Changes between Initial Version and Version 1 of Ticket #17037


Ignore:
Timestamp:
Mar 7, 2025, 2:45:43 PM (9 months ago)
Author:
Tom Goddard
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #17037

    • Property Component Unassigned → Window Toolkit
    • Property Owner set to Tom Goddard
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → Mac multi-display crash

  • Ticket #17037 – Description

    initial v1  
    32483248I | No description available 
    32493249 
    3250 
    3251 > modelfix
    3252 
    3253 Changed 25299 atom styles 
    3254 23699 atoms, 24145 bonds, 9 pseudobonds, 2970 residues, 2 models selected 
    3255 
    3256 > split #1
    3257 
    3258 Split ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) into 9 models 
    3259 Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb A #1.1 
    3260 --- 
    3261 Chain | Description 
    3262 A | No description available 
    3263  
    3264 Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb B #1.2 
    3265 --- 
    3266 Chain | Description 
    3267 B | No description available 
    3268  
    3269 Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb C #1.3 
    3270 --- 
    3271 Chain | Description 
    3272 C | No description available 
    3273  
    3274 Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb D #1.4 
    3275 --- 
    3276 Chain | Description 
    3277 D | No description available 
    3278  
    3279 Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb E #1.5 
    3280 --- 
    3281 Chain | Description 
    3282 E | No description available 
    3283  
    3284 Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb F #1.6 
    3285 --- 
    3286 Chain | Description 
    3287 F | No description available 
    3288  
    3289 Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb G #1.7 
    3290 --- 
    3291 Chain | Description 
    3292 G | No description available 
    3293  
    3294 Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb H #1.8 
    3295 --- 
    3296 Chain | Description 
    3297 H | No description available 
    3298  
    3299 Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb I #1.9 
    3300 --- 
    3301 Chain | Description 
    3302 I | No description available 
    3303  
    3304 
    3305 > hide #!1.1 models
    3306 
    3307 > hide #1.2 models
    3308 
    3309 > hide #!1.3 models
    3310 
    3311 > hide #!1.5 models
    3312 
    3313 > show #!1.5 models
    3314 
    3315 > hide #!1.6 models
    3316 
    3317 > select /G:548
    3318 
    3319 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3320 
    3321 > show sel atoms
    3322 
    3323 Unsupported scale factor (0.000000) detected on Display0 
    3324 
    3325 Unsupported scale factor (0.000000) detected on Display1 
    3326 
    3327 > open "/Users/jtbauer/Library/CloudStorage/OneDrive-
    3328 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    3329 > structures/Projects-maps/ylODC_54bp-
    3330 > oriC061_complete/cryosparc_P370_J327_even_better_Orc2WHD.mrc"
    3331 
    3332 Opened cryosparc_P370_J327_even_better_Orc2WHD.mrc as #2, grid size
    3333 440,440,440, pixel 0.827, shown at level 0.0402, step 2, values float32 
    3334 
    3335 > volume #2 step 1
    3336 
    3337 > volume #2 level 0.1468
    3338 
    3339 > select clear
    3340 
    3341 > ui mousemode right translate
    3342 
    3343 > ui mousemode right zoom
    3344 
    3345 > ui mousemode right translate
    3346 
    3347 > vop flip #2
    3348 
    3349 Opened cryosparc_P370_J327_even_better_Orc2WHD.mrc z flip as #3, grid size
    3350 440,440,440, pixel 0.827, shown at step 1, values float32 
    3351 
    3352 > save "/Users/jtbauer/Library/CloudStorage/OneDrive-
    3353 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    3354 > structures/Projects-maps/ylODC_54bp-
    3355 > oriC061_complete/cryosparc_P370_J327_FLIPPED_even_better_Orc2WHD.mrc" models
    3356 > #3
    3357 
    3358 Unsupported scale factor (0.000000) detected on Display1 
    3359 
    3360 > open "/Users/jtbauer/Library/CloudStorage/OneDrive-
    3361 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    3362 > structures/Projects-maps/ylODC_54bp-
    3363 > oriC061_complete/cryosparc_P370_J418_local_refine_even_better_Orc2WHD.mrc"
    3364 
    3365 Opened cryosparc_P370_J418_local_refine_even_better_Orc2WHD.mrc as #4, grid
    3366 size 440,440,440, pixel 0.827, shown at level 0.0436, step 2, values float32 
    3367 
    3368 > select ~sel & ##selected
    3369 
    3370 Nothing selected 
    3371 
    3372 > vop flip #4
    3373 
    3374 Opened cryosparc_P370_J418_local_refine_even_better_Orc2WHD.mrc z flip as #5,
    3375 grid size 440,440,440, pixel 0.827, shown at step 1, values float32 
    3376 
    3377 > close #4
    3378 
    3379 > volume #5 level 0.1372
    3380 
    3381 > volume #3 level 0.14
    3382 
    3383 > volume #5 level 0.14
    3384 
    3385 > volume #5 level 0.1
    3386 
    3387 > volume #3 level 0.1
    3388 
    3389 > volume #3 level 0.0813
    3390 
    3391 > volume #3 level 0.1
    3392 
    3393 > open "/Users/jtbauer/Library/CloudStorage/OneDrive-
    3394 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    3395 > structures/Projects-maps/ylODC_54bp-
    3396 > oriC061_complete/cryosparc_P370_J420_even_better_Orc2WHD-sharp.mrc"
    3397 
    3398 Opened cryosparc_P370_J420_even_better_Orc2WHD-sharp.mrc as #4, grid size
    3399 440,440,440, pixel 0.827, shown at level 0.0683, step 2, values float32 
    3400 
    3401 > close #5
    3402 
    3403 > vop flip #4
    3404 
    3405 Opened cryosparc_P370_J420_even_better_Orc2WHD-sharp.mrc z flip as #5, grid
    3406 size 440,440,440, pixel 0.827, shown at step 1, values float32 
    3407 
    3408 > close #4
    3409 
    3410 > volume #5 level 0.1
    3411 
    3412 > volume #5 level 0.12
    3413 
    3414 > volume #5 level 0.1
    3415 
    3416 > volume #5 level 0.095
    3417 
    3418 > volume #5 level 0.08
    3419 
    3420 > hide #!3 models
    3421 
    3422 > hide #!1 models
    3423 
    3424 > surface dust #5 size 8.27
    3425 
    3426 > close #5
    3427 
    3428 > open /Users/jtbauer/Library/CloudStorage/OneDrive-
    3429 > Personal/Documents/ROTATION_WORK/Joshua-
    3430 > Tor_Lab/test_a3d8f/test_a3d8f_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
    3431 
    3432 Chain information for
    3433 test_a3d8f_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb #4 
    3434 --- 
    3435 Chain | Description 
    3436 A | No description available 
    3437 B | No description available 
    3438  
    3439 Computing secondary structure 
    3440 
    3441 > select add #4
    3442 
    3443 6005 atoms, 6077 bonds, 374 residues, 1 model selected 
    3444 
    3445 > ui mousemode right select
    3446 
    3447 > select clear
    3448 
    3449 > open "/Users/jtbauer/Library/CloudStorage/OneDrive-
    3450 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/test_a3d8f/1j7v-crystal
    3451 > structure.pdb"
    3452 
    3453 1j7v-crystal structure.pdb title: 
