Changes between Initial Version and Version 1 of Ticket #14542


Ignore:
Timestamp:
Feb 5, 2024, 7:31:43 PM (21 months ago)
Author:
Tom Goddard
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #14542

    • Property Cc Eric Pettersen added
    • Property Component Unassigned → Logging
    • Property Owner set to Tom Goddard
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → Log does not scroll to bottom after new command

  • Ticket #14542 – Description

    initial v1  
    33443344> open CD20_2H7v16/STR7668v2_alito6vja_C178to187.pdb name CD20_2H7v16 id 102.1
    33453345
    3346 Summary of feedback from opening CD20_2H7v16/STR7668v2_alito6vja_C178to187.pdb 
    3347 --- 
    3348 warning | Ignored bad PDB record found on line 1 
    3349 HEADER STR7668 version_2 2023.12.13 
    3350  
    3351 CD20_2H7v16 title: 
    3352 Structure of 2H7.v16 Fab and 2103.826032.Hs_MS4A1.M1-P297.BiNTF-NAvi at 3.3 A
    3353 resolution. [more info...] 
    3354  
    3355 Chain information for CD20_2H7v16 #1 
    3356 --- 
    3357 Chain | Description 
    3358 C D | No description available 
    3359 H I | No description available 
    3360 L M | No description available 
    3361  
    3362 Non-standard residues in CD20_2H7v16 #1 
    3363 --- 
    3364 Y01 — (Y01) 
    3365  
    3366 
    3367 > open CD20_2H7v16/P69_W9_J181/J181_004_volume_denoised.mrc id 102.2
    3368 
    3369 Opened J181_004_volume_denoised.mrc as #1, grid size 480,480,480, pixel 0.838,
    3370 shown at level 0.0054, step 2, values float32 
    3371 
    3372 > volume #102.2 step 1 level 0.08 color #9999CC transparency 0.5
    3373 
    3374 > view matrix models
    3375 > #102.2,-0.2379,0.93572,0.26045,-39.485,0.96898,0.21017,0.12999,-107.2,0.066893,0.2833,-0.9567,274.92
    3376 
    3377 > open "CD20_2H7v16/crystal_structure/STR7487.2H7 Fab.pdb" name 2H7v16_XRay id
    3378 > 102.10
    3379 
    3380 Summary of feedback from opening CD20_2H7v16/crystal_structure/STR7487.2H7
    3381 Fab.pdb 
    3382 --- 
    3383 warning | Ignored bad PDB record found on line 1 
    3384 HEADER STR7487 version_1 2023.05.24 
    3385  
    3386 2H7v16_XRay title: 
    3387 Structure of 2H7 Fab at 2.45 A resolution. [more info...] 
    3388  
    3389 Chain information for 2H7v16_XRay #1 
    3390 --- 
    3391 Chain | Description 
    3392 A B X Y | No description available 
    3393  
    3394 Non-standard residues in 2H7v16_XRay #1 
    3395 --- 
    3396 CL — (CL) 
    3397  
    3398 
    3399 > matchmaker #102.10/A,B to #102.1/H,L
    3400 
    3401 Parameters 
    3402 --- 
    3403 Chain pairing | bb 
    3404 Alignment algorithm | Needleman-Wunsch 
    3405 Similarity matrix | BLOSUM-62 
    3406 SS fraction | 0.3 
    3407 Gap open (HH/SS/other) | 18/18/6 
    3408 Gap extend | 1 
    3409 SS matrix |  |  | H | S | O 
    3410 ---|---|---|--- 
    3411 H | 6 | -9 | -6 
    3412 S |  | 6 | -6 
    3413 O |  |  | 4 
    3414 Iteration cutoff | 2 
    3415  
    3416 Matchmaker CD20_2H7v16, chain L (#102.1) with 2H7v16_XRay, chain A (#102.10),
    3417 sequence alignment score = 1228.2 
    3418 RMSD between 208 pruned atom pairs is 0.731 angstroms; (across all 213 pairs:
    3419 0.804) 
    3420  
    3421 
    3422 > open CD20_2H7v166_D56A/STR7717v2_alito6vja.pdb name CD20_2H7v166_D56A id
    3423 > 103.1
    3424 
    3425 Summary of feedback from opening CD20_2H7v166_D56A/STR7717v2_alito6vja.pdb 
    3426 --- 
    3427 warning | Ignored bad PDB record found on line 1 
    3428 HEADER STR7717 version_2 2023.12.15 
    3429  
    3430 CD20_2H7v166_D56A title: 
    3431 Structure of 2H7v166_D56A Fab and Hs_CD20.M1-P297 at 3.7 A resolution . [more
    3432 info...] 
    3433  
    3434 Chain information for CD20_2H7v166_D56A #1 
    3435 --- 
    3436 Chain | Description 
    3437 C D | No description available 
    3438 H I | No description available 
    3439 L | No description available 
    3440 M | No description available 
    3441  
    3442 Non-standard residues in CD20_2H7v166_D56A #1 
    3443 --- 
    3444 Y01 — (Y01) 
    3445  
    3446 
    3447 > open CD20_2H7v166_D56A/cryosparc_P69_J433_007_volume_map_sharp.mrc id 103.2
    3448 
    3449 Opened cryosparc_P69_J433_007_volume_map_sharp.mrc as #1, grid size
    3450 300,300,300, pixel 1.28, shown at level 0.0592, step 2, values float32 
    3451 
    3452 > volume #103.2 step 1 level 0.355 color #9999CC transparency 0.5
    3453 
    3454 > view matrix models
    3455 > #103.2,0.00937853,0.99467855,-0.10259937,-18.50914227,-0.99948588,0.00617870,-0.03146112,352.75851684,-0.03065977,0.10284168,0.99422511,-49.28949280
    3456 
    3457 > open CD20_2H7v166_S92A_D56A/STR7729v2_alito6vja.pdb name
    3458 > CD20_2H7v166_S92A_D56A id 104.1
    3459 
    3460 Summary of feedback from opening
    3461 CD20_2H7v166_S92A_D56A/STR7729v2_alito6vja.pdb 
    3462 --- 
    3463 warning | Ignored bad PDB record found on line 1 
    3464 HEADER STR7729 version_2 2024.01.29 
    3465  
    3466 CD20_2H7v166_S92A_D56A title: 
    3467 Structure of 2H7v166 LC.S92A HC.D56A Fab and Hs_CD20.M1-P297 at 4.5 A
    3468 resolution. [more info...] 
    3469  
    3470 Chain information for CD20_2H7v166_S92A_D56A #1 
    3471 --- 
    3472 Chain | Description 
    3473 C D | No description available 
    3474 H | No description available 
    3475 I | No description available 
    3476 L M | No description available 
    3477  
    3478 
    3479 > open CD20_2H7v166_S92A_D56A/cryosparc_P69_J242_005_volume_map_sharp_flip.mrc
    3480 > id 104.2
    3481 
    3482 Opened cryosparc_P69_J242_005_volume_map_sharp_flip.mrc as #1, grid size
    3483 300,300,300, pixel 1.43, shown at level 0.0447, step 2, values float32 
    3484 
    3485 > volume #104.2 step 1 level 0.355 color #9999CC transparency 0.5
    3486 
    3487 > view matrix models
    3488 > #104.2,-0.00249470,0.97079708,0.23988915,-104.32503408,0.99657176,0.02225139,-0.07968446,-45.21631074,-0.08269530,0.23886796,-0.96752446,330.43463437
    3489 
    3490 > rename #101 CD20_RTX
    3491 
    3492 > rename #102 CD20_2H7v16
    3493 
    3494 > rename #103 CD20_2H7v166_D56A
    3495 
    3496 > rename #104 CD20_2H7v166_S92A_D56A
    3497 
    3498 > dssp
    3499 
    3500 > name CD20_RTX #101.1
    3501 
    3502 > name CD20_2H7v16 #102.1
    3503 
    3504 > name CD20_2H7v166_D56A #103.1
    3505 
    3506 > name CD20_2H7v166_S92A_D56A #104.1
    3507 
    3508 > name CD20 /C,D
    3509 
    3510 > name CD20_Monomer /C
    3511 
    3512 > name CD20_H1 /C,D:46-71
    3513 
    3514 > name CD20_ECL1 /C,D:72-79
    3515 
    3516 > name CD20_H2 /C,D:80-105
    3517 
    3518 > name CD20_ICL1 /C,D:106-112
    3519 
    3520 > name CD20_H3 /C,D:113-141
    3521 
    3522 > name CD20_ECL2 /C,D:142-187
    3523 
    3524 > name CD20_ECL2SS /C,D:167,183
    3525 
    3526 > name CD20_H4 /C,D:188-end
    3527 
    3528 > name CD20_DimerInt /C,D:62,200,65,196,69,192,73,188,76,185,58,54,50
    3529 
    3530 > name RTX CD20_RTX & /H,L,I,M
    3531 
    3532 > name RTX_H RTX & /H,I
    3533 
    3534 > name RTX_L RTX & /L,M
    3535 
    3536 > name RTX_Epitope CD20_RTX & /C,D:168-175
    3537 
    3538 > name RTX_V (RTX & /L,M:1-107) | (RTX & /H,I:1-111)
    3539 
    3540 > name RTX_C (RTX & /L,M:113-end) | (RTX & /H,I:119-end)
    3541 
    3542 > name H7v16 CD20_2H7v16 & /H,L,I,M
    3543 
    3544 > name H7v16_H H7v16 & /H,I
    3545 
    3546 > name H7v16_L H7v16 & /L,M
    3547 
    3548 > name H7v16_Epitope CD20_2H7v16 & /C,D:168-175
    3549 
    3550 > name H7v16_V (H7v16 & /L,M:1-107) | (H7v16 & /H,I:1-111)
    3551 
    3552 > name H7v16_C (H7v16 & /L,M:112-end) | (H7v16 & /H,I:119-end)
    3553 
    3554 > name H7v166_D56A CD20_2H7v166_D56A & /H,L,I,M
    3555 
    3556 > name H7v166_D56A_H H7v166_D56A & /H,I
    3557 
    3558 > name H7v166_D56A_L H7v166_D56A & /L,M
    3559 
    3560 > name H7v166_D56A_Epitope CD20_2H7v166_D56A & /C,D:168-175
    3561 
    3562 > name H7v166_D56A_V (H7v166_D56A & /L,M:1-107) | (H7v166_D56A & /H,I:1-111)
    3563 
    3564 > name H7v166_D56A_C (H7v166_D56A & /L,M:112-end) | (H7v166_D56A &
    3565 > /H,I:119-end)
    3566 
    3567 > name H7v166_S92A_D56A CD20_2H7v166_S92A_D56A & /H,L,I,M
    3568 
    3569 > name H7v166_S92A_D56A_H H7v166_S92A_D56A & /H,I
    3570 
    3571 > name H7v166_S92A_D56A_L H7v166_S92A_D56A & /L,M
    3572 
    3573 > name H7v166_S92A_D56A_Epitope CD20_2H7v166_S92A_D56A & /C,D:168-175
    3574 
    3575 > name H7v166_S92A_D56A_V (H7v166_S92A_D56A & /L,M:1-107) | (H7v166_S92A_D56A
    3576 > & /H,I:1-111)
    3577 
    3578 > name H7v166_S92A_D56A_C (H7v166_S92A_D56A & /L,M:112-end) |
    3579 > (H7v166_S92A_D56A & /H,I:119-end)
    3580 
    3581 > lighting soft
    3582 
    3583 > set bgColor white
    3584 
    3585 > camera ortho
    3586 
    3587 > style stick
    3588 
    3589 Changed 44237 atom styles 
    3590 
    3591 > color byhetero
    3592 
    3593 > open CD20_2H7_mutants_color.cxc
    3594 
    3595 > color CD20 burlywood
    3596 
    3597 > color modify CD20_H1 hue - 20
    3598 
    3599 > color modify CD20_H2 hue - 10
    3600 
    3601 > color modify CD20_H3 hue + 0
    3602 
    3603 > color modify CD20_H4 hue + 10
    3604 
    3605 > color modify CD20_ECL1 hue +10
    3606 
    3607 > color modify CD20_ECL2 hue + 40
    3608 
    3609 > color modify CD20 saturation + 80
    3610 
    3611 > color CD20_ECL2 rgb(127,165,90)
    3612 
    3613 > color CD20_H4 rgb(176,215,142)
    3614 
    3615 > color RTX plum
    3616 
    3617 > color modify RTX_H hue - 40
    3618 
    3619 > color H7v16 slate blue
    3620 
    3621 > color modify H7v16_H hue - 40
    3622 
    3623 > color H7v166_D56A dodger blue
    3624 
    3625 > color modify H7v166_D56A_H hue - 40
    3626 
    3627 > color H7v166_S92A_D56A purple
    3628 
    3629 > color modify H7v166_S92A_D56A_H hue - 40
    3630 
    3631 executed CD20_2H7_mutants_color.cxc 
    3632 
    3633 > hide
    3634 
    3635 > ribbon
    3636 
    3637 > show CD20_ECL2SS
    3638 
    3639 > style CD20_ECL2SS stick
    3640 
    3641 Changed 96 atom styles 
    3642 
    3643 > define axis fromPoint 155,155,70 toPoint 155,155,210 name sym_axis
    3644 
    3645 Axis 'sym_axis' centered at [155. 155. 140.] with direction [ 0. 0. 140.],
    3646 radius 1, and length 140 
    3647 
    3648 > marker #1.1 position 155,155,70
    3649 
    3650 > marker #1.1 position 155,155,210
    3651 
    3652 > select
    3653 > #101.1/C,D:73,74,75,76,77,78,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,184,185,186,187,188
    3654 
    3655 440 atoms, 446 bonds, 54 residues, 1 model selected 
    3656 
    3657 > define plane sel name membrane_plane
    3658 
    3659 Plane 'membrane_plane' placed at [154.99498409 155.00750455 153.73545455] with
    3660 normal [-5.66049107e-05 -2.68508756e-05 -9.99999998e-01] and radius 24.3 
    3661 
    3662 > rename ##name=membrane_plane id 10
    3663 
    3664 > open CD20_2H7v16/CD20_RTX_define_pseudo_symmetries.cxc
    3665 
    3666 > combine CD20_RTX name RTX_Va modelId 1001
    3667 
    3668 > select zone (RTX_V & /H,L) 0.1 #1001
    3669 
    3670 Selected 1711 atoms 
    3671 
    3672 > delete #1001 & ~sel
    3673 
    3674 > combine #1001 name RTX_Va_copy modelId 1002
    3675 
    3676 > combine CD20_RTX name RTX_Vb modelId 1003
    3677 
    3678 > select zone (RTX_V & /I,M) 0.1 #1003
    3679 
    3680 Selected 1711 atoms 
    3681 
    3682 > delete #1003 & ~sel
    3683 
    3684 > combine #1003 name RTX_Vb_copy modelId 1004
    3685 
    3686 > combine CD20_RTX name RTX_Ca modelId 1005
    3687 
    3688 > select zone (RTX_C & /H,L) 0.1 #1005
    3689 
    3690 Selected 1503 atoms 
    3691 
    3692 > delete #1005 & ~sel
    3693 
    3694 > combine #1005 name RTX_Ca_copy modelId 1006
    3695 
    3696 > combine CD20_RTX name RTX_Cb modelId 1007
    3697 
    3698 > select zone (RTX_C & /I,M) 0.1 #1007
    3699 
    3700 Selected 1503 atoms 
    3701 
    3702 > delete #1007 & ~sel
    3703 
    3704 > combine #1007 name RTX_Ca_copy modelId 1008
    3705 
    3706 > matchmaker #1002/L to #1001/H
    3707 
    3708 Parameters 
    3709 --- 
    3710 Chain pairing | bb 
    3711 Alignment algorithm | Needleman-Wunsch 
    3712 Similarity matrix | BLOSUM-62 
    3713 SS fraction | 0.3 
    3714 Gap open (HH/SS/other) | 18/18/6 
    3715 Gap extend | 1 
    3716 SS matrix |  |  | H | S | O 
    3717 ---|---|---|--- 
    3718 H | 6 | -9 | -6 
    3719 S |  | 6 | -6 
    3720 O |  |  | 4 
    3721 Iteration cutoff | 2 
    3722  
    3723 Matchmaker RTX_Va, chain H (#1001) with RTX_Va_copy, chain L (#1002), sequence
    3724 alignment score = 198.7 
    3725 RMSD between 57 pruned atom pairs is 0.694 angstroms; (across all 103 pairs:
    3726 4.421) 
    3727  
    3728 
    3729 > wait 1
    3730 
    3731 > measure rotation #1002 toModel #1001 showSlabs true
    3732 
    3733 Position of RTX_Va_copy #1002 relative to RTX_Va #1001 coordinates: 
    3734 Matrix rotation and translation 
    3735 0.65377294 -0.06463426 0.75392530 -36.97668460 
    3736 0.02426941 -0.99404163 -0.10626495 318.59247232 
    3737 0.75630149 0.08777047 -0.64830888 90.28955685 
    3738 Axis 0.90906034 -0.01113250 0.41651574 
    3739 Axis point 0.00000000 156.41772375 62.99337678 
    3740 Rotation angle (degrees) 173.87355102 
    3741 Shift along axis 0.44625393 
    3742  
    3743 
    3744 > close #1001 #1002
    3745 
    3746 > define axis #2 name axis_Va
    3747 
    3748 Axis 'rotation axis #2/axis_Va' centered at [137.08203113 154.73899552
    3749 125.80199389] with direction [ 0.90906034 -0.0111325 0.41651574], radius
    3750 0.65062, and length 52.0496 
    3751 
    3752 > rename #2 Va_rotation_axis id #101.3.1.1
    3753 
    3754 > rename #3 Va_rotation_slabs id #101.3.2.1
    3755 
    3756 > matchmaker #1004/M to #1003/I
    3757 
    3758 Parameters 
    3759 --- 
    3760 Chain pairing | bb 
    3761 Alignment algorithm | Needleman-Wunsch 
    3762 Similarity matrix | BLOSUM-62 
    3763 SS fraction | 0.3 
    3764 Gap open (HH/SS/other) | 18/18/6 
    3765 Gap extend | 1 
    3766 SS matrix |  |  | H | S | O 
    3767 ---|---|---|--- 
    3768 H | 6 | -9 | -6 
    3769 S |  | 6 | -6 
    3770 O |  |  | 4 
    3771 Iteration cutoff | 2 
    3772  
    3773 Matchmaker RTX_Vb, chain I (#1003) with RTX_Vb_copy, chain M (#1004), sequence
    3774 alignment score = 214.3 
    3775 RMSD between 57 pruned atom pairs is 0.703 angstroms; (across all 103 pairs:
    3776 4.448) 
    3777  
    3778 
    3779 > wait 1
    3780 
    3781 > measure rotation #1004 toModel #1003 showSlabs true
    3782 
    3783 Position of RTX_Vb_copy #1004 relative to RTX_Vb #1003 coordinates: 
    3784 Matrix rotation and translation 
    3785 0.65527690 -0.06129532 -0.75289778 163.48223927 
    3786 0.03113398 -0.99366393 0.10799385 290.56686667 
    3787 -0.75474688 -0.09420658 -0.64921665 352.74817189 
    3788 Axis -0.90945183 0.00831685 0.41572611 
    3789 Axis point 0.00000000 156.83903630 204.83255489 
    3790 Rotation angle (degrees) 173.61745932 
    3791 Shift along axis 0.38400661 
    3792  
    3793 
    3794 > close #1004 #1003
    3795 
    3796 > define axis #2 name axis_Vb
    3797 
    3798 Axis 'rotation axis #2/axis_Vb' centered at [172.9873955 155.25708275
    3799 125.75703344] with direction [-0.90945183 0.00831685 0.41572611], radius
    3800 0.648586, and length 51.8869 
    3801 
    3802 > rename #2 Vb_rotation_axis id #101.3.1.2
    3803 
    3804 > rename #3 Vb_rotation_slabs id #101.3.2.2
    3805 
    3806 > matchmaker #1006/L to #1005/H
    3807 
    3808 Parameters 
    3809 --- 
    3810 Chain pairing | bb 
    3811 Alignment algorithm | Needleman-Wunsch 
    3812 Similarity matrix | BLOSUM-62 
    3813 SS fraction | 0.3 
    3814 Gap open (HH/SS/other) | 18/18/6 
    3815 Gap extend | 1 
    3816 SS matrix |  |  | H | S | O 
    3817 ---|---|---|--- 
    3818 H | 6 | -9 | -6 
    3819 S |  | 6 | -6 
    3820 O |  |  | 4 
    3821 Iteration cutoff | 2 
    3822  
    3823 Matchmaker RTX_Ca, chain H (#1005) with RTX_Ca_copy, chain L (#1006), sequence
    3824 alignment score = 238.2 
    3825 RMSD between 50 pruned atom pairs is 0.795 angstroms; (across all 96 pairs:
    3826 3.308) 
    3827  
    3828 
    3829 > wait 1
    3830 
    3831 > measure rotation #1006 toModel #1005 showSlabs true
    3832 
    3833 Position of RTX_Ca_copy #1006 relative to RTX_Ca #1005 coordinates: 
    3834 Matrix rotation and translation 
    3835 0.37780344 0.24165354 0.89379423 -73.66252391 
    3836 0.01279825 -0.96661035 0.25593093 273.63534365 
    3837 0.92579737 -0.08525258 -0.36828146 68.27322422 
    3838 Axis -0.82796624 -0.07766353 -0.55537400 
    3839 Axis point 0.00000000 144.62953182 41.62502778 
    3840 Rotation angle (degrees) 168.10978391 
    3841 Shift along axis 1.82142171 
    3842  
    3843 
    3844 > close #1006 #1005
    3845 
    3846 > define axis #2 name axis_Ca
    3847 
    3848 Axis 'rotation axis #2/axis_Ca' centered at [102.30380142 154.22566542
    3849 110.24723578] with direction [-0.82796624 -0.07766353 -0.555374 ], radius
    3850 0.539289, and length 43.1431 
    3851 
    3852 > rename #2 Ca_rotation_axis id #101.3.1.3
    3853 
    3854 > rename #3 Ca_rotation_slabs id #101.3.2.3
    3855 
    3856 > matchmaker #1008/M to #1007/I
    3857 
    3858 Parameters 
    3859 --- 
    3860 Chain pairing | bb 
    3861 Alignment algorithm | Needleman-Wunsch 
    3862 Similarity matrix | BLOSUM-62 
    3863 SS fraction | 0.3 
    3864 Gap open (HH/SS/other) | 18/18/6 
    3865 Gap extend | 1 
    3866 SS matrix |  |  | H | S | O 
    3867 ---|---|---|--- 
    3868 H | 6 | -9 | -6 
    3869 S |  | 6 | -6 
    3870 O |  |  | 4 
    3871 Iteration cutoff | 2 
    3872  
    3873 Matchmaker RTX_Cb, chain I (#1007) with RTX_Ca_copy, chain M (#1008), sequence
    3874 alignment score = 238.2 
    3875 RMSD between 50 pruned atom pairs is 0.794 angstroms; (across all 96 pairs:
    3876 3.487) 
    3877  
    3878 
    3879 > wait 1
    3880 
    3881 > measure rotation #1008 toModel #1007 showSlabs true
    3882 
    3883 Position of RTX_Ca_copy #1008 relative to RTX_Cb #1007 coordinates: 
    3884 Matrix rotation and translation 
    3885 0.37961795 0.24211100 -0.89290116 191.06761259 
    3886 0.01296287 -0.96644625 -0.25654164 332.12351027 
    3887 -0.92505253 0.08581325 -0.37001879 328.82641259 
    3888 Axis 0.82850834 0.07780721 -0.55454483 
    3889 Axis point 0.00000000 136.30341759 249.27961172 
    3890 Rotation angle (degrees) 168.07628341 
    3891 Shift along axis 1.79372450 
    3892  
    3893 
    3894 > close #1008 #1007
    3895 
    3896 > define axis #2 name axis_Cb
    3897 
    3898 Axis 'rotation axis #2/axis_Cb' centered at [207.91438592 155.82915639
    3899 110.11643971] with direction [ 0.82850834 0.07780721 -0.55454483], radius
    3900 0.53918, and length 43.1344 
    3901 
    3902 > rename #2 Cb_rotation_axis id #101.3.1.4
    3903 
    3904 > rename #3 Cb_rotation_slabs id #101.3.2.4
    3905 
    3906 > rename #101.3 geometry
    3907 
    3908 > rename #101.3.1 rotation_axes
    3909 
    3910 > rename #101.3.2 rotation_slabs
    3911 
    3912 executed CD20_RTX_define_pseudo_symmetries.cxc 
    3913 
    3914 > open CD20_2H7v16/CD20_2H7v16_define_pseudo_symmetries.cxc
    3915 
    3916 > combine CD20_2H7v16 name 2H7_v16_Va modelId 1001
    3917 
    3918 > select zone (H7v16_V & /H,L) 0.1 #1001
    3919 
    3920 Selected 1754 atoms 
    3921 
    3922 > delete #1001 & ~sel
    3923 
    3924 > combine #1001 name 2H7_v16_Va_copy modelId 1002
    3925 
    3926 > combine CD20_2H7v16 name 2H7_v16_Vb modelId 1003
    3927 
    3928 > select zone (H7v16_V & /I,M) 0.1 #1003
    3929 
    3930 Selected 1710 atoms 
    3931 
    3932 > delete #1003 & ~sel
    3933 
    3934 > combine #1003 name 2H7_v16_Vb_copy modelId 1004
    3935 
    3936 > combine CD20_2H7v16 name 2H7_v16_Ca modelId 1005
    3937 
    3938 > select zone (H7v16_C & /H,L) 0.1 #1005
    3939 
    3940 Selected 1550 atoms 
    3941 
    3942 > delete #1005 & ~sel
    3943 
    3944 > combine #1005 name 2H7_v16_Ca_copy modelId 1006
    3945 
    3946 > combine CD20_2H7v16 name 2H7_v16_Cb modelId 1007
    3947 
    3948 > select zone (H7v16_C & /I,M) 0.1 #1007
    3949 
    3950 Selected 1550 atoms 
    3951 
    3952 > delete #1007 & ~sel
    3953 
    3954 > combine #1007 name 2H7_v16_Ca_copy modelId 1008
    3955 
    3956 > matchmaker #1002/L to #1001/H
    3957 
    3958 Parameters 
    3959 --- 
    3960 Chain pairing | bb 
    3961 Alignment algorithm | Needleman-Wunsch 
    3962 Similarity matrix | BLOSUM-62 
    3963 SS fraction | 0.3 
    3964 Gap open (HH/SS/other) | 18/18/6 
    3965 Gap extend | 1 
    3966 SS matrix |  |  | H | S | O 
    3967 ---|---|---|--- 
    3968 H | 6 | -9 | -6 
    3969 S |  | 6 | -6 
    3970 O |  |  | 4 
    3971 Iteration cutoff | 2 
    3972  
    3973 Matchmaker 2H7_v16_Va, chain H (#1001) with 2H7_v16_Va_copy, chain L (#1002),
    3974 sequence alignment score = 387.9 
    3975 RMSD between 66 pruned atom pairs is 0.856 angstroms; (across all 103 pairs:
    3976 5.340) 
    3977  
    3978 
    3979 > wait 1
    3980 
    3981 > measure rotation #1002 toModel #1001 showSlabs true
    3982 
    3983 Position of 2H7_v16_Va_copy #1002 relative to 2H7_v16_Va #1001 coordinates: 
    3984 Matrix rotation and translation 
    3985 0.58985298 0.00233427 0.80750728 -45.05678546 
    3986 0.12316682 -0.98855531 -0.08711100 297.16136614 
    3987 0.79806228 0.15084078 -0.58338980 65.44859378 
    3988 Axis 0.89106916 0.03536916 0.45248731 
    3989 Axis point 0.00000000 147.01172040 55.34624717 
    3990 Rotation angle (degrees) 172.32693090 
    3991 Shift along axis -0.02370559 
    3992  
    3993 
    3994 > close #1001 #1002
    3995 
    3996 > define axis #2 name axis_Va
    3997 
    3998 Axis 'rotation axis #2/axis_Va' centered at [138.16022152 152.49570671
    3999 125.5043786 ] with direction [0.89106916 0.03536916 0.45248731], radius
    4000 0.589874, and length 47.1899 
    4001 
    4002 > rename #2 Va_rotation_axis id #102.3.1.1
    4003 
    4004 > rename #3 Va_rotation_slabs id #102.3.2.1
    4005 
    4006 > matchmaker #1004/M to #1003/I
    4007 
    4008 Parameters 
    4009 --- 
    4010 Chain pairing | bb 
    4011 Alignment algorithm | Needleman-Wunsch 
    4012 Similarity matrix | BLOSUM-62 
    4013 SS fraction | 0.3 
    4014 Gap open (HH/SS/other) | 18/18/6 
    4015 Gap extend | 1 
    4016 SS matrix |  |  | H | S | O 
    4017 ---|---|---|--- 
    4018 H | 6 | -9 | -6 
    4019 S |  | 6 | -6 
    4020 O |  |  | 4 
    4021 Iteration cutoff | 2 
    4022  
    4023 Matchmaker 2H7_v16_Vb, chain I (#1003) with 2H7_v16_Vb_copy, chain M (#1004),
    4024 sequence alignment score = 378.3 
    4025 RMSD between 65 pruned atom pairs is 0.877 angstroms; (across all 97 pairs:
    4026 4.620) 
    4027  
    4028 
    4029 > wait 1
    4030 
    4031 > measure rotation #1004 toModel #1003 showSlabs true
    4032 
    4033 Position of 2H7_v16_Vb_copy #1004 relative to 2H7_v16_Vb #1003 coordinates: 
    4034 Matrix rotation and translation 
    4035 0.62864598 0.45103819 -0.63353672 71.77949524 
    4036 0.53321619 -0.84298968 -0.07105560 212.64664720 
    4037 -0.56611370 -0.29314322 -0.77044294 368.84403487 
    4038 Axis -0.90200560 -0.27383758 0.33376470 
    4039 Axis point -0.00000000 108.05935567 190.41757658 
    4040 Rotation angle (degrees) 172.92851049 
    4041 Shift along axis 0.13096924 
    4042  
    4043 
    4044 > close #1004 #1003
    4045 
    4046 > define axis #2 name axis_Vb
    4047 
    4048 Axis 'rotation axis #2/axis_Vb' centered at [174.414767 161.00949037
    4049 125.87973689] with direction [-0.9020056 -0.27383758 0.3337647 ], radius
    4050 0.594923, and length 47.5938 
    4051 
    4052 > rename #2 Vb_rotation_axis id #102.3.1.2
    4053 
    4054 > rename #3 Vb_rotation_slabs id #102.3.2.2
    4055 
    4056 > matchmaker #1006/L to #1005/H
    4057 
    4058 Parameters 
    4059 --- 
    4060 Chain pairing | bb 
    4061 Alignment algorithm | Needleman-Wunsch 
    4062 Similarity matrix | BLOSUM-62 
    4063 SS fraction | 0.3 
    4064 Gap open (HH/SS/other) | 18/18/6 
    4065 Gap extend | 1 
    4066 SS matrix |  |  | H | S | O 
    4067 ---|---|---|--- 
    4068 H | 6 | -9 | -6 
    4069 S |  | 6 | -6 
    4070 O |  |  | 4 
    4071 Iteration cutoff | 2 
    4072  
    4073 Matchmaker 2H7_v16_Ca, chain H (#1005) with 2H7_v16_Ca_copy, chain L (#1006),
    4074 sequence alignment score = 403.6 
    4075 RMSD between 58 pruned atom pairs is 1.037 angstroms; (across all 98 pairs:
    4076 3.184) 
    4077  
    4078 
    4079 > wait 1
    4080 
    4081 > measure rotation #1006 toModel #1005 showSlabs true
    4082 
    4083 Position of 2H7_v16_Ca_copy #1006 relative to 2H7_v16_Ca #1005 coordinates: 
    4084 Matrix rotation and translation 
    4085 -0.62547004 0.41276667 0.66212605 49.05674876 
    4086 0.08546501 -0.80725952 0.58397585 200.07354667 
    4087 0.77555333 0.42184801 0.46963954 -95.83522576 
    4088 Axis -0.42390521 -0.29657098 -0.85577452 
    4089 Axis point 59.57688139 113.83169245 0.00000000 
    4090 Rotation angle (degrees) 168.97535276 
    4091 Shift along axis 1.88192618 
    4092  
    4093 
    4094 > close #1006 #1005
    4095 
    4096 > define axis #2 name axis_Ca
    4097 
    4098 Axis 'rotation axis #2/axis_Ca' centered at [109.8807251 149.02507918
    4099 101.55276878] with direction [-0.42390521 -0.29657098 -0.85577452], radius
    4100 0.550437, and length 44.0349 
    4101 
    4102 > rename #2 Ca_rotation_axis id #102.3.1.3
    4103 
    4104 > rename #3 Ca_rotation_slabs id #102.3.2.3
    4105 
    4106 > matchmaker #1008/M to #1007/I
    4107 
    4108 Parameters 
    4109 --- 
    4110 Chain pairing | bb 
    4111 Alignment algorithm | Needleman-Wunsch 
    4112 Similarity matrix | BLOSUM-62 
    4113 SS fraction | 0.3 
    4114 Gap open (HH/SS/other) | 18/18/6 
    4115 Gap extend | 1 
    4116 SS matrix |  |  | H | S | O 
    4117 ---|---|---|--- 
    4118 H | 6 | -9 | -6 
    4119 S |  | 6 | -6 
    4120 O |  |  | 4 
    4121 Iteration cutoff | 2 
    4122  
    4123 Matchmaker 2H7_v16_Cb, chain I (#1007) with 2H7_v16_Ca_copy, chain M (#1008),
    4124 sequence alignment score = 396 
    4125 RMSD between 54 pruned atom pairs is 0.855 angstroms; (across all 98 pairs:
