
    8125 > select add #18/A:601@CL
    8126 
    8127 129 atoms, 13 residues, 1 model selected 
    8128 
    8129 > delete atoms sel
    8130 
    8131 > delete bonds sel
    8132 
    8133 > show #!19 models
    8134 
    8135 > hide #!18 atoms
    8136 
    8137 > show #!18 cartoons
    8138 
    8139 > hide #!19 models
    8140 
    8141 > show #!19 models
    8142 
    8143 > close #18-19
    8144 
    8145 > show #!20 models
    8146 
    8147 > show #!21 models
    8148 
    8149 > show #!17 models
    8150 
    8151 > hide #!17 models
    8152 
    8153 > show #!17 models
    8154 
    8155 > hide #!20 models
    8156 
    8157 > hide #!21 models
    8158 
    8159 > show #!12 models
    8160 
    8161 Drag select of 9 residues 
    8162 
    8163 > select up
    8164 
    8165 352 atoms, 352 bonds, 44 residues, 2 models selected 
    8166 
    8167 > select up
    8168 
    8169 6964 atoms, 7080 bonds, 898 residues, 2 models selected 
    8170 
    8171 > ui tool show Matchmaker
    8172 
    8173 > matchmaker #!12 & sel to #17 & sel
    8174 
    8175 Computing secondary structure 
    8176 [Repeated 1 time(s)]  Parameters 
    8177 --- 
    8178 Chain pairing | bb 
    8179 Alignment algorithm | Needleman-Wunsch 
    8180 Similarity matrix | BLOSUM-62 
    8181 SS fraction | 0.3 
    8182 Gap open (HH/SS/other) | 18/18/6 
    8183 Gap extend | 1 
    8184 SS matrix |  |  | H | S | O 
    8185 ---|---|---|--- 
    8186 H | 6 | -9 | -6 
    8187 S |  | 6 | -6 
    8188 O |  |  | 4 
    8189 Iteration cutoff | 2 
    8190  
    8191 Matchmaker combination, chain B (#17) with 4zyp_Mota_AM14.pdb, chain B (#12),
    8192 sequence alignment score = 2486.8 
    8193 RMSD between 449 pruned atom pairs is 0.000 angstroms; (across all 449 pairs:
    8194 0.000) 
    8195  
    8196 
    8197 > select clear
    8198 
    8199 > color #12 #d6d6d6ff
    8200 
    8201 > color #12 silver
    8202 
    8203 > color #12 darkgrey
    8204 
    8205 > color #12 silver
    8206 
    8207 > hide #!12 models
    8208 
    8209 > show #!12 models
    8210 
    8211 > hide #!12 models
    8212 
    8213 > hide #!17 models
    8214 
    8215 > show #!12 models
    8216 
    8217 > hide #!12 models
    8218 
    8219 > show #!17 models
    8220 
    8221 > show #!12 models
    8222 
    8223 > select #17/B:197
    8224 
    8225 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8226 Drag select of 7 residues 
    8227 
    8228 > select up
    8229 
    8230 61 atoms, 16 bonds, 7 residues, 2 models selected 
    8231 
    8232 > select up
    8233 
    8234 363 atoms, 364 bonds, 42 residues, 2 models selected 
    8235 
    8236 > select up
    8237 
    8238 10446 atoms, 10621 bonds, 1347 residues, 2 models selected 
    8239 
    8240 > select clear
    8241 
    8242 Drag select of 4 residues 
    8243 
    8244 > select up
    8245 
    8246 158 atoms, 158 bonds, 18 residues, 2 models selected 
    8247 
    8248 > select up
    8249 
    8250 6964 atoms, 7080 bonds, 898 residues, 2 models selected 
    8251 
    8252 > color sel gray
    8253 
    8254 > select clear
    8255 
    8256 > hide #12.1 models
    8257 
    8258 > hide #!17.1 models
    8259 
    8260 > select clear
    8261 
    8262 > show #!17.1 models
    8263 
    8264 > select #12/C:272
    8265 
    8266 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8267 
    8268 > select up
    8269 
    8270 80 atoms, 79 bonds, 10 residues, 1 model selected 
    8271 
    8272 > select up
    8273 
    8274 3482 atoms, 3541 bonds, 449 residues, 1 model selected 
    8275 
    8276 > color sel hot pink
    8277 
    8278 > select clear
    8279 
    8280 > select #12/C:56
    8281 
    8282 7 atoms, 6 bonds, 1 residue, 1 model selected 
    8283 
    8284 > select up
    8285 
    8286 82 atoms, 84 bonds, 10 residues, 1 model selected 
    8287 
    8288 > select up
    8289 
    8290 3482 atoms, 3541 bonds, 449 residues, 1 model selected 
    8291 
    8292 > color sel magenta
    8293 
    8294 > color sel orange
    8295 
    8296 > color sel hot pink
    8297 
    8298 > select clear
    8299 
    8300 Drag select of 125 residues 
    8301 
    8302 > view sel
    8303 
    8304 > select clear
    8305 
    8306 [Repeated 1 time(s)]
    8307 
    8308 > save "/Users/szhang3/OneDrive -