    3454 Human il-10 / il-10R1 complex [more info...] 
    3455  
    3456 Chain information for 1j7v-crystal structure.pdb #5 
    3457 --- 
    3458 Chain | Description | UniProt 
    3459 L | IL-10; cytokine synthesis inhibitory factor; CSIF | IL10_HUMAN 1-160 
    3460 R | IL-10R1; IL-10R-A | I10R1_HUMAN 1-214 
    3461  
    3462 13 atoms have alternate locations. Control/examine alternate locations with
    3463 Altloc Explorer [start tool...] or the altlocs command. 
    3464 
    3465 > matchmaker #4 to #5
    3466 
    3467 Computing secondary structure 
    3468 Parameters 
    3469 --- 
    3470 Chain pairing | bb 
    3471 Alignment algorithm | Needleman-Wunsch 
    3472 Similarity matrix | BLOSUM-62 
    3473 SS fraction | 0.3 
    3474 Gap open (HH/SS/other) | 18/18/6 
    3475 Gap extend | 1 
    3476 SS matrix |  |  | H | S | O 
    3477 ---|---|---|--- 
    3478 H | 6 | -9 | -6 
    3479 S |  | 6 | -6 
    3480 O |  |  | 4 
    3481 Iteration cutoff | 2 
    3482  
    3483 Matchmaker 1j7v-crystal structure.pdb, chain R (#5) with
    3484 test_a3d8f_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb, chain
    3485 B (#4), sequence alignment score = 1073 
    3486 RMSD between 192 pruned atom pairs is 0.747 angstroms; (across all 205 pairs:
    3487 1.150) 
    3488  
    3489 
    3490 > open /Users/jtbauer/Library/CloudStorage/OneDrive-
    3491 > Personal/Documents/ROTATION_WORK/Joshua-
    3492 > Tor_Lab/test_a3d8f/test_a3d8f_relaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb
    3493 
    3494 Chain information for
    3495 test_a3d8f_relaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb #6 
    3496 --- 
    3497 Chain | Description 
    3498 A | No description available 
    3499 B | No description available 
    3500  
    3501 Computing secondary structure 
    3502 
    3503 > select ~sel & ##selected
    3504 
    3505 Nothing selected 
    3506 
    3507 > matchmaker #6 to #5
    3508 
    3509 Computing secondary structure 
    3510 Parameters 
    3511 --- 
    3512 Chain pairing | bb 
    3513 Alignment algorithm | Needleman-Wunsch 
    3514 Similarity matrix | BLOSUM-62 
    3515 SS fraction | 0.3 
    3516 Gap open (HH/SS/other) | 18/18/6 
    3517 Gap extend | 1 
    3518 SS matrix |  |  | H | S | O 
    3519 ---|---|---|--- 
    3520 H | 6 | -9 | -6 
    3521 S |  | 6 | -6 
    3522 O |  |  | 4 
    3523 Iteration cutoff | 2 
    3524  
    3525 Matchmaker 1j7v-crystal structure.pdb, chain R (#5) with
    3526 test_a3d8f_relaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb, chain
    3527 B (#6), sequence alignment score = 1073 
    3528 RMSD between 191 pruned atom pairs is 0.713 angstroms; (across all 205 pairs:
    3529 1.091) 
    3530  
    3531 
    3532 > close #4
    3533 
    3534 > close #6
    3535 
    3536 > ui tool show "Unit Cell"
    3537 
    3538 > unitcell #5
    3539 
    3540 > unitcell delete #5
    3541 
    3542 > unitcell #5
    3543 
    3544 Drag select of 587 residues 
    3545 
    3546 > delete sel
    3547 
    3548 Drag select of 832 residues, 8 pseudobonds 
    3549 
    3550 > delete sel
    3551 
    3552 > open /Users/jtbauer/Library/CloudStorage/OneDrive-
    3553 > Personal/Documents/ROTATION_WORK/Joshua-
    3554 > Tor_Lab/test_a3d8f/test_566b6.result.zip
    3555 
    3556 Unrecognized file suffix '.zip' 
    3557 
    3558 > open /Users/jtbauer/Library/CloudStorage/OneDrive-
    3559 > Personal/Documents/ROTATION_WORK/Joshua-
    3560 > Tor_Lab/test_a3d8f/test_566b6/test_566b6_relaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb
    3561 
    3562 Chain information for
    3563 test_566b6_relaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb #6 
    3564 --- 
    3565 Chain | Description 
    3566 A B | No description available 
    3567 C D | No description available 
    3568  
    3569 Computing secondary structure 
    3570 
    3571 > hide #!4 models
    3572 
    3573 > show #!4 models
    3574 
    3575 > hide #5 models
    3576 
    3577 > show #5 models
    3578 
    3579 > hide #5 models
    3580 
    3581 > hide #!4 models
    3582 
    3583 > show #5 models
    3584 
    3585 > hide #5 models
    3586 
    3587 > show #!4 models
    3588 
    3589 > hide #!4 models
    3590 
    3591 > show #5 models
    3592 
    3593 > hide #5 models
    3594 
    3595 > show #!4 models
    3596 
    3597 > close #5
    3598 
    3599 > matchmaker #6 to #4
    3600 
    3601 Specify a single 'to' model only 
    3602 
    3603 > hide #4.1 models
    3604 
    3605 > show #4.1 models
    3606 
    3607 > hide #4.2 models
    3608 
    3609 > show #4.2 models
    3610 
    3611 > hide #!4.3 models
    3612 
    3613 > show #!4.3 models
    3614 
    3615 > hide #4.4 models
    3616 
    3617 > show #4.4 models
    3618 
    3619 > close #4
    3620 
    3621 > open "/Users/jtbauer/Library/CloudStorage/OneDrive-
    3622 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/test_a3d8f/1j7v-crystal
    3623 > structure.pdb" format pdb
    3624 
    3625 1j7v-crystal structure.pdb title: 
    3626 Human il-10 / il-10R1 complex [more info...] 
    3627  
    3628 Chain information for 1j7v-crystal structure.pdb #4 
    3629 --- 
    3630 Chain | Description | UniProt 
    3631 L | IL-10; cytokine synthesis inhibitory factor; CSIF | IL10_HUMAN 1-160 
    3632 R | IL-10R1; IL-10R-A | I10R1_HUMAN 1-214 
    3633  
    3634 13 atoms have alternate locations. Control/examine alternate locations with
    3635 Altloc Explorer [start tool...] or the altlocs command. 
    3636 
    3637 > unitcell #4
    3638 
    3639 > combine #5
    3640 
    3641 Remapping chain ID 'L' in 1j7v-crystal structure.pdb #2 #5.2 to 'M' 
    3642 Remapping chain ID 'R' in 1j7v-crystal structure.pdb #2 #5.2 to 'S' 
    3643 Remapping chain ID 'L' in 1j7v-crystal structure.pdb #3 #5.3 to 'N' 
    3644 Remapping chain ID 'R' in 1j7v-crystal structure.pdb #3 #5.3 to 'T' 
    3645 Remapping chain ID 'L' in 1j7v-crystal structure.pdb #4 #5.4 to 'O' 
    3646 Remapping chain ID 'R' in 1j7v-crystal structure.pdb #4 #5.4 to 'U' 
    3647 Remapping chain ID 'L' in 1j7v-crystal structure.pdb #5 #5.5 to 'P' 
    3648 Remapping chain ID 'R' in 1j7v-crystal structure.pdb #5 #5.5 to 'V' 
    3649 Remapping chain ID 'L' in 1j7v-crystal structure.pdb #6 #5.6 to 'Q' 
    3650 Remapping chain ID 'R' in 1j7v-crystal structure.pdb #6 #5.6 to 'W' 
    3651 
    3652 > hide #4 models
    3653 
    3654 > hide #!5 models
    3655 
    3656 > matchmaker #6 to #7
    3657 
    3658 Computing secondary structure 
    3659 Parameters 
    3660 --- 
    3661 Chain pairing | bb 
    3662 Alignment algorithm | Needleman-Wunsch 
    3663 Similarity matrix | BLOSUM-62 
    3664 SS fraction | 0.3 
    3665 Gap open (HH/SS/other) | 18/18/6 
    3666 Gap extend | 1 
    3667 SS matrix |  |  | H | S | O 
    3668 ---|---|---|--- 
    3669 H | 6 | -9 | -6 
    3670 S |  | 6 | -6 
    3671 O |  |  | 4 
    3672 Iteration cutoff | 2 
    3673  
    3674 Matchmaker combination, chain R (#7) with
    3675 test_566b6_relaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb, chain
    3676 C (#6), sequence alignment score = 1073 
    3677 RMSD between 194 pruned atom pairs is 0.648 angstroms; (across all 205 pairs:
    3678 1.044) 
    3679  
    3680 
    3681 > select add #6
    3682 
    3683 12010 atoms, 12154 bonds, 748 residues, 1 model selected 
    3684 
    3685 > ui mousemode right "translate selected models"
    3686 
    3687 > view matrix models
    3688 > #6,0.51645,0.16079,-0.84109,16.615,-0.7222,0.60956,-0.32692,27.053,0.46012,0.77627,0.43093,122.67
    3689 
    3690 > matchmaker #6 to #7
    3691 
    3692 Computing secondary structure 
    3693 Parameters 
    3694 --- 
    3695 Chain pairing | bb 
    3696 Alignment algorithm | Needleman-Wunsch 
    3697 Similarity matrix | BLOSUM-62 
    3698 SS fraction | 0.3 
    3699 Gap open (HH/SS/other) | 18/18/6 
    3700 Gap extend | 1 
    3701 SS matrix |  |  | H | S | O 
    3702 ---|---|---|--- 
    3703 H | 6 | -9 | -6 
    3704 S |  | 6 | -6 
    3705 O |  |  | 4 
    3706 Iteration cutoff | 2 
    3707  
    3708 Matchmaker combination, chain R (#7) with
    3709 test_566b6_relaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb, chain
    3710 C (#6), sequence alignment score = 1073 
    3711 RMSD between 194 pruned atom pairs is 0.648 angstroms; (across all 205 pairs:
    3712 1.044) 
    3713  
    3714 
    3715 > view matrix models
    3716 > #6,0.51645,0.16079,-0.84109,16.006,-0.7222,0.60956,-0.32692,15.467,0.46012,0.77627,0.43093,137.76
    3717 
    3718 > view matrix models
    3719 > #6,0.51645,0.16079,-0.84109,12.455,-0.7222,0.60956,-0.32692,-15.933,0.46012,0.77627,0.43093,154.19
    3720 
    3721 > view matrix models
    3722 > #6,0.51645,0.16079,-0.84109,7.4024,-0.7222,0.60956,-0.32692,10.581,0.46012,0.77627,0.43093,164.48
    3723 
    3724 > view matrix models