    4126 3.551) 
    4127  
    4128 
    4129 > wait 1
    4130 
    4131 > measure rotation #1008 toModel #1007 showSlabs true
    4132 
    4133 Position of 2H7_v16_Ca_copy #1008 relative to 2H7_v16_Cb #1007 coordinates: 
    4134 Matrix rotation and translation 
    4135 -0.62894249 0.48033740 -0.61131606 312.62038315 
    4136 0.14842286 -0.69766113 -0.70088487 336.12735996 
    4137 -0.76315267 -0.53154955 0.36749568 311.24709675 
    4138 Axis 0.42085200 0.37736216 -0.82491296 
    4139 Axis point 256.37284203 220.04020388 0.00000000 
    4140 Rotation angle (degrees) 168.39393838 
    4141 Shift along axis 1.65689588 
    4142  
    4143 
    4144 > close #1008 #1007
    4145 
    4146 > define axis #2 name axis_Cb
    4147 
    4148 Axis 'rotation axis #2/axis_Cb' centered at [202.74487059 171.95401837
    4149 105.11630914] with direction [ 0.420852 0.37736216 -0.82491296], radius
    4150 0.534846, and length 42.7877 
    4151 
    4152 > rename #2 Cb_rotation_axis id #102.3.1.4
    4153 
    4154 > rename #3 Cb_rotation_slabs id #102.3.2.4
    4155 
    4156 > rename #102.3 geometry
    4157 
    4158 > rename #102.3.1 rotation_axes
    4159 
    4160 > rename #102.3.2 rotation_slabs
    4161 
    4162 executed CD20_2H7v16_define_pseudo_symmetries.cxc 
    4163 
    4164 > open CD20_2H7v166_D56A/CD20_2H7v166_D56A_define_pseudo_symmetries.cxc
    4165 
    4166 > combine CD20_2H7v166_D56A name 2H7_v166_D56A_Va modelId 1001
    4167 
    4168 > select zone (H7v166_D56A_V & /H,L) 0.1 #1001
    4169 
    4170 Selected 1654 atoms 
    4171 
    4172 > delete #1001 & ~sel
    4173 
    4174 > combine #1001 name 2H7_v166_D56A_Va_copy modelId 1002
    4175 
    4176 > combine CD20_2H7v166_D56A name 2H7_v166_D56A_Vb modelId 1003
    4177 
    4178 > select zone (H7v166_D56A_V & /I,M) 0.1 #1003
    4179 
    4180 Selected 1678 atoms 
    4181 
    4182 > delete #1003 & ~sel
    4183 
    4184 > combine #1003 name 2H7_v166_D56A_Vb_copy modelId 1004
    4185 
    4186 > combine CD20_2H7v166_D56A name 2H7_v166_D56A_Ca modelId 1005
    4187 
    4188 > select zone (H7v166_D56A_C & /H,L) 0.1 #1005
    4189 
    4190 Selected 1550 atoms 
    4191 
    4192 > delete #1005 & ~sel
    4193 
    4194 > combine #1005 name 2H7_v166_D56A_Ca_copy modelId 1006
    4195 
    4196 > combine CD20_2H7v166_D56A name 2H7_v166_D56A_Cb modelId 1007
    4197 
    4198 > select zone (H7v166_D56A_C & /I,M) 0.1 #1007
    4199 
    4200 Selected 1550 atoms 
    4201 
    4202 > delete #1007 & ~sel
    4203 
    4204 > combine #1007 name 2H7_v166_D56A_Ca_copy modelId 1008
    4205 
    4206 > matchmaker #1002/L to #1001/H
    4207 
    4208 Parameters 
    4209 --- 
    4210 Chain pairing | bb 
    4211 Alignment algorithm | Needleman-Wunsch 
    4212 Similarity matrix | BLOSUM-62 
    4213 SS fraction | 0.3 
    4214 Gap open (HH/SS/other) | 18/18/6 
    4215 Gap extend | 1 
    4216 SS matrix |  |  | H | S | O 
    4217 ---|---|---|--- 
    4218 H | 6 | -9 | -6 
    4219 S |  | 6 | -6 
    4220 O |  |  | 4 
    4221 Iteration cutoff | 2 
    4222  
    4223 Matchmaker 2H7_v166_D56A_Va, chain H (#1001) with 2H7_v166_D56A_Va_copy, chain
    4224 L (#1002), sequence alignment score = 547.6 
    4225 RMSD between 74 pruned atom pairs is 0.966 angstroms; (across all 90 pairs:
    4226 2.607) 
    4227  
    4228 
    4229 > wait 1
    4230 
    4231 > measure rotation #1002 toModel #1001 showSlabs true
    4232 
    4233 Position of 2H7_v166_D56A_Va_copy #1002 relative to 2H7_v166_D56A_Va #1001
    4234 coordinates: 
    4235 Matrix rotation and translation 
    4236 0.73992366 -0.12116101 0.66168949 -29.70332856 
    4237 -0.06116680 -0.99168902 -0.11318795 332.06337928 
    4238 0.66990417 0.04327702 -0.74118520 123.44534698 
    4239 Axis 0.93259437 -0.04896279 0.35758970 
    4240 Axis point 0.00000000 162.47254458 74.89799404 
    4241 Rotation angle (degrees) 175.18797763 
    4242 Shift along axis 0.18287681 
    4243  
    4244 
    4245 > close #1001 #1002
    4246 
    4247 > define axis #2 name axis_Va
    4248 
    4249 Axis 'rotation axis #2/axis_Va' centered at [136.31725835 155.31565622
    4250 127.16685711] with direction [ 0.93259437 -0.04896279 0.3575897 ], radius
    4251 0.599212, and length 47.937 
    4252 
    4253 > rename #2 Va_rotation_axis id #103.3.1.1
    4254 
    4255 > rename #3 Va_rotation_slabs id #103.3.2.1
    4256 
    4257 > matchmaker #1004/M to #1003/I
    4258 
    4259 Parameters 
    4260 --- 
    4261 Chain pairing | bb 
    4262 Alignment algorithm | Needleman-Wunsch 
    4263 Similarity matrix | BLOSUM-62 
    4264 SS fraction | 0.3 
    4265 Gap open (HH/SS/other) | 18/18/6 
    4266 Gap extend | 1 
    4267 SS matrix |  |  | H | S | O 
    4268 ---|---|---|--- 
    4269 H | 6 | -9 | -6 
    4270 S |  | 6 | -6 
    4271 O |  |  | 4 
    4272 Iteration cutoff | 2 
    4273  
    4274 Matchmaker 2H7_v166_D56A_Vb, chain I (#1003) with 2H7_v166_D56A_Vb_copy, chain
    4275 M (#1004), sequence alignment score = 376.5 
    4276 RMSD between 70 pruned atom pairs is 0.891 angstroms; (across all 92 pairs:
    4277 3.886) 
    4278  
    4279 
    4280 > wait 1
    4281 
    4282 > measure rotation #1004 toModel #1003 showSlabs true
    4283 
    4284 Position of 2H7_v166_D56A_Vb_copy #1004 relative to 2H7_v166_D56A_Vb #1003
    4285 coordinates: 
    4286 Matrix rotation and translation 
    4287 0.72982969 -0.01372193 -0.68349128 135.94952936 
    4288 0.06485007 -0.99390027 0.08920045 287.47713002 
    4289 -0.68054617 -0.10942560 -0.72448806 354.00628960 
    4290 Axis -0.92979963 -0.01378652 0.36780781 
    4291 Axis point 0.00000000 152.92822789 195.61279282 
    4292 Rotation angle (degrees) 173.86847166 
    4293 Shift along axis -0.16285394 
    4294  
    4295 
    4296 > close #1004 #1003
    4297 
    4298 > define axis #2 name axis_Vb
    4299 
    4300 Axis 'rotation axis #2/axis_Vb' centered at [173.81620585 155.50547201
    4301 126.8550136 ] with direction [-0.92979963 -0.01378652 0.36780781], radius
    4302 0.597156, and length 47.7725 
    4303 
    4304 > rename #2 Vb_rotation_axis id #103.3.1.2
    4305 
    4306 > rename #3 Vb_rotation_slabs id #103.3.2.2
    4307 
    4308 > matchmaker #1006/L to #1005/H
    4309 
    4310 Parameters 
    4311 --- 
    4312 Chain pairing | bb 
    4313 Alignment algorithm | Needleman-Wunsch 
    4314 Similarity matrix | BLOSUM-62 
    4315 SS fraction | 0.3 
    4316 Gap open (HH/SS/other) | 18/18/6 
    4317 Gap extend | 1 
    4318 SS matrix |  |  | H | S | O 
    4319 ---|---|---|--- 
    4320 H | 6 | -9 | -6 
    4321 S |  | 6 | -6 
    4322 O |  |  | 4 
    4323 Iteration cutoff | 2 
    4324  
    4325 Matchmaker 2H7_v166_D56A_Ca, chain H (#1005) with 2H7_v166_D56A_Ca_copy, chain
    4326 L (#1006), sequence alignment score = 554.5 
    4327 RMSD between 57 pruned atom pairs is 0.959 angstroms; (across all 98 pairs:
    4328 3.119) 
    4329  
    4330 
    4331 > wait 1
    4332 
    4333 > measure rotation #1006 toModel #1005 showSlabs true
    4334 
    4335 Position of 2H7_v166_D56A_Ca_copy #1006 relative to 2H7_v166_D56A_Ca #1005
    4336 coordinates: 
    4337 Matrix rotation and translation 
    4338 -0.33391401 0.38072466 0.86229355 -12.40856576 
    4339 0.05205532 -0.90595556 0.42016042 245.78035810 
    4340 0.94116506 0.18518442 0.28269251 -52.33839393 
    4341 Axis -0.57081123 -0.19159720 -0.79841408 
    4342 Axis point 28.53870248 129.91224226 0.00000000 
    4343 Rotation angle (degrees) 168.12212217 
    4344 Shift along axis 1.77983022 
    4345  
    4346 
    4347 > close #1006 #1005
    4348 
    4349 > define axis #2 name axis_Ca
    4350 
    4351 Axis 'rotation axis #2/axis_Ca' centered at [104.79817162 155.50932275
    4352 106.6668468 ] with direction [-0.57081123 -0.1915972 -0.79841408], radius
    4353 0.56909, and length 45.5272 
    4354 
    4355 > rename #2 Ca_rotation_axis id #103.3.1.3
    4356 
    4357 > rename #3 Ca_rotation_slabs id #103.3.2.3
    4358 
    4359 > matchmaker #1008/M to #1007/I
    4360 
    4361 Parameters 
    4362 --- 
    4363 Chain pairing | bb 
    4364 Alignment algorithm | Needleman-Wunsch 
    4365 Similarity matrix | BLOSUM-62 
    4366 SS fraction | 0.3 
    4367 Gap open (HH/SS/other) | 18/18/6 
    4368 Gap extend | 1 
    4369 SS matrix |  |  | H | S | O 
    4370 ---|---|---|--- 
    4371 H | 6 | -9 | -6 
    4372 S |  | 6 | -6 
    4373 O |  |  | 4 
    4374 Iteration cutoff | 2 
    4375  
    4376 Matchmaker 2H7_v166_D56A_Cb, chain I (#1007) with 2H7_v166_D56A_Ca_copy, chain
    4377 M (#1008), sequence alignment score = 416.6 
    4378 RMSD between 55 pruned atom pairs is 0.882 angstroms; (across all 98 pairs:
    4379 3.361) 
    4380  
    4381 
    4382 > wait 1
    4383 
    4384 > measure rotation #1008 toModel #1007 showSlabs true
    4385 
    4386 Position of 2H7_v166_D56A_Ca_copy #1008 relative to 2H7_v166_D56A_Cb #1007
    4387 coordinates: 
    4388 Matrix rotation and translation 
    4389 -0.50667380 0.40781938 -0.75958213 323.22163731 
    4390 0.08178140 -0.85433688 -0.51324487 330.95129120 
    4391 -0.85825023 -0.32216741 0.39951808 287.19953324 
    4392 Axis 0.48922423 0.25262440 -0.83476977 
    4393 Axis point 265.28291179 189.90297685 0.00000000 
    4394 Rotation angle (degrees) 168.73855860 
    4395 Shift along axis 1.98873850 
    4396  
    4397 
    4398 > close #1008 #1007
    4399 
    4400 > define axis #2 name axis_Cb
    4401 
    4402 Axis 'rotation axis #2/axis_Cb' centered at [203.75015551 158.12884417
    4403 104.99415577] with direction [ 0.48922423 0.2526244 -0.83476977], radius
    4404 0.553583, and length 44.2867 
    4405 
    4406 > rename #2 Cb_rotation_axis id #103.3.1.4
    4407 
    4408 > rename #3 Cb_rotation_slabs id #103.3.2.4
    4409 
    4410 > rename #103.3 geometry
    4411 
    4412 > rename #103.3.1 rotation_axes
    4413 
    4414 > rename #103.3.2 rotation_slabs
    4415 
    4416 executed CD20_2H7v166_D56A_define_pseudo_symmetries.cxc 
    4417 
    4418 > open
    4419 > CD20_2H7v166_S92A_D56A/CD20_2H7v166_S92A_D56A_define_pseudo_symmetries.cxc
    4420 
    4421 > combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Va modelId 1001
    4422 
    4423 > select zone (H7v166_S92A_D56A_V & /H,L) 0.1 #1001
    4424 
    4425 Selected 1653 atoms 
    4426 
    4427 > delete #1001 & ~sel
    4428 
    4429 > combine #1001 name 2H7_v166_S92A_D56A_Va_copy modelId 1002
    4430 
    4431 > combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Vb modelId 1003
    4432 
    4433 > select zone (H7v166_S92A_D56A_V & /I,M) 0.1 #1003
    4434 
    4435 Selected 1678 atoms 
    4436 
    4437 > delete #1003 & ~sel
    4438 
    4439 > combine #1003 name 2H7_v166_S92A_D56A_Vb_copy modelId 1004
    4440 
    4441 > combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Ca modelId 1005
    4442 
    4443 > select zone (H7v166_S92A_D56A_C & /H,L) 0.1 #1005
    4444 
    4445 Selected 1461 atoms 
    4446 
    4447 > delete #1005 & ~sel
    4448 
    4449 > combine #1005 name 2H7_v166_S92A_D56A_Ca_copy modelId 1006
    4450 
    4451 > combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Cb modelId 1007
    4452 
    4453 > select zone (H7v166_S92A_D56A_C & /I,M) 0.1 #1007
    4454 
    4455 Selected 1550 atoms 
    4456 
    4457 > delete #1007 & ~sel
    4458 
    4459 > combine #1007 name 2H7_v166_S92A_D56A_Ca_copy modelId 1008
    4460 
    4461 > matchmaker #1002/L to #1001/H
    4462 
    4463 Parameters 
    4464 --- 
    4465 Chain pairing | bb 
    4466 Alignment algorithm | Needleman-Wunsch 
    4467 Similarity matrix | BLOSUM-62 
    4468 SS fraction | 0.3 
    4469 Gap open (HH/SS/other) | 18/18/6 
    4470 Gap extend | 1 
    4471 SS matrix |  |  | H | S | O 
    4472 ---|---|---|--- 
    4473 H | 6 | -9 | -6 
    4474 S |  | 6 | -6 
    4475 O |  |  | 4 
    4476 Iteration cutoff | 2 
    4477  
    4478 Matchmaker 2H7_v166_S92A_D56A_Va, chain H (#1001) with
    4479 2H7_v166_S92A_D56A_Va_copy, chain L (#1002), sequence alignment score = 221.1 
    4480 RMSD between 66 pruned atom pairs is 1.048 angstroms; (across all 87 pairs:
    4481 3.054) 
    4482  
    4483 
    4484 > wait 1
    4485 
    4486 > measure rotation #1002 toModel #1001 showSlabs true
    4487 
    4488 Position of 2H7_v166_S92A_D56A_Va_copy #1002 relative to 2H7_v166_S92A_D56A_Va
    4489 #1001 coordinates: 
    4490 Matrix rotation and translation 
    4491 0.71841270 -0.03882790 0.69453263 -43.77242719 
    4492 0.04474713 -0.99379351 -0.10184377 314.28607160 
    4493 0.69417640 0.10424420 -0.71221645 107.06747282 
    4494 Axis 0.92669760 0.00160183 0.37580447 
    4495 Axis point 0.00000000 153.96110044 71.86641580 
    4496 Rotation angle (degrees) 173.61580296 
    4497 Shift along axis 0.17606353 
    4498  
    4499 
    4500 > close #1001 #1002
    4501 
    4502 > define axis #2 name axis_Va
    4503 
    4504 Axis 'rotation axis #2/axis_Va' centered at [136.49236761 154.19703207
    4505 127.21828189] with direction [0.9266976 0.00160183 0.37580447], radius
    4506 0.603625, and length 48.29 
    4507 
    4508 > rename #2 Va_rotation_axis id #104.3.1.1
    4509 
    4510 > rename #3 Va_rotation_slabs id #104.3.2.1
    4511 
    4512 > matchmaker #1004/M to #1003/I
    4513 
    4514 Parameters 
    4515 --- 
    4516 Chain pairing | bb 
    4517 Alignment algorithm | Needleman-Wunsch 
    4518 Similarity matrix | BLOSUM-62 
    4519 SS fraction | 0.3 
    4520 Gap open (HH/SS/other) | 18/18/6 
    4521 Gap extend | 1 
    4522 SS matrix |  |  | H | S | O 
    4523 ---|---|---|--- 
    4524 H | 6 | -9 | -6 
    4525 S |  | 6 | -6 
    4526 O |  |  | 4 
    4527 Iteration cutoff | 2 
    4528  
    4529 Matchmaker 2H7_v166_S92A_D56A_Vb, chain I (#1003) with
    4530 2H7_v166_S92A_D56A_Vb_copy, chain M (#1004), sequence alignment score = 228.5 
    4531 RMSD between 66 pruned atom pairs is 1.088 angstroms; (across all 92 pairs:
    4532 3.936) 
    4533  
    4534 
    4535 > wait 1
    4536 
    4537 > measure rotation #1004 toModel #1003 showSlabs true
    4538 
    4539 Position of 2H7_v166_S92A_D56A_Vb_copy #1004 relative to 2H7_v166_S92A_D56A_Vb
    4540 #1003 coordinates: 
    4541 Matrix rotation and translation 
    4542 0.73661563 -0.07135580 -0.67253682 142.18618798 
    4543 0.02298296 -0.99120309 0.13033888 288.51761976 
    4544 -0.67592100 -0.11146654 -0.72849572 353.55093768 
    4545 Axis -0.93153019 0.01303723 0.36343024 
    4546 Axis point 0.00000000 157.62360929 194.41945478 
    4547 Rotation angle (degrees) 172.54257925 
    4548 Shift along axis -0.19815617 
    4549  
    4550 
    4551 > close #1004 #1003
    4552 
    4553 > define axis #2 name axis_Vb
    4554 
    4555 Axis 'rotation axis #2/axis_Vb' centered at [172.8655548 155.20426996
    4556 126.97712173] with direction [-0.93153019 0.01303723 0.36343024], radius
    4557 0.60681, and length 48.5448 
    4558 
    4559 > rename #2 Vb_rotation_axis id #104.3.1.2
    4560 
    4561 > rename #3 Vb_rotation_slabs id #104.3.2.2
    4562 
    4563 > matchmaker #1006/L to #1005/H
    4564 
    4565 Parameters 
    4566 --- 
    4567 Chain pairing | bb 
    4568 Alignment algorithm | Needleman-Wunsch 
    4569 Similarity matrix | BLOSUM-62 
    4570 SS fraction | 0.3 
    4571 Gap open (HH/SS/other) | 18/18/6 
    4572 Gap extend | 1 
    4573 SS matrix |  |  | H | S | O 
    4574 ---|---|---|--- 
    4575 H | 6 | -9 | -6 
    4576 S |  | 6 | -6 
    4577 O |  |  | 4 
    4578 Iteration cutoff | 2 
    4579  
    4580 Matchmaker 2H7_v166_S92A_D56A_Ca, chain H (#1005) with
    4581 2H7_v166_S92A_D56A_Ca_copy, chain L (#1006), sequence alignment score = 229.8 
    4582 RMSD between 50 pruned atom pairs is 0.885 angstroms; (across all 82 pairs:
    4583 3.058) 
    4584  
    4585 
    4586 > wait 1
    4587 
    4588 > measure rotation #1006 toModel #1005 showSlabs true
    4589 
    4590 Position of 2H7_v166_S92A_D56A_Ca_copy #1006 relative to 2H7_v166_S92A_D56A_Ca
    4591 #1005 coordinates: 
    4592 Matrix rotation and translation 
    4593 -0.43223566 0.39105435 0.81255697 5.34243089 
    4594 0.04124481 -0.89156204 0.45101662 236.01875124 
    4595 0.90081696 0.22845922 0.36923594 -64.79879197 
    4596 Axis -0.52502754 -0.20821113 -0.82522373 
    4597 Axis point 38.63388899 125.78498588 0.00000000 
    4598 Rotation angle (degrees) 167.76344751 
    4599 Shift along axis 1.52684600 
    4600  
    4601 
    4602 > close #1006 #1005
    4603 
    4604 > define axis #2 name axis_Ca
    4605 
    4606 Axis 'rotation axis #2/axis_Ca' centered at [105.63109625 152.35419104
    4607 105.30435297] with direction [-0.52502754 -0.20821113 -0.82522373], radius
    4608 0.532467, and length 42.5974 
    4609 
    4610 > rename #2 Ca_rotation_axis id #104.3.1.3
    4611 
    4612 > rename #3 Ca_rotation_slabs id #104.3.2.3
    4613 
    4614 > matchmaker #1008/M to #1007/I
    4615 
    4616 Parameters 
    4617 --- 
    4618 Chain pairing | bb 
    4619 Alignment algorithm | Needleman-Wunsch 
    4620 Similarity matrix | BLOSUM-62 
    4621 SS fraction | 0.3 
    4622 Gap open (HH/SS/other) | 18/18/6 
    4623 Gap extend | 1 
    4624 SS matrix |  |  | H | S | O 
    4625 ---|---|---|--- 
    4626 H | 6 | -9 | -6 
    4627 S |  | 6 | -6 
    4628 O |  |  | 4 
    4629 Iteration cutoff | 2 
    4630  
    4631 Matchmaker 2H7_v166_S92A_D56A_Cb, chain I (#1007) with
    4632 2H7_v166_S92A_D56A_Ca_copy, chain M (#1008), sequence alignment score = 226.4 
    4633 RMSD between 57 pruned atom pairs is 0.983 angstroms; (across all 98 pairs:
    4634 3.247) 
    4635  
    4636 
    4637 > wait 1
    4638 
    4639 > measure rotation #1008 toModel #1007 showSlabs true
    4640 
    4641 Position of 2H7_v166_S92A_D56A_Ca_copy #1008 relative to 2H7_v166_S92A_D56A_Cb
    4642 #1007 coordinates: 
    4643 Matrix rotation and translation 
    4644 -0.44691350 0.37987962 -0.80991345 321.97311814 
    4645 0.04334425 -0.89510032 -0.44375297 334.72634524 
    4646 -0.89352650 -0.23342428 0.38356682 282.18198422 
    4647 Axis 0.51860284 0.20616286 -0.82978790 
    4648 Axis point 269.80743377 182.59879005 0.00000000 
    4649 Rotation angle (degrees) 168.30019456 
    4650 Shift along axis 1.83311720 
    4651  
    4652 
    4653 > close #1008 #1007
    4654 
    4655 > define axis #2 name axis_Cb
    4656 
    4657 Axis 'rotation axis #2/axis_Cb' centered at [203.87433587 156.38806637
    4658 105.49592574] with direction [ 0.51860284 0.20616286 -0.8297879 ], radius
    4659 0.566216, and length 45.2973 
    4660 
    4661 > rename #2 Cb_rotation_axis id #104.3.1.4
    4662 
    4663 > rename #3 Cb_rotation_slabs id #104.3.2.4
    4664 
    4665 > rename #104.3 geometry
    4666 
    4667 > rename #104.3.1 rotation_axes
    4668 
    4669 > rename #104.3.2 rotation_slabs
    4670 
    4671 executed CD20_2H7v166_S92A_D56A_define_pseudo_symmetries.cxc 
    4672 
    4673 > open CD20_2H7_mutants_define_domain_centroids.cxc
    4674 
    4675 > define centroid RTX_C & /L name centroid_RTX_C_L
    4676 
    4677 Centroid 'centroid_RTX_C_L' placed at [ 99.24795328 158.51064899 116.56555556] 
    4678 
    4679 > rename ##name=centroid_RTX_C_L id 101.3.3.1
    4680 
    4681 > define centroid RTX_C & /M name centroid_RTX_C_M
    4682 
    4683 Centroid 'centroid_RTX_C_M' placed at [210.77360859 151.52862247 116.58115025] 
    4684 
    4685 > rename ##name=centroid_RTX_C_M id 101.3.3.2
    4686 
    4687 > define centroid RTX_C & /H name centroid_RTX_C_H
    4688 
    4689 Centroid 'centroid_RTX_C_H' placed at [106.64933474 150.8311308 104.33269761] 
    4690 
    4691 > rename ##name=centroid_RTX_C_H id 101.3.3.3
    4692 
    4693 > define centroid RTX_C & /I name centroid_RTX_C_I
    4694 
    4695 Centroid 'centroid_RTX_C_I' placed at [203.36467932 159.20700844 104.37016456] 
    4696 
    4697 > rename ##name=centroid_RTX_C_I id 101.3.3.4
    4698 
    4699 > define centroid RTX_V & /L name centroid_RTX_V_L
    4700 
    4701 Centroid 'centroid_RTX_V_L' placed at [134.90703015 166.45776759 126.23118216] 
    4702 
    4703 > rename ##name=centroid_RTX_V_L id 101.3.3.5
    4704 
    4705 > define centroid RTX_V & /M name centroid_RTX_V_M
    4706 
    4707 Centroid 'centroid_RTX_V_M' placed at [175.12986935 143.57538693 126.24564698] 
    4708 
    4709 > rename ##name=centroid_RTX_V_M id 101.3.3.6
    4710 
    4711 > define centroid RTX_V & /H name centroid_RTX_V_H
    4712 
    4713 Centroid 'centroid_RTX_V_H' placed at [138.39382732 143.61326339 125.48950601] 
    4714 
    4715 > rename ##name=centroid_RTX_V_H id 101.3.3.7
    4716 
    4717 > define centroid RTX_V & /I name centroid_RTX_V_I
    4718 
    4719 Centroid 'centroid_RTX_V_I' placed at [171.6143541 166.39779016 125.48935082] 
    4720 
    4721 > rename ##name=centroid_RTX_V_I id 101.3.3.8
    4722 
    4723 > rename #101.3.3 centroids
    4724 
    4725 > define centroid H7v16_C & /L name centroid_2H7v16_C_L
    4726 
    4727 Centroid 'centroid_2H7v16_C_L' placed at [105.06462233 154.79494479
    4728 104.71732873] 
    4729 
    4730 > rename ##name=centroid_2H7v16_C_L id 102.3.3.1
    4731 
    4732 > define centroid H7v16_C & /M name centroid_2H7v16_C_M
    4733 
    4734 Centroid 'centroid_2H7v16_C_M' placed at [208.42672522 167.55451192
    4735 109.46892346] 
    4736 
    4737 > rename ##name=centroid_2H7v16_C_M id 102.3.3.2
    4738 
    4739 > define centroid H7v16_C & /H name centroid_2H7v16_C_H
    4740 
    4741 Centroid 'centroid_2H7v16_C_H' placed at [115.17526428 144.82097344
    4742 100.10963479] 
    4743 
    4744 > rename ##name=centroid_2H7v16_C_H id 102.3.3.3
    4745 
    4746 > define centroid H7v16_C & /I name centroid_2H7v16_C_I
    4747 
    4748 Centroid 'centroid_2H7v16_C_I' placed at [196.31280478 174.43741833
    4749 103.22787118] 
    4750 
    4751 > rename ##name=centroid_2H7v16_C_I id 102.3.3.4
    4752 
    4753 > define centroid H7v16_V & /L name centroid_2H7v16_V_L
    4754 
    4755 Centroid 'centroid_2H7v16_V_L' placed at [136.25738614 163.8169901
    4756 124.64938243] 
    4757 
    4758 > rename ##name=centroid_2H7v16_V_L id 102.3.3.5
    4759 
    4760 > define centroid H7v16_V & /M name centroid_2H7v16_V_M
    4761 
    4762 Centroid 'centroid_2H7v16_V_M' placed at [179.26451702 150.74154843
    4763 126.48898691] 
    4764 
    4765 > rename ##name=centroid_2H7v16_V_M id 102.3.3.6
    4766 
    4767 > define centroid H7v16_V & /H name centroid_2H7v16_V_H
    4768 
    4769 Centroid 'centroid_2H7v16_V_H' placed at [139.25597569 141.97514482
    4770 126.96669027] 
    4771 
    4772 > rename ##name=centroid_2H7v16_V_H id 102.3.3.7
    4773 
    4774 > define centroid H7v16_V & /I name centroid_2H7v16_V_I
    4775 
    4776 Centroid 'centroid_2H7v16_V_I' placed at [169.61364905 170.56588689
    4777 126.76187738] 
    4778 
    4779 > rename ##name=centroid_2H7v16_V_I id 102.3.3.8
    4780 
    4781 > rename #102.3.3 centroids
    4782 
    4783 > define centroid H7v166_D56A_C & /L name centroid_2H7v166_D56A_C_L
    4784 
    4785 Centroid 'centroid_2H7v166_D56A_C_L' placed at [101.80191468 161.59134128
    4786 111.74271267] 
    4787 
    4788 > rename ##name=centroid_2H7v166_D56A_C_L id 103.3.3.1
    4789 
    4790 > define centroid H7v166_D56A_C & /M name centroid_2H7v166_D56A_C_M
    4791 
    4792 Centroid 'centroid_2H7v166_D56A_C_M' placed at [208.08802258 152.28425847
    4793 109.3226675 ] 
    4794 
    4795 > rename ##name=centroid_2H7v166_D56A_C_M id 103.3.3.2
    4796 
    4797 > define centroid H7v166_D56A_C & /H name centroid_2H7v166_D56A_C_H
    4798 
    4799 Centroid 'centroid_2H7v166_D56A_C_H' placed at [110.13903054 151.41048738
    4800 105.03944622] 
    4801 
    4802 > rename ##name=centroid_2H7v166_D56A_C_H id 103.3.3.3
    4803 
    4804 > define centroid H7v166_D56A_C & /I name centroid_2H7v166_D56A_C_I
    4805 
    4806 Centroid 'centroid_2H7v166_D56A_C_I' placed at [198.26240903 162.26559628
    4807 103.22947676] 
    4808 
    4809 > rename ##name=centroid_2H7v166_D56A_C_I id 103.3.3.4
    4810 
    4811 > define centroid H7v166_D56A_V & /L name centroid_2H7v166_D56A_V_L
    4812 
    4813 Centroid 'centroid_2H7v166_D56A_V_L' placed at [134.697663 166.81530949
    4814 127.91858459] 
    4815 
    4816 > rename ##name=centroid_2H7v166_D56A_V_L id 103.3.3.5
    4817 
    4818 > define centroid H7v166_D56A_V & /M name centroid_2H7v166_D56A_V_M
    4819 
    4820 Centroid 'centroid_2H7v166_D56A_V_M' placed at [176.0024767 144.42140479
    4821 127.2169787 ] 
    4822 
    4823 > rename ##name=centroid_2H7v166_D56A_V_M id 103.3.3.6
    4824 
    4825 > define centroid H7v166_D56A_V & /H name centroid_2H7v166_D56A_V_H
    4826 
    4827 Centroid 'centroid_2H7v166_D56A_V_H' placed at [137.53539482 144.47796656
    4828 127.54490507] 
    4829 
    4830 > rename ##name=centroid_2H7v166_D56A_V_H id 103.3.3.7
    4831 
    4832 > define centroid H7v166_D56A_V & /I name centroid_2H7v166_D56A_V_I
    4833 
    4834 Centroid 'centroid_2H7v166_D56A_V_I' placed at [172.57552427 166.28897087
    4835 127.29650809] 
    4836 
    4837 > rename ##name=centroid_2H7v166_D56A_V_I id 103.3.3.8
    4838 
    4839 > rename #103.3.3 centroids
    4840 
    4841 > define centroid CD20 & /C name centroid_CD20_C
    4842 
    4843 Centroid 'centroid_CD20_C' placed at [144.8538135 155.45678354 168.48594241] 
    4844 
    4845 > rename ##name=centroid_CD20_C id 101.3.3.9
    4846 
    4847 > define centroid CD20 & /D name centroid_CD20_D
    4848 
    4849 Centroid 'centroid_CD20_D' placed at [165.21501485 155.16108662 168.7605414 ] 
    4850 
    4851 > rename ##name=centroid_CD20_D id 101.3.3.10
    4852 
    4853 executed CD20_2H7_mutants_define_domain_centroids.cxc 
    4854 
    4855 > turn x 90
    4856 
    4857 > view
    4858 
    4859 > hide #101 models
    4860 
    4861 > hide #!102.2 models
    4862 
    4863 > ~ribbon #102.10/X,Y
    4864 
    4865 executed CD20_2H7_mutants_setup.cxc 
    4866 
    4867 > help angle
    4868 
    4869 > open /Users/rohoua/work/Genentech/CD20/CD20_2H7v166/STR7730.pdb
    4870 
    4871 Summary of feedback from opening
    4872 /Users/rohoua/work/Genentech/CD20/CD20_2H7v166/STR7730.pdb 
    4873 --- 
    4874 warning | Ignored bad PDB record found on line 1 
    4875 HEADER STR7730 version_1 2024.01.12 
    4876  
    4877 STR7730.pdb title: 
    4878 Structure of 2H7v166 Fab and Hs_CD20.M1-P297 at 5.2 A resolution. [more
    4879 info...] 