    8309 > Moderna/RSV/MAbs/101/101_trimer_monomer_3fabs.png" width 651 height 661
    8310 > supersample 3 transparentBackground true
    8311 
    8312 > movie record
    8313 
    8314 > turn y 2 180
    8315 
    8316 > wait 180
    8317 
    8318 > movie encode /Users/szhang3/Desktop/movie1.mp4
    8319 
    8320 Movie saved to /Users/szhang3/Desktop/movie1.mp4 
    8321  
    8322 
    8323 > show #!16 models
    8324 
    8325 > movie record
    8326 
    8327 > turn y 2 180
    8328 
    8329 > wait 180
    8330 
    8331 > movie encode /Users/szhang3/Desktop/movie2.mp4
    8332 
    8333 Movie saved to /Users/szhang3/Desktop/movie2.mp4 
    8334  
    8335 
    8336 > lighting soft
    8337 
    8338 > lighting simple
    8339 
    8340 > movie record
    8341 
    8342 > turn y 2 180
    8343 
    8344 > wait 180
    8345 
    8346 > movie encode /Users/szhang3/Desktop/movie3.mp4
    8347 
    8348 Movie saved to /Users/szhang3/Desktop/movie3.mp4 
    8349  
    8350 
    8351 > save "/Users/szhang3/OneDrive - Moderna/RSV/MAbs/fitting.cxs" includeMaps
    8352 > true
    8353 
    8354 > show #!21 models
    8355 
    8356 > hide #!17 models
    8357 
    8358 > show #!17 models
    8359 
    8360 > close #21
    8361 
    8362 > hide #!17 models
    8363 
    8364 > show #!17 models
    8365 
    8366 > hide #!12 models
    8367 
    8368 > show #!12 models
    8369 
    8370 > hide #!12 models
    8371 
    8372 > hide #!17 models
    8373 
    8374 > hide #!16 models
    8375 
    8376 > show #!15 models
    8377 
    8378 > hide #!15 models
    8379 
    8380 > close #15
    8381 
    8382 > show #!20 models
    8383 
    8384 > hide #!20 models
    8385 
    8386 > close #20
    8387 
    8388 > show #!17 models
    8389 
    8390 > show #!16 models
    8391 
    8392 > show #!14 models
    8393 
    8394 > show #!13 models
    8395 
    8396 > hide #!13 models
    8397 
    8398 > show #!13 models
    8399 
    8400 > hide #!16 models
    8401 
    8402 > hide #!17 models
    8403 
    8404 > hide #!14 models
    8405 
    8406 > hide #!13 models
    8407 
    8408 > show #!13 models
    8409 
    8410 > select add #13
    8411 
    8412 5 models selected 
    8413 
    8414 > view sel
    8415 
    8416 Window position QRect(1795,566 600x300) outside any known screen, using
    8417 primary screen 
    8418 
    8419 No displayed objects specified. 
    8420 
    8421 > close #13
    8422 
    8423 > show #!14 models
    8424 
    8425 > show #!12 models
    8426 
    8427 > hide #!14 models
    8428 
    8429 > show #!14 models
    8430 
    8431 > hide #!12 models
    8432 
    8433 > hide #!14 models
    8434 
    8435 > show #!12 models
    8436 
    8437 > show #!14 models
    8438 
    8439 > show #!17 models
    8440 
    8441 > hide #!14 models
    8442 
    8443 > hide #!17 models
    8444 
    8445 > hide #!12 models
    8446 
    8447 > show #!14 models
    8448 
    8449 > hide #!14 models
    8450 
    8451 > show #!17 models
    8452 
    8453 > hide #!17 models
    8454 
    8455 > show #!14 models
    8456 
    8457 > show #!12 models
    8458 
    8459 > hide #!12 models
    8460 
    8461 > hide #!14 models
    8462 
    8463 > show #!12 models
    8464 
    8465 > hide #!12 models
    8466 
    8467 > show #!14 models
    8468 
    8469 > close #14
    8470 
    8471 > show #!12 models
    8472 
    8473 > hide #!12 models
    8474 
    8475 > show #!11 models
    8476 
    8477 > hide #!11 models
    8478 
    8479 > show #!10 models
    8480 
    8481 > hide #!10 models
    8482 
    8483 > show #!12 models
    8484 
    8485 > show #!16 models
    8486 
    8487 > show #!17 models
    8488 
    8489 > open /Users/szhang3/Library/CloudStorage/OneDrive-
    8490 > Moderna/RSV/MAbs/102/102_RSVA-PreF-trimer.pdb
    8491 
    8492 Chain information for 102_RSVA-PreF-trimer.pdb #13 
    8493 --- 
    8494 Chain | Description 
    8495 A B C | No description available 
    8496 D G M | No description available 
    8497 E L R | No description available 
    8498  
    8499 
    8500 > open /Users/szhang3/Library/CloudStorage/OneDrive-
    8501 > Moderna/RSV/MAbs/102/cryosparc_P141_J36_001_volume_map.mrc
    8502 
    8503 Opened cryosparc_P141_J36_001_volume_map.mrc as #14, grid size 256,256,256,
    8504 pixel 2, shown at level 0.0693, step 1, values float32 
    8505 