    3725 > #6,0.51645,0.16079,-0.84109,77.402,-0.7222,0.60956,-0.32692,32.484,0.46012,0.77627,0.43093,91.425
    3726 
    3727 > close #6
    3728 
    3729 > open /Users/jtbauer/Library/CloudStorage/OneDrive-
    3730 > Personal/Documents/ROTATION_WORK/Joshua-
    3731 > Tor_Lab/test_a3d8f/test_566b6/test_566b6_relaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb
    3732 
    3733 Chain information for
    3734 test_566b6_relaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb #6 
    3735 --- 
    3736 Chain | Description 
    3737 A B | No description available 
    3738 C D | No description available 
    3739  
    3740 Computing secondary structure 
    3741 
    3742 > matchmaker #6 to #7
    3743 
    3744 Computing secondary structure 
    3745 Parameters 
    3746 --- 
    3747 Chain pairing | bb 
    3748 Alignment algorithm | Needleman-Wunsch 
    3749 Similarity matrix | BLOSUM-62 
    3750 SS fraction | 0.3 
    3751 Gap open (HH/SS/other) | 18/18/6 
    3752 Gap extend | 1 
    3753 SS matrix |  |  | H | S | O 
    3754 ---|---|---|--- 
    3755 H | 6 | -9 | -6 
    3756 S |  | 6 | -6 
    3757 O |  |  | 4 
    3758 Iteration cutoff | 2 
    3759  
    3760 Matchmaker combination, chain R (#7) with
    3761 test_566b6_relaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb, chain
    3762 C (#6), sequence alignment score = 1052 
    3763 RMSD between 190 pruned atom pairs is 0.752 angstroms; (across all 205 pairs:
    3764 1.415) 
    3765  
    3766 
    3767 > close #6
    3768 
    3769 > open /Users/jtbauer/Library/CloudStorage/OneDrive-
    3770 > Personal/Documents/ROTATION_WORK/Joshua-
    3771 > Tor_Lab/test_a3d8f/test_566b6/test_566b6_relaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb
    3772 
    3773 Chain information for
    3774 test_566b6_relaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb #6 
    3775 --- 
    3776 Chain | Description 
    3777 A B | No description available 
    3778 C D | No description available 
    3779  
    3780 Computing secondary structure 
    3781 
    3782 > matchmaker #6 to #7
    3783 
    3784 Computing secondary structure 
    3785 Parameters 
    3786 --- 
    3787 Chain pairing | bb 
    3788 Alignment algorithm | Needleman-Wunsch 
    3789 Similarity matrix | BLOSUM-62 
    3790 SS fraction | 0.3 
    3791 Gap open (HH/SS/other) | 18/18/6 
    3792 Gap extend | 1 
    3793 SS matrix |  |  | H | S | O 
    3794 ---|---|---|--- 
    3795 H | 6 | -9 | -6 
    3796 S |  | 6 | -6 
    3797 O |  |  | 4 
    3798 Iteration cutoff | 2 
    3799  
    3800 Matchmaker combination, chain R (#7) with
    3801 test_566b6_relaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb, chain
    3802 D (#6), sequence alignment score = 1073 
    3803 RMSD between 196 pruned atom pairs is 0.731 angstroms; (across all 205 pairs:
    3804 1.005) 
    3805  
    3806 
    3807 > close #6
    3808 
    3809 > open /Users/jtbauer/Library/CloudStorage/OneDrive-
    3810 > Personal/Documents/ROTATION_WORK/Joshua-
    3811 > Tor_Lab/test_a3d8f/test_566b6/test_566b6_relaxed_rank_004_alphafold2_multimer_v3_model_4_seed_000.pdb
    3812 
    3813 Chain information for
    3814 test_566b6_relaxed_rank_004_alphafold2_multimer_v3_model_4_seed_000.pdb #6 
    3815 --- 
    3816 Chain | Description 
    3817 A B | No description available 
    3818 C D | No description available 
    3819  
    3820 Computing secondary structure 
    3821 
    3822 > matchmaker #6 to #7
    3823 
    3824 Computing secondary structure 
    3825 Parameters 
    3826 --- 
    3827 Chain pairing | bb 
    3828 Alignment algorithm | Needleman-Wunsch 
    3829 Similarity matrix | BLOSUM-62 
    3830 SS fraction | 0.3 
    3831 Gap open (HH/SS/other) | 18/18/6 
    3832 Gap extend | 1 
    3833 SS matrix |  |  | H | S | O 
    3834 ---|---|---|--- 
    3835 H | 6 | -9 | -6 
    3836 S |  | 6 | -6 
    3837 O |  |  | 4 
    3838 Iteration cutoff | 2 
    3839  
    3840 Matchmaker combination, chain R (#7) with
    3841 test_566b6_relaxed_rank_004_alphafold2_multimer_v3_model_4_seed_000.pdb, chain
    3842 C (#6), sequence alignment score = 1073 
    3843 RMSD between 193 pruned atom pairs is 0.707 angstroms; (across all 205 pairs:
    3844 1.082) 
    3845  
    3846 
    3847 > close #6
    3848 
    3849 > open /Users/jtbauer/Library/CloudStorage/OneDrive-
    3850 > Personal/Documents/ROTATION_WORK/Joshua-
    3851 > Tor_Lab/test_a3d8f/test_566b6/test_566b6_relaxed_rank_005_alphafold2_multimer_v3_model_5_seed_000.pdb
    3852 
    3853 Chain information for
    3854 test_566b6_relaxed_rank_005_alphafold2_multimer_v3_model_5_seed_000.pdb #6 
    3855 --- 
    3856 Chain | Description 
    3857 A B | No description available 
    3858 C D | No description available 
    3859  
    3860 Computing secondary structure 
    3861 
    3862 > matchmaker #6 to #7
    3863 
    3864 Computing secondary structure 
    3865 Parameters 
    3866 --- 
    3867 Chain pairing | bb 
    3868 Alignment algorithm | Needleman-Wunsch 
    3869 Similarity matrix | BLOSUM-62 
    3870 SS fraction | 0.3 
    3871 Gap open (HH/SS/other) | 18/18/6 
    3872 Gap extend | 1 
    3873 SS matrix |  |  | H | S | O 
    3874 ---|---|---|--- 
    3875 H | 6 | -9 | -6 
    3876 S |  | 6 | -6 
    3877 O |  |  | 4 
    3878 Iteration cutoff | 2 
    3879  
    3880 Matchmaker combination, chain R (#7) with
    3881 test_566b6_relaxed_rank_005_alphafold2_multimer_v3_model_5_seed_000.pdb, chain
    3882 C (#6), sequence alignment score = 1073 
    3883 RMSD between 192 pruned atom pairs is 0.722 angstroms; (across all 205 pairs:
    3884 1.163) 
    3885  
    3886 
    3887 > close #6
    3888 
    3889 > close #7
    3890 
    3891 > close #5
    3892 
    3893 > close #4
    3894 
    3895 > close #1
    3896 
    3897 > close
    3898 
    3899 > open "/Users/jtbauer/Library/CloudStorage/OneDrive-
    3900 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    3901 > structures/PDBs/ylODC_54bp-
    3902 > oriC061_complete/ylODC_54bpOriC061_rev29_PostPhenix.pdb"
    3903 
    3904 Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb #1 
    3905 --- 
    3906 Chain | Description 
    3907 A | No description available 
    3908 B | No description available 
    3909 C | No description available 
    3910 D | No description available 
    3911 E | No description available 
    3912 F | No description available 
    3913 G | No description available 
    3914 H | No description available 
    3915 I | No description available 
    3916  
    3917 
    3918 > modelfix
    3919 
    3920 Changed 25299 atom styles 
    3921 23699 atoms, 24145 bonds, 9 pseudobonds, 2970 residues, 2 models selected 
    3922 
    3923 > hide #!1 models
    3924 
    3925 > open /Users/jtbauer/Library/CloudStorage/OneDrive-
    3926 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/7jk3-dmODC_GCrich.pdb
    3927 
    3928 7jk3-dmODC_GCrich.pdb title: 
    3929 Structure of drosophila orc bound to GC-rich DNA and CDC6 [more info...] 
    3930  
    3931 Chain information for 7jk3-dmODC_GCrich.pdb #2 
    3932 --- 
    3933 Chain | Description | UniProt 
    3934 A | DMORC1 | ORC1_DROME 440-924 
    3935 B | DMORC2 | ORC2_DROME 1-618 
    3936 C | origin recognition complex subunit 3 | Q7K2L1_DROME 1-721 
    3937 D | ORC4 | Q9W102_DROME 1-459 
    3938 E | ORC5 | ORC5_DROME 1-460 
    3939 F | ORC6 | ORC6_DROME 1-257 
    3940 G | CDC6 | Q9VSM9_DROME 242-662 
    3941 H | DNA (33-mer) |   
    3942 I | DNA (33-mer) |   
    3943  
    3944 Non-standard residues in 7jk3-dmODC_GCrich.pdb #2 
    3945 --- 
    3946 ATP — adenosine-5'-triphosphate 
    3947 MG — magnesium ion 
    3948  
    3949 
    3950 > close #2
    3951 
    3952 > open /Users/jtbauer/Library/CloudStorage/OneDrive-
    3953 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/hsORC1-6_CDC6_60bpDNA.pdb
    3954 
    3955 Chain information for hsORC1-6_CDC6_60bpDNA.pdb #2 
    3956 --- 
    3957 Chain | Description 
    3958 A | No description available 
    3959 B | No description available 
    3960 C | No description available 
    3961 D | No description available 
    3962 E | No description available 
    3963 F | No description available 
    3964 G | No description available 
    3965 H | No description available 
    3966 I | No description available 
    3967  
    3968 
    3969 > modelfix
    3970 
    3971 Changed 46715 atom styles 
    3972 43798 atoms, 44629 bonds, 22 pseudobonds, 5455 residues, 4 models selected 
    3973 Computing secondary structure 
    3974 
    3975 > open /Users/jtbauer/Library/CloudStorage/OneDrive-
    3976 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/7mca-assembly1.cif
    3977 
    3978 7mca-assembly1.cif title: 
    3979 Structure of the S. cerevisiae origin recognition complex bound to the
    3980 replication initiator Cdc6 and the ARS1 origin DNA. [more info...] 