    4880  
    4881 Chain information for STR7730.pdb #2 
    4882 --- 
    4883 Chain | Description 
    4884 C | No description available 
    4885 D | No description available 
    4886 H I | No description available 
    4887 L | No description available 
    4888 M | No description available 
    4889  
    4890 
    4891 > matchmaker #2 to #103.1
    4892 
    4893 Parameters 
    4894 --- 
    4895 Chain pairing | bb 
    4896 Alignment algorithm | Needleman-Wunsch 
    4897 Similarity matrix | BLOSUM-62 
    4898 SS fraction | 0.3 
    4899 Gap open (HH/SS/other) | 18/18/6 
    4900 Gap extend | 1 
    4901 SS matrix |  |  | H | S | O 
    4902 ---|---|---|--- 
    4903 H | 6 | -9 | -6 
    4904 S |  | 6 | -6 
    4905 O |  |  | 4 
    4906 Iteration cutoff | 2 
    4907  
    4908 Matchmaker CD20_2H7v166_D56A, chain I (#103.1) with STR7730.pdb, chain H (#2),
    4909 sequence alignment score = 1988.6 
    4910 RMSD between 214 pruned atom pairs is 0.839 angstroms; (across all 229 pairs:
    4911 1.558) 
    4912  
    4913 
    4914 > save /Users/rohoua/work/Genentech/CD20/CD20_2H7v166/STR7730_alito6vja.pdb
    4915 > models #2
    4916 
    4917 > help martrix
    4918 
    4919 No help found for 'martrix' 
    4920 
    4921 > help view matrix
    4922 
    4923 > view matrix
    4924 
    4925 view matrix camera 1,0,0,148.16,0,1.1102e-16,1,424.33,0,-1,1.1102e-16,137.41 
    4926 view matrix models
    4927 #101,1,0,0,0,0,1,0,0,0,0,1,0,#101.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.3,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.4,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.3,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.4,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.4.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.3,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.4,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.5,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.6,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.7,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.8,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.9,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.10,1,0,0,0,0,1,0,0,0,0,1,0,#102,1,0,0,0,0,1,0,0,0,0,1,0,#102.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.2,-0.2379,0.93572,0.26045,-39.485,0.96898,0.21017,0.12999,-107.2,0.066893,0.2833,-0.9567,274.92,#102.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.10,0.76603,0.10593,0.63402,98.602,-0.63362,-0.041732,0.77252,142.28,0.10829,-0.9935,0.035152,135.31,#102.10.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.3,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.4,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.3,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.4,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.4.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.3,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.4,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.5,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.6,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.7,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.8,1,0,0,0,0,1,0,0,0,0,1,0,#103,1,0,0,0,0,1,0,0,0,0,1,0,#103.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.2,0.0093785,0.99468,-0.1026,-18.509,-0.99949,0.0061787,-0.031461,352.76,-0.03066,0.10284,0.99423,-49.289,#103.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.3,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.4,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.3,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.4,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.4.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.3,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.4,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.5,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.6,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.7,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.8,1,0,0,0,0,1,0,0,0,0,1,0,#104,1,0,0,0,0,1,0,0,0,0,1,0,#104.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.2,-0.0024947,0.9708,0.23989,-104.33,0.99657,0.022251,-0.079684,-45.216,-0.082695,0.23887,-0.96752,330.43,#104.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.3,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.4,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.3,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.4,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.4.2,1,0,0,0,0,1,0,0,0,0,1,0,#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#10,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.094232,-0.75331,-0.65088,436.99,-0.99412,-0.036109,-0.10213,396.76,0.053436,0.65667,-0.75228,168.36 
    4928  
    4929 
    4930 > close
    4931 
    4932 > open /Users/rohoua/work/Genentech/CD20/CD20_2H7_mutants_setup.cxc format cmd
    4933 
    4934 > close
    4935 
    4936 > cd /Users/rohoua/work/Genentech/CD20
    4937 
    4938 Current working directory is: /Users/rohoua/work/Genentech/CD20 
    4939 
    4940 > open pdb:6vja name CD20_RTX id 101.1
    4941 
    4942 CD20_RTX title: 
    4943 Structure of CD20 in complex with rituximab Fab [more info...] 
    4944  
    4945 Chain information for CD20_RTX #1 
    4946 --- 
    4947 Chain | Description | UniProt 
    4948 C D | B-lymphocyte antigen CD20 | CD20_HUMAN 41-297 
    4949 H I | Rituximab Fab heavy chain | 
    4950 L M | Rituximab Fab light chain | 
    4951  
    4952 Non-standard residues in CD20_RTX #1 
    4953 --- 
    4954 Y01 — cholesterol hemisuccinate 
    4955  
    4956 
    4957 > open CD20_2H7v16/STR7668v2_alito6vja_C178to187.pdb name CD20_2H7v16 id 102.1
    4958 
    4959 Summary of feedback from opening CD20_2H7v16/STR7668v2_alito6vja_C178to187.pdb 
    4960 --- 
    4961 warning | Ignored bad PDB record found on line 1 
    4962 HEADER STR7668 version_2 2023.12.13 
    4963  
    4964 CD20_2H7v16 title: 
    4965 Structure of 2H7.v16 Fab and 2103.826032.Hs_MS4A1.M1-P297.BiNTF-NAvi at 3.3 A
    4966 resolution. [more info...] 
    4967  
    4968 Chain information for CD20_2H7v16 #1 
    4969 --- 
    4970 Chain | Description 
    4971 C D | No description available 
    4972 H I | No description available 
    4973 L M | No description available 
    4974  
    4975 Non-standard residues in CD20_2H7v16 #1 
    4976 --- 
    4977 Y01 — (Y01) 
    4978  
    4979 
    4980 > open CD20_2H7v16/P69_W9_J181/J181_004_volume_denoised.mrc id 102.2
    4981 
    4982 Opened J181_004_volume_denoised.mrc as #1, grid size 480,480,480, pixel 0.838,
    4983 shown at level 0.0054, step 2, values float32 
    4984 
    4985 > volume #102.2 step 1 level 0.08 color #9999CC transparency 0.5
    4986 
    4987 > view matrix models
    4988 > #102.2,-0.2379,0.93572,0.26045,-39.485,0.96898,0.21017,0.12999,-107.2,0.066893,0.2833,-0.9567,274.92
    4989 
    4990 > open "CD20_2H7v16/crystal_structure/STR7487.2H7 Fab.pdb" name 2H7v16_XRay id
    4991 > 102.10
    4992 
    4993 Summary of feedback from opening CD20_2H7v16/crystal_structure/STR7487.2H7
    4994 Fab.pdb 
    4995 --- 
    4996 warning | Ignored bad PDB record found on line 1 
    4997 HEADER STR7487 version_1 2023.05.24 
    4998  
    4999 2H7v16_XRay title: 
    5000 Structure of 2H7 Fab at 2.45 A resolution. [more info...] 
    5001  
    5002 Chain information for 2H7v16_XRay #1 
    5003 --- 
    5004 Chain | Description 
    5005 A B X Y | No description available 
    5006  
    5007 Non-standard residues in 2H7v16_XRay #1 
    5008 --- 
    5009 CL — (CL) 
    5010  
    5011 
    5012 > matchmaker #102.10/A,B to #102.1/H,L
    5013 
    5014 Parameters 
    5015 --- 
    5016 Chain pairing | bb 
    5017 Alignment algorithm | Needleman-Wunsch 
    5018 Similarity matrix | BLOSUM-62 
    5019 SS fraction | 0.3 
    5020 Gap open (HH/SS/other) | 18/18/6 
    5021 Gap extend | 1 
    5022 SS matrix |  |  | H | S | O 
    5023 ---|---|---|--- 
    5024 H | 6 | -9 | -6 
    5025 S |  | 6 | -6 
    5026 O |  |  | 4 
    5027 Iteration cutoff | 2 
    5028  
    5029 Matchmaker CD20_2H7v16, chain L (#102.1) with 2H7v16_XRay, chain A (#102.10),
    5030 sequence alignment score = 1228.2 
    5031 RMSD between 208 pruned atom pairs is 0.731 angstroms; (across all 213 pairs:
    5032 0.804) 
    5033  
    5034 
    5035 > open CD20_2H7v166_D56A/STR7717v2_alito6vja.pdb name CD20_2H7v166_D56A id
    5036 > 103.1
    5037 
    5038 Summary of feedback from opening CD20_2H7v166_D56A/STR7717v2_alito6vja.pdb 
    5039 --- 
    5040 warning | Ignored bad PDB record found on line 1 
    5041 HEADER STR7717 version_2 2023.12.15 
    5042  
    5043 CD20_2H7v166_D56A title: 
    5044 Structure of 2H7v166_D56A Fab and Hs_CD20.M1-P297 at 3.7 A resolution . [more
    5045 info...] 
    5046  
    5047 Chain information for CD20_2H7v166_D56A #1 
    5048 --- 
    5049 Chain | Description 
    5050 C D | No description available 
    5051 H I | No description available 
    5052 L | No description available 
    5053 M | No description available 
    5054  
    5055 Non-standard residues in CD20_2H7v166_D56A #1 
    5056 --- 
    5057 Y01 — (Y01) 
    5058  
    5059 
    5060 > open CD20_2H7v166_D56A/cryosparc_P69_J433_007_volume_map_sharp.mrc id 103.2
    5061 
    5062 Opened cryosparc_P69_J433_007_volume_map_sharp.mrc as #1, grid size
    5063 300,300,300, pixel 1.28, shown at level 0.0592, step 2, values float32 
    5064 
    5065 > volume #103.2 step 1 level 0.355 color #9999CC transparency 0.5
    5066 
    5067 > view matrix models
    5068 > #103.2,0.00937853,0.99467855,-0.10259937,-18.50914227,-0.99948588,0.00617870,-0.03146112,352.75851684,-0.03065977,0.10284168,0.99422511,-49.28949280
    5069 
    5070 > open CD20_2H7v166_S92A_D56A/STR7729v2_alito6vja.pdb name
    5071 > CD20_2H7v166_S92A_D56A id 104.1
    5072 
    5073 Summary of feedback from opening
    5074 CD20_2H7v166_S92A_D56A/STR7729v2_alito6vja.pdb 
    5075 --- 
    5076 warning | Ignored bad PDB record found on line 1 
    5077 HEADER STR7729 version_2 2024.01.29 
    5078  
    5079 CD20_2H7v166_S92A_D56A title: 
    5080 Structure of 2H7v166 LC.S92A HC.D56A Fab and Hs_CD20.M1-P297 at 4.5 A
    5081 resolution. [more info...] 
    5082  
    5083 Chain information for CD20_2H7v166_S92A_D56A #1 
    5084 --- 
    5085 Chain | Description 
    5086 C D | No description available 
    5087 H | No description available 
    5088 I | No description available 
    5089 L M | No description available 
    5090  
    5091 
    5092 > open CD20_2H7v166_S92A_D56A/cryosparc_P69_J242_005_volume_map_sharp_flip.mrc
    5093 > id 104.2
    5094 
    5095 Opened cryosparc_P69_J242_005_volume_map_sharp_flip.mrc as #1, grid size
    5096 300,300,300, pixel 1.43, shown at level 0.0447, step 2, values float32 
    5097 
    5098 > volume #104.2 step 1 level 0.355 color #9999CC transparency 0.5
    5099 
    5100 > view matrix models
    5101 > #104.2,-0.00249470,0.97079708,0.23988915,-104.32503408,0.99657176,0.02225139,-0.07968446,-45.21631074,-0.08269530,0.23886796,-0.96752446,330.43463437
    5102 
    5103 > open CD20_2H7v166/STR7730_alito6vja.pdb name CD20_2H7v166 id 105.1
    5104 
    5105 Summary of feedback from opening CD20_2H7v166/STR7730_alito6vja.pdb 
    5106 --- 
    5107 warning | Ignored bad PDB record found on line 1 
    5108 HEADER STR7730 version_1 2024.01.12 
    5109  
    5110 CD20_2H7v166 title: 
    5111 Structure of 2H7v166 Fab and Hs_CD20.M1-P297 at 5.2 A resolution. [more
    5112 info...] 
    5113  
    5114 Chain information for CD20_2H7v166 #1 
    5115 --- 
    5116 Chain | Description 
    5117 C | No description available 
    5118 D | No description available 
    5119 H I | No description available 
    5120 L | No description available 
    5121 M | No description available 
    5122  
    5123 
    5124 > open CD20_2H7v166/cryosparc_P71_J138_006_volume_map_sharp.mrc id 105.2
    5125 
    5126 Opened cryosparc_P71_J138_006_volume_map_sharp.mrc as #1, grid size
    5127 300,300,300, pixel 1.43, shown at level 0.0428, step 2, values float32 
    5128 
    5129 > volume #105.2 step 1 level 0.355 color #9999CC transparency 0.5
    5130 
    5131 > view matrix models
    5132 > #105.2,0.094232,-0.75331,-0.65088,436.99,-0.99412,-0.036109,-0.10213,396.76,0.053436,0.65667,-0.75228,168.36
    5133 
    5134 > rename #101 CD20_RTX
    5135 
    5136 > rename #102 CD20_2H7v16
    5137 
    5138 > rename #103 CD20_2H7v166_D56A
    5139 
    5140 > rename #104 CD20_2H7v166_S92A_D56A
    5141 
    5142 > dssp
    5143 
    5144 > name CD20_RTX #101.1
    5145 
    5146 > name CD20_2H7v16 #102.1
    5147 
    5148 > name CD20_2H7v166_D56A #103.1
    5149 
    5150 > name CD20_2H7v166_S92A_D56A #104.1
    5151 
    5152 > name CD20 /C,D
    5153 
    5154 > name CD20_Monomer /C
    5155 
    5156 > name CD20_H1 /C,D:46-71
    5157 
    5158 > name CD20_ECL1 /C,D:72-79
    5159 
    5160 > name CD20_H2 /C,D:80-105
    5161 
    5162 > name CD20_ICL1 /C,D:106-112
    5163 
    5164 > name CD20_H3 /C,D:113-141
    5165 
    5166 > name CD20_ECL2 /C,D:142-187
    5167 
    5168 > name CD20_ECL2SS /C,D:167,183
    5169 
    5170 > name CD20_H4 /C,D:188-end
    5171 
    5172 > name CD20_DimerInt /C,D:62,200,65,196,69,192,73,188,76,185,58,54,50
    5173 
    5174 > name RTX CD20_RTX & /H,L,I,M
    5175 
    5176 > name RTX_H RTX & /H,I
    5177 
    5178 > name RTX_L RTX & /L,M
    5179 
    5180 > name RTX_Epitope CD20_RTX & /C,D:168-175
    5181 
    5182 > name RTX_V (RTX & /L,M:1-107) | (RTX & /H,I:1-111)
    5183 
    5184 > name RTX_C (RTX & /L,M:113-end) | (RTX & /H,I:119-end)
    5185 
    5186 > name H7v16 CD20_2H7v16 & /H,L,I,M
    5187 
    5188 > name H7v16_H H7v16 & /H,I
    5189 
    5190 > name H7v16_L H7v16 & /L,M
    5191 
    5192 > name H7v16_Epitope CD20_2H7v16 & /C,D:168-175
    5193 
    5194 > name H7v16_V (H7v16 & /L,M:1-107) | (H7v16 & /H,I:1-111)
    5195 
    5196 > name H7v16_C (H7v16 & /L,M:112-end) | (H7v16 & /H,I:119-end)
    5197 
    5198 > name H7v166_D56A CD20_2H7v166_D56A & /H,L,I,M
    5199 
    5200 > name H7v166_D56A_H H7v166_D56A & /H,I
    5201 
    5202 > name H7v166_D56A_L H7v166_D56A & /L,M
    5203 
    5204 > name H7v166_D56A_Epitope CD20_2H7v166_D56A & /C,D:168-175
    5205 
    5206 > name H7v166_D56A_V (H7v166_D56A & /L,M:1-107) | (H7v166_D56A & /H,I:1-111)
    5207 
    5208 > name H7v166_D56A_C (H7v166_D56A & /L,M:112-end) | (H7v166_D56A &
    5209 > /H,I:119-end)
    5210 
    5211 > name H7v166_S92A_D56A CD20_2H7v166_S92A_D56A & /H,L,I,M
    5212 
    5213 > name H7v166_S92A_D56A_H H7v166_S92A_D56A & /H,I
    5214 
    5215 > name H7v166_S92A_D56A_L H7v166_S92A_D56A & /L,M
    5216 
    5217 > name H7v166_S92A_D56A_Epitope CD20_2H7v166_S92A_D56A & /C,D:168-175
    5218 
    5219 > name H7v166_S92A_D56A_V (H7v166_S92A_D56A & /L,M:1-107) | (H7v166_S92A_D56A
    5220 > & /H,I:1-111)
    5221 
    5222 > name H7v166_S92A_D56A_C (H7v166_S92A_D56A & /L,M:112-end) |
    5223 > (H7v166_S92A_D56A & /H,I:119-end)
    5224 
    5225 > lighting soft
    5226 
    5227 > set bgColor white
    5228 
    5229 > camera ortho
    5230 
    5231 > style stick
    5232 
    5233 Changed 53488 atom styles 
    5234 
    5235 > color byhetero
    5236 
    5237 > open CD20_2H7_mutants_color.cxc
    5238 
    5239 > color CD20 burlywood
    5240 
    5241 > color modify CD20_H1 hue - 20
    5242 
    5243 > color modify CD20_H2 hue - 10
    5244 
    5245 > color modify CD20_H3 hue + 0
    5246 
    5247 > color modify CD20_H4 hue + 10
    5248 
    5249 > color modify CD20_ECL1 hue +10
    5250 
    5251 > color modify CD20_ECL2 hue + 40
    5252 
    5253 > color modify CD20 saturation + 80
    5254 
    5255 > color CD20_ECL2 rgb(127,165,90)
    5256 
    5257 > color CD20_H4 rgb(176,215,142)
    5258 
    5259 > color RTX plum
    5260 
    5261 > color modify RTX_H hue - 40
    5262 
    5263 > color H7v16 slate blue
    5264 
    5265 > color modify H7v16_H hue - 40
    5266 
    5267 > color H7v166_D56A dodger blue
    5268 
    5269 > color modify H7v166_D56A_H hue - 40
    5270 
    5271 > color H7v166_S92A_D56A purple
    5272 
    5273 > color modify H7v166_S92A_D56A_H hue - 40
    5274 
    5275 executed CD20_2H7_mutants_color.cxc 
    5276 
    5277 > hide
    5278 
    5279 > ribbon
    5280 
    5281 > show CD20_ECL2SS
    5282 
    5283 > style CD20_ECL2SS stick
    5284 
    5285 Changed 120 atom styles 
    5286 
    5287 > define axis fromPoint 155,155,70 toPoint 155,155,210 name sym_axis
    5288 
    5289 Axis 'sym_axis' centered at [155. 155. 140.] with direction [ 0. 0. 140.],
    5290 radius 1, and length 140 
    5291 
    5292 > marker #1.1 position 155,155,70
    5293 
    5294 > marker #1.1 position 155,155,210
    5295 
    5296 > select
    5297 > #101.1/C,D:73,74,75,76,77,78,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,184,185,186,187,188
    5298 
    5299 440 atoms, 446 bonds, 54 residues, 1 model selected 
    5300 
    5301 > define plane sel name membrane_plane
    5302 
    5303 Plane 'membrane_plane' placed at [154.99498409 155.00750455 153.73545455] with
    5304 normal [-5.66049107e-05 -2.68508756e-05 -9.99999998e-01] and radius 24.3 
    5305 
    5306 > rename ##name=membrane_plane id 10
    5307 
    5308 > open CD20_2H7v16/CD20_RTX_define_pseudo_symmetries.cxc
    5309 
    5310 > combine CD20_RTX name RTX_Va modelId 1001
    5311 
    5312 > select zone (RTX_V & /H,L) 0.1 #1001
    5313 
    5314 Selected 1711 atoms 
    5315 
    5316 > delete #1001 & ~sel
    5317 
    5318 > combine #1001 name RTX_Va_copy modelId 1002
    5319 
    5320 > combine CD20_RTX name RTX_Vb modelId 1003
    5321 
    5322 > select zone (RTX_V & /I,M) 0.1 #1003
    5323 
    5324 Selected 1711 atoms 
    5325 
    5326 > delete #1003 & ~sel
    5327 
    5328 > combine #1003 name RTX_Vb_copy modelId 1004
    5329 
    5330 > combine CD20_RTX name RTX_Ca modelId 1005
    5331 
    5332 > select zone (RTX_C & /H,L) 0.1 #1005
    5333 
    5334 Selected 1503 atoms 
    5335 
    5336 > delete #1005 & ~sel
    5337 
    5338 > combine #1005 name RTX_Ca_copy modelId 1006
    5339 
    5340 > combine CD20_RTX name RTX_Cb modelId 1007
    5341 
    5342 > select zone (RTX_C & /I,M) 0.1 #1007
    5343 
    5344 Selected 1503 atoms 
    5345 
    5346 > delete #1007 & ~sel
    5347 
    5348 > combine #1007 name RTX_Ca_copy modelId 1008
    5349 
    5350 > matchmaker #1002/L to #1001/H
    5351 
    5352 Parameters 
    5353 --- 
    5354 Chain pairing | bb 
    5355 Alignment algorithm | Needleman-Wunsch 
    5356 Similarity matrix | BLOSUM-62 
    5357 SS fraction | 0.3 
    5358 Gap open (HH/SS/other) | 18/18/6 
    5359 Gap extend | 1 
    5360 SS matrix |  |  | H | S | O 
    5361 ---|---|---|--- 
    5362 H | 6 | -9 | -6 
    5363 S |  | 6 | -6 
    5364 O |  |  | 4 
    5365 Iteration cutoff | 2 
    5366  
    5367 Matchmaker RTX_Va, chain H (#1001) with RTX_Va_copy, chain L (#1002), sequence
    5368 alignment score = 198.7 
    5369 RMSD between 57 pruned atom pairs is 0.694 angstroms; (across all 103 pairs:
    5370 4.421) 
    5371  
    5372 
    5373 > wait 1
    5374 
    5375 > measure rotation #1002 toModel #1001 showSlabs true
    5376 
    5377 Position of RTX_Va_copy #1002 relative to RTX_Va #1001 coordinates: 
    5378 Matrix rotation and translation 
    5379 0.65377294 -0.06463426 0.75392530 -36.97668460 
    5380 0.02426941 -0.99404163 -0.10626495 318.59247232 
    5381 0.75630149 0.08777047 -0.64830888 90.28955685 
    5382 Axis 0.90906034 -0.01113250 0.41651574 
    5383 Axis point 0.00000000 156.41772375 62.99337678 
    5384 Rotation angle (degrees) 173.87355102 
    5385 Shift along axis 0.44625393 
    5386  
    5387 
    5388 > close #1001 #1002
    5389 
    5390 > define axis #2 name axis_Va
    5391 
    5392 Axis 'rotation axis #2/axis_Va' centered at [137.08203113 154.73899552
    5393 125.80199389] with direction [ 0.90906034 -0.0111325 0.41651574], radius
    5394 0.65062, and length 52.0496 
    5395 
    5396 > rename #2 Va_rotation_axis id #101.3.1.1
    5397 
    5398 > rename #3 Va_rotation_slabs id #101.3.2.1
    5399 
    5400 > matchmaker #1004/M to #1003/I
    5401 
    5402 Parameters 
    5403 --- 
    5404 Chain pairing | bb 
    5405 Alignment algorithm | Needleman-Wunsch 
    5406 Similarity matrix | BLOSUM-62 
    5407 SS fraction | 0.3 
    5408 Gap open (HH/SS/other) | 18/18/6 
    5409 Gap extend | 1 
    5410 SS matrix |  |  | H | S | O 
    5411 ---|---|---|--- 
    5412 H | 6 | -9 | -6 
    5413 S |  | 6 | -6 
    5414 O |  |  | 4 
    5415 Iteration cutoff | 2 
    5416  
    5417 Matchmaker RTX_Vb, chain I (#1003) with RTX_Vb_copy, chain M (#1004), sequence
    5418 alignment score = 214.3 
    5419 RMSD between 57 pruned atom pairs is 0.703 angstroms; (across all 103 pairs:
    5420 4.448) 
    5421  
    5422 
    5423 > wait 1
    5424 
    5425 > measure rotation #1004 toModel #1003 showSlabs true
    5426 
    5427 Position of RTX_Vb_copy #1004 relative to RTX_Vb #1003 coordinates: 
    5428 Matrix rotation and translation 
    5429 0.65527690 -0.06129532 -0.75289778 163.48223927 
    5430 0.03113398 -0.99366393 0.10799385 290.56686667 
    5431 -0.75474688 -0.09420658 -0.64921665 352.74817189 
    5432 Axis -0.90945183 0.00831685 0.41572611 
    5433 Axis point 0.00000000 156.83903630 204.83255489 
    5434 Rotation angle (degrees) 173.61745932 
    5435 Shift along axis 0.38400661 
    5436  
    5437 
    5438 > close #1004 #1003
    5439 
    5440 > define axis #2 name axis_Vb
    5441 
    5442 Axis 'rotation axis #2/axis_Vb' centered at [172.9873955 155.25708275
    5443 125.75703344] with direction [-0.90945183 0.00831685 0.41572611], radius
    5444 0.648586, and length 51.8869 
    5445 
    5446 > rename #2 Vb_rotation_axis id #101.3.1.2
    5447 
    5448 > rename #3 Vb_rotation_slabs id #101.3.2.2
    5449 
    5450 > matchmaker #1006/L to #1005/H
    5451 
    5452 Parameters 
    5453 --- 
    5454 Chain pairing | bb 
    5455 Alignment algorithm | Needleman-Wunsch 
    5456 Similarity matrix | BLOSUM-62 
    5457 SS fraction | 0.3 
    5458 Gap open (HH/SS/other) | 18/18/6 
    5459 Gap extend | 1 
    5460 SS matrix |  |  | H | S | O 
    5461 ---|---|---|--- 
    5462 H | 6 | -9 | -6 
    5463 S |  | 6 | -6 
    5464 O |  |  | 4 
    5465 Iteration cutoff | 2 
    5466  
    5467 Matchmaker RTX_Ca, chain H (#1005) with RTX_Ca_copy, chain L (#1006), sequence
    5468 alignment score = 238.2 
    5469 RMSD between 50 pruned atom pairs is 0.795 angstroms; (across all 96 pairs:
    5470 3.308) 
    5471  
    5472 
    5473 > wait 1
    5474 
    5475 > measure rotation #1006 toModel #1005 showSlabs true
    5476 
    5477 Position of RTX_Ca_copy #1006 relative to RTX_Ca #1005 coordinates: 
    5478 Matrix rotation and translation 
    5479 0.37780344 0.24165354 0.89379423 -73.66252391 
    5480 0.01279825 -0.96661035 0.25593093 273.63534365 
    5481 0.92579737 -0.08525258 -0.36828146 68.27322422 
    5482 Axis -0.82796624 -0.07766353 -0.55537400 
    5483 Axis point 0.00000000 144.62953182 41.62502778 
    5484 Rotation angle (degrees) 168.10978391 
    5485 Shift along axis 1.82142171 
    5486  
    5487 
    5488 > close #1006 #1005
    5489 
    5490 > define axis #2 name axis_Ca
    5491 
    5492 Axis 'rotation axis #2/axis_Ca' centered at [102.30380142 154.22566542