    8506 > volume #14 level 0.7208
    8507 
    8508 > volume #14 level 1.044
    8509 
    8510 > transparency 50
    8511 
    8512 > hide #!17 models
    8513 
    8514 > show #!17 models
    8515 
    8516 > hide #!12 models
    8517 
    8518 > show #!12 models
    8519 
    8520 > hide #!12 models
    8521 
    8522 > hide #!13 models
    8523 
    8524 > show #!13 models
    8525 
    8526 > hide #!14 models
    8527 
    8528 > show #!14 models
    8529 
    8530 > show #!12 models
    8531 
    8532 > hide #!12 models
    8533 
    8534 > show #!11 models
    8535 
    8536 > hide #!11 models
    8537 
    8538 > show #!11 models
    8539 
    8540 > hide #!11 models
    8541 
    8542 > show #!12 models
    8543 
    8544 > hide #!17 models
    8545 
    8546 > show #!17 models
    8547 
    8548 > hide #!12 models
    8549 
    8550 > show #!12 models
    8551 
    8552 > hide #!12 models
    8553 
    8554 > hide #!13 models
    8555 
    8556 > show #!13 models
    8557 
    8558 > show #!12 models
    8559 
    8560 > hide #!12 models
    8561 
    8562 > show #!12 models
    8563 
    8564 > hide #!13 models
    8565 
    8566 > show #!13 models
    8567 
    8568 > hide #!13 models
    8569 
    8570 > show #!13 models
    8571 
    8572 > select add #12
    8573 
    8574 10446 atoms, 10621 bonds, 3 pseudobonds, 1347 residues, 2 models selected 
    8575 
    8576 > select subtract #12
    8577 
    8578 Nothing selected 
    8579 
    8580 > select add #13
    8581 
    8582 20544 atoms, 20995 bonds, 6 pseudobonds, 2658 residues, 2 models selected 
    8583 
    8584 > color #13 #424242ff
    8585 
    8586 > color #13 #00f900ff
    8587 
    8588 > color #13 #008f00ff
    8589 
    8590 > color #13 #919191ff
    8591 
    8592 > color #13 #009193ff
    8593 
    8594 > color #13 #4f8f00ff
    8595 
    8596 > color #13 #9437ffff
    8597 
    8598 > ui mousemode right "rotate selected models"
    8599 
    8600 > ui mousemode right zoom
    8601 
    8602 > ui mousemode right "translate selected models"
    8603 
    8604 > view matrix models #13,1,0,0,556.84,0,1,0,181.23,0,0,1,-206.43
    8605 
    8606 > view matrix models #13,1,0,0,513.32,0,1,0,205.36,0,0,1,-202.66
    8607 
    8608 > view matrix models #13,1,0,0,503.7,0,1,0,238.02,0,0,1,-237.5
    8609 
    8610 > view matrix models #13,1,0,0,501.73,0,1,0,236.59,0,0,1,-240.18
    8611 
    8612 > ui mousemode right zoom
    8613 
    8614 > hide #!12 models
    8615 
    8616 > hide #!14 models
    8617 
    8618 > show #!14 models
    8619 
    8620 > hide #!16 models
    8621 
    8622 > hide #!17 models
    8623 
    8624 > ui tool show "Side View"
    8625 
    8626 > hide sel atoms
    8627 
    8628 > show sel cartoons
    8629 
    8630 > ui mousemode right "rotate selected models"
    8631 
    8632 > view matrix models
    8633 > #13,0.4947,0.047412,0.86777,-59.308,-0.29285,0.94921,0.11509,98.704,-0.81823,-0.31106,0.48346,-220.74
    8634 
    8635 > ui mousemode right "translate selected models"
    8636 
    8637 > view matrix models
    8638 > #13,0.4947,0.047412,0.86777,-23.35,-0.29285,0.94921,0.11509,117.35,-0.81823,-0.31106,0.48346,-204.85
    8639 
    8640 > fitmap #13 inMap #14
    8641 
    8642 Fit molecule 102_RSVA-PreF-trimer.pdb (#13) to map
    8643 cryosparc_P141_J36_001_volume_map.mrc (#14) using 20544 atoms 
    8644 average map value = 1.953, steps = 100 
    8645 shifted from previous position = 14.8 
    8646 rotated from previous position = 13.6 degrees 
    8647 atoms outside contour = 2141, contour level = 1.0438 
    8648  
    8649 Position of 102_RSVA-PreF-trimer.pdb (#13) relative to
    8650 cryosparc_P141_J36_001_volume_map.mrc (#14) coordinates: 
    8651 Matrix rotation and translation 
    8652 0.55034274 0.16955768 0.81754088 11.73024931 
    8653 -0.19355143 0.97839830 -0.07262672 220.25650910 
    8654 -0.81219501 -0.11826661 0.57127252 -254.99367436 
    8655 Axis -0.02732403 0.97570255 -0.21738890 
    8656 Axis point -177.74270461 0.00000000 -121.13339893 
    8657 Rotation angle (degrees) 56.63252247 
    8658 Shift along axis 270.01711300 
    8659  
    8660 
    8661 > show #!16 models
    8662 
    8663 > show #!12 models
    8664 
    8665 > hide #!16 models
    8666 
    8667 > select add #14
    8668 
    8669 20544 atoms, 20995 bonds, 6 pseudobonds, 2658 residues, 4 models selected 