    3981  
    3982 Chain information for 7mca-assembly1.cif #3 
    3983 --- 
    3984 Chain | Description 
    3985 A | Origin recognition complex subunit 1 
    3986 B | Origin recognition complex subunit 2 
    3987 C | Origin recognition complex subunit 3 
    3988 D | Origin recognition complex subunit 4 
    3989 E | Origin recognition complex subunit 5 
    3990 F | Origin recognition complex subunit 6 
    3991 G | DNA (85-MER) 
    3992 H | DNA (85-MER) 
    3993 I | Cell division control protein 6 
    3994  
    3995 Non-standard residues in 7mca-assembly1.cif #3 
    3996 --- 
    3997 AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
    3998 5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate);
    3999 adenosine-5'-diphosphate monothiophosphate) 
    4000 MG — magnesium ion 
    4001  
    4002 
    4003 > modelfix
    4004 
    4005 Changed 71407 atom styles 
    4006 66312 atoms, 67574 bonds, 36 pseudobonds, 8215 residues, 6 models selected 
    4007 
    4008 > newcolor #3/A #3/B #3/C #3/D #3/E #3/F #3/I #3/G #3/H
    4009 
    4010 > select #1/H,I
    4011 
    4012 1476 atoms, 1654 bonds, 72 residues, 1 model selected 
    4013 
    4014 > show #!1 models
    4015 
    4016 > ui mousemode right select
    4017 
    4018 > select clear
    4019 
    4020 > matchmaker #2,3 to #1
    4021 
    4022 Computing secondary structure 
    4023 Parameters 
    4024 --- 
    4025 Chain pairing | bb 
    4026 Alignment algorithm | Needleman-Wunsch 
    4027 Similarity matrix | BLOSUM-62 
    4028 SS fraction | 0.3 
    4029 Gap open (HH/SS/other) | 18/18/6 
    4030 Gap extend | 1 
    4031 SS matrix |  |  | H | S | O 
    4032 ---|---|---|--- 
    4033 H | 6 | -9 | -6 
    4034 S |  | 6 | -6 
    4035 O |  |  | 4 
    4036 Iteration cutoff | 2 
    4037  
    4038 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain C (#1) with
    4039 hsORC1-6_CDC6_60bpDNA.pdb, chain C (#2), sequence alignment score = 967.1 
    4040 RMSD between 139 pruned atom pairs is 1.275 angstroms; (across all 568 pairs:
    4041 7.882) 
    4042  
    4043 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca-
    4044 assembly1.cif, chain A (#3), sequence alignment score = 943 
    4045 RMSD between 228 pruned atom pairs is 1.005 angstroms; (across all 394 pairs:
    4046 5.169) 
    4047  
    4048 
    4049 > matchmaker #2,3 to #1/C:180-260,/D,/E
    4050 
    4051 Invalid "to" argument: only initial part "#1/C:180-260" of atom specifier
    4052 valid 
    4053 
    4054 > matchmaker #2,3 to (#1/C:140-300 | #1/D:360-end | #1/E:307-end)
    4055 
    4056 Computing secondary structure 
    4057 Parameters 
    4058 --- 
    4059 Chain pairing | bb 
    4060 Alignment algorithm | Needleman-Wunsch 
    4061 Similarity matrix | BLOSUM-62 
    4062 SS fraction | 0.3 
    4063 Gap open (HH/SS/other) | 18/18/6 
    4064 Gap extend | 1 
    4065 SS matrix |  |  | H | S | O 
    4066 ---|---|---|--- 
    4067 H | 6 | -9 | -6 
    4068 S |  | 6 | -6 
    4069 O |  |  | 4 
    4070 Iteration cutoff | 2 
    4071  
    4072 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain E (#1) with
    4073 hsORC1-6_CDC6_60bpDNA.pdb, chain E (#2), sequence alignment score = 281.2 
    4074 RMSD between 99 pruned atom pairs is 0.965 angstroms; (across all 120 pairs:
    4075 3.490) 
    4076  
    4077 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain E (#1) with 7mca-
    4078 assembly1.cif, chain E (#3), sequence alignment score = 312.4 
    4079 RMSD between 101 pruned atom pairs is 0.945 angstroms; (across all 138 pairs:
    4080 3.466) 
    4081  
    4082 
    4083 > matchmaker #2,3 to (#1/A:300-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end)
    4084 
    4085 Computing secondary structure 
    4086 Parameters 
    4087 --- 
    4088 Chain pairing | bb 
    4089 Alignment algorithm | Needleman-Wunsch 
    4090 Similarity matrix | BLOSUM-62 
    4091 SS fraction | 0.3 
    4092 Gap open (HH/SS/other) | 18/18/6 
    4093 Gap extend | 1 
    4094 SS matrix |  |  | H | S | O 
    4095 ---|---|---|--- 
    4096 H | 6 | -9 | -6 
    4097 S |  | 6 | -6 
    4098 O |  |  | 4 
    4099 Iteration cutoff | 2 
    4100  
    4101 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with
    4102 hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 836.2 
    4103 RMSD between 200 pruned atom pairs is 1.167 angstroms; (across all 283 pairs:
    4104 2.305) 
    4105  
    4106 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca-
    4107 assembly1.cif, chain A (#3), sequence alignment score = 700.3 
    4108 RMSD between 218 pruned atom pairs is 0.943 angstroms; (across all 276 pairs:
    4109 5.480) 
    4110  
    4111 
    4112 > matchmaker #2,3 to (#1/A:400-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end)
    4113 
    4114 Computing secondary structure 
    4115 Parameters 
    4116 --- 
    4117 Chain pairing | bb 
    4118 Alignment algorithm | Needleman-Wunsch 
    4119 Similarity matrix | BLOSUM-62 
    4120 SS fraction | 0.3 
    4121 Gap open (HH/SS/other) | 18/18/6 
    4122 Gap extend | 1 
    4123 SS matrix |  |  | H | S | O 
    4124 ---|---|---|--- 
    4125 H | 6 | -9 | -6 
    4126 S |  | 6 | -6 
    4127 O |  |  | 4 
    4128 Iteration cutoff | 2 
    4129  
    4130 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with
    4131 hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 582.4 
    4132 RMSD between 128 pruned atom pairs is 1.051 angstroms; (across all 196 pairs:
    4133 2.238) 
    4134  
    4135 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca-
    4136 assembly1.cif, chain A (#3), sequence alignment score = 527.5 
    4137 RMSD between 164 pruned atom pairs is 0.962 angstroms; (across all 191 pairs:
    4138 2.175) 
    4139  
    4140 
    4141 > matchmaker #2,3 to (#1/A:500-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end)
    4142 
    4143 Computing secondary structure 
    4144 Parameters 
    4145 --- 
    4146 Chain pairing | bb 
    4147 Alignment algorithm | Needleman-Wunsch 
    4148 Similarity matrix | BLOSUM-62 
    4149 SS fraction | 0.3 
    4150 Gap open (HH/SS/other) | 18/18/6 
    4151 Gap extend | 1 
    4152 SS matrix |  |  | H | S | O 
    4153 ---|---|---|--- 
    4154 H | 6 | -9 | -6 
    4155 S |  | 6 | -6 
    4156 O |  |  | 4 
    4157 Iteration cutoff | 2 
    4158  
    4159 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with
    4160 hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 284.5 
    4161 RMSD between 68 pruned atom pairs is 1.060 angstroms; (across all 96 pairs:
    4162 2.171) 
    4163  
    4164 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain E (#1) with 7mca-
    4165 assembly1.cif, chain E (#3), sequence alignment score = 312.4 
    4166 RMSD between 101 pruned atom pairs is 0.945 angstroms; (across all 138 pairs:
    4167 3.466) 
    4168  
    4169 
    4170 > matchmaker #2,3 to (#1/A:400-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end)
    4171 
    4172 Computing secondary structure 
    4173 Parameters 
    4174 --- 
    4175 Chain pairing | bb 
    4176 Alignment algorithm | Needleman-Wunsch 
    4177 Similarity matrix | BLOSUM-62 
    4178 SS fraction | 0.3 
    4179 Gap open (HH/SS/other) | 18/18/6 
    4180 Gap extend | 1 
    4181 SS matrix |  |  | H | S | O 
    4182 ---|---|---|--- 
    4183 H | 6 | -9 | -6 
    4184 S |  | 6 | -6 
    4185 O |  |  | 4 
    4186 Iteration cutoff | 2 
    4187  
    4188 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with
    4189 hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 582.4 
    4190 RMSD between 128 pruned atom pairs is 1.051 angstroms; (across all 196 pairs:
    4191 2.238) 
    4192  
    4193 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca-
    4194 assembly1.cif, chain A (#3), sequence alignment score = 527.5 
    4195 RMSD between 164 pruned atom pairs is 0.962 angstroms; (across all 191 pairs:
    4196 2.175) 
    4197  
    4198 
    4199 > select ~nucleic
    4200 
    4201 66692 atoms, 67966 bonds, 38 pseudobonds, 8239 residues, 7 models selected 
    4202 
    4203 > show sel surfaces
    4204 
    4205 > transparency 30 surfaces
    4206 
    4207 > transparency 70 surfaces
    4208 
    4209 > hide sel cartoons
    4210 
    4211 > matchmaker #2,3 to (#1/A:500-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end)
    4212 
    4213 Computing secondary structure 
    4214 Parameters 
    4215 --- 
    4216 Chain pairing | bb 
    4217 Alignment algorithm | Needleman-Wunsch 
    4218 Similarity matrix | BLOSUM-62 
    4219 SS fraction | 0.3 
    4220 Gap open (HH/SS/other) | 18/18/6 
    4221 Gap extend | 1 
    4222 SS matrix |  |  | H | S | O 
    4223 ---|---|---|--- 
    4224 H | 6 | -9 | -6 
    4225 S |  | 6 | -6 
    4226 O |  |  | 4 
    4227 Iteration cutoff | 2 
    4228  
    4229 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with
    4230 hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 284.5 
    4231 RMSD between 68 pruned atom pairs is 1.060 angstroms; (across all 96 pairs:
    4232 2.171) 
    4233  
    4234 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain E (#1) with 7mca-
    4235 assembly1.cif, chain E (#3), sequence alignment score = 312.4 
    4236 RMSD between 101 pruned atom pairs is 0.945 angstroms; (across all 138 pairs:
    4237 3.466) 
    4238  
    4239 
    4240 > matchmaker #2,3 to (#1/A:400-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end)
    4241 
    4242 Computing secondary structure 
    4243 Parameters 
    4244 --- 
    4245 Chain pairing | bb 
    4246 Alignment algorithm | Needleman-Wunsch 
    4247 Similarity matrix | BLOSUM-62 
    4248 SS fraction | 0.3 
    4249 Gap open (HH/SS/other) | 18/18/6 
    4250 Gap extend | 1 
    4251 SS matrix |  |  | H | S | O 
    4252 ---|---|---|--- 
    4253 H | 6 | -9 | -6 
    4254 S |  | 6 | -6 
    4255 O |  |  | 4 
    4256 Iteration cutoff | 2 
    4257  
    4258 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with
    4259 hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 582.4 
    4260 RMSD between 128 pruned atom pairs is 1.051 angstroms; (across all 196 pairs:
    4261 2.238) 
    4262  
    4263 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca-
    4264 assembly1.cif, chain A (#3), sequence alignment score = 527.5 
    4265 RMSD between 164 pruned atom pairs is 0.962 angstroms; (across all 191 pairs:
    4266 2.175) 
    4267  
    4268 
    4269 > matchmaker #2,3 to (#1/A:400-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end)
    4270 
    4271 Computing secondary structure 
    4272 Parameters 
    4273 --- 
    4274 Chain pairing | bb 
    4275 Alignment algorithm | Needleman-Wunsch 
    4276 Similarity matrix | BLOSUM-62 
    4277 SS fraction | 0.3 
    4278 Gap open (HH/SS/other) | 18/18/6 
    4279 Gap extend | 1 
    4280 SS matrix |  |  | H | S | O 
    4281 ---|---|---|--- 
    4282 H | 6 | -9 | -6 
    4283 S |  | 6 | -6 
    4284 O |  |  | 4 