    5493 110.24723578] with direction [-0.82796624 -0.07766353 -0.555374 ], radius
    5494 0.539289, and length 43.1431 
    5495 
    5496 > rename #2 Ca_rotation_axis id #101.3.1.3
    5497 
    5498 > rename #3 Ca_rotation_slabs id #101.3.2.3
    5499 
    5500 > matchmaker #1008/M to #1007/I
    5501 
    5502 Parameters 
    5503 --- 
    5504 Chain pairing | bb 
    5505 Alignment algorithm | Needleman-Wunsch 
    5506 Similarity matrix | BLOSUM-62 
    5507 SS fraction | 0.3 
    5508 Gap open (HH/SS/other) | 18/18/6 
    5509 Gap extend | 1 
    5510 SS matrix |  |  | H | S | O 
    5511 ---|---|---|--- 
    5512 H | 6 | -9 | -6 
    5513 S |  | 6 | -6 
    5514 O |  |  | 4 
    5515 Iteration cutoff | 2 
    5516  
    5517 Matchmaker RTX_Cb, chain I (#1007) with RTX_Ca_copy, chain M (#1008), sequence
    5518 alignment score = 238.2 
    5519 RMSD between 50 pruned atom pairs is 0.794 angstroms; (across all 96 pairs:
    5520 3.487) 
    5521  
    5522 
    5523 > wait 1
    5524 
    5525 > measure rotation #1008 toModel #1007 showSlabs true
    5526 
    5527 Position of RTX_Ca_copy #1008 relative to RTX_Cb #1007 coordinates: 
    5528 Matrix rotation and translation 
    5529 0.37961795 0.24211100 -0.89290116 191.06761259 
    5530 0.01296287 -0.96644625 -0.25654164 332.12351027 
    5531 -0.92505253 0.08581325 -0.37001879 328.82641259 
    5532 Axis 0.82850834 0.07780721 -0.55454483 
    5533 Axis point 0.00000000 136.30341759 249.27961172 
    5534 Rotation angle (degrees) 168.07628341 
    5535 Shift along axis 1.79372450 
    5536  
    5537 
    5538 > close #1008 #1007
    5539 
    5540 > define axis #2 name axis_Cb
    5541 
    5542 Axis 'rotation axis #2/axis_Cb' centered at [207.91438592 155.82915639
    5543 110.11643971] with direction [ 0.82850834 0.07780721 -0.55454483], radius
    5544 0.53918, and length 43.1344 
    5545 
    5546 > rename #2 Cb_rotation_axis id #101.3.1.4
    5547 
    5548 > rename #3 Cb_rotation_slabs id #101.3.2.4
    5549 
    5550 > rename #101.3 geometry
    5551 
    5552 > rename #101.3.1 rotation_axes
    5553 
    5554 > rename #101.3.2 rotation_slabs
    5555 
    5556 executed CD20_RTX_define_pseudo_symmetries.cxc 
    5557 
    5558 > open CD20_2H7v16/CD20_2H7v16_define_pseudo_symmetries.cxc
    5559 
    5560 > combine CD20_2H7v16 name 2H7_v16_Va modelId 1001
    5561 
    5562 > select zone (H7v16_V & /H,L) 0.1 #1001
    5563 
    5564 Selected 1754 atoms 
    5565 
    5566 > delete #1001 & ~sel
    5567 
    5568 > combine #1001 name 2H7_v16_Va_copy modelId 1002
    5569 
    5570 > combine CD20_2H7v16 name 2H7_v16_Vb modelId 1003
    5571 
    5572 > select zone (H7v16_V & /I,M) 0.1 #1003
    5573 
    5574 Selected 1710 atoms 
    5575 
    5576 > delete #1003 & ~sel
    5577 
    5578 > combine #1003 name 2H7_v16_Vb_copy modelId 1004
    5579 
    5580 > combine CD20_2H7v16 name 2H7_v16_Ca modelId 1005
    5581 
    5582 > select zone (H7v16_C & /H,L) 0.1 #1005
    5583 
    5584 Selected 1550 atoms 
    5585 
    5586 > delete #1005 & ~sel
    5587 
    5588 > combine #1005 name 2H7_v16_Ca_copy modelId 1006
    5589 
    5590 > combine CD20_2H7v16 name 2H7_v16_Cb modelId 1007
    5591 
    5592 > select zone (H7v16_C & /I,M) 0.1 #1007
    5593 
    5594 Selected 1550 atoms 
    5595 
    5596 > delete #1007 & ~sel
    5597 
    5598 > combine #1007 name 2H7_v16_Ca_copy modelId 1008
    5599 
    5600 > matchmaker #1002/L to #1001/H
    5601 
    5602 Parameters 
    5603 --- 
    5604 Chain pairing | bb 
    5605 Alignment algorithm | Needleman-Wunsch 
    5606 Similarity matrix | BLOSUM-62 
    5607 SS fraction | 0.3 
    5608 Gap open (HH/SS/other) | 18/18/6 
    5609 Gap extend | 1 
    5610 SS matrix |  |  | H | S | O 
    5611 ---|---|---|--- 
    5612 H | 6 | -9 | -6 
    5613 S |  | 6 | -6 
    5614 O |  |  | 4 
    5615 Iteration cutoff | 2 
    5616  
    5617 Matchmaker 2H7_v16_Va, chain H (#1001) with 2H7_v16_Va_copy, chain L (#1002),
    5618 sequence alignment score = 387.9 
    5619 RMSD between 66 pruned atom pairs is 0.856 angstroms; (across all 103 pairs:
    5620 5.340) 
    5621  
    5622 
    5623 > wait 1
    5624 
    5625 > measure rotation #1002 toModel #1001 showSlabs true
    5626 
    5627 Position of 2H7_v16_Va_copy #1002 relative to 2H7_v16_Va #1001 coordinates: 
    5628 Matrix rotation and translation 
    5629 0.58985298 0.00233427 0.80750728 -45.05678546 
    5630 0.12316682 -0.98855531 -0.08711100 297.16136614 
    5631 0.79806228 0.15084078 -0.58338980 65.44859378 
    5632 Axis 0.89106916 0.03536916 0.45248731 
    5633 Axis point 0.00000000 147.01172040 55.34624717 
    5634 Rotation angle (degrees) 172.32693090 
    5635 Shift along axis -0.02370559 
    5636  
    5637 
    5638 > close #1001 #1002
    5639 
    5640 > define axis #2 name axis_Va
    5641 
    5642 Axis 'rotation axis #2/axis_Va' centered at [138.16022152 152.49570671
    5643 125.5043786 ] with direction [0.89106916 0.03536916 0.45248731], radius
    5644 0.589874, and length 47.1899 
    5645 
    5646 > rename #2 Va_rotation_axis id #102.3.1.1
    5647 
    5648 > rename #3 Va_rotation_slabs id #102.3.2.1
    5649 
    5650 > matchmaker #1004/M to #1003/I
    5651 
    5652 Parameters 
    5653 --- 
    5654 Chain pairing | bb 
    5655 Alignment algorithm | Needleman-Wunsch 
    5656 Similarity matrix | BLOSUM-62 
    5657 SS fraction | 0.3 
    5658 Gap open (HH/SS/other) | 18/18/6 
    5659 Gap extend | 1 
    5660 SS matrix |  |  | H | S | O 
    5661 ---|---|---|--- 
    5662 H | 6 | -9 | -6 
    5663 S |  | 6 | -6 
    5664 O |  |  | 4 
    5665 Iteration cutoff | 2 
    5666  
    5667 Matchmaker 2H7_v16_Vb, chain I (#1003) with 2H7_v16_Vb_copy, chain M (#1004),
    5668 sequence alignment score = 378.3 
    5669 RMSD between 65 pruned atom pairs is 0.877 angstroms; (across all 97 pairs:
    5670 4.620) 
    5671  
    5672 
    5673 > wait 1
    5674 
    5675 > measure rotation #1004 toModel #1003 showSlabs true
    5676 
    5677 Position of 2H7_v16_Vb_copy #1004 relative to 2H7_v16_Vb #1003 coordinates: 
    5678 Matrix rotation and translation 
    5679 0.62864598 0.45103819 -0.63353672 71.77949524 
    5680 0.53321619 -0.84298968 -0.07105560 212.64664720 
    5681 -0.56611370 -0.29314322 -0.77044294 368.84403487 
    5682 Axis -0.90200560 -0.27383758 0.33376470 
    5683 Axis point -0.00000000 108.05935567 190.41757658 
    5684 Rotation angle (degrees) 172.92851049 
    5685 Shift along axis 0.13096924 
    5686  
    5687 
    5688 > close #1004 #1003
    5689 
    5690 > define axis #2 name axis_Vb
    5691 
    5692 Axis 'rotation axis #2/axis_Vb' centered at [174.414767 161.00949037
    5693 125.87973689] with direction [-0.9020056 -0.27383758 0.3337647 ], radius
    5694 0.594923, and length 47.5938 
    5695 
    5696 > rename #2 Vb_rotation_axis id #102.3.1.2
    5697 
    5698 > rename #3 Vb_rotation_slabs id #102.3.2.2
    5699 
    5700 > matchmaker #1006/L to #1005/H
    5701 
    5702 Parameters 
    5703 --- 
    5704 Chain pairing | bb 
    5705 Alignment algorithm | Needleman-Wunsch 
    5706 Similarity matrix | BLOSUM-62 
    5707 SS fraction | 0.3 
    5708 Gap open (HH/SS/other) | 18/18/6 
    5709 Gap extend | 1 
    5710 SS matrix |  |  | H | S | O 
    5711 ---|---|---|--- 
    5712 H | 6 | -9 | -6 
    5713 S |  | 6 | -6 
    5714 O |  |  | 4 
    5715 Iteration cutoff | 2 
    5716  
    5717 Matchmaker 2H7_v16_Ca, chain H (#1005) with 2H7_v16_Ca_copy, chain L (#1006),
    5718 sequence alignment score = 403.6 
    5719 RMSD between 58 pruned atom pairs is 1.037 angstroms; (across all 98 pairs:
    5720 3.184) 
    5721  
    5722 
    5723 > wait 1
    5724 
    5725 > measure rotation #1006 toModel #1005 showSlabs true
    5726 
    5727 Position of 2H7_v16_Ca_copy #1006 relative to 2H7_v16_Ca #1005 coordinates: 
    5728 Matrix rotation and translation 
    5729 -0.62547004 0.41276667 0.66212605 49.05674876 
    5730 0.08546501 -0.80725952 0.58397585 200.07354667 
    5731 0.77555333 0.42184801 0.46963954 -95.83522576 
    5732 Axis -0.42390521 -0.29657098 -0.85577452 
    5733 Axis point 59.57688139 113.83169245 0.00000000 
    5734 Rotation angle (degrees) 168.97535276 
    5735 Shift along axis 1.88192618 
    5736  
    5737 
    5738 > close #1006 #1005
    5739 
    5740 > define axis #2 name axis_Ca
    5741 
    5742 Axis 'rotation axis #2/axis_Ca' centered at [109.8807251 149.02507918
    5743 101.55276878] with direction [-0.42390521 -0.29657098 -0.85577452], radius
    5744 0.550437, and length 44.0349 
    5745 
    5746 > rename #2 Ca_rotation_axis id #102.3.1.3
    5747 
    5748 > rename #3 Ca_rotation_slabs id #102.3.2.3
    5749 
    5750 > matchmaker #1008/M to #1007/I
    5751 
    5752 Parameters 
    5753 --- 
    5754 Chain pairing | bb 
    5755 Alignment algorithm | Needleman-Wunsch 
    5756 Similarity matrix | BLOSUM-62 
    5757 SS fraction | 0.3 
    5758 Gap open (HH/SS/other) | 18/18/6 
    5759 Gap extend | 1 
    5760 SS matrix |  |  | H | S | O 
    5761 ---|---|---|--- 
    5762 H | 6 | -9 | -6 
    5763 S |  | 6 | -6 
    5764 O |  |  | 4 
    5765 Iteration cutoff | 2 
    5766  
    5767 Matchmaker 2H7_v16_Cb, chain I (#1007) with 2H7_v16_Ca_copy, chain M (#1008),
    5768 sequence alignment score = 396 
    5769 RMSD between 54 pruned atom pairs is 0.855 angstroms; (across all 98 pairs:
    5770 3.551) 
    5771  
    5772 
    5773 > wait 1
    5774 
    5775 > measure rotation #1008 toModel #1007 showSlabs true
    5776 
    5777 Position of 2H7_v16_Ca_copy #1008 relative to 2H7_v16_Cb #1007 coordinates: 
    5778 Matrix rotation and translation 
    5779 -0.62894249 0.48033740 -0.61131606 312.62038315 
    5780 0.14842286 -0.69766113 -0.70088487 336.12735996 
    5781 -0.76315267 -0.53154955 0.36749568 311.24709675 
    5782 Axis 0.42085200 0.37736216 -0.82491296 
    5783 Axis point 256.37284203 220.04020388 0.00000000 
    5784 Rotation angle (degrees) 168.39393838 
    5785 Shift along axis 1.65689588 
    5786  
    5787 
    5788 > close #1008 #1007
    5789 
    5790 > define axis #2 name axis_Cb
    5791 
    5792 Axis 'rotation axis #2/axis_Cb' centered at [202.74487059 171.95401837
    5793 105.11630914] with direction [ 0.420852 0.37736216 -0.82491296], radius
    5794 0.534846, and length 42.7877 
    5795 
    5796 > rename #2 Cb_rotation_axis id #102.3.1.4
    5797 
    5798 > rename #3 Cb_rotation_slabs id #102.3.2.4
    5799 
    5800 > rename #102.3 geometry
    5801 
    5802 > rename #102.3.1 rotation_axes
    5803 
    5804 > rename #102.3.2 rotation_slabs
    5805 
    5806 executed CD20_2H7v16_define_pseudo_symmetries.cxc 
    5807 
    5808 > open CD20_2H7v166_D56A/CD20_2H7v166_D56A_define_pseudo_symmetries.cxc
    5809 
    5810 > combine CD20_2H7v166_D56A name 2H7_v166_D56A_Va modelId 1001
    5811 
    5812 > select zone (H7v166_D56A_V & /H,L) 0.1 #1001
    5813 
    5814 Selected 1654 atoms 
    5815 
    5816 > delete #1001 & ~sel
    5817 
    5818 > combine #1001 name 2H7_v166_D56A_Va_copy modelId 1002
    5819 
    5820 > combine CD20_2H7v166_D56A name 2H7_v166_D56A_Vb modelId 1003
    5821 
    5822 > select zone (H7v166_D56A_V & /I,M) 0.1 #1003
    5823 
    5824 Selected 1678 atoms 
    5825 
    5826 > delete #1003 & ~sel
    5827 
    5828 > combine #1003 name 2H7_v166_D56A_Vb_copy modelId 1004
    5829 
    5830 > combine CD20_2H7v166_D56A name 2H7_v166_D56A_Ca modelId 1005
    5831 
    5832 > select zone (H7v166_D56A_C & /H,L) 0.1 #1005
    5833 
    5834 Selected 1550 atoms 
    5835 
    5836 > delete #1005 & ~sel
    5837 
    5838 > combine #1005 name 2H7_v166_D56A_Ca_copy modelId 1006
    5839 
    5840 > combine CD20_2H7v166_D56A name 2H7_v166_D56A_Cb modelId 1007
    5841 
    5842 > select zone (H7v166_D56A_C & /I,M) 0.1 #1007
    5843 
    5844 Selected 1550 atoms 
    5845 
    5846 > delete #1007 & ~sel
    5847 
    5848 > combine #1007 name 2H7_v166_D56A_Ca_copy modelId 1008
    5849 
    5850 > matchmaker #1002/L to #1001/H
    5851 
    5852 Parameters 
    5853 --- 
    5854 Chain pairing | bb 
    5855 Alignment algorithm | Needleman-Wunsch 
    5856 Similarity matrix | BLOSUM-62 
    5857 SS fraction | 0.3 
    5858 Gap open (HH/SS/other) | 18/18/6 
    5859 Gap extend | 1 
    5860 SS matrix |  |  | H | S | O 
    5861 ---|---|---|--- 
    5862 H | 6 | -9 | -6 
    5863 S |  | 6 | -6 
    5864 O |  |  | 4 
    5865 Iteration cutoff | 2 
    5866  
    5867 Matchmaker 2H7_v166_D56A_Va, chain H (#1001) with 2H7_v166_D56A_Va_copy, chain
    5868 L (#1002), sequence alignment score = 547.6 
    5869 RMSD between 74 pruned atom pairs is 0.966 angstroms; (across all 90 pairs:
    5870 2.607) 
    5871  
    5872 
    5873 > wait 1
    5874 
    5875 > measure rotation #1002 toModel #1001 showSlabs true
    5876 
    5877 Position of 2H7_v166_D56A_Va_copy #1002 relative to 2H7_v166_D56A_Va #1001
    5878 coordinates: 
    5879 Matrix rotation and translation 
    5880 0.73992366 -0.12116101 0.66168949 -29.70332856 
    5881 -0.06116680 -0.99168902 -0.11318795 332.06337928 
    5882 0.66990417 0.04327702 -0.74118520 123.44534698 
    5883 Axis 0.93259437 -0.04896279 0.35758970 
    5884 Axis point 0.00000000 162.47254458 74.89799404 
    5885 Rotation angle (degrees) 175.18797763 
    5886 Shift along axis 0.18287681 
    5887  
    5888 
    5889 > close #1001 #1002
    5890 
    5891 > define axis #2 name axis_Va
    5892 
    5893 Axis 'rotation axis #2/axis_Va' centered at [136.31725835 155.31565622
    5894 127.16685711] with direction [ 0.93259437 -0.04896279 0.3575897 ], radius
    5895 0.599212, and length 47.937 
    5896 
    5897 > rename #2 Va_rotation_axis id #103.3.1.1
    5898 
    5899 > rename #3 Va_rotation_slabs id #103.3.2.1
    5900 
    5901 > matchmaker #1004/M to #1003/I
    5902 
    5903 Parameters 
    5904 --- 
    5905 Chain pairing | bb 
    5906 Alignment algorithm | Needleman-Wunsch 
    5907 Similarity matrix | BLOSUM-62 
    5908 SS fraction | 0.3 
    5909 Gap open (HH/SS/other) | 18/18/6 
    5910 Gap extend | 1 
    5911 SS matrix |  |  | H | S | O 
    5912 ---|---|---|--- 
    5913 H | 6 | -9 | -6 
    5914 S |  | 6 | -6 
    5915 O |  |  | 4 
    5916 Iteration cutoff | 2 
    5917  
    5918 Matchmaker 2H7_v166_D56A_Vb, chain I (#1003) with 2H7_v166_D56A_Vb_copy, chain
    5919 M (#1004), sequence alignment score = 376.5 
    5920 RMSD between 70 pruned atom pairs is 0.891 angstroms; (across all 92 pairs:
    5921 3.886) 
    5922  
    5923 
    5924 > wait 1
    5925 
    5926 > measure rotation #1004 toModel #1003 showSlabs true
    5927 
    5928 Position of 2H7_v166_D56A_Vb_copy #1004 relative to 2H7_v166_D56A_Vb #1003
    5929 coordinates: 
    5930 Matrix rotation and translation 
    5931 0.72982969 -0.01372193 -0.68349128 135.94952936 
    5932 0.06485007 -0.99390027 0.08920045 287.47713002 
    5933 -0.68054617 -0.10942560 -0.72448806 354.00628960 
    5934 Axis -0.92979963 -0.01378652 0.36780781 
    5935 Axis point 0.00000000 152.92822789 195.61279282 
    5936 Rotation angle (degrees) 173.86847166 
    5937 Shift along axis -0.16285394 
    5938  
    5939 
    5940 > close #1004 #1003
    5941 
    5942 > define axis #2 name axis_Vb
    5943 
    5944 Axis 'rotation axis #2/axis_Vb' centered at [173.81620585 155.50547201
    5945 126.8550136 ] with direction [-0.92979963 -0.01378652 0.36780781], radius
    5946 0.597156, and length 47.7725 
    5947 
    5948 > rename #2 Vb_rotation_axis id #103.3.1.2
    5949 
    5950 > rename #3 Vb_rotation_slabs id #103.3.2.2
    5951 
    5952 > matchmaker #1006/L to #1005/H
    5953 
    5954 Parameters 
    5955 --- 
    5956 Chain pairing | bb 
    5957 Alignment algorithm | Needleman-Wunsch 
    5958 Similarity matrix | BLOSUM-62 
    5959 SS fraction | 0.3 
    5960 Gap open (HH/SS/other) | 18/18/6 
    5961 Gap extend | 1 
    5962 SS matrix |  |  | H | S | O 
    5963 ---|---|---|--- 
    5964 H | 6 | -9 | -6 
    5965 S |  | 6 | -6 
    5966 O |  |  | 4 
    5967 Iteration cutoff | 2 
    5968  
    5969 Matchmaker 2H7_v166_D56A_Ca, chain H (#1005) with 2H7_v166_D56A_Ca_copy, chain
    5970 L (#1006), sequence alignment score = 554.5 
    5971 RMSD between 57 pruned atom pairs is 0.959 angstroms; (across all 98 pairs:
    5972 3.119) 
    5973  
    5974 
    5975 > wait 1
    5976 
    5977 > measure rotation #1006 toModel #1005 showSlabs true
    5978 
    5979 Position of 2H7_v166_D56A_Ca_copy #1006 relative to 2H7_v166_D56A_Ca #1005
    5980 coordinates: 
    5981 Matrix rotation and translation 
    5982 -0.33391401 0.38072466 0.86229355 -12.40856576 
    5983 0.05205532 -0.90595556 0.42016042 245.78035810 
    5984 0.94116506 0.18518442 0.28269251 -52.33839393 
    5985 Axis -0.57081123 -0.19159720 -0.79841408 
    5986 Axis point 28.53870248 129.91224226 0.00000000 
    5987 Rotation angle (degrees) 168.12212217 
    5988 Shift along axis 1.77983022 
    5989  
    5990 
    5991 > close #1006 #1005
    5992 
    5993 > define axis #2 name axis_Ca
    5994 
    5995 Axis 'rotation axis #2/axis_Ca' centered at [104.79817162 155.50932275
    5996 106.6668468 ] with direction [-0.57081123 -0.1915972 -0.79841408], radius
    5997 0.56909, and length 45.5272 
    5998 
    5999 > rename #2 Ca_rotation_axis id #103.3.1.3
    6000 
    6001 > rename #3 Ca_rotation_slabs id #103.3.2.3
    6002 
    6003 > matchmaker #1008/M to #1007/I
    6004 
    6005 Parameters 
    6006 --- 
    6007 Chain pairing | bb 
    6008 Alignment algorithm | Needleman-Wunsch 
    6009 Similarity matrix | BLOSUM-62 
    6010 SS fraction | 0.3 
    6011 Gap open (HH/SS/other) | 18/18/6 
    6012 Gap extend | 1 
    6013 SS matrix |  |  | H | S | O 
    6014 ---|---|---|--- 
    6015 H | 6 | -9 | -6 
    6016 S |  | 6 | -6 
    6017 O |  |  | 4 
    6018 Iteration cutoff | 2 
    6019  
    6020 Matchmaker 2H7_v166_D56A_Cb, chain I (#1007) with 2H7_v166_D56A_Ca_copy, chain
    6021 M (#1008), sequence alignment score = 416.6 
    6022 RMSD between 55 pruned atom pairs is 0.882 angstroms; (across all 98 pairs:
    6023 3.361) 
    6024  
    6025 
    6026 > wait 1
    6027 
    6028 > measure rotation #1008 toModel #1007 showSlabs true
    6029 
    6030 Position of 2H7_v166_D56A_Ca_copy #1008 relative to 2H7_v166_D56A_Cb #1007
    6031 coordinates: 
    6032 Matrix rotation and translation 
    6033 -0.50667380 0.40781938 -0.75958213 323.22163731 
    6034 0.08178140 -0.85433688 -0.51324487 330.95129120 
    6035 -0.85825023 -0.32216741 0.39951808 287.19953324 
    6036 Axis 0.48922423 0.25262440 -0.83476977 
    6037 Axis point 265.28291179 189.90297685 0.00000000 
    6038 Rotation angle (degrees) 168.73855860 
    6039 Shift along axis 1.98873850 
    6040  
    6041 
    6042 > close #1008 #1007
    6043 
    6044 > define axis #2 name axis_Cb
    6045 
    6046 Axis 'rotation axis #2/axis_Cb' centered at [203.75015551 158.12884417
    6047 104.99415577] with direction [ 0.48922423 0.2526244 -0.83476977], radius
    6048 0.553583, and length 44.2867 
    6049 
    6050 > rename #2 Cb_rotation_axis id #103.3.1.4
    6051 
    6052 > rename #3 Cb_rotation_slabs id #103.3.2.4
    6053 
    6054 > rename #103.3 geometry
    6055 
    6056 > rename #103.3.1 rotation_axes
    6057 
    6058 > rename #103.3.2 rotation_slabs
    6059 
    6060 executed CD20_2H7v166_D56A_define_pseudo_symmetries.cxc 
    6061 
    6062 > open
    6063 > CD20_2H7v166_S92A_D56A/CD20_2H7v166_S92A_D56A_define_pseudo_symmetries.cxc
    6064 
    6065 > combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Va modelId 1001
    6066 
    6067 > select zone (H7v166_S92A_D56A_V & /H,L) 0.1 #1001
    6068 
    6069 Selected 1653 atoms 
    6070 
    6071 > delete #1001 & ~sel
    6072 
    6073 > combine #1001 name 2H7_v166_S92A_D56A_Va_copy modelId 1002
    6074 
    6075 > combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Vb modelId 1003
    6076 
    6077 > select zone (H7v166_S92A_D56A_V & /I,M) 0.1 #1003
    6078 
    6079 Selected 1678 atoms 
    6080 
    6081 > delete #1003 & ~sel
    6082 
    6083 > combine #1003 name 2H7_v166_S92A_D56A_Vb_copy modelId 1004
    6084 
    6085 > combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Ca modelId 1005
    6086 
    6087 > select zone (H7v166_S92A_D56A_C & /H,L) 0.1 #1005
    6088 
    6089 Selected 1461 atoms 
    6090 
    6091 > delete #1005 & ~sel
    6092 
    6093 > combine #1005 name 2H7_v166_S92A_D56A_Ca_copy modelId 1006
    6094 
    6095 > combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Cb modelId 1007
    6096 
    6097 > select zone (H7v166_S92A_D56A_C & /I,M) 0.1 #1007
    6098 
    6099 Selected 1550 atoms 
    6100 
    6101 > delete #1007 & ~sel
    6102 
    6103 > combine #1007 name 2H7_v166_S92A_D56A_Ca_copy modelId 1008
    6104 
    6105 > matchmaker #1002/L to #1001/H
    6106 
    6107 Parameters 
    6108 --- 
    6109 Chain pairing | bb 
    6110 Alignment algorithm | Needleman-Wunsch 
    6111 Similarity matrix | BLOSUM-62 
    6112 SS fraction | 0.3 
    6113 Gap open (HH/SS/other) | 18/18/6 
    6114 Gap extend | 1 
    6115 SS matrix |  |  | H | S | O 
    6116 ---|---|---|--- 
    6117 H | 6 | -9 | -6 
    6118 S |  | 6 | -6 
    6119 O |  |  | 4 
    6120 Iteration cutoff | 2 
    6121  
    6122 Matchmaker 2H7_v166_S92A_D56A_Va, chain H (#1001) with
    6123 2H7_v166_S92A_D56A_Va_copy, chain L (#1002), sequence alignment score = 221.1 
    6124 RMSD between 66 pruned atom pairs is 1.048 angstroms; (across all 87 pairs:
    6125 3.054) 
    6126  
    6127 
    6128 > wait 1
    6129 
    6130 > measure rotation #1002 toModel #1001 showSlabs true
    6131 
    6132 Position of 2H7_v166_S92A_D56A_Va_copy #1002 relative to 2H7_v166_S92A_D56A_Va
    6133 #1001 coordinates: 
    6134 Matrix rotation and translation 
    6135 0.71841270 -0.03882790 0.69453263 -43.77242719 
    6136 0.04474713 -0.99379351 -0.10184377 314.28607160 
    6137 0.69417640 0.10424420 -0.71221645 107.06747282 
    6138 Axis 0.92669760 0.00160183 0.37580447 
    6139 Axis point 0.00000000 153.96110044 71.86641580 
    6140 Rotation angle (degrees) 173.61580296 
    6141 Shift along axis 0.17606353 
    6142  
    6143 
    6144 > close #1001 #1002
    6145 
    6146 > define axis #2 name axis_Va
    6147 
    6148 Axis 'rotation axis #2/axis_Va' centered at [136.49236761 154.19703207
    6149 127.21828189] with direction [0.9266976 0.00160183 0.37580447], radius
    6150 0.603625, and length 48.29 
    6151 
    6152 > rename #2 Va_rotation_axis id #104.3.1.1
    6153 
    6154 > rename #3 Va_rotation_slabs id #104.3.2.1
    6155 
    6156 > matchmaker #1004/M to #1003/I
    6157 
    6158 Parameters 
    6159 --- 
    6160 Chain pairing | bb 
    6161 Alignment algorithm | Needleman-Wunsch 
    6162 Similarity matrix | BLOSUM-62 
    6163 SS fraction | 0.3 
    6164 Gap open (HH/SS/other) | 18/18/6 
    6165 Gap extend | 1 
    6166 SS matrix |  |  | H | S | O 
    6167 ---|---|---|--- 
    6168 H | 6 | -9 | -6 
    6169 S |  | 6 | -6 
    6170 O |  |  | 4 
    6171 Iteration cutoff | 2 
    6172  
    6173 Matchmaker 2H7_v166_S92A_D56A_Vb, chain I (#1003) with
    6174 2H7_v166_S92A_D56A_Vb_copy, chain M (#1004), sequence alignment score = 228.5 
    6175 RMSD between 66 pruned atom pairs is 1.088 angstroms; (across all 92 pairs:
    6176 3.936) 
    6177  
    6178 
    6179 > wait 1
    6180 
    6181 > measure rotation #1004 toModel #1003 showSlabs true
    6182 
    6183 Position of 2H7_v166_S92A_D56A_Vb_copy #1004 relative to 2H7_v166_S92A_D56A_Vb