    8670 
    8671 > ui mousemode right "rotate selected models"
    8672 
    8673 > view matrix models
    8674 > #13,0.1273,0.63314,0.7635,-79.993,-0.94959,-0.14454,0.27819,-160.39,0.28649,-0.76042,0.58283,46.734,#14,0.8016,0.53938,0.25789,-142.44,-0.31968,0.022173,0.94727,80.019,0.50522,-0.84177,0.1902,274.71
    8675 
    8676 > ui mousemode right "translate selected models"
    8677 
    8678 > view matrix models
    8679 > #13,0.1273,0.63314,0.7635,-112.25,-0.94959,-0.14454,0.27819,-185.42,0.28649,-0.76042,0.58283,13.296,#14,0.8016,0.53938,0.25789,-174.7,-0.31968,0.022173,0.94727,54.989,0.50522,-0.84177,0.1902,241.28
    8680 
    8681 > view matrix models
    8682 > #13,0.1273,0.63314,0.7635,-136.19,-0.94959,-0.14454,0.27819,-177.84,0.28649,-0.76042,0.58283,18.694,#14,0.8016,0.53938,0.25789,-198.63,-0.31968,0.022173,0.94727,62.577,0.50522,-0.84177,0.1902,246.67
    8683 
    8684 > view matrix models
    8685 > #13,0.1273,0.63314,0.7635,-139.11,-0.94959,-0.14454,0.27819,-177.31,0.28649,-0.76042,0.58283,36.077,#14,0.8016,0.53938,0.25789,-201.55,-0.31968,0.022173,0.94727,63.1,0.50522,-0.84177,0.1902,264.06
    8686 
    8687 > view matrix models
    8688 > #13,0.1273,0.63314,0.7635,-131.93,-0.94959,-0.14454,0.27819,-182.03,0.28649,-0.76042,0.58283,39.082,#14,0.8016,0.53938,0.25789,-194.37,-0.31968,0.022173,0.94727,58.381,0.50522,-0.84177,0.1902,267.06
    8689 
    8690 > ui tool show Matchmaker
    8691 
    8692 > matchmaker #!13 & sel to #12 & sel
    8693 
    8694 No 'to' model specified 
    8695 
    8696 > select add #12
    8697 
    8698 30990 atoms, 31616 bonds, 9 pseudobonds, 4005 residues, 6 models selected 
    8699 
    8700 > ui tool show Matchmaker
    8701 
    8702 > matchmaker #!13 & sel to #12 & sel
    8703 
    8704 Computing secondary structure 
    8705 [Repeated 1 time(s)]  Parameters 
    8706 --- 
    8707 Chain pairing | bb 
    8708 Alignment algorithm | Needleman-Wunsch 
    8709 Similarity matrix | BLOSUM-62 
    8710 SS fraction | 0.3 
    8711 Gap open (HH/SS/other) | 18/18/6 
    8712 Gap extend | 1 
    8713 SS matrix |  |  | H | S | O 
    8714 ---|---|---|--- 
    8715 H | 6 | -9 | -6 
    8716 S |  | 6 | -6 
    8717 O |  |  | 4 
    8718 Iteration cutoff | 2 
    8719  
    8720 Matchmaker 4zyp_Mota_AM14.pdb, chain A (#12) with 102_RSVA-PreF-trimer.pdb,
    8721 chain A (#13), sequence alignment score = 2489.2 
    8722 RMSD between 449 pruned atom pairs is 0.001 angstroms; (across all 449 pairs:
    8723 0.001) 
    8724  
    8725 
    8726 > ui tool show "Fit in Map"
    8727 
    8728 > fitmap #16 inMap #8
    8729 
    8730 Fit map P141_J33_zflip_101_RSVA-mono_MEDI_Mota.mrc in map preF_DS-
    8731 Cav1_20A_7mpg_Box208_0-045.mrc using 44648 points 
    8732 correlation = 0.7033, correlation about mean = 0.2694, overlap = 9030 
    8733 steps = 336, shift = 36.7, angle = 52.8 degrees 
    8734  
    8735 Position of P141_J33_zflip_101_RSVA-mono_MEDI_Mota.mrc (#16) relative to
    8736 preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates: 
    8737 Matrix rotation and translation 
    8738 0.63499761 -0.60502993 0.48032990 106.67366773 
    8739 0.45142417 0.79518516 0.40484167 -149.98927774 
    8740 -0.62689254 -0.04024096 0.77806581 168.17260938 
    8741 Axis -0.27926224 0.69471464 0.66286060 
    8742 Axis point 288.45766169 0.00000000 10.20458531 
    8743 Rotation angle (degrees) 52.83414700 
    8744 Shift along axis -22.51467756 
    8745  
    8746 
    8747 > show #!8 models
    8748 
    8749 > hide #!8 models
    8750 
    8751 > show #!8 models
    8752 
    8753 > fitmap #16 inMap #8
    8754 
    8755 Fit map P141_J33_zflip_101_RSVA-mono_MEDI_Mota.mrc in map preF_DS-
    8756 Cav1_20A_7mpg_Box208_0-045.mrc using 44648 points 
    8757 correlation = 0.7034, correlation about mean = 0.2698, overlap = 9030 
    8758 steps = 48, shift = 0.0587, angle = 0.134 degrees 
    8759  
    8760 Position of P141_J33_zflip_101_RSVA-mono_MEDI_Mota.mrc (#16) relative to
    8761 preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates: 
    8762 Matrix rotation and translation 
    8763 0.63600736 -0.60429647 0.47991710 106.40988355 
    8764 0.44966402 0.79563234 0.40592050 -150.05527072 
    8765 -0.62713389 -0.04236698 0.77775840 168.73735361 
    8766 Axis -0.28142708 0.69498735 0.66165806 