    4285 Iteration cutoff | 2 
    4286  
    4287 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with
    4288 hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 582.4 
    4289 RMSD between 128 pruned atom pairs is 1.051 angstroms; (across all 196 pairs:
    4290 2.238) 
    4291  
    4292 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca-
    4293 assembly1.cif, chain A (#3), sequence alignment score = 527.5 
    4294 RMSD between 164 pruned atom pairs is 0.962 angstroms; (across all 191 pairs:
    4295 2.175) 
    4296  
    4297 
    4298 > matchmaker #2,3 to #1
    4299 
    4300 Computing secondary structure 
    4301 Parameters 
    4302 --- 
    4303 Chain pairing | bb 
    4304 Alignment algorithm | Needleman-Wunsch 
    4305 Similarity matrix | BLOSUM-62 
    4306 SS fraction | 0.3 
    4307 Gap open (HH/SS/other) | 18/18/6 
    4308 Gap extend | 1 
    4309 SS matrix |  |  | H | S | O 
    4310 ---|---|---|--- 
    4311 H | 6 | -9 | -6 
    4312 S |  | 6 | -6 
    4313 O |  |  | 4 
    4314 Iteration cutoff | 2 
    4315  
    4316 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain C (#1) with
    4317 hsORC1-6_CDC6_60bpDNA.pdb, chain C (#2), sequence alignment score = 967.1 
    4318 RMSD between 139 pruned atom pairs is 1.275 angstroms; (across all 568 pairs:
    4319 7.882) 
    4320  
    4321 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca-
    4322 assembly1.cif, chain A (#3), sequence alignment score = 943 
    4323 RMSD between 228 pruned atom pairs is 1.005 angstroms; (across all 394 pairs:
    4324 5.169) 
    4325  
    4326 Drag select of ylODC_54bpOriC061_rev29_PostPhenix.pdb_A SES surface, 7 of
    4327 358676 triangles, ylODC_54bpOriC061_rev29_PostPhenix.pdb_D SES surface, 18 of
    4328 396086 triangles, hsORC1-6_CDC6_60bpDNA.pdb_D SES surface, 38 of 440036
    4329 triangles 
    4330 
    4331 > select #2/A:901@C5'
    4332 
    4333 1 atom, 1 residue, 1 model selected 
    4334 
    4335 > select up
    4336 
    4337 31 atoms, 33 bonds, 1 residue, 1 model selected 
    4338 
    4339 > select up
    4340 
    4341 3061 atoms, 3113 bonds, 385 residues, 1 model selected 
    4342 
    4343 > select down
    4344 
    4345 31 atoms, 33 bonds, 1 residue, 2 models selected 
    4346 
    4347 > select clear
    4348 
    4349 > matchmaker #2,3 to (#1/A:500-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end)
    4350 
    4351 Computing secondary structure 
    4352 Parameters 
    4353 --- 
    4354 Chain pairing | bb 
    4355 Alignment algorithm | Needleman-Wunsch 
    4356 Similarity matrix | BLOSUM-62 
    4357 SS fraction | 0.3 
    4358 Gap open (HH/SS/other) | 18/18/6 
    4359 Gap extend | 1 
    4360 SS matrix |  |  | H | S | O 
    4361 ---|---|---|--- 
    4362 H | 6 | -9 | -6 
    4363 S |  | 6 | -6 
    4364 O |  |  | 4 
    4365 Iteration cutoff | 2 
    4366  
    4367 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with
    4368 hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 284.5 
    4369 RMSD between 68 pruned atom pairs is 1.060 angstroms; (across all 96 pairs:
    4370 2.171) 
    4371  
    4372 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain E (#1) with 7mca-
    4373 assembly1.cif, chain E (#3), sequence alignment score = 312.4 
    4374 RMSD between 101 pruned atom pairs is 0.945 angstroms; (across all 138 pairs:
    4375 3.466) 
    4376  
    4377 
    4378 > matchmaker #2,3 to (#1/A:400-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end)
    4379 
    4380 Computing secondary structure 
    4381 Parameters 
    4382 --- 
    4383 Chain pairing | bb 
    4384 Alignment algorithm | Needleman-Wunsch 
    4385 Similarity matrix | BLOSUM-62 
    4386 SS fraction | 0.3 
    4387 Gap open (HH/SS/other) | 18/18/6 
    4388 Gap extend | 1 
    4389 SS matrix |  |  | H | S | O 
    4390 ---|---|---|--- 
    4391 H | 6 | -9 | -6 
    4392 S |  | 6 | -6 
    4393 O |  |  | 4 
    4394 Iteration cutoff | 2 
    4395  
    4396 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with
    4397 hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 582.4 
    4398 RMSD between 128 pruned atom pairs is 1.051 angstroms; (across all 196 pairs:
    4399 2.238) 
    4400  
    4401 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca-
    4402 assembly1.cif, chain A (#3), sequence alignment score = 527.5 
    4403 RMSD between 164 pruned atom pairs is 0.962 angstroms; (across all 191 pairs:
    4404 2.175) 
    4405  
    4406 
    4407 > matchmaker #2,3 to #1
    4408 
    4409 Computing secondary structure 
    4410 Parameters 
    4411 --- 
    4412 Chain pairing | bb 
    4413 Alignment algorithm | Needleman-Wunsch 
    4414 Similarity matrix | BLOSUM-62 
    4415 SS fraction | 0.3 
    4416 Gap open (HH/SS/other) | 18/18/6 
    4417 Gap extend | 1 
    4418 SS matrix |  |  | H | S | O 
    4419 ---|---|---|--- 
    4420 H | 6 | -9 | -6 
    4421 S |  | 6 | -6 
    4422 O |  |  | 4 
    4423 Iteration cutoff | 2 
    4424  
    4425 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain C (#1) with
    4426 hsORC1-6_CDC6_60bpDNA.pdb, chain C (#2), sequence alignment score = 967.1 
    4427 RMSD between 139 pruned atom pairs is 1.275 angstroms; (across all 568 pairs:
    4428 7.882) 
    4429  
    4430 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca-
    4431 assembly1.cif, chain A (#3), sequence alignment score = 943 
    4432 RMSD between 228 pruned atom pairs is 1.005 angstroms; (across all 394 pairs:
    4433 5.169) 
    4434  
    4435 
    4436 > matchmaker #2,3 to (#1/A:400-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end)
    4437 
    4438 Computing secondary structure 
    4439 Parameters 
    4440 --- 
    4441 Chain pairing | bb 
    4442 Alignment algorithm | Needleman-Wunsch 
    4443 Similarity matrix | BLOSUM-62 
    4444 SS fraction | 0.3 
    4445 Gap open (HH/SS/other) | 18/18/6 
    4446 Gap extend | 1 
    4447 SS matrix |  |  | H | S | O 
    4448 ---|---|---|--- 
    4449 H | 6 | -9 | -6 
    4450 S |  | 6 | -6 
    4451 O |  |  | 4 
    4452 Iteration cutoff | 2 
    4453  
    4454 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with
    4455 hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 582.4 
    4456 RMSD between 128 pruned atom pairs is 1.051 angstroms; (across all 196 pairs:
    4457 2.238) 
    4458  
    4459 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca-
    4460 assembly1.cif, chain A (#3), sequence alignment score = 527.5 
    4461 RMSD between 164 pruned atom pairs is 0.962 angstroms; (across all 191 pairs:
    4462 2.175) 
    4463  
    4464 
    4465 > select #2
    4466 
    4467 21416 atoms, 21948 bonds, 13 pseudobonds, 2551 residues, 2 models selected 
    4468 
    4469 > show sel atoms
    4470 
    4471 > undo
    4472 
    4473 > show sel cartoons
    4474 
    4475 > select clear
    4476 
    4477 > matchmaker #2,3 to #1
    4478 
    4479 Computing secondary structure 
    4480 Parameters 
    4481 --- 
    4482 Chain pairing | bb 
    4483 Alignment algorithm | Needleman-Wunsch 
    4484 Similarity matrix | BLOSUM-62 
    4485 SS fraction | 0.3 
    4486 Gap open (HH/SS/other) | 18/18/6 
    4487 Gap extend | 1 
    4488 SS matrix |  |  | H | S | O 
    4489 ---|---|---|--- 
    4490 H | 6 | -9 | -6 
    4491 S |  | 6 | -6 
    4492 O |  |  | 4 
    4493 Iteration cutoff | 2 
    4494  
    4495 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain C (#1) with
    4496 hsORC1-6_CDC6_60bpDNA.pdb, chain C (#2), sequence alignment score = 967.1 
    4497 RMSD between 139 pruned atom pairs is 1.275 angstroms; (across all 568 pairs:
    4498 7.882) 
    4499  
    4500 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca-
    4501 assembly1.cif, chain A (#3), sequence alignment score = 943 
    4502 RMSD between 228 pruned atom pairs is 1.005 angstroms; (across all 394 pairs:
    4503 5.169) 
    4504  
    4505 
    4506 > matchmaker #2,3 to (#1/A:400-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end)
    4507 
    4508 Computing secondary structure 
    4509 Parameters 
    4510 --- 
    4511 Chain pairing | bb 
    4512 Alignment algorithm | Needleman-Wunsch 
    4513 Similarity matrix | BLOSUM-62 
    4514 SS fraction | 0.3 
    4515 Gap open (HH/SS/other) | 18/18/6 
    4516 Gap extend | 1 
    4517 SS matrix |  |  | H | S | O 
    4518 ---|---|---|--- 
    4519 H | 6 | -9 | -6 
    4520 S |  | 6 | -6 
    4521 O |  |  | 4 
    4522 Iteration cutoff | 2 
    4523  
    4524 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with
    4525 hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 582.4 
    4526 RMSD between 128 pruned atom pairs is 1.051 angstroms; (across all 196 pairs:
    4527 2.238) 
    4528  
    4529 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca-
    4530 assembly1.cif, chain A (#3), sequence alignment score = 527.5 
    4531 RMSD between 164 pruned atom pairs is 0.962 angstroms; (across all 191 pairs:
    4532 2.175) 
    4533  
    4534 
    4535 > hide #!2 models
    4536 
    4537 > show #!2 models
    4538 
    4539 > hide #!2 models
    4540 
    4541 > show #!2 models
    4542 
    4543 > select add #2
    4544 
    4545 21416 atoms, 21948 bonds, 13 pseudobonds, 2551 residues, 2 models selected 
    4546 
    4547 > hide sel surfaces
    4548 
    4549 > select clear
    4550 
    4551 > matchmaker #2,3 to #1
    4552 
    4553 Computing secondary structure 
    4554 Parameters 
    4555 --- 
    4556 Chain pairing | bb 
    4557 Alignment algorithm | Needleman-Wunsch 
    4558 Similarity matrix | BLOSUM-62 
    4559 SS fraction | 0.3 
    4560 Gap open (HH/SS/other) | 18/18/6 
    4561 Gap extend | 1 
    4562 SS matrix |  |  | H | S | O 
    4563 ---|---|---|--- 
    4564 H | 6 | -9 | -6 
    4565 S |  | 6 | -6 
    4566 O |  |  | 4 
    4567 Iteration cutoff | 2 
    4568  
    4569 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain C (#1) with
    4570 hsORC1-6_CDC6_60bpDNA.pdb, chain C (#2), sequence alignment score = 967.1 
    4571 RMSD between 139 pruned atom pairs is 1.275 angstroms; (across all 568 pairs:
    4572 7.882) 
    4573  
    4574 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca-
    4575 assembly1.cif, chain A (#3), sequence alignment score = 943 
    4576 RMSD between 228 pruned atom pairs is 1.005 angstroms; (across all 394 pairs:
    4577 5.169) 
    4578  
    4579 
    4580 > matchmaker #2,3 to (#1/A:400-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end)
    4581 
    4582 Computing secondary structure 
    4583 Parameters 
    4584 --- 
    4585 Chain pairing | bb 
    4586 Alignment algorithm | Needleman-Wunsch 
    4587 Similarity matrix | BLOSUM-62 
    4588 SS fraction | 0.3 
    4589 Gap open (HH/SS/other) | 18/18/6 
    4590 Gap extend | 1 
    4591 SS matrix |  |  | H | S | O 
    4592 ---|---|---|--- 
    4593 H | 6 | -9 | -6 
    4594 S |  | 6 | -6 
    4595 O |  |  | 4 
    4596 Iteration cutoff | 2 
    4597  