    6184 #1003 coordinates: 
    6185 Matrix rotation and translation 
    6186 0.73661563 -0.07135580 -0.67253682 142.18618798 
    6187 0.02298296 -0.99120309 0.13033888 288.51761976 
    6188 -0.67592100 -0.11146654 -0.72849572 353.55093768 
    6189 Axis -0.93153019 0.01303723 0.36343024 
    6190 Axis point 0.00000000 157.62360929 194.41945478 
    6191 Rotation angle (degrees) 172.54257925 
    6192 Shift along axis -0.19815617 
    6193  
    6194 
    6195 > close #1004 #1003
    6196 
    6197 > define axis #2 name axis_Vb
    6198 
    6199 Axis 'rotation axis #2/axis_Vb' centered at [172.8655548 155.20426996
    6200 126.97712173] with direction [-0.93153019 0.01303723 0.36343024], radius
    6201 0.60681, and length 48.5448 
    6202 
    6203 > rename #2 Vb_rotation_axis id #104.3.1.2
    6204 
    6205 > rename #3 Vb_rotation_slabs id #104.3.2.2
    6206 
    6207 > matchmaker #1006/L to #1005/H
    6208 
    6209 Parameters 
    6210 --- 
    6211 Chain pairing | bb 
    6212 Alignment algorithm | Needleman-Wunsch 
    6213 Similarity matrix | BLOSUM-62 
    6214 SS fraction | 0.3 
    6215 Gap open (HH/SS/other) | 18/18/6 
    6216 Gap extend | 1 
    6217 SS matrix |  |  | H | S | O 
    6218 ---|---|---|--- 
    6219 H | 6 | -9 | -6 
    6220 S |  | 6 | -6 
    6221 O |  |  | 4 
    6222 Iteration cutoff | 2 
    6223  
    6224 Matchmaker 2H7_v166_S92A_D56A_Ca, chain H (#1005) with
    6225 2H7_v166_S92A_D56A_Ca_copy, chain L (#1006), sequence alignment score = 229.8 
    6226 RMSD between 50 pruned atom pairs is 0.885 angstroms; (across all 82 pairs:
    6227 3.058) 
    6228  
    6229 
    6230 > wait 1
    6231 
    6232 > measure rotation #1006 toModel #1005 showSlabs true
    6233 
    6234 Position of 2H7_v166_S92A_D56A_Ca_copy #1006 relative to 2H7_v166_S92A_D56A_Ca
    6235 #1005 coordinates: 
    6236 Matrix rotation and translation 
    6237 -0.43223566 0.39105435 0.81255697 5.34243089 
    6238 0.04124481 -0.89156204 0.45101662 236.01875124 
    6239 0.90081696 0.22845922 0.36923594 -64.79879197 
    6240 Axis -0.52502754 -0.20821113 -0.82522373 
    6241 Axis point 38.63388899 125.78498588 0.00000000 
    6242 Rotation angle (degrees) 167.76344751 
    6243 Shift along axis 1.52684600 
    6244  
    6245 
    6246 > close #1006 #1005
    6247 
    6248 > define axis #2 name axis_Ca
    6249 
    6250 Axis 'rotation axis #2/axis_Ca' centered at [105.63109625 152.35419104
    6251 105.30435297] with direction [-0.52502754 -0.20821113 -0.82522373], radius
    6252 0.532467, and length 42.5974 
    6253 
    6254 > rename #2 Ca_rotation_axis id #104.3.1.3
    6255 
    6256 > rename #3 Ca_rotation_slabs id #104.3.2.3
    6257 
    6258 > matchmaker #1008/M to #1007/I
    6259 
    6260 Parameters 
    6261 --- 
    6262 Chain pairing | bb 
    6263 Alignment algorithm | Needleman-Wunsch 
    6264 Similarity matrix | BLOSUM-62 
    6265 SS fraction | 0.3 
    6266 Gap open (HH/SS/other) | 18/18/6 
    6267 Gap extend | 1 
    6268 SS matrix |  |  | H | S | O 
    6269 ---|---|---|--- 
    6270 H | 6 | -9 | -6 
    6271 S |  | 6 | -6 
    6272 O |  |  | 4 
    6273 Iteration cutoff | 2 
    6274  
    6275 Matchmaker 2H7_v166_S92A_D56A_Cb, chain I (#1007) with
    6276 2H7_v166_S92A_D56A_Ca_copy, chain M (#1008), sequence alignment score = 226.4 
    6277 RMSD between 57 pruned atom pairs is 0.983 angstroms; (across all 98 pairs:
    6278 3.247) 
    6279  
    6280 
    6281 > wait 1
    6282 
    6283 > measure rotation #1008 toModel #1007 showSlabs true
    6284 
    6285 Position of 2H7_v166_S92A_D56A_Ca_copy #1008 relative to 2H7_v166_S92A_D56A_Cb
    6286 #1007 coordinates: 
    6287 Matrix rotation and translation 
    6288 -0.44691350 0.37987962 -0.80991345 321.97311814 
    6289 0.04334425 -0.89510032 -0.44375297 334.72634524 
    6290 -0.89352650 -0.23342428 0.38356682 282.18198422 
    6291 Axis 0.51860284 0.20616286 -0.82978790 
    6292 Axis point 269.80743377 182.59879005 0.00000000 
    6293 Rotation angle (degrees) 168.30019456 
    6294 Shift along axis 1.83311720 
    6295  
    6296 
    6297 > close #1008 #1007
    6298 
    6299 > define axis #2 name axis_Cb
    6300 
    6301 Axis 'rotation axis #2/axis_Cb' centered at [203.87433587 156.38806637
    6302 105.49592574] with direction [ 0.51860284 0.20616286 -0.8297879 ], radius
    6303 0.566216, and length 45.2973 
    6304 
    6305 > rename #2 Cb_rotation_axis id #104.3.1.4
    6306 
    6307 > rename #3 Cb_rotation_slabs id #104.3.2.4
    6308 
    6309 > rename #104.3 geometry
    6310 
    6311 > rename #104.3.1 rotation_axes
    6312 
    6313 > rename #104.3.2 rotation_slabs
    6314 
    6315 executed CD20_2H7v166_S92A_D56A_define_pseudo_symmetries.cxc 
    6316 
    6317 > open CD20_2H7_mutants_define_domain_centroids.cxc
    6318 
    6319 > define centroid RTX_C & /L name centroid_RTX_C_L
    6320 
    6321 Centroid 'centroid_RTX_C_L' placed at [ 99.24795328 158.51064899 116.56555556] 
    6322 
    6323 > rename ##name=centroid_RTX_C_L id 101.3.3.1
    6324 
    6325 > define centroid RTX_C & /M name centroid_RTX_C_M
    6326 
    6327 Centroid 'centroid_RTX_C_M' placed at [210.77360859 151.52862247 116.58115025] 
    6328 
    6329 > rename ##name=centroid_RTX_C_M id 101.3.3.2
    6330 
    6331 > define centroid RTX_C & /H name centroid_RTX_C_H
    6332 
    6333 Centroid 'centroid_RTX_C_H' placed at [106.64933474 150.8311308 104.33269761] 
    6334 
    6335 > rename ##name=centroid_RTX_C_H id 101.3.3.3
    6336 
    6337 > define centroid RTX_C & /I name centroid_RTX_C_I
    6338 
    6339 Centroid 'centroid_RTX_C_I' placed at [203.36467932 159.20700844 104.37016456] 
    6340 
    6341 > rename ##name=centroid_RTX_C_I id 101.3.3.4
    6342 
    6343 > define centroid RTX_V & /L name centroid_RTX_V_L
    6344 
    6345 Centroid 'centroid_RTX_V_L' placed at [134.90703015 166.45776759 126.23118216] 
    6346 
    6347 > rename ##name=centroid_RTX_V_L id 101.3.3.5
    6348 
    6349 > define centroid RTX_V & /M name centroid_RTX_V_M
    6350 
    6351 Centroid 'centroid_RTX_V_M' placed at [175.12986935 143.57538693 126.24564698] 
    6352 
    6353 > rename ##name=centroid_RTX_V_M id 101.3.3.6
    6354 
    6355 > define centroid RTX_V & /H name centroid_RTX_V_H
    6356 
    6357 Centroid 'centroid_RTX_V_H' placed at [138.39382732 143.61326339 125.48950601] 
    6358 
    6359 > rename ##name=centroid_RTX_V_H id 101.3.3.7
    6360 
    6361 > define centroid RTX_V & /I name centroid_RTX_V_I
    6362 
    6363 Centroid 'centroid_RTX_V_I' placed at [171.6143541 166.39779016 125.48935082] 
    6364 
    6365 > rename ##name=centroid_RTX_V_I id 101.3.3.8
    6366 
    6367 > rename #101.3.3 centroids
    6368 
    6369 > define centroid H7v16_C & /L name centroid_2H7v16_C_L
    6370 
    6371 Centroid 'centroid_2H7v16_C_L' placed at [105.06462233 154.79494479
    6372 104.71732873] 
    6373 
    6374 > rename ##name=centroid_2H7v16_C_L id 102.3.3.1
    6375 
    6376 > define centroid H7v16_C & /M name centroid_2H7v16_C_M
    6377 
    6378 Centroid 'centroid_2H7v16_C_M' placed at [208.42672522 167.55451192
    6379 109.46892346] 
    6380 
    6381 > rename ##name=centroid_2H7v16_C_M id 102.3.3.2
    6382 
    6383 > define centroid H7v16_C & /H name centroid_2H7v16_C_H
    6384 
    6385 Centroid 'centroid_2H7v16_C_H' placed at [115.17526428 144.82097344
    6386 100.10963479] 
    6387 
    6388 > rename ##name=centroid_2H7v16_C_H id 102.3.3.3
    6389 
    6390 > define centroid H7v16_C & /I name centroid_2H7v16_C_I
    6391 
    6392 Centroid 'centroid_2H7v16_C_I' placed at [196.31280478 174.43741833
    6393 103.22787118] 
    6394 
    6395 > rename ##name=centroid_2H7v16_C_I id 102.3.3.4
    6396 
    6397 > define centroid H7v16_V & /L name centroid_2H7v16_V_L
    6398 
    6399 Centroid 'centroid_2H7v16_V_L' placed at [136.25738614 163.8169901
    6400 124.64938243] 
    6401 
    6402 > rename ##name=centroid_2H7v16_V_L id 102.3.3.5
    6403 
    6404 > define centroid H7v16_V & /M name centroid_2H7v16_V_M
    6405 
    6406 Centroid 'centroid_2H7v16_V_M' placed at [179.26451702 150.74154843
    6407 126.48898691] 
    6408 
    6409 > rename ##name=centroid_2H7v16_V_M id 102.3.3.6
    6410 
    6411 > define centroid H7v16_V & /H name centroid_2H7v16_V_H
    6412 
    6413 Centroid 'centroid_2H7v16_V_H' placed at [139.25597569 141.97514482
    6414 126.96669027] 
    6415 
    6416 > rename ##name=centroid_2H7v16_V_H id 102.3.3.7
    6417 
    6418 > define centroid H7v16_V & /I name centroid_2H7v16_V_I
    6419 
    6420 Centroid 'centroid_2H7v16_V_I' placed at [169.61364905 170.56588689
    6421 126.76187738] 
    6422 
    6423 > rename ##name=centroid_2H7v16_V_I id 102.3.3.8
    6424 
    6425 > rename #102.3.3 centroids
    6426 
    6427 > define centroid H7v166_D56A_C & /L name centroid_2H7v166_D56A_C_L
    6428 
    6429 Centroid 'centroid_2H7v166_D56A_C_L' placed at [101.80191468 161.59134128
    6430 111.74271267] 
    6431 
    6432 > rename ##name=centroid_2H7v166_D56A_C_L id 103.3.3.1
    6433 
    6434 > define centroid H7v166_D56A_C & /M name centroid_2H7v166_D56A_C_M
    6435 
    6436 Centroid 'centroid_2H7v166_D56A_C_M' placed at [208.08802258 152.28425847
    6437 109.3226675 ] 
    6438 
    6439 > rename ##name=centroid_2H7v166_D56A_C_M id 103.3.3.2
    6440 
    6441 > define centroid H7v166_D56A_C & /H name centroid_2H7v166_D56A_C_H
    6442 
    6443 Centroid 'centroid_2H7v166_D56A_C_H' placed at [110.13903054 151.41048738
    6444 105.03944622] 
    6445 
    6446 > rename ##name=centroid_2H7v166_D56A_C_H id 103.3.3.3
    6447 
    6448 > define centroid H7v166_D56A_C & /I name centroid_2H7v166_D56A_C_I
    6449 
    6450 Centroid 'centroid_2H7v166_D56A_C_I' placed at [198.26240903 162.26559628
    6451 103.22947676] 
    6452 
    6453 > rename ##name=centroid_2H7v166_D56A_C_I id 103.3.3.4
    6454 
    6455 > define centroid H7v166_D56A_V & /L name centroid_2H7v166_D56A_V_L
    6456 
    6457 Centroid 'centroid_2H7v166_D56A_V_L' placed at [134.697663 166.81530949
    6458 127.91858459] 
    6459 
    6460 > rename ##name=centroid_2H7v166_D56A_V_L id 103.3.3.5
    6461 
    6462 > define centroid H7v166_D56A_V & /M name centroid_2H7v166_D56A_V_M
    6463 
    6464 Centroid 'centroid_2H7v166_D56A_V_M' placed at [176.0024767 144.42140479
    6465 127.2169787 ] 
    6466 
    6467 > rename ##name=centroid_2H7v166_D56A_V_M id 103.3.3.6
    6468 
    6469 > define centroid H7v166_D56A_V & /H name centroid_2H7v166_D56A_V_H
    6470 
    6471 Centroid 'centroid_2H7v166_D56A_V_H' placed at [137.53539482 144.47796656
    6472 127.54490507] 
    6473 
    6474 > rename ##name=centroid_2H7v166_D56A_V_H id 103.3.3.7
    6475 
    6476 > define centroid H7v166_D56A_V & /I name centroid_2H7v166_D56A_V_I
    6477 
    6478 Centroid 'centroid_2H7v166_D56A_V_I' placed at [172.57552427 166.28897087
    6479 127.29650809] 
    6480 
    6481 > rename ##name=centroid_2H7v166_D56A_V_I id 103.3.3.8
    6482 
    6483 > rename #103.3.3 centroids
    6484 
    6485 > define centroid CD20 & /C name centroid_CD20_C
    6486 
    6487 Centroid 'centroid_CD20_C' placed at [149.05372941 155.2359381 168.42928274] 
    6488 
    6489 > rename ##name=centroid_CD20_C id 101.3.3.9
    6490 
    6491 > define centroid CD20 & /D name centroid_CD20_D
    6492 
    6493 Centroid 'centroid_CD20_D' placed at [161.37843923 154.64721755 168.73475111] 
    6494 
    6495 > rename ##name=centroid_CD20_D id 101.3.3.10
    6496 
    6497 executed CD20_2H7_mutants_define_domain_centroids.cxc 
    6498 
    6499 > turn x 90
    6500 
    6501 > view
    6502 
    6503 > hide #101 models
    6504 
    6505 > hide #!102.2 models
    6506 
    6507 > ~ribbon #102.10/X,Y
    6508 
    6509 executed CD20_2H7_mutants_setup.cxc 
    6510 
    6511 > hide #!104 models
    6512 
    6513 > hide #!103 models
    6514 
    6515 > hide #!102 models
    6516 
    6517 > hide #!105 models
    6518 
    6519 > show #!105 models
    6520 
    6521 > show #!104 models
    6522 
    6523 > hide #!104 models
    6524 
    6525 > hide #!104.3 models
    6526 
    6527 > show #!104 models
    6528 
    6529 > hide #!104 models
    6530 
    6531 > show #!104 models
    6532 
    6533 > hide #!104 models
    6534 
    6535 > show #!104 models
    6536 
    6537 > hide #!104 models
    6538 
    6539 > show #!104 models
    6540 
    6541 > hide #!104 models
    6542 
    6543 > show #!104 models
    6544 
    6545 > hide #!104 models
    6546 
    6547 > show #!104 models
    6548 
    6549 > hide #!104 models
    6550 
    6551 > show #!104 models
    6552 
    6553 > hide #!104 models
    6554 
    6555 > show #!103 models
    6556 
    6557 > hide #!103 models
    6558 
    6559 > show #!103 models
    6560 
    6561 > hide #!103.3 models
    6562 
    6563 > hide #!103 models
    6564 
    6565 > show #!103 models
    6566 
    6567 > hide #!103 models
    6568 
    6569 > show #!103 models
    6570 
    6571 > hide #!103 models
    6572 
    6573 > show #!103 models
    6574 
    6575 > hide #!103 models
    6576 
    6577 > show #!103 models
    6578 
    6579 > hide #!105.2 models
    6580 
    6581 > hide #!103.2 models
    6582 
    6583 > hide #!103 models
    6584 
    6585 > show #!103 models
    6586 
    6587 > hide #!103 models
    6588 
    6589 > show #!103 models
    6590 
    6591 > hide #!103 models
    6592 
    6593 > show #!103 models
    6594 
    6595 > hide #!103 models
    6596 
    6597 > show #!103 models
    6598 
    6599 > hide #!103 models
    6600 
    6601 > show #!103 models
    6602 
    6603 > hide #!103 models
    6604 
    6605 > show #!103 models
    6606 
    6607 > hide #!103 models
    6608 
    6609 > show #!103 models
    6610 
    6611 > hide #!103 models
    6612 
    6613 > show #!103 models
    6614 
    6615 > hide #!103 models
    6616 
    6617 > show #!103 models
    6618 
    6619 > hide #!103 models
    6620 
    6621 > show #!102 models
    6622 
    6623 > hide #!102.10 models
    6624 
    6625 > hide #!102.3 models
    6626 
    6627 > hide #!102 models
    6628 
    6629 > show #!102 models
    6630 
    6631 > hide #!102 models
    6632 
    6633 > hide #!103.1 models
    6634 
    6635 > show #!101 models
    6636 
    6637 > hide #!101 models
    6638 
    6639 > show #!101 models
    6640 
    6641 > show #101.1 models
    6642 
    6643 > hide #!101 models
    6644 
    6645 > show #!101 models
    6646 
    6647 > hide #!101 models
    6648 
    6649 > show #!101 models
    6650 
    6651 > hide #!101 models
    6652 
    6653 > show #!101 models
    6654 
    6655 > hide #!101 models
    6656 
    6657 > show #!101 models
    6658 
    6659 > hide #!101 models
    6660 
    6661 > show #!101 models
    6662 
    6663 > hide #!101 models
    6664 
    6665 > show #!101 models
    6666 
    6667 > hide #!101 models
    6668 
    6669 > show #!101 models
    6670 
    6671 > hide #!101 models
    6672 
    6673 > show #!101 models
    6674 
    6675 > hide #!101 models
    6676 
    6677 > hide #10 models
    6678 
    6679 > show #10 models
    6680 
    6681 > show #!101 models
    6682 
    6683 > hide #!101 models
    6684 
    6685 > show #!101 models
    6686 
    6687 > hide #!105 models
    6688 
    6689 > select add #105
    6690 
    6691 9251 atoms, 9491 bonds, 1207 residues, 4 models selected 
    6692 
    6693 > select subtract #105
    6694 
    6695 Nothing selected 
    6696 
    6697 > show #!105 models
    6698 
    6699 > hide #!105 models
    6700 
    6701 > show #!105 models
    6702 
    6703 > hide #!105 models
    6704 
    6705 > show #!105 models
    6706 
    6707 > hide #!105 models
    6708 
    6709 > show #!105 models
    6710 
    6711 > hide #!105 models
    6712 
    6713 > show #!105 models
    6714 
    6715 > hide #!105 models
    6716 
    6717 > show #!105 models
    6718 
    6719 > hide #!105 models
    6720 
    6721 > show #!105 models
    6722 
    6723 > hide #!105 models
    6724 
    6725 > show #!105 models
    6726 
    6727 > hide #!105 models
    6728 
    6729 > show #!105 models
    6730 
    6731 > hide #!105 models
    6732 
    6733 > show #!105 models
    6734 
    6735 > hide #!105 models
    6736 
    6737 > show #!105 models
    6738 
    6739 > hide #!105 models
    6740 
    6741 > show #!105 models
    6742 
    6743 > hide #!105 models
    6744 
    6745 > show #!105 models
    6746 
    6747 > hide #!105 models
    6748 
    6749 > show #!105 models
    6750 
    6751 > hide #!105 models
    6752 
    6753 > show #!105 models
    6754 
    6755 > hide #!105 models
    6756 
    6757 > show #!105 models
    6758 
    6759 > hide #!105 models
    6760 
    6761 > show #!105 models
    6762 
    6763 > hide #!105 models
    6764 
    6765 > show #!105 models
    6766 
    6767 > hide #!105 models
    6768 
    6769 > show #!105 models
    6770 
    6771 > hide #!105 models
    6772 
    6773 > show #!105 models
    6774 
    6775 > hide #!105 models
    6776 
    6777 > show #!105 models
    6778 
    6779 > hide #!105 models
    6780 
    6781 > show #!105 models
    6782 
    6783 > hide #!105 models
    6784 
    6785 > show #!105 models
    6786 
    6787 > hide #!105 models
    6788 
    6789 > show #!105 models
    6790 
    6791 > hide #!105 models
    6792 
    6793 > show #!105 models
    6794 
    6795 > hide #!105 models
    6796 
    6797 > show #!105 models
    6798 
    6799 > hide #!105 models
    6800 
    6801 > matchmaker #105.1/C,D to #101.1/C,D
    6802 
    6803 Parameters 
    6804 --- 
    6805 Chain pairing | bb 
    6806 Alignment algorithm | Needleman-Wunsch 
    6807 Similarity matrix | BLOSUM-62 
    6808 SS fraction | 0.3 
    6809 Gap open (HH/SS/other) | 18/18/6 
    6810 Gap extend | 1 
    6811 SS matrix |  |  | H | S | O 
    6812 ---|---|---|--- 
    6813 H | 6 | -9 | -6 
    6814 S |  | 6 | -6 
    6815 O |  |  | 4 
    6816 Iteration cutoff | 2 
    6817  
    6818 Matchmaker CD20_RTX, chain D (#101.1) with CD20_2H7v166, chain D (#105.1),
    6819 sequence alignment score = 1150.4 
    6820 RMSD between 148 pruned atom pairs is 0.878 angstroms; (across all 158 pairs:
    6821 1.117) 
    6822  
    6823 
    6824 > show #!105 models
    6825 
    6826 > hide #!105 models
    6827 
    6828 > show #!105 models
    6829 
    6830 > hide #!105 models
    6831 
    6832 > show #!105 models
    6833 
    6834 > hide #!105 models
    6835 
    6836 > show #!105 models
    6837 
    6838 > hide #!105 models
    6839 
    6840 > show #!105 models
    6841 
    6842 > hide #!105 models
    6843 
    6844 > show #!105 models
    6845 
    6846 > hide #!105 models
    6847 
    6848 > show #!105 models
    6849 
    6850 > hide #!105 models
    6851 
    6852 > show #!105 models
    6853 
    6854 > hide #!105 models
    6855 
    6856 > show #!105 models
    6857 
    6858 > hide #!105 models
    6859 
    6860 > show #!105 models
    6861 
    6862 > hide #!105 models
    6863 
    6864 > show #!105 models
    6865 
    6866 > hide #!105 models
    6867 
    6868 > show #!105 models
    6869 
    6870 > hide #!105 models
    6871 
    6872 > save /Users/rohoua/work/Genentech/CD20/CD20_2H7v166/STR7730_alito6vja.pdb
    6873 > models #105.1
    6874 
    6875 > view matrix
    6876 
    6877 view matrix camera
    6878 0.30758,0.083643,0.94784,441.19,-0.95125,0.0031095,0.30841,241.21,0.022849,-0.99649,0.080522,159.68 
    6879 view matrix models
    6880 #101,1,0,0,0,0,1,0,0,0,0,1,0,#101.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.3,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.4,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.3,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.4,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.4.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.3,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.4,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.5,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.6,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.7,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.8,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.9,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.10,1,0,0,0,0,1,0,0,0,0,1,0,#102,1,0,0,0,0,1,0,0,0,0,1,0,#102.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.2,-0.2379,0.93572,0.26045,-39.485,0.96898,0.21017,0.12999,-107.2,0.066893,0.2833,-0.9567,274.92,#102.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.10,0.76603,0.10593,0.63402,98.602,-0.63362,-0.041732,0.77252,142.28,0.10829,-0.9935,0.035152,135.31,#102.10.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.3,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.4,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.3,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.4,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.4.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.3,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.4,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.5,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.6,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.7,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.8,1,0,0,0,0,1,0,0,0,0,1,0,#103,1,0,0,0,0,1,0,0,0,0,1,0,#103.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.2,0.0093785,0.99468,-0.1026,-18.509,-0.99949,0.0061787,-0.031461,352.76,-0.03066,0.10284,0.99423,-49.289,#103.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.3,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.4,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.3,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.4,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.4.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.3,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.4,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.5,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.6,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.7,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.8,1,0,0,0,0,1,0,0,0,0,1,0,#104,1,0,0,0,0,1,0,0,0,0,1,0,#104.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.2,-0.0024947,0.9708,0.23989,-104.33,0.99657,0.022251,-0.079684,-45.216,-0.082695,0.23887,-0.96752,330.43,#104.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.3,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.4,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.3,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.4,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.4.2,1,0,0,0,0,1,0,0,0,0,1,0,#105,1,0,0,0,0,1,0,0,0,0,1,0,#105.1,-0.9972,-0.068777,0.029474,316.4,0.068287,-0.99752,-0.017317,300.18,0.030591,-0.015255,0.99942,-2.5792,#105.2,0.094232,-0.75331,-0.65088,436.99,-0.99412,-0.036109,-0.10213,396.76,0.053436,0.65667,-0.75228,168.36,#105.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#10,1,0,0,0,0,1,0,0,0,0,1,0 
    6881  
    6882 
    6883 > ui tool show Log
    6884 
    6885 > open /Users/rohoua/work/Genentech/CD20/CD20_2H7v166/STR7730.pdb
    6886 
    6887 Summary of feedback from opening
    6888 /Users/rohoua/work/Genentech/CD20/CD20_2H7v166/STR7730.pdb 
    6889 --- 
    6890 warning | Ignored bad PDB record found on line 1 
    6891 HEADER STR7730 version_1 2024.01.12 
    6892  
    6893 STR7730.pdb title: 
    6894 Structure of 2H7v166 Fab and Hs_CD20.M1-P297 at 5.2 A resolution. [more
    6895 info...] 