    8767 Axis point 289.07522752 0.00000000 10.76828252 
    8768 Rotation angle (degrees) 52.79281114 
    8769 Shift along axis -22.58670798 
    8770  
    8771 
    8772 > view matrix models
    8773 > #12,-0.18088,-0.9835,0.0018353,203.97,-0.71723,0.13063,-0.68448,241.88,0.67295,-0.12512,-0.72903,207.89,#13,0.046808,0.77485,0.63041,-92.939,-0.92342,-0.20709,0.32311,-192.36,0.38091,-0.59726,0.70583,3.4601,#14,0.8016,0.53938,0.25789,-194.43,-0.31968,0.022173,0.94727,58.108,0.50522,-0.84177,0.1902,267
    8774 
    8775 > hide #!8 models
    8776 
    8777 > select subtract #12
    8778 
    8779 20544 atoms, 20995 bonds, 6 pseudobonds, 2658 residues, 4 models selected 
    8780 
    8781 > select subtract #13
    8782 
    8783 2 models selected 
    8784 
    8785 > view matrix models
    8786 > #14,0.8016,0.53938,0.25789,-190.17,-0.31968,0.022173,0.94727,58.653,0.50522,-0.84177,0.1902,271.8
    8787 
    8788 > ui mousemode right "rotate selected models"
    8789 
    8790 > view matrix models
    8791 > #14,0.60959,0.74841,0.2613,-190.74,-0.48817,0.09471,0.86759,104.99,0.62457,-0.65644,0.42309,138.99
    8792 
    8793 > view matrix models
    8794 > #14,0.70486,0.64145,0.30284,-200.49,-0.40622,0.015028,0.91365,91.122,0.58151,-0.76701,0.27117,214.19
    8795 
    8796 > view matrix models
    8797 > #14,0.54437,0.78241,0.30249,-192.19,-0.33229,-0.12996,0.93418,101.13,0.77022,-0.60906,0.18924,148.52
    8798 
    8799 > ui mousemode right "translate selected models"
    8800 
    8801 > view matrix models
    8802 > #14,0.54437,0.78241,0.30249,-195.72,-0.33229,-0.12996,0.93418,109.69,0.77022,-0.60906,0.18924,136.41
    8803 
    8804 > view matrix models
    8805 > #14,0.54437,0.78241,0.30249,-197.76,-0.33229,-0.12996,0.93418,110.08,0.77022,-0.60906,0.18924,142.84
    8806 
    8807 > view matrix models
    8808 > #14,0.54437,0.78241,0.30249,-199.71,-0.33229,-0.12996,0.93418,111.7,0.77022,-0.60906,0.18924,136.18
    8809 
    8810 > ui mousemode right "rotate selected models"
    8811 
    8812 > view matrix models
    8813 > #14,0.63312,0.71043,0.30731,-206.86,-0.34688,-0.094512,0.93313,107.36,0.69197,-0.69739,0.1866,177.95
    8814 
    8815 > view matrix models
    8816 > #14,0.71087,0.64088,0.28972,-206.15,-0.33815,-0.049762,0.93977,92.873,0.6167,-0.76603,0.18134,214.95
    8817 
    8818 > ui mousemode right "translate selected models"
    8819 
    8820 > view matrix models
    8821 > #14,0.71087,0.64088,0.28972,-203.43,-0.33815,-0.049762,0.93977,86.714,0.6167,-0.76603,0.18134,218.04
    8822 
    8823 > fitmap #16 inMap #8
    8824 
    8825 Fit map P141_J33_zflip_101_RSVA-mono_MEDI_Mota.mrc in map preF_DS-
    8826 Cav1_20A_7mpg_Box208_0-045.mrc using 44648 points 
    8827 correlation = 0.7033, correlation about mean = 0.2694, overlap = 9030 
    8828 steps = 44, shift = 0.0593, angle = 0.13 degrees 
    8829  
    8830 Position of P141_J33_zflip_101_RSVA-mono_MEDI_Mota.mrc (#16) relative to
    8831 preF_DS-Cav1_20A_7mpg_Box208_0-045.mrc (#8) coordinates: 
    8832 Matrix rotation and translation 
    8833 0.63516113 -0.60490130 0.48027571 106.62440954 
    8834 0.45135795 0.79528046 0.40472829 -149.96457081 
    8835 -0.62677455 -0.04029141 0.77815825 168.13836967 
    8836 Axis -0.27926942 0.69472270 0.66284912 
    8837 Axis point 288.45373559 0.00000000 10.20493332 
    8838 Rotation angle (degrees) 52.82151862 
    8839 Shift along axis -22.51035962 
    8840  
    8841 
    8842 > fitmap #13 inMap #14
    8843 
    8844 Fit molecule 102_RSVA-PreF-trimer.pdb (#13) to map
    8845 cryosparc_P141_J36_001_volume_map.mrc (#14) using 20544 atoms 
    8846 average map value = 1.953, steps = 68 
    8847 shifted from previous position = 3.94 
    8848 rotated from previous position = 5.86 degrees 
    8849 atoms outside contour = 2141, contour level = 1.0438 
    8850  
    8851 Position of 102_RSVA-PreF-trimer.pdb (#13) relative to
    8852 cryosparc_P141_J36_001_volume_map.mrc (#14) coordinates: 
    8853 Matrix rotation and translation 
    8854 0.55030849 0.16967080 0.81754047 11.70550044 
    8855 -0.19361573 0.97837844 -0.07272286 220.29854429 
    8856 -0.81220289 -0.11826868 0.57126088 -254.98994277 
    8857 Axis -0.02726701 0.97568173 -0.21748948 
    8858 Axis point -177.71371795 0.00000000 -121.07794582 
    8859 Rotation angle (degrees) 56.63477800 