    4598 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with
    4599 hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 582.4 
    4600 RMSD between 128 pruned atom pairs is 1.051 angstroms; (across all 196 pairs:
    4601 2.238) 
    4602  
    4603 Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca-
    4604 assembly1.cif, chain A (#3), sequence alignment score = 527.5 
    4605 RMSD between 164 pruned atom pairs is 0.962 angstroms; (across all 191 pairs:
    4606 2.175) 
    4607  
    4608 
    4609 > select add #2
    4610 
    4611 21416 atoms, 21948 bonds, 13 pseudobonds, 2551 residues, 2 models selected 
    4612 
    4613 > select ~nucleic
    4614 
    4615 66692 atoms, 67966 bonds, 38 pseudobonds, 8239 residues, 7 models selected 
    4616 
    4617 > show sel surfaces
    4618 
    4619 > select clear
    4620 
    4621 > select ~nucleic
    4622 
    4623 66692 atoms, 67966 bonds, 38 pseudobonds, 8239 residues, 7 models selected 
    4624 
    4625 > hide sel cartoons
    4626 
    4627 > hide sel atoms
    4628 
    4629 > select clear
    4630 
    4631 > color #1 FFFF80
    4632 
    4633 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    4634 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    4635 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    4636 
    4637 > color #1 #FFFF80
    4638 
    4639 > color #1 #FF8080
    4640 
    4641 > color #2 #8080FF
    4642 
    4643 > color #2 #0080FF
    4644 
    4645 > color #3 #0080FF
    4646 
    4647 > color #3 lime
    4648 
    4649 > lighting full
    4650 
    4651 > graphics silhouettes false
    4652 
    4653 > lighting shadows false
    4654 
    4655 > lighting shadows true
    4656 
    4657 > lighting full
    4658 
    4659 > transparency 75 surfaces
    4660 
    4661 > hide #!2 models
    4662 
    4663 > hide #!3 models
    4664 
    4665 > show #!2 models
    4666 
    4667 > show #!3 models
    4668 
    4669 > nucleotides atoms
    4670 
    4671 > style nucleic stick
    4672 
    4673 Changed 4715 atom styles 
    4674 
    4675 > nucleotides fill
    4676 
    4677 > style nucleic stick
    4678 
    4679 Changed 4715 atom styles 
    4680 
    4681 > nucleotides tube/slab shape box
    4682 
    4683 > hide #!2 models
    4684 
    4685 > hide #!3 models
    4686 
    4687 > show #!3 models
    4688 
    4689 > show #!2 models
    4690 
    4691 > hide #!2 models
    4692 
    4693 > hide #!1 models
    4694 
    4695 > show #!1 models
    4696 
    4697 > show #!2 models
    4698 
    4699 > lighting soft
    4700 
    4701 > hide #!2 models
    4702 
    4703 > hide #!1 models
    4704 
    4705 > | #3/I) /Z /Z
    4706 
    4707 Expected fewer arguments 
    4708 
    4709 >
    4710 
    4711 Missing or invalid eighth argument: Expected a text string 
    4712 
    4713 > newcolor /A /B /C /D /E /F #1/G /Z /Z
    4714 
    4715 > newcolor /A /B /C /D /E /F #2/G /Z /Z
    4716 
    4717 > newcolor /A /B /C /D /E /F #3/I /Z /Z
    4718 
    4719 > transparency 75 surfaces
    4720 
    4721 > show #!2 models
    4722 
    4723 > hide #!3 models
    4724 
    4725 > show #!3 models
    4726 
    4727 > hide #!2 models
    4728 
    4729 > hide #!3 models
    4730 
    4731 > show #!2 models
    4732 
    4733 > show #!3 models
    4734 
    4735 > color #3 #0080FF
    4736 
    4737 > color #2 lime
    4738 
    4739 > newcolor /A /B /C /D /E /F #3/I /Z /Z
    4740 
    4741 > newcolor /A /B /C /D /E /F #2/G /Z /Z
    4742 
    4743 > transparency 75 surfaces
    4744 
    4745 > hide #!3 models
    4746 
    4747 > hide #!2 models
    4748 
    4749 > show #!1 models
    4750 
    4751 > show #!2 models
    4752 
    4753 > show #!3 models
    4754 
    4755 > hide #!2 models
    4756 
    4757 > hide #!3 models
    4758 
    4759 > show #!2 models
    4760 
    4761 > show #!3 models
    4762 
    4763 > hide #!2 models
    4764 
    4765 > hide #!3 models
    4766 
    4767 > save "/Users/jtbauer/Library/CloudStorage/OneDrive-
    4768 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/figures for
    4769 > posterpub/ylODC_54oriC_bend_updated.png" supersample 3
    4770 
    4771 > show #!2 models
    4772 
    4773 > hide #!1 models
    4774 
    4775 > save "/Users/jtbauer/Library/CloudStorage/OneDrive-
    4776 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/figures for
    4777 > posterpub/hsODC_bend_updated.png" supersample 3
    4778 
    4779 > show #!3 models
    4780 
    4781 > hide #!2 models
    4782 
    4783 > save "/Users/jtbauer/Library/CloudStorage/OneDrive-
    4784 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/figures for
    4785 > posterpub/scODC_bend_updated.png" supersample 3
    4786 
    4787 > show #!1 models
    4788 
    4789 > show #!2 models
    4790 
    4791 > transparency 50 surfaces
    4792 
    4793 > hide #!2 models
    4794 
    4795 > hide #!3 models
    4796 
    4797 > save "/Users/jtbauer/Library/CloudStorage/OneDrive-
    4798 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/figures for
    4799 > posterpub/ylODC_54oriC_bend_updated2.png" supersample 3
    4800 
    4801 > show #!2 models
    4802 
    4803 > hide #!1 models
    4804 
    4805 > save "/Users/jtbauer/Library/CloudStorage/OneDrive-
    4806 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/figures for
    4807 > posterpub/hsODC_bend_updated2.png" supersample 3
    4808 
    4809 > hide #!2 models
    4810 
    4811 > show #!3 models
    4812 
    4813 > save "/Users/jtbauer/Library/CloudStorage/OneDrive-
    4814 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/figures for
    4815 > posterpub/scODC_bend_updated2.png" supersample 3
    4816 
    4817 > ui tool show "Side View"
    4818 
    4819 > show #!1 models
    4820 
    4821 > hide #!3 models
    4822 
    4823 > show #!2 models
    4824 
    4825 > hide #!1 models
    4826 
    4827 > lighting full
    4828 
    4829 > show #!1 models
    4830 
    4831 > hide #!2 models
    4832 
    4833 > show #!3 models
    4834 
    4835 > hide #!1 models
    4836 
    4837 > show #!2 models
    4838 
    4839 > hide #!2 models
    4840 
    4841 > show #!2 models
    4842 
    4843 > hide #!2 models
    4844 
    4845 > show #!2 models
    4846 
    4847 > hide #!2 models
    4848 
    4849 > show #!2 models
    4850 
    4851 > hide #!2 models
    4852 
    4853 > show #!1 models
    4854 
    4855 > hide #!3 models
    4856 
    4857 > show #!2 models
    4858 
    4859 > hide #!2 models
    4860 
    4861 > show #!2 models
    4862 
    4863 > hide #!2 models
    4864 
    4865 > show #!2 models
    4866 
    4867 > hide #!1 models
    4868 
    4869 > show #!1 models
    4870 
    4871 > hide #!2 models
    4872 
    4873 > show #!2 models
    4874 
    4875 > hide #!2 models
    4876 
    4877 > show #!2 models
    4878 
    4879 > hide #!2 models
    4880 
    4881 > show #!2 models
    4882 
    4883 > hide #!2 models
    4884 
    4885 > show #!2 models
    4886 
    4887 > hide #!2 models
    4888 
    4889 > show #!2 models
    4890 
    4891 > show #!1-2 cartoons
    4892 
    4893 > hide #!1 models
    4894 
    4895 > show #!1 models
    4896 
    4897 > hide #!1 models
    4898 
    4899 > show #!1 models
    4900 
    4901 > close #2-3
    4902 
    4903 > hide surfaces
    4904 
    4905 > select /A,B,C,E,F
    4906 
    4907 16637 atoms, 16971 bonds, 4 pseudobonds, 2073 residues, 3 models selected 
    4908 
    4909 > hide sel cartoons
    4910 
    4911 > select /D:465
    4912 
    4913 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4914 
    4915 > show sel atoms
    4916 
    4917 > select /G:557
    4918 
    4919 11 atoms, 10 bonds, 1 residue, 1 model selected 
    4920 
    4921 > show sel atoms
    4922 
    4923 > select /G:548
    4924 
    4925 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4926 
    4927 > show sel atoms
    4928 
    4929 > select clear
    4930 
    4931 > lighting shadows false
    4932 
    4933 > modelfix
    4934 
    4935 Changed 25299 atom styles 
    4936 23699 atoms, 24145 bonds, 9 pseudobonds, 2970 residues, 2 models selected 
    4937 
    4938 > select /A,B,C,E,F
    4939 
    4940 16637 atoms, 16971 bonds, 4 pseudobonds, 2073 residues, 3 models selected 
    4941 
    4942 > hide sel cartoons
    4943 
    4944 > select clear
    4945 
    4946 > select /D:465
    4947 
    4948 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4949 
    4950 > show sel atoms
    4951 
    4952 > select /G:560
    4953 
    4954 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4955 
    4956 > select /G:557
    4957 
    4958 11 atoms, 10 bonds, 1 residue, 1 model selected 
    4959 
    4960 > show sel atoms
    4961 
    4962 > select /G:548
    4963 
    4964 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4965 
    4966 > show sel atoms
    4967 
    4968 > select clear
    4969 
    4970 > nucleotides tube/slab shape box
    4971 
    4972 > nucleotides fill
    4973 
    4974 > style nucleic stick
    4975 
    4976 Changed 1476 atom styles 
    4977 
    4978 > nucleotides fill
    4979 
    4980 > style nucleic stick
    4981 
    4982 Changed 1476 atom styles 
    4983 
    4984 > nucleotides ladder
    4985 
    4986 > nucleotides fill
    4987 
    4988 > style nucleic stick
    4989 
    4990 Changed 1476 atom styles 
    4991 
    4992 > nucleotides fill
    4993 
    4994 > style nucleic stick
    4995 
    4996 Changed 1476 atom styles 
    4997 
    4998 > nucleotides atoms
    4999 
    5000 > style nucleic stick
    5001 
    5002 Changed 1476 atom styles 
    5003 
    5004 > select clear
    5005 
    5006 > save "/Users/jtbauer/Library/CloudStorage/OneDrive-
    5007 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/figures for
    5008 > posterpub/Orc4-Cdc6-element-54bpOriC061-ver1.png" supersample 3
    5009 
    5010 > open "/Users/jtbauer/Library/CloudStorage/OneDrive-
    5011 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    5012 > structures/PDBs/ylODC_54bp-
    5013 > oriC061_complete/ylODC_54bpOriC061_rev30_PostPhenix.pdb"
    5014 
    5015 Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb #2 
    5016 --- 
    5017 Chain | Description 
    5018 A | No description available 
    5019 B | No description available 
    5020 C | No description available 
    5021 D | No description available 
    5022 E | No description available 
    5023 F | No description available 
    5024 G | No description available 
    5025 H | No description available 
    5026 I | No description available 
    5027  
    5028 
    5029 > modelfix
    5030 
    5031 Changed 50598 atom styles 
    5032 47398 atoms, 48290 bonds, 18 pseudobonds, 5940 residues, 4 models selected 
    5033 
    5034 > select /A,B,C,E,F
    5035 
    5036 33274 atoms, 33942 bonds, 8 pseudobonds, 4146 residues, 6 models selected 
    5037 
    5038 > hide sel cartoons
    5039 
    5040 > select ~nucleic
    5041 
    5042 47646 atoms, 48546 bonds, 22 pseudobonds, 5956 residues, 6 models selected 