    6896  
    6897 Chain information for STR7730.pdb #2 
    6898 --- 
    6899 Chain | Description 
    6900 C | No description available 
    6901 D | No description available 
    6902 H I | No description available 
    6903 L | No description available 
    6904 M | No description available 
    6905  
    6906 
    6907 > matchmaker #2 to #105.1
    6908 
    6909 Parameters 
    6910 --- 
    6911 Chain pairing | bb 
    6912 Alignment algorithm | Needleman-Wunsch 
    6913 Similarity matrix | BLOSUM-62 
    6914 SS fraction | 0.3 
    6915 Gap open (HH/SS/other) | 18/18/6 
    6916 Gap extend | 1 
    6917 SS matrix |  |  | H | S | O 
    6918 ---|---|---|--- 
    6919 H | 6 | -9 | -6 
    6920 S |  | 6 | -6 
    6921 O |  |  | 4 
    6922 Iteration cutoff | 2 
    6923  
    6924 Matchmaker CD20_2H7v166, chain C (#105.1) with STR7730.pdb, chain C (#2),
    6925 sequence alignment score = 2082.4 
    6926 RMSD between 166 pruned atom pairs is 0.001 angstroms; (across all 166 pairs:
    6927 0.001) 
    6928  
    6929 
    6930 > view matrix
    6931 
    6932 view matrix camera
    6933 0.30758,0.083643,0.94784,441.19,-0.95125,0.0031095,0.30841,241.21,0.022849,-0.99649,0.080522,159.68 
    6934 view matrix models
    6935 #101,1,0,0,0,0,1,0,0,0,0,1,0,#101.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.3,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.4,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.1.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.3,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.4,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.2.4.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.3,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.4,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.5,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.6,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.7,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.8,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.9,1,0,0,0,0,1,0,0,0,0,1,0,#101.3.3.10,1,0,0,0,0,1,0,0,0,0,1,0,#102,1,0,0,0,0,1,0,0,0,0,1,0,#102.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.2,-0.2379,0.93572,0.26045,-39.485,0.96898,0.21017,0.12999,-107.2,0.066893,0.2833,-0.9567,274.92,#102.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.10,0.76603,0.10593,0.63402,98.602,-0.63362,-0.041732,0.77252,142.28,0.10829,-0.9935,0.035152,135.31,#102.10.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.3,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.4,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.1.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.3,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.4,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.2.4.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.3,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.4,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.5,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.6,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.7,1,0,0,0,0,1,0,0,0,0,1,0,#102.3.3.8,1,0,0,0,0,1,0,0,0,0,1,0,#103,1,0,0,0,0,1,0,0,0,0,1,0,#103.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.2,0.0093785,0.99468,-0.1026,-18.509,-0.99949,0.0061787,-0.031461,352.76,-0.03066,0.10284,0.99423,-49.289,#103.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.3,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.4,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.1.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.3,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.4,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.2.4.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.3,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.4,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.5,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.6,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.7,1,0,0,0,0,1,0,0,0,0,1,0,#103.3.3.8,1,0,0,0,0,1,0,0,0,0,1,0,#104,1,0,0,0,0,1,0,0,0,0,1,0,#104.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.2,-0.0024947,0.9708,0.23989,-104.33,0.99657,0.022251,-0.079684,-45.216,-0.082695,0.23887,-0.96752,330.43,#104.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.3,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.4,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.1.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.2.2,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.3,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.3.2,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.4,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#104.3.2.4.2,1,0,0,0,0,1,0,0,0,0,1,0,#105,1,0,0,0,0,1,0,0,0,0,1,0,#105.1,-0.9972,-0.068777,0.029474,316.4,0.068287,-0.99752,-0.017317,300.18,0.030591,-0.015255,0.99942,-2.5792,#105.2,0.094232,-0.75331,-0.65088,436.99,-0.99412,-0.036109,-0.10213,396.76,0.053436,0.65667,-0.75228,168.36,#105.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#10,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.024025,0.77304,0.6339,-141.69,0.99715,-0.026789,0.070462,-68.674,0.071451,0.63379,-0.7702,173 
    6936  
    6937 
    6938 > close
    6939 
    6940 > open /Users/rohoua/work/Genentech/CD20/CD20_2H7_mutants_setup.cxc format cmd
    6941 
    6942 > close
    6943 
    6944 > cd /Users/rohoua/work/Genentech/CD20
    6945 
    6946 Current working directory is: /Users/rohoua/work/Genentech/CD20 
    6947 
    6948 > open pdb:6vja name CD20_RTX id 101.1
    6949 
    6950 CD20_RTX title: 
    6951 Structure of CD20 in complex with rituximab Fab [more info...] 
    6952  
    6953 Chain information for CD20_RTX #1 
    6954 --- 
    6955 Chain | Description | UniProt 
    6956 C D | B-lymphocyte antigen CD20 | CD20_HUMAN 41-297 
    6957 H I | Rituximab Fab heavy chain | 
    6958 L M | Rituximab Fab light chain | 
    6959  
    6960 Non-standard residues in CD20_RTX #1 
    6961 --- 
    6962 Y01 — cholesterol hemisuccinate 
    6963  
    6964 
    6965 > open CD20_2H7v16/STR7668v2_alito6vja_C178to187.pdb name CD20_2H7v16 id 102.1
    6966 
    6967 Summary of feedback from opening CD20_2H7v16/STR7668v2_alito6vja_C178to187.pdb 
    6968 --- 
    6969 warning | Ignored bad PDB record found on line 1 
    6970 HEADER STR7668 version_2 2023.12.13 
    6971  
    6972 CD20_2H7v16 title: 
    6973 Structure of 2H7.v16 Fab and 2103.826032.Hs_MS4A1.M1-P297.BiNTF-NAvi at 3.3 A
    6974 resolution. [more info...] 
    6975  
    6976 Chain information for CD20_2H7v16 #1 
    6977 --- 
    6978 Chain | Description 
    6979 C D | No description available 
    6980 H I | No description available 
    6981 L M | No description available 
    6982  
    6983 Non-standard residues in CD20_2H7v16 #1 
    6984 --- 
    6985 Y01 — (Y01) 
    6986  
    6987 
    6988 > open CD20_2H7v16/P69_W9_J181/J181_004_volume_denoised.mrc id 102.2
    6989 
    6990 Opened J181_004_volume_denoised.mrc as #1, grid size 480,480,480, pixel 0.838,
    6991 shown at level 0.0054, step 2, values float32 
    6992 
    6993 > volume #102.2 step 1 level 0.08 color #9999CC transparency 0.5
    6994 
    6995 > view matrix models
    6996 > #102.2,-0.2379,0.93572,0.26045,-39.485,0.96898,0.21017,0.12999,-107.2,0.066893,0.2833,-0.9567,274.92
    6997 
    6998 > open "CD20_2H7v16/crystal_structure/STR7487.2H7 Fab.pdb" name 2H7v16_XRay id
    6999 > 102.10
    7000 
    7001 Summary of feedback from opening CD20_2H7v16/crystal_structure/STR7487.2H7
    7002 Fab.pdb 
    7003 --- 
    7004 warning | Ignored bad PDB record found on line 1 
    7005 HEADER STR7487 version_1 2023.05.24 
    7006  
    7007 2H7v16_XRay title: 
    7008 Structure of 2H7 Fab at 2.45 A resolution. [more info...] 
    7009  
    7010 Chain information for 2H7v16_XRay #1 
    7011 --- 
    7012 Chain | Description 
    7013 A B X Y | No description available 
    7014  
    7015 Non-standard residues in 2H7v16_XRay #1 
    7016 --- 
    7017 CL — (CL) 
    7018  
    7019 
    7020 > matchmaker #102.10/A,B to #102.1/H,L
    7021 
    7022 Parameters 
    7023 --- 
    7024 Chain pairing | bb 
    7025 Alignment algorithm | Needleman-Wunsch 
    7026 Similarity matrix | BLOSUM-62 
    7027 SS fraction | 0.3 
    7028 Gap open (HH/SS/other) | 18/18/6 
    7029 Gap extend | 1 
    7030 SS matrix |  |  | H | S | O 
    7031 ---|---|---|--- 
    7032 H | 6 | -9 | -6 
    7033 S |  | 6 | -6 
    7034 O |  |  | 4 
    7035 Iteration cutoff | 2 
    7036  
    7037 Matchmaker CD20_2H7v16, chain L (#102.1) with 2H7v16_XRay, chain A (#102.10),
    7038 sequence alignment score = 1228.2 
    7039 RMSD between 208 pruned atom pairs is 0.731 angstroms; (across all 213 pairs:
    7040 0.804) 
    7041  
    7042 
    7043 > open CD20_2H7v166_D56A/STR7717v2_alito6vja.pdb name CD20_2H7v166_D56A id
    7044 > 103.1
    7045 
    7046 Summary of feedback from opening CD20_2H7v166_D56A/STR7717v2_alito6vja.pdb 
    7047 --- 
    7048 warning | Ignored bad PDB record found on line 1 
    7049 HEADER STR7717 version_2 2023.12.15 
    7050  
    7051 CD20_2H7v166_D56A title: 
    7052 Structure of 2H7v166_D56A Fab and Hs_CD20.M1-P297 at 3.7 A resolution . [more
    7053 info...] 
    7054  
    7055 Chain information for CD20_2H7v166_D56A #1 
    7056 --- 
    7057 Chain | Description 
    7058 C D | No description available 
    7059 H I | No description available 
    7060 L | No description available 
    7061 M | No description available 
    7062  
    7063 Non-standard residues in CD20_2H7v166_D56A #1 
    7064 --- 
    7065 Y01 — (Y01) 
    7066  
    7067 
    7068 > open CD20_2H7v166_D56A/cryosparc_P69_J433_007_volume_map_sharp.mrc id 103.2
    7069 
    7070 Opened cryosparc_P69_J433_007_volume_map_sharp.mrc as #1, grid size
    7071 300,300,300, pixel 1.28, shown at level 0.0592, step 2, values float32 
    7072 
    7073 > volume #103.2 step 1 level 0.355 color #9999CC transparency 0.5
    7074 
    7075 > view matrix models
    7076 > #103.2,0.00937853,0.99467855,-0.10259937,-18.50914227,-0.99948588,0.00617870,-0.03146112,352.75851684,-0.03065977,0.10284168,0.99422511,-49.28949280
    7077 
    7078 > open CD20_2H7v166_S92A_D56A/STR7729v2_alito6vja.pdb name
    7079 > CD20_2H7v166_S92A_D56A id 104.1
    7080 
    7081 Summary of feedback from opening
    7082 CD20_2H7v166_S92A_D56A/STR7729v2_alito6vja.pdb 
    7083 --- 
    7084 warning | Ignored bad PDB record found on line 1 
    7085 HEADER STR7729 version_2 2024.01.29 
    7086  
    7087 CD20_2H7v166_S92A_D56A title: 
    7088 Structure of 2H7v166 LC.S92A HC.D56A Fab and Hs_CD20.M1-P297 at 4.5 A
    7089 resolution. [more info...] 
    7090  
    7091 Chain information for CD20_2H7v166_S92A_D56A #1 
    7092 --- 
    7093 Chain | Description 
    7094 C D | No description available 
    7095 H | No description available 
    7096 I | No description available 
    7097 L M | No description available 
    7098  
    7099 
    7100 > open CD20_2H7v166_S92A_D56A/cryosparc_P69_J242_005_volume_map_sharp_flip.mrc
    7101 > id 104.2
    7102 
    7103 Opened cryosparc_P69_J242_005_volume_map_sharp_flip.mrc as #1, grid size
    7104 300,300,300, pixel 1.43, shown at level 0.0447, step 2, values float32 
    7105 
    7106 > volume #104.2 step 1 level 0.355 color #9999CC transparency 0.5
    7107 
    7108 > view matrix models
    7109 > #104.2,-0.00249470,0.97079708,0.23988915,-104.32503408,0.99657176,0.02225139,-0.07968446,-45.21631074,-0.08269530,0.23886796,-0.96752446,330.43463437
    7110 
    7111 > open CD20_2H7v166/STR7730_alito6vja.pdb name CD20_2H7v166 id 105.1
    7112 
    7113 Summary of feedback from opening CD20_2H7v166/STR7730_alito6vja.pdb 
    7114 --- 
    7115 warning | Ignored bad PDB record found on line 1 
    7116 HEADER STR7730 version_1 2024.01.12 
    7117  
    7118 CD20_2H7v166 title: 
    7119 Structure of 2H7v166 Fab and Hs_CD20.M1-P297 at 5.2 A resolution. [more
    7120 info...] 
    7121  
    7122 Chain information for CD20_2H7v166 #1 
    7123 --- 
    7124 Chain | Description 
    7125 C | No description available 
    7126 D | No description available 
    7127 H I | No description available 
    7128 L | No description available 
    7129 M | No description available 
    7130  
    7131 
    7132 > open CD20_2H7v166/cryosparc_P71_J138_006_volume_map_sharp.mrc id 105.2
    7133 
    7134 Opened cryosparc_P71_J138_006_volume_map_sharp.mrc as #1, grid size
    7135 300,300,300, pixel 1.43, shown at level 0.0428, step 2, values float32 
    7136 
    7137 > volume #105.2 step 1 level 0.355 color #9999CC transparency 0.5
    7138 
    7139 > view matrix models
    7140 > #105.2,-0.024025,0.77304,0.6339,-141.69,0.99715,-0.026789,0.070462,-68.674,0.071451,0.63379,-0.7702,173
    7141 
    7142 > rename #101 CD20_RTX
    7143 
    7144 > rename #102 CD20_2H7v16
    7145 
    7146 > rename #103 CD20_2H7v166_D56A
    7147 
    7148 > rename #104 CD20_2H7v166_S92A_D56A
    7149 
    7150 > dssp
    7151 
    7152 > name CD20_RTX #101.1
    7153 
    7154 > name CD20_2H7v16 #102.1
    7155 
    7156 > name CD20_2H7v166_D56A #103.1
    7157 
    7158 > name CD20_2H7v166_S92A_D56A #104.1
    7159 
    7160 > name CD20 /C,D
    7161 
    7162 > name CD20_Monomer /C
    7163 
    7164 > name CD20_H1 /C,D:46-71
    7165 
    7166 > name CD20_ECL1 /C,D:72-79
    7167 
    7168 > name CD20_H2 /C,D:80-105
    7169 
    7170 > name CD20_ICL1 /C,D:106-112
    7171 
    7172 > name CD20_H3 /C,D:113-141
    7173 
    7174 > name CD20_ECL2 /C,D:142-187
    7175 
    7176 > name CD20_ECL2SS /C,D:167,183
    7177 
    7178 > name CD20_H4 /C,D:188-end
    7179 
    7180 > name CD20_DimerInt /C,D:62,200,65,196,69,192,73,188,76,185,58,54,50
    7181 
    7182 > name RTX CD20_RTX & /H,L,I,M
    7183 
    7184 > name RTX_H RTX & /H,I
    7185 
    7186 > name RTX_L RTX & /L,M
    7187 
    7188 > name RTX_Epitope CD20_RTX & /C,D:168-175
    7189 
    7190 > name RTX_V (RTX & /L,M:1-107) | (RTX & /H,I:1-111)
    7191 
    7192 > name RTX_C (RTX & /L,M:113-end) | (RTX & /H,I:119-end)
    7193 
    7194 > name H7v16 CD20_2H7v16 & /H,L,I,M
    7195 
    7196 > name H7v16_H H7v16 & /H,I
    7197 
    7198 > name H7v16_L H7v16 & /L,M
    7199 
    7200 > name H7v16_Epitope CD20_2H7v16 & /C,D:168-175
    7201 
    7202 > name H7v16_V (H7v16 & /L,M:1-107) | (H7v16 & /H,I:1-111)
    7203 
    7204 > name H7v16_C (H7v16 & /L,M:112-end) | (H7v16 & /H,I:119-end)
    7205 
    7206 > name H7v166_D56A CD20_2H7v166_D56A & /H,L,I,M
    7207 
    7208 > name H7v166_D56A_H H7v166_D56A & /H,I
    7209 
    7210 > name H7v166_D56A_L H7v166_D56A & /L,M
    7211 
    7212 > name H7v166_D56A_Epitope CD20_2H7v166_D56A & /C,D:168-175
    7213 
    7214 > name H7v166_D56A_V (H7v166_D56A & /L,M:1-107) | (H7v166_D56A & /H,I:1-111)
    7215 
    7216 > name H7v166_D56A_C (H7v166_D56A & /L,M:112-end) | (H7v166_D56A &
    7217 > /H,I:119-end)
    7218 
    7219 > name H7v166_S92A_D56A CD20_2H7v166_S92A_D56A & /H,L,I,M
    7220 
    7221 > name H7v166_S92A_D56A_H H7v166_S92A_D56A & /H,I
    7222 
    7223 > name H7v166_S92A_D56A_L H7v166_S92A_D56A & /L,M
    7224 
    7225 > name H7v166_S92A_D56A_Epitope CD20_2H7v166_S92A_D56A & /C,D:168-175
    7226 
    7227 > name H7v166_S92A_D56A_V (H7v166_S92A_D56A & /L,M:1-107) | (H7v166_S92A_D56A
    7228 > & /H,I:1-111)
    7229 
    7230 > name H7v166_S92A_D56A_C (H7v166_S92A_D56A & /L,M:112-end) |
    7231 > (H7v166_S92A_D56A & /H,I:119-end)
    7232 
    7233 > lighting soft
    7234 
    7235 > set bgColor white
    7236 
    7237 > camera ortho
    7238 
    7239 > style stick
    7240 
    7241 Changed 53488 atom styles 
    7242 
    7243 > color byhetero
    7244 
    7245 > open CD20_2H7_mutants_color.cxc
    7246 
    7247 > color CD20 burlywood
    7248 
    7249 > color modify CD20_H1 hue - 20
    7250 
    7251 > color modify CD20_H2 hue - 10
    7252 
    7253 > color modify CD20_H3 hue + 0
    7254 
    7255 > color modify CD20_H4 hue + 10
    7256 
    7257 > color modify CD20_ECL1 hue +10
    7258 
    7259 > color modify CD20_ECL2 hue + 40
    7260 
    7261 > color modify CD20 saturation + 80
    7262 
    7263 > color CD20_ECL2 rgb(127,165,90)
    7264 
    7265 > color CD20_H4 rgb(176,215,142)
    7266 
    7267 > color RTX plum
    7268 
    7269 > color modify RTX_H hue - 40
    7270 
    7271 > color H7v16 slate blue
    7272 
    7273 > color modify H7v16_H hue - 40
    7274 
    7275 > color H7v166_D56A dodger blue
    7276 
    7277 > color modify H7v166_D56A_H hue - 40
    7278 
    7279 > color H7v166_S92A_D56A purple
    7280 
    7281 > color modify H7v166_S92A_D56A_H hue - 40
    7282 
    7283 executed CD20_2H7_mutants_color.cxc 
    7284 
    7285 > hide
    7286 
    7287 > ribbon
    7288 
    7289 > show CD20_ECL2SS
    7290 
    7291 > style CD20_ECL2SS stick
    7292 
    7293 Changed 120 atom styles 
    7294 
    7295 > define axis fromPoint 155,155,70 toPoint 155,155,210 name sym_axis
    7296 
    7297 Axis 'sym_axis' centered at [155. 155. 140.] with direction [ 0. 0. 140.],
    7298 radius 1, and length 140 
    7299 
    7300 > marker #1.1 position 155,155,70
    7301 
    7302 > marker #1.1 position 155,155,210
    7303 
    7304 > select
    7305 > #101.1/C,D:73,74,75,76,77,78,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,184,185,186,187,188
    7306 
    7307 440 atoms, 446 bonds, 54 residues, 1 model selected 
    7308 
    7309 > define plane sel name membrane_plane
    7310 
    7311 Plane 'membrane_plane' placed at [154.99498409 155.00750455 153.73545455] with
    7312 normal [-5.66049107e-05 -2.68508756e-05 -9.99999998e-01] and radius 24.3 
    7313 
    7314 > rename ##name=membrane_plane id 10
    7315 
    7316 > open CD20_2H7v16/CD20_RTX_define_pseudo_symmetries.cxc
    7317 
    7318 > combine CD20_RTX name RTX_Va modelId 1001
    7319 
    7320 > select zone (RTX_V & /H,L) 0.1 #1001
    7321 
    7322 Selected 1711 atoms 
    7323 
    7324 > delete #1001 & ~sel
    7325 
    7326 > combine #1001 name RTX_Va_copy modelId 1002
    7327 
    7328 > combine CD20_RTX name RTX_Vb modelId 1003
    7329 
    7330 > select zone (RTX_V & /I,M) 0.1 #1003
    7331 
    7332 Selected 1711 atoms 
    7333 
    7334 > delete #1003 & ~sel
    7335 
    7336 > combine #1003 name RTX_Vb_copy modelId 1004
    7337 
    7338 > combine CD20_RTX name RTX_Ca modelId 1005
    7339 
    7340 > select zone (RTX_C & /H,L) 0.1 #1005
    7341 
    7342 Selected 1503 atoms 
    7343 
    7344 > delete #1005 & ~sel
    7345 
    7346 > combine #1005 name RTX_Ca_copy modelId 1006
    7347 
    7348 > combine CD20_RTX name RTX_Cb modelId 1007
    7349 
    7350 > select zone (RTX_C & /I,M) 0.1 #1007
    7351 
    7352 Selected 1503 atoms 
    7353 
    7354 > delete #1007 & ~sel
    7355 
    7356 > combine #1007 name RTX_Ca_copy modelId 1008
    7357 
    7358 > matchmaker #1002/L to #1001/H
    7359 
    7360 Parameters 
    7361 --- 
    7362 Chain pairing | bb 
    7363 Alignment algorithm | Needleman-Wunsch 
    7364 Similarity matrix | BLOSUM-62 
    7365 SS fraction | 0.3 
    7366 Gap open (HH/SS/other) | 18/18/6 
    7367 Gap extend | 1 
    7368 SS matrix |  |  | H | S | O 
    7369 ---|---|---|--- 
    7370 H | 6 | -9 | -6 
    7371 S |  | 6 | -6 
    7372 O |  |  | 4 
    7373 Iteration cutoff | 2 
    7374  
    7375 Matchmaker RTX_Va, chain H (#1001) with RTX_Va_copy, chain L (#1002), sequence
    7376 alignment score = 198.7 
    7377 RMSD between 57 pruned atom pairs is 0.694 angstroms; (across all 103 pairs:
    7378 4.421) 
    7379  
    7380 
    7381 > wait 1
    7382 
    7383 > measure rotation #1002 toModel #1001 showSlabs true
    7384 
    7385 Position of RTX_Va_copy #1002 relative to RTX_Va #1001 coordinates: 
    7386 Matrix rotation and translation 
    7387 0.65377294 -0.06463426 0.75392530 -36.97668460 
    7388 0.02426941 -0.99404163 -0.10626495 318.59247232 
    7389 0.75630149 0.08777047 -0.64830888 90.28955685 
    7390 Axis 0.90906034 -0.01113250 0.41651574 
    7391 Axis point 0.00000000 156.41772375 62.99337678 
    7392 Rotation angle (degrees) 173.87355102 
    7393 Shift along axis 0.44625393 
    7394  
    7395 
    7396 > close #1001 #1002
    7397 
    7398 > define axis #2 name axis_Va
    7399 
    7400 Axis 'rotation axis #2/axis_Va' centered at [137.08203113 154.73899552
    7401 125.80199389] with direction [ 0.90906034 -0.0111325 0.41651574], radius
    7402 0.65062, and length 52.0496 
    7403 
    7404 > rename #2 Va_rotation_axis id #101.3.1.1
    7405 
    7406 > rename #3 Va_rotation_slabs id #101.3.2.1
    7407 
    7408 > matchmaker #1004/M to #1003/I
    7409 
    7410 Parameters 
    7411 --- 
    7412 Chain pairing | bb 
    7413 Alignment algorithm | Needleman-Wunsch 
    7414 Similarity matrix | BLOSUM-62 
    7415 SS fraction | 0.3 
    7416 Gap open (HH/SS/other) | 18/18/6 
    7417 Gap extend | 1 
    7418 SS matrix |  |  | H | S | O 
    7419 ---|---|---|--- 
    7420 H | 6 | -9 | -6 
    7421 S |  | 6 | -6 
    7422 O |  |  | 4 
    7423 Iteration cutoff | 2 
    7424  
    7425 Matchmaker RTX_Vb, chain I (#1003) with RTX_Vb_copy, chain M (#1004), sequence
    7426 alignment score = 214.3 
    7427 RMSD between 57 pruned atom pairs is 0.703 angstroms; (across all 103 pairs:
    7428 4.448) 
    7429  
    7430 
    7431 > wait 1
    7432 
    7433 > measure rotation #1004 toModel #1003 showSlabs true
    7434 
    7435 Position of RTX_Vb_copy #1004 relative to RTX_Vb #1003 coordinates: 
    7436 Matrix rotation and translation 
    7437 0.65527690 -0.06129532 -0.75289778 163.48223927 
    7438 0.03113398 -0.99366393 0.10799385 290.56686667 
    7439 -0.75474688 -0.09420658 -0.64921665 352.74817189 
    7440 Axis -0.90945183 0.00831685 0.41572611 
    7441 Axis point 0.00000000 156.83903630 204.83255489 
    7442 Rotation angle (degrees) 173.61745932 
    7443 Shift along axis 0.38400661 
    7444  
    7445 
    7446 > close #1004 #1003
    7447 
    7448 > define axis #2 name axis_Vb
    7449 
    7450 Axis 'rotation axis #2/axis_Vb' centered at [172.9873955 155.25708275
    7451 125.75703344] with direction [-0.90945183 0.00831685 0.41572611], radius
    7452 0.648586, and length 51.8869 
    7453 
    7454 > rename #2 Vb_rotation_axis id #101.3.1.2
    7455 
    7456 > rename #3 Vb_rotation_slabs id #101.3.2.2
    7457 
    7458 > matchmaker #1006/L to #1005/H
    7459 
    7460 Parameters 
    7461 --- 
    7462 Chain pairing | bb 
    7463 Alignment algorithm | Needleman-Wunsch 
    7464 Similarity matrix | BLOSUM-62 
    7465 SS fraction | 0.3 
    7466 Gap open (HH/SS/other) | 18/18/6 
    7467 Gap extend | 1 
    7468 SS matrix |  |  | H | S | O 
    7469 ---|---|---|--- 
    7470 H | 6 | -9 | -6 
    7471 S |  | 6 | -6 
    7472 O |  |  | 4 
    7473 Iteration cutoff | 2 
    7474  
    7475 Matchmaker RTX_Ca, chain H (#1005) with RTX_Ca_copy, chain L (#1006), sequence
    7476 alignment score = 238.2 
    7477 RMSD between 50 pruned atom pairs is 0.795 angstroms; (across all 96 pairs:
    7478 3.308) 
    7479  
    7480 
    7481 > wait 1
    7482 
    7483 > measure rotation #1006 toModel #1005 showSlabs true
    7484 
    7485 Position of RTX_Ca_copy #1006 relative to RTX_Ca #1005 coordinates: 
    7486 Matrix rotation and translation 
    7487 0.37780344 0.24165354 0.89379423 -73.66252391 
    7488 0.01279825 -0.96661035 0.25593093 273.63534365 
    7489 0.92579737 -0.08525258 -0.36828146 68.27322422 
    7490 Axis -0.82796624 -0.07766353 -0.55537400 
    7491 Axis point 0.00000000 144.62953182 41.62502778 
    7492 Rotation angle (degrees) 168.10978391 
    7493 Shift along axis 1.82142171 
    7494  
    7495 
    7496 > close #1006 #1005
    7497 
    7498 > define axis #2 name axis_Ca
    7499 
    7500 Axis 'rotation axis #2/axis_Ca' centered at [102.30380142 154.22566542
    7501 110.24723578] with direction [-0.82796624 -0.07766353 -0.555374 ], radius
    7502 0.539289, and length 43.1431 
    7503 
    7504 > rename #2 Ca_rotation_axis id #101.3.1.3
    7505 