    8860 Shift along axis 270.07971981 
    8861  
    8862 
    8863 > select clear
    8864 
    8865 > hide #!14 models
    8866 
    8867 > hide #!12 models
    8868 
    8869 > show #!14 models
    8870 
    8871 > hide #!14 models
    8872 
    8873 > ui mousemode right zoom
    8874 
    8875 > select clear
    8876 
    8877 [Repeated 1 time(s)]Drag select of 178 residues 
    8878 
    8879 > select up
    8880 
    8881 2123 atoms, 2148 bonds, 274 residues, 1 model selected 
    8882 
    8883 > select up
    8884 
    8885 13683 atoms, 13942 bonds, 1771 residues, 1 model selected 
    8886 
    8887 > color sel light gray
    8888 
    8889 > select clear
    8890 
    8891 > show #!14 models
    8892 
    8893 > select clear
    8894 
    8895 > color #14 #ff8ad8ff models
    8896 
    8897 > color #14 #ff9ae4ff models
    8898 
    8899 > color #14 #ffd7f5ff models
    8900 
    8901 > transparency 50
    8902 
    8903 > save "/Users/szhang3/OneDrive - Moderna/RSV/MAbs/fitting.cxs" includeMaps
    8904 > true
    8905 
    8906 > vop resample #14 onGrid #8
    8907 
    8908 Opened cryosparc_P141_J36_001_volume_map.mrc resampled as #15, grid size
    8909 208,208,208, pixel 2, shown at step 1, values float32 
    8910 
    8911 > close #14
    8912 
    8913 > transparency 50
    8914 
    8915 > volume #15 color #f7d5f280
    8916 
    8917 > save "/Users/szhang3/OneDrive -
    8918 > Moderna/RSV/MAbs/102/cryosparc_P141_J36_001_volume_map.mrc" models #15
    8919 
    8920 > save "/Users/szhang3/OneDrive - Moderna/RSV/MAbs/102/102_RSVA-PreF-
    8921 > trimer.pdb" models #13 relModel #15
    8922 
    8923 > save "/Users/szhang3/OneDrive - Moderna/RSV/MAbs/fitting.cxs" includeMaps
    8924 > true
    8925 
    8926 ——— End of log from Tue Jun 17 10:45:24 2025 ———
    8927 
    8928 opened ChimeraX session 
    8929 
    8930 > show #!17 models
    8931 
    8932 > hide #!17 models
    8933 
    8934 > hide #!15 models
    8935 
    8936 > hide #!13 models
    8937 
    8938 > show #!16 models
    8939 
    8940 > show #!17 models
    8941 
    8942 > ui mousemode right "rotate selected models"
    8943 
    8944 > select add #17
    8945 
    8946 13451 atoms, 13769 bonds, 4 pseudobonds, 1751 residues, 3 models selected 
    8947 
    8948 > view matrix models
    8949 > #17,-0.40062,0.51626,-0.75695,335.76,0.73058,-0.3186,-0.60395,309.45,-0.55296,-0.79497,-0.24953,559.08
    8950 
    8951 > ui mousemode right "rotate selected models"
    8952 
    8953 > view matrix models
    8954 > #17,-0.54804,0.83396,-0.064578,107.3,-0.11531,-0.15179,-0.98166,501.63,-0.82847,-0.53054,0.17935,430.99
    8955 
    8956 > ui mousemode right "translate selected models"
    8957 
    8958 > view matrix models
    8959 > #17,-0.54804,0.83396,-0.064578,139.28,-0.11531,-0.15179,-0.98166,494.56,-0.82847,-0.53054,0.17935,436.13
    8960 
    8961 > view matrix models
    8962 > #17,-0.54804,0.83396,-0.064578,144.52,-0.11531,-0.15179,-0.98166,495.92,-0.82847,-0.53054,0.17935,428.28
    8963 
    8964 > view matrix models
    8965 > #17,-0.54804,0.83396,-0.064578,140.24,-0.11531,-0.15179,-0.98166,493.11,-0.82847,-0.53054,0.17935,425.39
    8966 
    8967 > view matrix models
    8968 > #17,-0.54804,0.83396,-0.064578,143.97,-0.11531,-0.15179,-0.98166,495.1,-0.82847,-0.53054,0.17935,422.32
    8969 
    8970 > ui tool show "Fit in Map"
    8971 
    8972 > fitmap #17 inMap #16
    8973 
    8974 Fit molecule combination (#17) to map P141_J33_zflip_101_RSVA-
    8975 mono_MEDI_Mota.mrc (#16) using 13451 atoms 
    8976 average map value = 1.686, steps = 96 
    8977 shifted from previous position = 2.18 
    8978 rotated from previous position = 11.3 degrees 
    8979 atoms outside contour = 1214, contour level = 1.1617 
    8980  
    8981 Position of combination (#17) relative to P141_J33_zflip_101_RSVA-
    8982 mono_MEDI_Mota.mrc (#16) coordinates: 
    8983 Matrix rotation and translation 
    8984 -0.05730192 0.79167018 -0.60825553 185.35262834 
    8985 0.35538881 -0.55317279 -0.75345779 457.02248045 
    8986 -0.93296048 -0.25934179 -0.24965286 501.51117550 
    8987 Axis 0.67245318 0.44189801 -0.59374478 
    8988 Axis point 0.00000000 94.20404151 395.46741439 
    8989 Rotation angle (degrees) 158.44476131 
    8990 Shift along axis 28.82864470 
    8991  
    8992 