    5043 
    5044 > hide sel atoms
    5045 
    5046 > select clear
    5047 
    5048 Drag select of 10 residues 
    5049 
    5050 > select clear
    5051 
    5052 Drag select of 2 residues 
    5053 
    5054 > show sel atoms
    5055 
    5056 > select #2/D:465@NZ
    5057 
    5058 1 atom, 1 residue, 1 model selected 
    5059 
    5060 > ui tool show "Add Hydrogens"
    5061 
    5062 > addh #!2
    5063 
    5064 Summary of feedback from adding hydrogens to
    5065 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2 
    5066 --- 
    5067 warnings | Not adding hydrogens to ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/H DG 8 P because it is missing heavy-atom bond partners 
    5068 Not adding hydrogens to ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/I DG 13 P
    5069 because it is missing heavy-atom bond partners 
    5070 notes | Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain A determined from SEQRES records 
    5071 Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain B determined
    5072 from SEQRES records 
    5073 No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain
    5074 C; guessing termini instead 
    5075 No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain
    5076 D; guessing termini instead 
    5077 No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain
    5078 E; guessing termini instead 
    5079 No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain
    5080 F; guessing termini instead 
    5081 No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain
    5082 G; guessing termini instead 
    5083 Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain H determined
    5084 from SEQRES records 
    5085 Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain I determined
    5086 from SEQRES records 
    5087 Chain-initial residues that are actual N termini:
    5088 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/A PRO 299,
    5089 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/B PRO 106,
    5090 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/C THR 6,
    5091 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D VAL 34,
    5092 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/E MET 1,
    5093 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/F PRO 179,
    5094 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G PRO 93,
    5095 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/C THR 6,
    5096 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/C ASN 72,
    5097 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D VAL 34,
    5098 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D GLN 127,
    5099 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D LEU 296,
    5100 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D PHE 436,
    5101 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/E MET 1,
    5102 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/E ASP 319,
    5103 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/F PRO 179,
    5104 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/F GLY 316,
    5105 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G PRO 93,
    5106 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G ALA 213,
    5107 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G THR 386,
    5108 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G VAL 439 
    5109 Chain-initial residues that are not actual N termini:
    5110 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/C ASN 72,
    5111 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D GLN 127,
    5112 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D LEU 296,
    5113 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D PHE 436,
    5114 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/E ASP 319,
    5115 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/F GLY 316,
    5116 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G ALA 213,
    5117 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G THR 386,
    5118 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G VAL 439 
    5119 Chain-final residues that are actual C termini:
    5120 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/A LEU 718,
    5121 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/B LEU 507,
    5122 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/C LEU 685,
    5123 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D ARG 511,
    5124 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/C ARG 29,
    5125 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/C LEU 685,
    5126 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D SER 123,
    5127 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D MET 285,
    5128 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D LEU 420,
    5129 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D ARG 511,
    5130 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/E MET 300,
    5131 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/E ASN 464,
    5132 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/F THR 307,
    5133 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/F LYS 349,
    5134 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G GLY 207,
    5135 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G HIS 335,
    5136 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G ASN 434,
    5137 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G LYS 602 
    5138 Chain-final residues that are not actual C termini:
    5139 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/C ARG 29,
    5140 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D SER 123,
    5141 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D MET 285,
    5142 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D LEU 420,
    5143 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/E ASN 464,
    5144 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/E MET 300,
    5145 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/F LYS 349,
    5146 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/F THR 307,
    5147 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G LYS 602,
    5148 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G GLY 207,
    5149 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G HIS 335,
    5150 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G ASN 434 
    5151 Chain-initial residues that are not actual 5' termini:
    5152 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/I DG 13 
    5153 Missing OXT added to C-terminal residue ylODC_54bpOriC061_rev30_PostPhenix.pdb
    5154 #2/B LEU 507 
    5155 Missing OXT added to C-terminal residue ylODC_54bpOriC061_rev30_PostPhenix.pdb
    5156 #2/C ARG 29 
    5157 Missing OXT added to C-terminal residue ylODC_54bpOriC061_rev30_PostPhenix.pdb
    5158 #2/D SER 123 
    5159 Missing OXT added to C-terminal residue ylODC_54bpOriC061_rev30_PostPhenix.pdb
    5160 #2/D MET 285 
    5161 Missing OXT added to C-terminal residue ylODC_54bpOriC061_rev30_PostPhenix.pdb
    5162 #2/D LEU 420 
    5163 8 messages similar to the above omitted 
    5164 3052 hydrogen bonds 
    5165 Adding 'H' to ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/C ASN 72 
    5166 Adding 'H' to ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D GLN 127 
    5167 Adding 'H' to ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D LEU 296 
    5168 Adding 'H' to ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D PHE 436 
    5169 Adding 'H' to ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/E ASP 319 
    5170 4 messages similar to the above omitted 
    5171 24712 hydrogens added 
    5172  
    5173 
    5174 > select #1/D:465@CE
    5175 
    5176 1 atom, 1 residue, 1 model selected 
    5177 
    5178 > ui tool show "Add Hydrogens"
    5179 
    5180 > addh #!1
    5181 
    5182 Summary of feedback from adding hydrogens to
    5183 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1 
    5184 --- 
    5185 warnings | Not adding hydrogens to ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/H DG 8 P because it is missing heavy-atom bond partners 
    5186 Not adding hydrogens to ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/I DG 13 P
    5187 because it is missing heavy-atom bond partners 
    5188 notes | Termini for ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) chain A determined from SEQRES records 
    5189 Termini for ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) chain B determined
    5190 from SEQRES records 
    5191 No usable SEQRES records for ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) chain
    5192 C; guessing termini instead 
    5193 No usable SEQRES records for ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) chain
    5194 D; guessing termini instead 
    5195 No usable SEQRES records for ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) chain
    5196 E; guessing termini instead 
    5197 No usable SEQRES records for ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) chain
    5198 F; guessing termini instead 
    5199 No usable SEQRES records for ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) chain
    5200 G; guessing termini instead 
    5201 Termini for ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) chain H determined
    5202 from SEQRES records 
    5203 Termini for ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) chain I determined
    5204 from SEQRES records 
    5205 Chain-initial residues that are actual N termini:
    5206 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/A PRO 299,
    5207 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/B PRO 106,
    5208 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/C THR 6,
    5209 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D VAL 34,
    5210 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/E MET 1,
    5211 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/F PRO 179,
    5212 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G PRO 93,
    5213 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/C THR 6,
    5214 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/C ASN 72,
    5215 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D VAL 34,
    5216 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D GLN 127,
    5217 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D LEU 296,
    5218 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D PHE 436,
    5219 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/E MET 1,
    5220 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/E ASP 319,
    5221 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/F PRO 179,
    5222 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/F GLY 316,
    5223 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G PRO 93,
    5224 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G ALA 213,