    7506 > rename #3 Ca_rotation_slabs id #101.3.2.3
    7507 
    7508 > matchmaker #1008/M to #1007/I
    7509 
    7510 Parameters 
    7511 --- 
    7512 Chain pairing | bb 
    7513 Alignment algorithm | Needleman-Wunsch 
    7514 Similarity matrix | BLOSUM-62 
    7515 SS fraction | 0.3 
    7516 Gap open (HH/SS/other) | 18/18/6 
    7517 Gap extend | 1 
    7518 SS matrix |  |  | H | S | O 
    7519 ---|---|---|--- 
    7520 H | 6 | -9 | -6 
    7521 S |  | 6 | -6 
    7522 O |  |  | 4 
    7523 Iteration cutoff | 2 
    7524  
    7525 Matchmaker RTX_Cb, chain I (#1007) with RTX_Ca_copy, chain M (#1008), sequence
    7526 alignment score = 238.2 
    7527 RMSD between 50 pruned atom pairs is 0.794 angstroms; (across all 96 pairs:
    7528 3.487) 
    7529  
    7530 
    7531 > wait 1
    7532 
    7533 > measure rotation #1008 toModel #1007 showSlabs true
    7534 
    7535 Position of RTX_Ca_copy #1008 relative to RTX_Cb #1007 coordinates: 
    7536 Matrix rotation and translation 
    7537 0.37961795 0.24211100 -0.89290116 191.06761259 
    7538 0.01296287 -0.96644625 -0.25654164 332.12351027 
    7539 -0.92505253 0.08581325 -0.37001879 328.82641259 
    7540 Axis 0.82850834 0.07780721 -0.55454483 
    7541 Axis point 0.00000000 136.30341759 249.27961172 
    7542 Rotation angle (degrees) 168.07628341 
    7543 Shift along axis 1.79372450 
    7544  
    7545 
    7546 > close #1008 #1007
    7547 
    7548 > define axis #2 name axis_Cb
    7549 
    7550 Axis 'rotation axis #2/axis_Cb' centered at [207.91438592 155.82915639
    7551 110.11643971] with direction [ 0.82850834 0.07780721 -0.55454483], radius
    7552 0.53918, and length 43.1344 
    7553 
    7554 > rename #2 Cb_rotation_axis id #101.3.1.4
    7555 
    7556 > rename #3 Cb_rotation_slabs id #101.3.2.4
    7557 
    7558 > rename #101.3 geometry
    7559 
    7560 > rename #101.3.1 rotation_axes
    7561 
    7562 > rename #101.3.2 rotation_slabs
    7563 
    7564 executed CD20_RTX_define_pseudo_symmetries.cxc 
    7565 
    7566 > open CD20_2H7v16/CD20_2H7v16_define_pseudo_symmetries.cxc
    7567 
    7568 > combine CD20_2H7v16 name 2H7_v16_Va modelId 1001
    7569 
    7570 > select zone (H7v16_V & /H,L) 0.1 #1001
    7571 
    7572 Selected 1754 atoms 
    7573 
    7574 > delete #1001 & ~sel
    7575 
    7576 > combine #1001 name 2H7_v16_Va_copy modelId 1002
    7577 
    7578 > combine CD20_2H7v16 name 2H7_v16_Vb modelId 1003
    7579 
    7580 > select zone (H7v16_V & /I,M) 0.1 #1003
    7581 
    7582 Selected 1710 atoms 
    7583 
    7584 > delete #1003 & ~sel
    7585 
    7586 > combine #1003 name 2H7_v16_Vb_copy modelId 1004
    7587 
    7588 > combine CD20_2H7v16 name 2H7_v16_Ca modelId 1005
    7589 
    7590 > select zone (H7v16_C & /H,L) 0.1 #1005
    7591 
    7592 Selected 1550 atoms 
    7593 
    7594 > delete #1005 & ~sel
    7595 
    7596 > combine #1005 name 2H7_v16_Ca_copy modelId 1006
    7597 
    7598 > combine CD20_2H7v16 name 2H7_v16_Cb modelId 1007
    7599 
    7600 > select zone (H7v16_C & /I,M) 0.1 #1007
    7601 
    7602 Selected 1550 atoms 
    7603 
    7604 > delete #1007 & ~sel
    7605 
    7606 > combine #1007 name 2H7_v16_Ca_copy modelId 1008
    7607 
    7608 > matchmaker #1002/L to #1001/H
    7609 
    7610 Parameters 
    7611 --- 
    7612 Chain pairing | bb 
    7613 Alignment algorithm | Needleman-Wunsch 
    7614 Similarity matrix | BLOSUM-62 
    7615 SS fraction | 0.3 
    7616 Gap open (HH/SS/other) | 18/18/6 
    7617 Gap extend | 1 
    7618 SS matrix |  |  | H | S | O 
    7619 ---|---|---|--- 
    7620 H | 6 | -9 | -6 
    7621 S |  | 6 | -6 
    7622 O |  |  | 4 
    7623 Iteration cutoff | 2 
    7624  
    7625 Matchmaker 2H7_v16_Va, chain H (#1001) with 2H7_v16_Va_copy, chain L (#1002),
    7626 sequence alignment score = 387.9 
    7627 RMSD between 66 pruned atom pairs is 0.856 angstroms; (across all 103 pairs:
    7628 5.340) 
    7629  
    7630 
    7631 > wait 1
    7632 
    7633 > measure rotation #1002 toModel #1001 showSlabs true
    7634 
    7635 Position of 2H7_v16_Va_copy #1002 relative to 2H7_v16_Va #1001 coordinates: 
    7636 Matrix rotation and translation 
    7637 0.58985298 0.00233427 0.80750728 -45.05678546 
    7638 0.12316682 -0.98855531 -0.08711100 297.16136614 
    7639 0.79806228 0.15084078 -0.58338980 65.44859378 
    7640 Axis 0.89106916 0.03536916 0.45248731 
    7641 Axis point 0.00000000 147.01172040 55.34624717 
    7642 Rotation angle (degrees) 172.32693090 
    7643 Shift along axis -0.02370559 
    7644  
    7645 
    7646 > close #1001 #1002
    7647 
    7648 > define axis #2 name axis_Va
    7649 
    7650 Axis 'rotation axis #2/axis_Va' centered at [138.16022152 152.49570671
    7651 125.5043786 ] with direction [0.89106916 0.03536916 0.45248731], radius
    7652 0.589874, and length 47.1899 
    7653 
    7654 > rename #2 Va_rotation_axis id #102.3.1.1
    7655 
    7656 > rename #3 Va_rotation_slabs id #102.3.2.1
    7657 
    7658 > matchmaker #1004/M to #1003/I
    7659 
    7660 Parameters 
    7661 --- 
    7662 Chain pairing | bb 
    7663 Alignment algorithm | Needleman-Wunsch 
    7664 Similarity matrix | BLOSUM-62 
    7665 SS fraction | 0.3 
    7666 Gap open (HH/SS/other) | 18/18/6 
    7667 Gap extend | 1 
    7668 SS matrix |  |  | H | S | O 
    7669 ---|---|---|--- 
    7670 H | 6 | -9 | -6 
    7671 S |  | 6 | -6 
    7672 O |  |  | 4 
    7673 Iteration cutoff | 2 
    7674  
    7675 Matchmaker 2H7_v16_Vb, chain I (#1003) with 2H7_v16_Vb_copy, chain M (#1004),
    7676 sequence alignment score = 378.3 
    7677 RMSD between 65 pruned atom pairs is 0.877 angstroms; (across all 97 pairs:
    7678 4.620) 
    7679  
    7680 
    7681 > wait 1
    7682 
    7683 > measure rotation #1004 toModel #1003 showSlabs true
    7684 
    7685 Position of 2H7_v16_Vb_copy #1004 relative to 2H7_v16_Vb #1003 coordinates: 
    7686 Matrix rotation and translation 
    7687 0.62864598 0.45103819 -0.63353672 71.77949524 
    7688 0.53321619 -0.84298968 -0.07105560 212.64664720 
    7689 -0.56611370 -0.29314322 -0.77044294 368.84403487 
    7690 Axis -0.90200560 -0.27383758 0.33376470 
    7691 Axis point -0.00000000 108.05935567 190.41757658 
    7692 Rotation angle (degrees) 172.92851049 
    7693 Shift along axis 0.13096924 
    7694  
    7695 
    7696 > close #1004 #1003
    7697 
    7698 > define axis #2 name axis_Vb
    7699 
    7700 Axis 'rotation axis #2/axis_Vb' centered at [174.414767 161.00949037
    7701 125.87973689] with direction [-0.9020056 -0.27383758 0.3337647 ], radius
    7702 0.594923, and length 47.5938 
    7703 
    7704 > rename #2 Vb_rotation_axis id #102.3.1.2
    7705 
    7706 > rename #3 Vb_rotation_slabs id #102.3.2.2
    7707 
    7708 > matchmaker #1006/L to #1005/H
    7709 
    7710 Parameters 
    7711 --- 
    7712 Chain pairing | bb 
    7713 Alignment algorithm | Needleman-Wunsch 
    7714 Similarity matrix | BLOSUM-62 
    7715 SS fraction | 0.3 
    7716 Gap open (HH/SS/other) | 18/18/6 
    7717 Gap extend | 1 
    7718 SS matrix |  |  | H | S | O 
    7719 ---|---|---|--- 
    7720 H | 6 | -9 | -6 
    7721 S |  | 6 | -6 
    7722 O |  |  | 4 
    7723 Iteration cutoff | 2 
    7724  
    7725 Matchmaker 2H7_v16_Ca, chain H (#1005) with 2H7_v16_Ca_copy, chain L (#1006),
    7726 sequence alignment score = 403.6 
    7727 RMSD between 58 pruned atom pairs is 1.037 angstroms; (across all 98 pairs:
    7728 3.184) 
    7729  
    7730 
    7731 > wait 1
    7732 
    7733 > measure rotation #1006 toModel #1005 showSlabs true
    7734 
    7735 Position of 2H7_v16_Ca_copy #1006 relative to 2H7_v16_Ca #1005 coordinates: 
    7736 Matrix rotation and translation 
    7737 -0.62547004 0.41276667 0.66212605 49.05674876 
    7738 0.08546501 -0.80725952 0.58397585 200.07354667 
    7739 0.77555333 0.42184801 0.46963954 -95.83522576 
    7740 Axis -0.42390521 -0.29657098 -0.85577452 
    7741 Axis point 59.57688139 113.83169245 0.00000000 
    7742 Rotation angle (degrees) 168.97535276 
    7743 Shift along axis 1.88192618 
    7744  
    7745 
    7746 > close #1006 #1005
    7747 
    7748 > define axis #2 name axis_Ca
    7749 
    7750 Axis 'rotation axis #2/axis_Ca' centered at [109.8807251 149.02507918
    7751 101.55276878] with direction [-0.42390521 -0.29657098 -0.85577452], radius
    7752 0.550437, and length 44.0349 
    7753 
    7754 > rename #2 Ca_rotation_axis id #102.3.1.3
    7755 
    7756 > rename #3 Ca_rotation_slabs id #102.3.2.3
    7757 
    7758 > matchmaker #1008/M to #1007/I
    7759 
    7760 Parameters 
    7761 --- 
    7762 Chain pairing | bb 
    7763 Alignment algorithm | Needleman-Wunsch 
    7764 Similarity matrix | BLOSUM-62 
    7765 SS fraction | 0.3 
    7766 Gap open (HH/SS/other) | 18/18/6 
    7767 Gap extend | 1 
    7768 SS matrix |  |  | H | S | O 
    7769 ---|---|---|--- 
    7770 H | 6 | -9 | -6 
    7771 S |  | 6 | -6 
    7772 O |  |  | 4 
    7773 Iteration cutoff | 2 
    7774  
    7775 Matchmaker 2H7_v16_Cb, chain I (#1007) with 2H7_v16_Ca_copy, chain M (#1008),
    7776 sequence alignment score = 396 
    7777 RMSD between 54 pruned atom pairs is 0.855 angstroms; (across all 98 pairs:
    7778 3.551) 
    7779  
    7780 
    7781 > wait 1
    7782 
    7783 > measure rotation #1008 toModel #1007 showSlabs true
    7784 
    7785 Position of 2H7_v16_Ca_copy #1008 relative to 2H7_v16_Cb #1007 coordinates: 
    7786 Matrix rotation and translation 
    7787 -0.62894249 0.48033740 -0.61131606 312.62038315 
    7788 0.14842286 -0.69766113 -0.70088487 336.12735996 
    7789 -0.76315267 -0.53154955 0.36749568 311.24709675 
    7790 Axis 0.42085200 0.37736216 -0.82491296 
    7791 Axis point 256.37284203 220.04020388 0.00000000 
    7792 Rotation angle (degrees) 168.39393838 
    7793 Shift along axis 1.65689588 
    7794  
    7795 
    7796 > close #1008 #1007
    7797 
    7798 > define axis #2 name axis_Cb
    7799 
    7800 Axis 'rotation axis #2/axis_Cb' centered at [202.74487059 171.95401837
    7801 105.11630914] with direction [ 0.420852 0.37736216 -0.82491296], radius
    7802 0.534846, and length 42.7877 
    7803 
    7804 > rename #2 Cb_rotation_axis id #102.3.1.4
    7805 
    7806 > rename #3 Cb_rotation_slabs id #102.3.2.4
    7807 
    7808 > rename #102.3 geometry
    7809 
    7810 > rename #102.3.1 rotation_axes
    7811 
    7812 > rename #102.3.2 rotation_slabs
    7813 
    7814 executed CD20_2H7v16_define_pseudo_symmetries.cxc 
    7815 
    7816 > open CD20_2H7v166_D56A/CD20_2H7v166_D56A_define_pseudo_symmetries.cxc
    7817 
    7818 > combine CD20_2H7v166_D56A name 2H7_v166_D56A_Va modelId 1001
    7819 
    7820 > select zone (H7v166_D56A_V & /H,L) 0.1 #1001
    7821 
    7822 Selected 1654 atoms 
    7823 
    7824 > delete #1001 & ~sel
    7825 
    7826 > combine #1001 name 2H7_v166_D56A_Va_copy modelId 1002
    7827 
    7828 > combine CD20_2H7v166_D56A name 2H7_v166_D56A_Vb modelId 1003
    7829 
    7830 > select zone (H7v166_D56A_V & /I,M) 0.1 #1003
    7831 
    7832 Selected 1678 atoms 
    7833 
    7834 > delete #1003 & ~sel
    7835 
    7836 > combine #1003 name 2H7_v166_D56A_Vb_copy modelId 1004
    7837 
    7838 > combine CD20_2H7v166_D56A name 2H7_v166_D56A_Ca modelId 1005
    7839 
    7840 > select zone (H7v166_D56A_C & /H,L) 0.1 #1005
    7841 
    7842 Selected 1550 atoms 
    7843 
    7844 > delete #1005 & ~sel
    7845 
    7846 > combine #1005 name 2H7_v166_D56A_Ca_copy modelId 1006
    7847 
    7848 > combine CD20_2H7v166_D56A name 2H7_v166_D56A_Cb modelId 1007
    7849 
    7850 > select zone (H7v166_D56A_C & /I,M) 0.1 #1007
    7851 
    7852 Selected 1550 atoms 
    7853 
    7854 > delete #1007 & ~sel
    7855 
    7856 > combine #1007 name 2H7_v166_D56A_Ca_copy modelId 1008
    7857 
    7858 > matchmaker #1002/L to #1001/H
    7859 
    7860 Parameters 
    7861 --- 
    7862 Chain pairing | bb 
    7863 Alignment algorithm | Needleman-Wunsch 
    7864 Similarity matrix | BLOSUM-62 
    7865 SS fraction | 0.3 
    7866 Gap open (HH/SS/other) | 18/18/6 
    7867 Gap extend | 1 
    7868 SS matrix |  |  | H | S | O 
    7869 ---|---|---|--- 
    7870 H | 6 | -9 | -6 
    7871 S |  | 6 | -6 
    7872 O |  |  | 4 
    7873 Iteration cutoff | 2 
    7874  
    7875 Matchmaker 2H7_v166_D56A_Va, chain H (#1001) with 2H7_v166_D56A_Va_copy, chain
    7876 L (#1002), sequence alignment score = 547.6 
    7877 RMSD between 74 pruned atom pairs is 0.966 angstroms; (across all 90 pairs:
    7878 2.607) 
    7879  
    7880 
    7881 > wait 1
    7882 
    7883 > measure rotation #1002 toModel #1001 showSlabs true
    7884 
    7885 Position of 2H7_v166_D56A_Va_copy #1002 relative to 2H7_v166_D56A_Va #1001
    7886 coordinates: 
    7887 Matrix rotation and translation 
    7888 0.73992366 -0.12116101 0.66168949 -29.70332856 
    7889 -0.06116680 -0.99168902 -0.11318795 332.06337928 
    7890 0.66990417 0.04327702 -0.74118520 123.44534698 
    7891 Axis 0.93259437 -0.04896279 0.35758970 
    7892 Axis point 0.00000000 162.47254458 74.89799404 
    7893 Rotation angle (degrees) 175.18797763 
    7894 Shift along axis 0.18287681 
    7895  
    7896 
    7897 > close #1001 #1002
    7898 
    7899 > define axis #2 name axis_Va
    7900 
    7901 Axis 'rotation axis #2/axis_Va' centered at [136.31725835 155.31565622
    7902 127.16685711] with direction [ 0.93259437 -0.04896279 0.3575897 ], radius
    7903 0.599212, and length 47.937 
    7904 
    7905 > rename #2 Va_rotation_axis id #103.3.1.1
    7906 
    7907 > rename #3 Va_rotation_slabs id #103.3.2.1
    7908 
    7909 > matchmaker #1004/M to #1003/I
    7910 
    7911 Parameters 
    7912 --- 
    7913 Chain pairing | bb 
    7914 Alignment algorithm | Needleman-Wunsch 
    7915 Similarity matrix | BLOSUM-62 
    7916 SS fraction | 0.3 
    7917 Gap open (HH/SS/other) | 18/18/6 
    7918 Gap extend | 1 
    7919 SS matrix |  |  | H | S | O 
    7920 ---|---|---|--- 
    7921 H | 6 | -9 | -6 
    7922 S |  | 6 | -6 
    7923 O |  |  | 4 
    7924 Iteration cutoff | 2 
    7925  
    7926 Matchmaker 2H7_v166_D56A_Vb, chain I (#1003) with 2H7_v166_D56A_Vb_copy, chain
    7927 M (#1004), sequence alignment score = 376.5 
    7928 RMSD between 70 pruned atom pairs is 0.891 angstroms; (across all 92 pairs:
    7929 3.886) 
    7930  
    7931 
    7932 > wait 1
    7933 
    7934 > measure rotation #1004 toModel #1003 showSlabs true
    7935 
    7936 Position of 2H7_v166_D56A_Vb_copy #1004 relative to 2H7_v166_D56A_Vb #1003
    7937 coordinates: 
    7938 Matrix rotation and translation 
    7939 0.72982969 -0.01372193 -0.68349128 135.94952936 
    7940 0.06485007 -0.99390027 0.08920045 287.47713002 
    7941 -0.68054617 -0.10942560 -0.72448806 354.00628960 
    7942 Axis -0.92979963 -0.01378652 0.36780781 
    7943 Axis point 0.00000000 152.92822789 195.61279282 
    7944 Rotation angle (degrees) 173.86847166 
    7945 Shift along axis -0.16285394 
    7946  
    7947 
    7948 > close #1004 #1003
    7949 
    7950 > define axis #2 name axis_Vb
    7951 
    7952 Axis 'rotation axis #2/axis_Vb' centered at [173.81620585 155.50547201
    7953 126.8550136 ] with direction [-0.92979963 -0.01378652 0.36780781], radius
    7954 0.597156, and length 47.7725 
    7955 
    7956 > rename #2 Vb_rotation_axis id #103.3.1.2
    7957 
    7958 > rename #3 Vb_rotation_slabs id #103.3.2.2
    7959 
    7960 > matchmaker #1006/L to #1005/H
    7961 
    7962 Parameters 
    7963 --- 
    7964 Chain pairing | bb 
    7965 Alignment algorithm | Needleman-Wunsch 
    7966 Similarity matrix | BLOSUM-62 
    7967 SS fraction | 0.3 
    7968 Gap open (HH/SS/other) | 18/18/6 
    7969 Gap extend | 1 
    7970 SS matrix |  |  | H | S | O 
    7971 ---|---|---|--- 
    7972 H | 6 | -9 | -6 
    7973 S |  | 6 | -6 
    7974 O |  |  | 4 
    7975 Iteration cutoff | 2 
    7976  
    7977 Matchmaker 2H7_v166_D56A_Ca, chain H (#1005) with 2H7_v166_D56A_Ca_copy, chain
    7978 L (#1006), sequence alignment score = 554.5 
    7979 RMSD between 57 pruned atom pairs is 0.959 angstroms; (across all 98 pairs:
    7980 3.119) 
    7981  
    7982 
    7983 > wait 1
    7984 
    7985 > measure rotation #1006 toModel #1005 showSlabs true
    7986 
    7987 Position of 2H7_v166_D56A_Ca_copy #1006 relative to 2H7_v166_D56A_Ca #1005
    7988 coordinates: 
    7989 Matrix rotation and translation 
    7990 -0.33391401 0.38072466 0.86229355 -12.40856576 
    7991 0.05205532 -0.90595556 0.42016042 245.78035810 
    7992 0.94116506 0.18518442 0.28269251 -52.33839393 
    7993 Axis -0.57081123 -0.19159720 -0.79841408 
    7994 Axis point 28.53870248 129.91224226 0.00000000 
    7995 Rotation angle (degrees) 168.12212217 
    7996 Shift along axis 1.77983022 
    7997  
    7998 
    7999 > close #1006 #1005
    8000 
    8001 > define axis #2 name axis_Ca
    8002 
    8003 Axis 'rotation axis #2/axis_Ca' centered at [104.79817162 155.50932275
    8004 106.6668468 ] with direction [-0.57081123 -0.1915972 -0.79841408], radius
    8005 0.56909, and length 45.5272 
    8006 
    8007 > rename #2 Ca_rotation_axis id #103.3.1.3
    8008 
    8009 > rename #3 Ca_rotation_slabs id #103.3.2.3
    8010 
    8011 > matchmaker #1008/M to #1007/I
    8012 
    8013 Parameters 
    8014 --- 
    8015 Chain pairing | bb 
    8016 Alignment algorithm | Needleman-Wunsch 
    8017 Similarity matrix | BLOSUM-62 
    8018 SS fraction | 0.3 
    8019 Gap open (HH/SS/other) | 18/18/6 
    8020 Gap extend | 1 
    8021 SS matrix |  |  | H | S | O 
    8022 ---|---|---|--- 
    8023 H | 6 | -9 | -6 
    8024 S |  | 6 | -6 
    8025 O |  |  | 4 
    8026 Iteration cutoff | 2 
    8027  
    8028 Matchmaker 2H7_v166_D56A_Cb, chain I (#1007) with 2H7_v166_D56A_Ca_copy, chain
    8029 M (#1008), sequence alignment score = 416.6 
    8030 RMSD between 55 pruned atom pairs is 0.882 angstroms; (across all 98 pairs:
    8031 3.361) 
    8032  
    8033 
    8034 > wait 1
    8035 
    8036 > measure rotation #1008 toModel #1007 showSlabs true
    8037 
    8038 Position of 2H7_v166_D56A_Ca_copy #1008 relative to 2H7_v166_D56A_Cb #1007
    8039 coordinates: 
    8040 Matrix rotation and translation 
    8041 -0.50667380 0.40781938 -0.75958213 323.22163731 
    8042 0.08178140 -0.85433688 -0.51324487 330.95129120 
    8043 -0.85825023 -0.32216741 0.39951808 287.19953324 
    8044 Axis 0.48922423 0.25262440 -0.83476977 
    8045 Axis point 265.28291179 189.90297685 0.00000000 
    8046 Rotation angle (degrees) 168.73855860 
    8047 Shift along axis 1.98873850 
    8048  
    8049 
    8050 > close #1008 #1007
    8051 
    8052 > define axis #2 name axis_Cb
    8053 
    8054 Axis 'rotation axis #2/axis_Cb' centered at [203.75015551 158.12884417
    8055 104.99415577] with direction [ 0.48922423 0.2526244 -0.83476977], radius
    8056 0.553583, and length 44.2867 
    8057 
    8058 > rename #2 Cb_rotation_axis id #103.3.1.4
    8059 
    8060 > rename #3 Cb_rotation_slabs id #103.3.2.4
    8061 
    8062 > rename #103.3 geometry
    8063 
    8064 > rename #103.3.1 rotation_axes
    8065 
    8066 > rename #103.3.2 rotation_slabs
    8067 
    8068 executed CD20_2H7v166_D56A_define_pseudo_symmetries.cxc 
    8069 
    8070 > open
    8071 > CD20_2H7v166_S92A_D56A/CD20_2H7v166_S92A_D56A_define_pseudo_symmetries.cxc
    8072 
    8073 > combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Va modelId 1001
    8074 
    8075 > select zone (H7v166_S92A_D56A_V & /H,L) 0.1 #1001
    8076 
    8077 Selected 1653 atoms 
    8078 
    8079 > delete #1001 & ~sel
    8080 
    8081 > combine #1001 name 2H7_v166_S92A_D56A_Va_copy modelId 1002
    8082 
    8083 > combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Vb modelId 1003
    8084 
    8085 > select zone (H7v166_S92A_D56A_V & /I,M) 0.1 #1003
    8086 
    8087 Selected 1678 atoms 
    8088 
    8089 > delete #1003 & ~sel
    8090 
    8091 > combine #1003 name 2H7_v166_S92A_D56A_Vb_copy modelId 1004
    8092 
    8093 > combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Ca modelId 1005
    8094 
    8095 > select zone (H7v166_S92A_D56A_C & /H,L) 0.1 #1005
    8096 
    8097 Selected 1461 atoms 
    8098 
    8099 > delete #1005 & ~sel
    8100 
    8101 > combine #1005 name 2H7_v166_S92A_D56A_Ca_copy modelId 1006
    8102 
    8103 > combine CD20_2H7v166_S92A_D56A name 2H7_v166_S92A_D56A_Cb modelId 1007
    8104 
    8105 > select zone (H7v166_S92A_D56A_C & /I,M) 0.1 #1007
    8106 
    8107 Selected 1550 atoms 
    8108 
    8109 > delete #1007 & ~sel
    8110 
    8111 > combine #1007 name 2H7_v166_S92A_D56A_Ca_copy modelId 1008
    8112 
    8113 > matchmaker #1002/L to #1001/H
    8114 
    8115 Parameters 
    8116 --- 
    8117 Chain pairing | bb 
    8118 Alignment algorithm | Needleman-Wunsch 
    8119 Similarity matrix | BLOSUM-62 
    8120 SS fraction | 0.3 
    8121 Gap open (HH/SS/other) | 18/18/6 
    8122 Gap extend | 1 
    8123 SS matrix |  |  | H | S | O 
    8124 ---|---|---|--- 
    8125 H | 6 | -9 | -6 
    8126 S |  | 6 | -6 
    8127 O |  |  | 4 
    8128 Iteration cutoff | 2 
    8129  
    8130 Matchmaker 2H7_v166_S92A_D56A_Va, chain H (#1001) with
    8131 2H7_v166_S92A_D56A_Va_copy, chain L (#1002), sequence alignment score = 221.1 
    8132 RMSD between 66 pruned atom pairs is 1.048 angstroms; (across all 87 pairs:
    8133 3.054) 
    8134  
    8135 
    8136 > wait 1
    8137 
    8138 > measure rotation #1002 toModel #1001 showSlabs true
    8139 
    8140 Position of 2H7_v166_S92A_D56A_Va_copy #1002 relative to 2H7_v166_S92A_D56A_Va
    8141 #1001 coordinates: 
    8142 Matrix rotation and translation 
    8143 0.71841270 -0.03882790 0.69453263 -43.77242719 
    8144 0.04474713 -0.99379351 -0.10184377 314.28607160 
    8145 0.69417640 0.10424420 -0.71221645 107.06747282 
    8146 Axis 0.92669760 0.00160183 0.37580447 
    8147 Axis point 0.00000000 153.96110044 71.86641580 
    8148 Rotation angle (degrees) 173.61580296 
    8149 Shift along axis 0.17606353 
    8150  
    8151 
    8152 > close #1001 #1002
    8153 
    8154 > define axis #2 name axis_Va
    8155 
    8156 Axis 'rotation axis #2/axis_Va' centered at [136.49236761 154.19703207
    8157 127.21828189] with direction [0.9266976 0.00160183 0.37580447], radius
    8158 0.603625, and length 48.29 
    8159 
    8160 > rename #2 Va_rotation_axis id #104.3.1.1
    8161 
    8162 > rename #3 Va_rotation_slabs id #104.3.2.1
    8163 
    8164 > matchmaker #1004/M to #1003/I
    8165 
    8166 Parameters 
    8167 --- 
    8168 Chain pairing | bb 
    8169 Alignment algorithm | Needleman-Wunsch 
    8170 Similarity matrix | BLOSUM-62 
    8171 SS fraction | 0.3 
    8172 Gap open (HH/SS/other) | 18/18/6 
    8173 Gap extend | 1 
    8174 SS matrix |  |  | H | S | O 
    8175 ---|---|---|--- 
    8176 H | 6 | -9 | -6 
    8177 S |  | 6 | -6 
    8178 O |  |  | 4 
    8179 Iteration cutoff | 2 
    8180  
    8181 Matchmaker 2H7_v166_S92A_D56A_Vb, chain I (#1003) with
    8182 2H7_v166_S92A_D56A_Vb_copy, chain M (#1004), sequence alignment score = 228.5 
    8183 RMSD between 66 pruned atom pairs is 1.088 angstroms; (across all 92 pairs:
    8184 3.936) 
    8185  
    8186 
    8187 > wait 1
    8188 
    8189 > measure rotation #1004 toModel #1003 showSlabs true
    8190 
    8191 Position of 2H7_v166_S92A_D56A_Vb_copy #1004 relative to 2H7_v166_S92A_D56A_Vb
    8192 #1003 coordinates: 
    8193 Matrix rotation and translation 
    8194 0.73661563 -0.07135580 -0.67253682 142.18618798 
    8195 0.02298296 -0.99120309 0.13033888 288.51761976 
    8196 -0.67592100 -0.11146654 -0.72849572 353.55093768 
    8197 Axis -0.93153019 0.01303723 0.36343024 
    8198 Axis point 0.00000000 157.62360929 194.41945478 
    8199 Rotation angle (degrees) 172.54257925 
    8200 Shift along axis -0.19815617 
    8201  
    8202 
    8203 > close #1004 #1003
    8204 
    8205 > define axis #2 name axis_Vb
    8206 
    8207 Axis 'rotation axis #2/axis_Vb' centered at [172.8655548 155.20426996