    8993 > open /Users/szhang3/Library/CloudStorage/OneDrive-
    8994 > Moderna/RSV/MAbs/101/P141_J33_zflip_101_RSVA-mono_MEDI_Mota.mrc
    8995 
    8996 Opened P141_J33_zflip_101_RSVA-mono_MEDI_Mota.mrc as #14, grid size
    8997 208,208,208, pixel 2, shown at level 0.0913, step 1, values float32 
    8998 
    8999 > close #16
    9000 
    9001 > close #17
    9002 
    9003 > close #14
    9004 
    9005 > open /Users/szhang3/Library/CloudStorage/OneDrive-
    9006 > Moderna/RSV/MAbs/101/101_RSVA-mono_MEDI_Mota.pdb
    9007 
    9008 Chain information for 101_RSVA-mono_MEDI_Mota.pdb #14 
    9009 --- 
    9010 Chain | Description 
    9011 B | No description available 
    9012 C G | No description available 
    9013 D J | No description available 
    9014 H | No description available 
    9015 L | No description available 
    9016  
    9017 
    9018 > open /Users/szhang3/Library/CloudStorage/OneDrive-
    9019 > Moderna/RSV/MAbs/101/P141_J33_zflip_101_RSVA-mono_MEDI_Mota.mrc
    9020 
    9021 Opened P141_J33_zflip_101_RSVA-mono_MEDI_Mota.mrc as #16, grid size
    9022 208,208,208, pixel 2, shown at level 0.0913, step 1, values float32 
    9023 
    9024 > volume #16 level 0.5128
    9025 
    9026 > hide #!16 models
    9027 
    9028 > select #14/F:612@CL
    9029 
    9030 1 atom, 1 residue, 1 model selected 
    9031 
    9032 > select add #14/A:601@CL
    9033 
    9034 2 atoms, 2 residues, 1 model selected 
    9035 
    9036 > select add #14/I:5@C3
    9037 
    9038 3 atoms, 3 residues, 1 model selected 
    9039 Drag select of 127 atoms 
    9040 
    9041 > select up
    9042 
    9043 129 atoms, 137 bonds, 13 residues, 1 model selected 
    9044 
    9045 > delete atoms sel
    9046 
    9047 > delete bonds sel
    9048 
    9049 > hide #!14 atoms
    9050 
    9051 > show #!14 cartoons
    9052 
    9053 > show #!15 models
    9054 
    9055 > hide #!15 models
    9056 
    9057 > show #!16 models
    9058 
    9059 > color #16 #a6ca8cff models
    9060 
    9061 > transparency 80
    9062 
    9063 > open /Users/szhang3/Library/CloudStorage/OneDrive-
    9064 > Moderna/RSV/MAbs/101/AF_101_fab/101mab/ranked_0.pdb
    9065 
    9066 Chain information for ranked_0.pdb #17 
    9067 --- 
    9068 Chain | Description 
    9069 A | No description available 
    9070 B | No description available 
    9071  
    9072 Computing secondary structure 
    9073 
    9074 > select add #17
    9075 
    9076 3452 atoms, 3494 bonds, 225 residues, 1 model selected 
    9077 
    9078 > view matrix models #17,1,0,0,-50.437,0,1,0,-69.652,0,0,1,86.791
    9079 
    9080 > ui mousemode right zoom
    9081 
    9082 > hide #!16 models
    9083 
    9084 Drag select of 297 residues 
    9085 
    9086 > select clear
    9087 
    9088 Drag select of 308 residues, 1 pseudobonds 
    9089 
    9090 > select up
    9091 
    9092 2746 atoms, 2811 bonds, 1 pseudobond, 363 residues, 2 models selected 
    9093 
    9094 > select up
    9095 
    9096 3237 atoms, 3321 bonds, 1 pseudobond, 424 residues, 2 models selected 
    9097 Drag select of 225 residues 
    9098 
    9099 > ui tool show Matchmaker
    9100 
    9101 > matchmaker #17 & sel to #14 & sel
    9102 
    9103 Computing secondary structure 
    9104 Parameters 
    9105 --- 
    9106 Chain pairing | bb 
    9107 Alignment algorithm | Needleman-Wunsch 
    9108 Similarity matrix | BLOSUM-62 
    9109 SS fraction | 0.3 
    9110 Gap open (HH/SS/other) | 18/18/6 
    9111 Gap extend | 1 
    9112 SS matrix |  |  | H | S | O 
    9113 ---|---|---|--- 
    9114 H | 6 | -9 | -6 
    9115 S |  | 6 | -6 
    9116 O |  |  | 4 
    9117 Iteration cutoff | 2 
    9118  
    9119 Matchmaker 101_RSVA-mono_MEDI_Mota.pdb, chain D (#14) with ranked_0.pdb, chain
    9120 A (#17), sequence alignment score = 394.8 
    9121 RMSD between 114 pruned atom pairs is 0.714 angstroms; (across all 118 pairs:
    9122 1.289) 
    9123  
    9124 
    9125 > select clear
    9126 
    9127 > hide #17 models
    9128 
    9129 > select clear
    9130 
    9131 > show #17 models
    9132 
    9133 > hide #17 models
    9134 
    9135 > show #17 models
    9136 
    9137 > select #14/C:108
    9138 
    9139 11 atoms, 10 bonds, 1 residue, 1 model selected 
    9140 
    9141 > select #14/D:113
    9142 
    9143 6 atoms, 5 bonds, 1 residue, 1 model selected 
    9144 
    9145 > select add #14/C:108
    9146 
    9147 17 atoms, 15 bonds, 2 residues, 1 model selected 
    9148 
    9149 > hide #17 models
    9150 
    9151 Drag select of 120 residues 
    9152 
    9153 > delete atoms sel
    9154 
    9155 > delete bonds sel
    9156 
    9157 > select clear
    9158 
    9159 > select #14/D:43
    9160 
    9161 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9162 Drag select of 64 residues, 1 pseudobonds 
    9163 
    9164 > delete atoms (#!14 & sel)
    9165 
    9166 > delete bonds (#!14 & sel)
    9167 
    9168 > select clear
    9169 
    9170 Drag select of 39 residues, 5 pseudobonds 
    9171 
    9172 > delete atoms (#!14 & sel)
    9173 
    9174 > delete bonds (#!14 & sel)
    9175 
    9176 Drag select of 2 residues, 1 pseudobonds 
    9177 
    9178 > delete atoms (#!14 & sel)
    9179 
    9180 > delete bonds (#!14 & sel)
    9181 
    9182 > hide #14.1 models
    9183 
    9184 > select clear
    9185 
    9186 > show #!16 models
    9187 
    9188 > show #17 models
    9189 
    9190 > fitmap #17 inMap #16
    9191 
    9192 Fit molecule ranked_0.pdb (#17) to map P141_J33_zflip_101_RSVA-
    9193 mono_MEDI_Mota.mrc (#16) using 3452 atoms 
    9194 average map value = 1.994, steps = 60 
    9195 shifted from previous position = 2.12 
    9196 rotated from previous position = 12.3 degrees 
    9197 atoms outside contour = 0, contour level = 0.51284 
    9198  
    9199 Position of ranked_0.pdb (#17) relative to P141_J33_zflip_101_RSVA-
    9200 mono_MEDI_Mota.mrc (#16) coordinates: 
    9201 Matrix rotation and translation 
    9202 -0.20789049 0.96779263 0.14198230 194.92116740 
    9203 0.88526058 0.24789487 -0.39352490 238.81782755 
    9204 -0.41604718 0.04388125 -0.90828364 246.10281057 
    9205 Axis 0.61277199 0.78175589 -0.11562099 
    9206 Axis point 36.69811989 0.00000000 137.78918834 
    9207 Rotation angle (degrees) 159.08958826 
    9208 Shift along axis 277.68482618 
    9209  
    9210 
    9211 > volume #16 level 1.817
    9212 
    9213 > volume #16 level 1.078
    9214 
    9215 > select #16
    9216 
    9217 2 models selected 
    9218 
    9219 > hide #!16 models
    9220 
    9221 > select subtract #16
    9222 
    9223 Nothing selected 
    9224 
    9225 > select #14/B:197
    9226 
    9227 8 atoms, 7 bonds, 1 residue, 1 model selected 
    9228 
    9229 > select #14/B:166
    9230 
    9231 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9232 
    9233 > select up
    9234 
    9235 73 atoms, 72 bonds, 10 residues, 1 model selected 
    9236 
    9237 > select up
    9238 
    9239 3482 atoms, 3540 bonds, 449 residues, 1 model selected 
    9240 
    9241 > color sel gray
    9242 
    9243 > select clear
    9244 
    9245 Drag select of 306 residues 
    9246 
    9247 > select up
    9248 
    9249 2787 atoms, 2841 bonds, 370 residues, 1 model selected 
    9250 
    9251 > select up
    9252 
    9253 3237 atoms, 3313 bonds, 428 residues, 1 model selected 
    9254 
    9255 > select up
    9256 
    9257 11590 atoms, 11841 bonds, 1514 residues, 1 model selected 
    9258 
    9259 > select down
    9260 
    9261 3237 atoms, 3313 bonds, 428 residues, 1 model selected 
    9262 
    9263 > color sel orange red
    9264 
    9265 > color sel red
    9266 
    9267 > select clear
    9268 
    9269 Drag select of 256 residues 
    9270 
    9271 > select up
    9272 
    9273 2321 atoms, 2376 bonds, 310 residues, 1 model selected 
    9274 
    9275 > select up
    9276 
    9277 3237 atoms, 3321 bonds, 424 residues, 1 model selected 
    9278 
    9279 > select up
    9280 
    9281 11590 atoms, 11841 bonds, 1514 residues, 1 model selected 
    9282 
    9283 > select down
    9284 
    9285 3237 atoms, 3321 bonds, 424 residues, 1 model selected 
    9286 
    9287 > color sel yellow
    9288 
    9289 Drag select of 278 residues 
    9290 
    9291 > select up
    9292 
    9293 3852 atoms, 3898 bonds, 338 residues, 2 models selected 
    9294 
    9295 > select up
    9296 
    9297 4957 atoms, 5024 bonds, 425 residues, 2 models selected 
    9298 
    9299 > color sel forest green
    9300 
    9301 > select clear
    9302 
    9303 > select #14/D:114
     1473[deleted to fit within ticket limits]
     1474
    93041475
    930514765 atoms, 4 bonds, 1 residue, 1 model selected