    8208 126.97712173] with direction [-0.93153019 0.01303723 0.36343024], radius
    8209 0.60681, and length 48.5448 
    8210 
    8211 > rename #2 Vb_rotation_axis id #104.3.1.2
    8212 
    8213 > rename #3 Vb_rotation_slabs id #104.3.2.2
    8214 
    8215 > matchmaker #1006/L to #1005/H
    8216 
    8217 Parameters 
    8218 --- 
    8219 Chain pairing | bb 
    8220 Alignment algorithm | Needleman-Wunsch 
    8221 Similarity matrix | BLOSUM-62 
    8222 SS fraction | 0.3 
    8223 Gap open (HH/SS/other) | 18/18/6 
    8224 Gap extend | 1 
    8225 SS matrix |  |  | H | S | O 
    8226 ---|---|---|--- 
    8227 H | 6 | -9 | -6 
    8228 S |  | 6 | -6 
    8229 O |  |  | 4 
    8230 Iteration cutoff | 2 
    8231  
    8232 Matchmaker 2H7_v166_S92A_D56A_Ca, chain H (#1005) with
    8233 2H7_v166_S92A_D56A_Ca_copy, chain L (#1006), sequence alignment score = 229.8 
    8234 RMSD between 50 pruned atom pairs is 0.885 angstroms; (across all 82 pairs:
    8235 3.058) 
    8236  
    8237 
    8238 > wait 1
    8239 
    8240 > measure rotation #1006 toModel #1005 showSlabs true
    8241 
    8242 Position of 2H7_v166_S92A_D56A_Ca_copy #1006 relative to 2H7_v166_S92A_D56A_Ca
    8243 #1005 coordinates: 
    8244 Matrix rotation and translation 
    8245 -0.43223566 0.39105435 0.81255697 5.34243089 
    8246 0.04124481 -0.89156204 0.45101662 236.01875124 
    8247 0.90081696 0.22845922 0.36923594 -64.79879197 
    8248 Axis -0.52502754 -0.20821113 -0.82522373 
    8249 Axis point 38.63388899 125.78498588 0.00000000 
    8250 Rotation angle (degrees) 167.76344751 
    8251 Shift along axis 1.52684600 
    8252  
    8253 
    8254 > close #1006 #1005
    8255 
    8256 > define axis #2 name axis_Ca
    8257 
    8258 Axis 'rotation axis #2/axis_Ca' centered at [105.63109625 152.35419104
    8259 105.30435297] with direction [-0.52502754 -0.20821113 -0.82522373], radius
    8260 0.532467, and length 42.5974 
    8261 
    8262 > rename #2 Ca_rotation_axis id #104.3.1.3
    8263 
    8264 > rename #3 Ca_rotation_slabs id #104.3.2.3
    8265 
    8266 > matchmaker #1008/M to #1007/I
    8267 
    8268 Parameters 
    8269 --- 
    8270 Chain pairing | bb 
    8271 Alignment algorithm | Needleman-Wunsch 
    8272 Similarity matrix | BLOSUM-62 
    8273 SS fraction | 0.3 
    8274 Gap open (HH/SS/other) | 18/18/6 
    8275 Gap extend | 1 
    8276 SS matrix |  |  | H | S | O 
    8277 ---|---|---|--- 
    8278 H | 6 | -9 | -6 
    8279 S |  | 6 | -6 
    8280 O |  |  | 4 
    8281 Iteration cutoff | 2 
    8282  
    8283 Matchmaker 2H7_v166_S92A_D56A_Cb, chain I (#1007) with
    8284 2H7_v166_S92A_D56A_Ca_copy, chain M (#1008), sequence alignment score = 226.4 
    8285 RMSD between 57 pruned atom pairs is 0.983 angstroms; (across all 98 pairs:
    8286 3.247) 
    8287  
    8288 
    8289 > wait 1
    8290 
    8291 > measure rotation #1008 toModel #1007 showSlabs true
    8292 
    8293 Position of 2H7_v166_S92A_D56A_Ca_copy #1008 relative to 2H7_v166_S92A_D56A_Cb
    8294 #1007 coordinates: 
    8295 Matrix rotation and translation 
    8296 -0.44691350 0.37987962 -0.80991345 321.97311814 
    8297 0.04334425 -0.89510032 -0.44375297 334.72634524 
    8298 -0.89352650 -0.23342428 0.38356682 282.18198422 
    8299 Axis 0.51860284 0.20616286 -0.82978790 
    8300 Axis point 269.80743377 182.59879005 0.00000000 
    8301 Rotation angle (degrees) 168.30019456 
    8302 Shift along axis 1.83311720 
    8303  
    8304 
    8305 > close #1008 #1007
    8306 
    8307 > define axis #2 name axis_Cb
    8308 
    8309 Axis 'rotation axis #2/axis_Cb' centered at [203.87433587 156.38806637
    8310 105.49592574] with direction [ 0.51860284 0.20616286 -0.8297879 ], radius
    8311 0.566216, and length 45.2973 
    8312 
    8313 > rename #2 Cb_rotation_axis id #104.3.1.4
    8314 
    8315 > rename #3 Cb_rotation_slabs id #104.3.2.4
    8316 
    8317 > rename #104.3 geometry
    8318 
    8319 > rename #104.3.1 rotation_axes
    8320 
    8321 > rename #104.3.2 rotation_slabs
    8322 
    8323 executed CD20_2H7v166_S92A_D56A_define_pseudo_symmetries.cxc 
    8324 
    8325 > open CD20_2H7_mutants_define_domain_centroids.cxc
    8326 
    8327 > define centroid RTX_C & /L name centroid_RTX_C_L
    8328 
    8329 Centroid 'centroid_RTX_C_L' placed at [ 99.24795328 158.51064899 116.56555556] 
    8330 
    8331 > rename ##name=centroid_RTX_C_L id 101.3.3.1
    8332 
    8333 > define centroid RTX_C & /M name centroid_RTX_C_M
    8334 
    8335 Centroid 'centroid_RTX_C_M' placed at [210.77360859 151.52862247 116.58115025] 
    8336 
    8337 > rename ##name=centroid_RTX_C_M id 101.3.3.2
    8338 
    8339 > define centroid RTX_C & /H name centroid_RTX_C_H
    8340 
    8341 Centroid 'centroid_RTX_C_H' placed at [106.64933474 150.8311308 104.33269761] 
    8342 
    8343 > rename ##name=centroid_RTX_C_H id 101.3.3.3
    8344 
    8345 > define centroid RTX_C & /I name centroid_RTX_C_I
    8346 
    8347 Centroid 'centroid_RTX_C_I' placed at [203.36467932 159.20700844 104.37016456] 
    8348 
    8349 > rename ##name=centroid_RTX_C_I id 101.3.3.4
    8350 
    8351 > define centroid RTX_V & /L name centroid_RTX_V_L
    8352 
    8353 Centroid 'centroid_RTX_V_L' placed at [134.90703015 166.45776759 126.23118216] 
    8354 
    8355 > rename ##name=centroid_RTX_V_L id 101.3.3.5
    8356 
    8357 > define centroid RTX_V & /M name centroid_RTX_V_M
    8358 
    8359 Centroid 'centroid_RTX_V_M' placed at [175.12986935 143.57538693 126.24564698] 
    8360 
    8361 > rename ##name=centroid_RTX_V_M id 101.3.3.6
    8362 
    8363 > define centroid RTX_V & /H name centroid_RTX_V_H
    8364 
    8365 Centroid 'centroid_RTX_V_H' placed at [138.39382732 143.61326339 125.48950601] 
    8366 
    8367 > rename ##name=centroid_RTX_V_H id 101.3.3.7
    8368 
    8369 > define centroid RTX_V & /I name centroid_RTX_V_I
    8370 
    8371 Centroid 'centroid_RTX_V_I' placed at [171.6143541 166.39779016 125.48935082] 
    8372 
    8373 > rename ##name=centroid_RTX_V_I id 101.3.3.8
    8374 
    8375 > rename #101.3.3 centroids
    8376 
    8377 > define centroid H7v16_C & /L name centroid_2H7v16_C_L
    8378 
    8379 Centroid 'centroid_2H7v16_C_L' placed at [105.06462233 154.79494479
    8380 104.71732873] 
    8381 
    8382 > rename ##name=centroid_2H7v16_C_L id 102.3.3.1
    8383 
    8384 > define centroid H7v16_C & /M name centroid_2H7v16_C_M
    8385 
    8386 Centroid 'centroid_2H7v16_C_M' placed at [208.42672522 167.55451192
    8387 109.46892346] 
    8388 
    8389 > rename ##name=centroid_2H7v16_C_M id 102.3.3.2
    8390 
    8391 > define centroid H7v16_C & /H name centroid_2H7v16_C_H
    8392 
    8393 Centroid 'centroid_2H7v16_C_H' placed at [115.17526428 144.82097344
    8394 100.10963479] 
    8395 
    8396 > rename ##name=centroid_2H7v16_C_H id 102.3.3.3
    8397 
    8398 > define centroid H7v16_C & /I name centroid_2H7v16_C_I
    8399 
    8400 Centroid 'centroid_2H7v16_C_I' placed at [196.31280478 174.43741833
    8401 103.22787118] 
    8402 
    8403 > rename ##name=centroid_2H7v16_C_I id 102.3.3.4
    8404 
    8405 > define centroid H7v16_V & /L name centroid_2H7v16_V_L
    8406 
    8407 Centroid 'centroid_2H7v16_V_L' placed at [136.25738614 163.8169901
    8408 124.64938243] 
    8409 
    8410 > rename ##name=centroid_2H7v16_V_L id 102.3.3.5
    8411 
    8412 > define centroid H7v16_V & /M name centroid_2H7v16_V_M
    8413 
    8414 Centroid 'centroid_2H7v16_V_M' placed at [179.26451702 150.74154843
    8415 126.48898691] 
    8416 
    8417 > rename ##name=centroid_2H7v16_V_M id 102.3.3.6
    8418 
    8419 > define centroid H7v16_V & /H name centroid_2H7v16_V_H
    8420 
    8421 Centroid 'centroid_2H7v16_V_H' placed at [139.25597569 141.97514482
    8422 126.96669027] 
    8423 
    8424 > rename ##name=centroid_2H7v16_V_H id 102.3.3.7
    8425 
    8426 > define centroid H7v16_V & /I name centroid_2H7v16_V_I
    8427 
    8428 Centroid 'centroid_2H7v16_V_I' placed at [169.61364905 170.56588689
    8429 126.76187738] 
    8430 
    8431 > rename ##name=centroid_2H7v16_V_I id 102.3.3.8
    8432 
    8433 > rename #102.3.3 centroids
    8434 
    8435 > define centroid H7v166_D56A_C & /L name centroid_2H7v166_D56A_C_L
    8436 
    8437 Centroid 'centroid_2H7v166_D56A_C_L' placed at [101.80191468 161.59134128
    8438 111.74271267] 
    8439 
    8440 > rename ##name=centroid_2H7v166_D56A_C_L id 103.3.3.1
    8441 
    8442 > define centroid H7v166_D56A_C & /M name centroid_2H7v166_D56A_C_M
    8443 
    8444 Centroid 'centroid_2H7v166_D56A_C_M' placed at [208.08802258 152.28425847
    8445 109.3226675 ] 
    8446 
    8447 > rename ##name=centroid_2H7v166_D56A_C_M id 103.3.3.2
    8448 
    8449 > define centroid H7v166_D56A_C & /H name centroid_2H7v166_D56A_C_H
    8450 
    8451 Centroid 'centroid_2H7v166_D56A_C_H' placed at [110.13903054 151.41048738
    8452 105.03944622] 
    8453 
    8454 > rename ##name=centroid_2H7v166_D56A_C_H id 103.3.3.3
    8455 
    8456 > define centroid H7v166_D56A_C & /I name centroid_2H7v166_D56A_C_I
    8457 
    8458 Centroid 'centroid_2H7v166_D56A_C_I' placed at [198.26240903 162.26559628
    8459 103.22947676] 
    8460 
    8461 > rename ##name=centroid_2H7v166_D56A_C_I id 103.3.3.4
    8462 
    8463 > define centroid H7v166_D56A_V & /L name centroid_2H7v166_D56A_V_L
    8464 
    8465 Centroid 'centroid_2H7v166_D56A_V_L' placed at [134.697663 166.81530949
    8466 127.91858459] 
    8467 
    8468 > rename ##name=centroid_2H7v166_D56A_V_L id 103.3.3.5
    8469 
    8470 > define centroid H7v166_D56A_V & /M name centroid_2H7v166_D56A_V_M
    8471 
    8472 Centroid 'centroid_2H7v166_D56A_V_M' placed at [176.0024767 144.42140479
    8473 127.2169787 ] 
    8474 
    8475 > rename ##name=centroid_2H7v166_D56A_V_M id 103.3.3.6
    8476 
    8477 > define centroid H7v166_D56A_V & /H name centroid_2H7v166_D56A_V_H
    8478 
    8479 Centroid 'centroid_2H7v166_D56A_V_H' placed at [137.53539482 144.47796656
    8480 127.54490507] 
    8481 
    8482 > rename ##name=centroid_2H7v166_D56A_V_H id 103.3.3.7
    8483 
    8484 > define centroid H7v166_D56A_V & /I name centroid_2H7v166_D56A_V_I
    8485 
    8486 Centroid 'centroid_2H7v166_D56A_V_I' placed at [172.57552427 166.28897087
    8487 127.29650809] 
    8488 
    8489 > rename ##name=centroid_2H7v166_D56A_V_I id 103.3.3.8
    8490 
    8491 > rename #103.3.3 centroids
    8492 
    8493 > define centroid CD20 & /C name centroid_CD20_C
    8494 
    8495 Centroid 'centroid_CD20_C' placed at [144.71880576 155.32713058 168.44437979] 
    8496 
    8497 > rename ##name=centroid_CD20_C id 101.3.3.9
    8498 
    8499 > define centroid CD20 & /D name centroid_CD20_D
    8500 
    8501 Centroid 'centroid_CD20_D' placed at [165.28259991 155.13681165 168.62706115] 
    8502 
    8503 > rename ##name=centroid_CD20_D id 101.3.3.10
    8504 
    8505 executed CD20_2H7_mutants_define_domain_centroids.cxc 
    8506 
    8507 > turn x 90
    8508 
    8509 > view
    8510 
    8511 > hide #101 models
    8512 
    8513 > hide #!102.2 models
    8514 
    8515 > ~ribbon #102.10/X,Y
    8516 
    8517 executed CD20_2H7_mutants_setup.cxc 
    8518 
    8519 > hide #!105 models
    8520 
    8521 > show #!105 models
    8522 
    8523 > hide #!104 models
    8524 
    8525 > hide #!103 models
    8526 
    8527 > hide #!102 models
    8528 
    8529 > hide #!105.2 models
    8530 
    8531 > show #!101 models
    8532 
    8533 > show #101.1 models
    8534 
    8535 > hide #!101 models
    8536 
    8537 > show #!101 models
    8538 
    8539 > hide #!101 models
    8540 
    8541 > show #!101 models
    8542 
    8543 > hide #!101 models
    8544 
    8545 > show #!101 models
    8546 
    8547 > hide #!101 models
    8548 
    8549 > show #!101 models
    8550 
    8551 > hide #!101 models
    8552 
    8553 > show #!101 models
    8554 
    8555 > hide #!105 models
    8556 
    8557 > show #!104 models
    8558 
    8559 > hide #!104 models
    8560 
    8561 > show #!104 models
    8562 
    8563 > hide #!104.2 models
    8564 
    8565 > hide #!104.3 models
    8566 
    8567 > hide #!104 models
    8568 
    8569 > show #!104 models
    8570 
    8571 > hide #!104 models
    8572 
    8573 > show #!104 models
    8574 
    8575 > hide #!104 models
    8576 
    8577 > show #!104 models
    8578 
    8579 > hide #!104 models
    8580 
    8581 > show #!104 models
    8582 
    8583 > hide #!104 models
    8584 
    8585 > show #!104 models
    8586 
    8587 > hide #!104 models
    8588 
    8589 > show #!104 models
    8590 
    8591 > hide #!104 models
    8592 
    8593 > show #!104 models
    8594 
    8595 > hide #!104 models
    8596 
    8597 > show #!104 models
    8598 
    8599 > hide #!104 models
    8600 
    8601 > show #!104 models
    8602 
    8603 > hide #!104 models
    8604 
    8605 > show #!104 models
    8606 
    8607 > hide #!104 models
    8608 
    8609 > show #!105 models
    8610 
    8611 > hide #!105 models
    8612 
    8613 > show #!103 models
    8614 
    8615 > hide #!103.3 models
    8616 
    8617 > hide #!103.2 models
    8618 
    8619 > hide #!103.1 models
    8620 
    8621 > show #!103.1 models
    8622 
    8623 > show #!104 models
    8624 
    8625 > hide #!104 models
    8626 
    8627 > show #!104 models
    8628 
    8629 > hide #!104 models
    8630 
    8631 > hide #!103 models
    8632 
    8633 > show #!103 models
    8634 
    8635 > hide #!103 models
    8636 
    8637 > show #!103 models
    8638 
    8639 > hide #!103 models
    8640 
    8641 > show #!102 models
    8642 
    8643 > hide #!102 models
    8644 
    8645 > show #!102 models
    8646 
    8647 > hide #!102 models
    8648 
    8649 > show #!102 models
    8650 
    8651 > hide #!102 models
    8652 
    8653 > show #!102 models
    8654 
    8655 > hide #!102 models
    8656 
    8657 > show #!102 models
    8658 
    8659 > hide #!102 models
    8660 
    8661 > show #!102 models
    8662 
    8663 > hide #!102 models
    8664 
    8665 > show #!102 models
    8666 
    8667 > show #!104 models
    8668 
    8669 > hide #!104 models
    8670 
    8671 > show #!104 models
    8672 
    8673 > hide #!104 models
    8674 
    8675 > show #!104 models
    8676 
    8677 > hide #!104 models
    8678 
    8679 > show #!103 models
    8680 
    8681 > hide #!103 models
    8682 
    8683 > show #!103 models
    8684 
    8685 > hide #!103 models
    8686 
    8687 > hide #!102 models
    8688 
    8689 > show #!102 models
    8690 
    8691 > hide #!102 models
    8692 
    8693 > show #!102 models
    8694 
    8695 > hide #!102 models
    8696 
    8697 > show #!102 models
    8698 
    8699 > hide #!102 models
    8700 
    8701 > show #!102 models
    8702 
    8703 > hide #!102 models
    8704 
    8705 > show #!105 models
    8706 
    8707 > show #!105.2 models
    8708 
    8709 > hide #!101 models
    8710 
    8711 > select #105.1/L:48
    8712 
    8713 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8714 
    8715 > select #105.1/L:49
    8716 
    8717 12 atoms, 12 bonds, 1 residue, 1 model selected 
    8718 
    8719 > select #105.1/L:60
    8720 
    8721 6 atoms, 5 bonds, 1 residue, 1 model selected 
    8722 
    8723 > select add #105.1/L:48
    8724 
    8725 14 atoms, 12 bonds, 2 residues, 1 model selected 
    8726 
    8727 > select subtract #105.1/L:48
    8728 
    8729 6 atoms, 5 bonds, 1 residue, 1 model selected 
    8730 
    8731 > select #105.1/L:49
    8732 
    8733 12 atoms, 12 bonds, 1 residue, 1 model selected 
    8734 
    8735 > select #105.1/L:49-60
    8736 
    8737 81 atoms, 83 bonds, 12 residues, 1 model selected 
    8738 
    8739 > delete sel
    8740 
    8741 > save /Users/rohoua/work/Genentech/CD20/CD20_2H7v166/STR7730_alito6vja_v2.pdb
    8742 > models #105.1
    8743 
    8744 > close
    8745 
    8746 > open /Users/rohoua/work/Genentech/CD20/CD20_2H7_mutants_setup.cxc format cmd
    8747 
    8748 > close
    8749 
    8750 > cd /Users/rohoua/work/Genentech/CD20
    8751 
    8752 Current working directory is: /Users/rohoua/work/Genentech/CD20 
    8753 
    8754 > open pdb:6vja name CD20_RTX id 101.1
    8755 
    8756 CD20_RTX title: 
    8757 Structure of CD20 in complex with rituximab Fab [more info...] 
    8758  
    8759 Chain information for CD20_RTX #1 
    8760 --- 
    8761 Chain | Description | UniProt 
    8762 C D | B-lymphocyte antigen CD20 | CD20_HUMAN 41-297 
    8763 H I | Rituximab Fab heavy chain | 
    8764 L M | Rituximab Fab light chain | 
    8765  
    8766 Non-standard residues in CD20_RTX #1 
    8767 --- 
    8768 Y01 — cholesterol hemisuccinate 
    8769  
    8770 
    8771 > open CD20_2H7v16/STR7668v2_alito6vja_C178to187.pdb name CD20_2H7v16 id 102.1
    8772 
    8773 Summary of feedback from opening CD20_2H7v16/STR7668v2_alito6vja_C178to187.pdb 
    8774 --- 
    8775 warning | Ignored bad PDB record found on line 1 
    8776 HEADER STR7668 version_2 2023.12.13 
    8777  
    8778 CD20_2H7v16 title: 
    8779 Structure of 2H7.v16 Fab and 2103.826032.Hs_MS4A1.M1-P297.BiNTF-NAvi at 3.3 A
    8780 resolution. [more info...] 
    8781  
    8782 Chain information for CD20_2H7v16 #1 
    8783 --- 
    8784 Chain | Description 
    8785 C D | No description available 
    8786 H I | No description available 
    8787 L M | No description available 
    8788  
    8789 Non-standard residues in CD20_2H7v16 #1 
    8790 --- 
    8791 Y01 — (Y01) 
    8792  
    8793 
    8794 > open CD20_2H7v16/P69_W9_J181/J181_004_volume_denoised.mrc id 102.2
    8795 
    8796 Opened J181_004_volume_denoised.mrc as #1, grid size 480,480,480, pixel 0.838,
    8797 shown at level 0.0054, step 2, values float32 
    8798 
    8799 > volume #102.2 step 1 level 0.08 color #9999CC transparency 0.5
    8800 
    8801 > view matrix models
    8802 > #102.2,-0.2379,0.93572,0.26045,-39.485,0.96898,0.21017,0.12999,-107.2,0.066893,0.2833,-0.9567,274.92
    8803 
    8804 > open "CD20_2H7v16/crystal_structure/STR7487.2H7 Fab.pdb" name 2H7v16_XRay id
    8805 > 102.10
    8806 
    8807 Summary of feedback from opening CD20_2H7v16/crystal_structure/STR7487.2H7
    8808 Fab.pdb 
    8809 --- 
    8810 warning | Ignored bad PDB record found on line 1 
    8811 HEADER STR7487 version_1 2023.05.24 
    8812  
    8813 2H7v16_XRay title: 
    8814 Structure of 2H7 Fab at 2.45 A resolution. [more info...] 
    8815  
    8816 Chain information for 2H7v16_XRay #1 
    8817 --- 
    8818 Chain | Description 
    8819 A B X Y | No description available 
    8820  
    8821 Non-standard residues in 2H7v16_XRay #1 
    8822 --- 
    8823 CL — (CL) 
    8824  
    8825 
    8826 > matchmaker #102.10/A,B to #102.1/H,L
    8827 
    8828 Parameters 
    8829 --- 
    8830 Chain pairing | bb 
    8831 Alignment algorithm | Needleman-Wunsch 
    8832 Similarity matrix | BLOSUM-62 
    8833 SS fraction | 0.3 
    8834 Gap open (HH/SS/other) | 18/18/6 
    8835 Gap extend | 1 
    8836 SS matrix |  |  | H | S | O 
    8837 ---|---|---|--- 
    8838 H | 6 | -9 | -6 
    8839 S |  | 6 | -6 
    8840 O |  |  | 4 
    8841 Iteration cutoff | 2 
    8842  
    8843 Matchmaker CD20_2H7v16, chain L (#102.1) with 2H7v16_XRay, chain A (#102.10),
    8844 sequence alignment score = 1228.2 
    8845 RMSD between 208 pruned atom pairs is 0.731 angstroms; (across all 213 pairs:
    8846 0.804) 
    8847  
    8848 
    8849 > open CD20_2H7v166_D56A/STR7717v2_alito6vja.pdb name CD20_2H7v166_D56A id
    8850 > 103.1
    8851 
    8852 Summary of feedback from opening CD20_2H7v166_D56A/STR7717v2_alito6vja.pdb 
    8853 --- 
    8854 warning | Ignored bad PDB record found on line 1 
    8855 HEADER STR7717 version_2 2023.12.15 
    8856  
    8857 CD20_2H7v166_D56A title: 
    8858 Structure of 2H7v166_D56A Fab and Hs_CD20.M1-P297 at 3.7 A resolution . [more
    8859 info...] 
    8860  
    8861 Chain information for CD20_2H7v166_D56A #1 
    8862 --- 
    8863 Chain | Description 
    8864 C D | No description available 
    8865 H I | No description available 
    8866 L | No description available 
    8867 M | No description available 
    8868  
    8869 Non-standard residues in CD20_2H7v166_D56A #1 
    8870 --- 
    8871 Y01 — (Y01) 
    8872  
    8873 
    8874 > open CD20_2H7v166_D56A/cryosparc_P69_J433_007_volume_map_sharp.mrc id 103.2
    8875 
    8876 Opened cryosparc_P69_J433_007_volume_map_sharp.mrc as #1, grid size
    8877 300,300,300, pixel 1.28, shown at level 0.0592, step 2, values float32 
    8878 
    8879 > volume #103.2 step 1 level 0.355 color #9999CC transparency 0.5
    8880 
    8881 > view matrix models
    8882 > #103.2,0.00937853,0.99467855,-0.10259937,-18.50914227,-0.99948588,0.00617870,-0.03146112,352.75851684,-0.03065977,0.10284168,0.99422511,-49.28949280
    8883 
    8884 > open CD20_2H7v166_S92A_D56A/STR7729v2_alito6vja.pdb name
    8885 > CD20_2H7v166_S92A_D56A id 104.1
    8886 
    8887 Summary of feedback from opening
    8888 CD20_2H7v166_S92A_D56A/STR7729v2_alito6vja.pdb 
    8889 --- 
    8890 warning | Ignored bad PDB record found on line 1 
    8891 HEADER STR7729 version_2 2024.01.29 
    8892  
    8893 CD20_2H7v166_S92A_D56A title: 
    8894 Structure of 2H7v166 LC.S92A HC.D56A Fab and Hs_CD20.M1-P297 at 4.5 A
    8895 resolution. [more info...] 
    8896  
    8897 Chain information for CD20_2H7v166_S92A_D56A #1 
    8898 --- 
    8899 Chain | Description 
    8900 C D | No description available 
    8901 H | No description available 
    8902 I | No description available 
    8903 L M | No description available 
    8904  
    8905 
    8906 > open CD20_2H7v166_S92A_D56A/cryosparc_P69_J242_005_volume_map_sharp_flip.mrc
    8907 > id 104.2
    8908 
    8909 Opened cryosparc_P69_J242_005_volume_map_sharp_flip.mrc as #1, grid size
    8910 300,300,300, pixel 1.43, shown at level 0.0447, step 2, values float32 
    8911 
    8912 > volume #104.2 step 1 level 0.355 color #9999CC transparency 0.5
    8913 
    8914 > view matrix models
    8915 > #104.2,-0.00249470,0.97079708,0.23988915,-104.32503408,0.99657176,0.02225139,-0.07968446,-45.21631074,-0.08269530,0.23886796,-0.96752446,330.43463437
    8916 
    8917 > open CD20_2H7v166/STR7730_alito6vja_v2.pdb name CD20_2H7v166 id 105.1
    8918 
    8919 Summary of feedback from opening CD20_2H7v166/STR7730_alito6vja_v2.pdb 
    8920 --- 
    8921 warning | Ignored bad PDB record found on line 1 
    8922 HEADER STR7730 version_1 2024.01.12 
    8923  
    8924 CD20_2H7v166 title: 
    8925 Structure of 2H7v166 Fab and Hs_CD20.M1-P297 at 5.2 A resolution. [more
    8926 info...] 
    8927  
    8928 Chain information for CD20_2H7v166 #1 
    8929 --- 
    8930 Chain | Description 
    8931 C | No description available 
    8932 D | No description available 
    8933 H I | No description available 
    8934 L | No description available 
    8935 M | No description available 
    8936  
    8937 
    8938 > open CD20_2H7v166/cryosparc_P71_J138_006_volume_map_sharp.mrc id 105.2
    8939 
    8940 Opened cryosparc_P71_J138_006_volume_map_sharp.mrc as #1, grid size
    8941 300,300,300, pixel 1.43, shown at level 0.0428, step 2, values float32 
    8942 
    8943 > volume #105.2 step 1 level 0.355 color #9999CC transparency 0.5
    8944 
    8945 > view matrix models
    8946 > #105.2,-0.024025,0.77304,0.6339,-141.69,0.99715,-0.026789,0.070462,-68.674,0.071451,0.63379,-0.7702,173
    8947 
    8948 > rename #101 CD20_RTX
    8949 
    8950 > rename #102 CD20_2H7v16
    8951 
    8952 > rename #103 CD20_2H7v166_D56A
    8953 
    8954 > rename #104 CD20_2H7v166_S92A_D56A
    8955 
    8956 > rename #105 CD20_2H7v166
    8957 
    8958 > dssp
    8959 
    8960 > name CD20_RTX #101.1
    8961 
    8962 > name CD20_2H7v16 #102.1
    8963 
    8964 > name CD20_2H7v166_D56A #103.1
     3346**** Deleted thousands of lines here.  Full text is attached as description.txt *****
    89653347
    89663348> name CD20_2H7v166_S92A_D56A #104.1