    5225 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G THR 386,
    5226 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G VAL 439 
    5227 Chain-initial residues that are not actual N termini:
    5228 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/C ASN 72,
    5229 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D GLN 127,
    5230 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D LEU 296,
    5231 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D PHE 436,
    5232 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/E ASP 319,
    5233 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/F GLY 316,
    5234 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G ALA 213,
    5235 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G THR 386,
    5236 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G VAL 439 
    5237 Chain-final residues that are actual C termini:
    5238 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/A LEU 718,
    5239 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/B LEU 507,
    5240 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/C LEU 685,
    5241 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D ARG 511,
    5242 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/C ARG 29,
    5243 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/C LEU 685,
    5244 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D SER 123,
    5245 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D MET 285,
    5246 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D LEU 420,
    5247 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D ARG 511,
    5248 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/E MET 300,
    5249 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/E ASN 464,
    5250 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/F THR 307,
    5251 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/F LYS 349,
    5252 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G GLY 207,
    5253 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G HIS 335,
    5254 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G ASN 434,
    5255 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G LYS 602 
    5256 Chain-final residues that are not actual C termini:
    5257 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/C ARG 29,
    5258 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D SER 123,
    5259 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D MET 285,
    5260 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D LEU 420,
    5261 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/E ASN 464,
    5262 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/E MET 300,
    5263 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/F LYS 349,
    5264 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/F THR 307,
    5265 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G LYS 602,
    5266 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G GLY 207,
    5267 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G HIS 335,
    5268 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G ASN 434 
    5269 Chain-initial residues that are not actual 5' termini:
    5270 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/I DG 13 
    5271 Missing OXT added to C-terminal residue ylODC_54bpOriC061_rev29_PostPhenix.pdb
    5272 #1/B LEU 507 
    5273 Missing OXT added to C-terminal residue ylODC_54bpOriC061_rev29_PostPhenix.pdb
    5274 #1/C ARG 29 
    5275 Missing OXT added to C-terminal residue ylODC_54bpOriC061_rev29_PostPhenix.pdb
    5276 #1/D SER 123 
    5277 Missing OXT added to C-terminal residue ylODC_54bpOriC061_rev29_PostPhenix.pdb
    5278 #1/D MET 285 
    5279 Missing OXT added to C-terminal residue ylODC_54bpOriC061_rev29_PostPhenix.pdb
    5280 #1/D LEU 420 
    5281 8 messages similar to the above omitted 
    5282 3042 hydrogen bonds 
    5283 Adding 'H' to ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/C ASN 72 
    5284 Adding 'H' to ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D GLN 127 
    5285 Adding 'H' to ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D LEU 296 
    5286 Adding 'H' to ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D PHE 436 
    5287 Adding 'H' to ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/E ASP 319 
    5288 4 messages similar to the above omitted 
    5289 24712 hydrogens added 
    5290  
    5291 
    5292 > ui tool show H-Bonds
    5293 
    5294 > select #1/D:465
    5295 
    5296 22 atoms, 21 bonds, 1 residue, 1 model selected 
    5297 
    5298 > hbonds sel restrict #1/H,I twoColors true intraRes false reveal true log
    5299 > true
    5300    
    5301    
    5302     Finding intermodel H-bonds
    5303     Finding intramodel H-bonds
    5304     Constraints relaxed by 0.4 angstroms and 20 degrees
    5305     Models used:
    5306         1 ylODC_54bpOriC061_rev29_PostPhenix.pdb
    5307    
    5308     2 H-bonds
    5309     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    5310     ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D LYS 465 NZ  ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/I DG 31 O6  ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D LYS 465 HZ1  2.845  1.875
    5311     ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D LYS 465 NZ  ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/I DG 32 N7  ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D LYS 465 HZ2  3.459  2.599
    5312    
    5313 
    5314  
    5315 2 hydrogen bonds found 
    5316 0 strict hydrogen bonds found 
    5317 
    5318 > select #2/D:465
    5319 
    5320 22 atoms, 21 bonds, 1 residue, 1 model selected 
    5321 
    5322 > ui tool show H-Bonds
    5323 
    5324 > hbonds sel restrict #2/H,I twoColors true intraRes false reveal true log
    5325 > true
    5326    
    5327    
    5328     Finding intermodel H-bonds
    5329     Finding intramodel H-bonds
    5330     Constraints relaxed by 0.4 angstroms and 20 degrees
    5331     Models used:
    5332         2 ylODC_54bpOriC061_rev30_PostPhenix.pdb
    5333    
    5334     2 H-bonds
    5335     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    5336     ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D LYS 465 NZ  ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/I DG 31 O6  ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D LYS 465 HZ1  2.363  1.498
    5337     ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D LYS 465 NZ  ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/I DG 32 O6  ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D LYS 465 HZ2  2.546  1.684
    5338    
    5339 
    5340  
    5341 2 hydrogen bonds found 
    5342 0 strict hydrogen bonds found 
    5343 
    5344 > ui tool show "Side View"
    5345 
    5346 > close #2
    5347 
    5348 > open "/Users/jtbauer/Library/CloudStorage/OneDrive-
    5349 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    5350 > structures/PDBs/ylODC_54bp-
    5351 > oriC061_complete/ylODC_54bpOriC061_rev30_PostPhenix.pdb" format pdb
    5352 
    5353 Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb #2 
    5354 --- 
    5355 Chain | Description 
    5356 A | No description available 
    5357 B | No description available 
    5358 C | No description available 
    5359 D | No description available 
    5360 E | No description available 
    5361 F | No description available 
    5362 G | No description available 
    5363 H | No description available 
    5364 I | No description available 
    5365  
    5366 
    5367 > modelfix
    5368 
    5369 Changed 75323 atom styles 
    5370 71260 atoms, 72152 bonds, 18 pseudobonds, 5940 residues, 4 models selected 
    5371 
    5372 > close #1
    5373 
    5374 > select /A,B,C,E,F
    5375 
    5376 16637 atoms, 16971 bonds, 4 pseudobonds, 2073 residues, 3 models selected 
    5377 
    5378 > hide sel cartoons
    5379 
    5380 > select clear
    5381 
    5382 > select ~nucleic
    5383 
    5384 23823 atoms, 24273 bonds, 11 pseudobonds, 2978 residues, 3 models selected 
    5385 
    5386 > hide sel atoms
    5387 
    5388 > select clear
    5389 
    5390 > select /D:465
    5391 
    5392 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5393 
    5394 > show sel atoms
    5395 
    5396 > select /G:548
    5397 
    5398 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5399 
    5400 > show sel atoms
    5401 
    5402 > select /G:557
    5403 
    5404 11 atoms, 10 bonds, 1 residue, 1 model selected 
    5405 
    5406 > show sel atoms
    5407 
    5408 > select clear
    5409 
    5410 > save "/Users/jtbauer/Library/CloudStorage/OneDrive-
    5411 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/figures for
    5412 > posterpub/Orc4-Cdc6-element-54bpOriC061-ver1.png" supersample 3
    5413 
    5414 > select clear
    5415 
    5416 > select /A,B,C,E,F
    5417 
    5418 16637 atoms, 16971 bonds, 4 pseudobonds, 2073 residues, 3 models selected 
    5419 
    5420 > show sel atoms
    5421 
    5422 > undo
    5423 
    5424 > show sel cartoons
    5425 
    5426 > color sel #808080
    5427 
    5428 > color sel #AAAAAA
    5429 
    5430 > color sel #BBBBBB
    5431 
    5432 > transparency 70 r
    5433 
    5434 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
    5435 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword 
    5436 
    5437 > transparency 70 cartoons
    5438 
    5439 > select clear
    5440 
    5441 > undo
    5442 
    5443 > transparency 0 ribbons
    5444 
    5445 > transparency 0 r
    5446 
    5447 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
    5448 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword 
    5449 
    5450 > transparency 0 sel
    5451 
    5452 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
    5453 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword 
    5454 
    5455 > transparency sel 70 target c
    5456 
    5457 > transparency sel 90 target c
    5458 
    5459 > transparency sel 80 target c
    5460 
    5461 > transparency sel 75 target c
    5462 
    5463 > select clear
    5464 
    5465 > select /A,B,C,E,F
    5466 
    5467 16637 atoms, 16971 bonds, 4 pseudobonds, 2073 residues, 3 models selected 
    5468 
    5469 > hide sel cartoons
    5470 
    5471 > show sel cartoons
    5472 
    5473 > select clear
    5474 
    5475 > turn x 2 180
    5476 
    5477 > wait 180
    5478 
    5479 > turn y 2 180
    5480 
    5481 > wait 180
    5482 
    5483 > turn y 2 180
    5484 
    5485 > wait 180
    5486 
    5487 > select /A,B,C,E,F
    5488 
    5489 16637 atoms, 16971 bonds, 4 pseudobonds, 2073 residues, 3 models selected 
    5490 
    5491 > hide sel cartoons
    5492 
    5493 > select up
    5494 
    5495 25299 atoms, 25927 bonds, 11 pseudobonds, 3050 residues, 3 models selected 
    5496 
    5497 > select up
    5498 
    5499 25299 atoms, 25927 bonds, 11 pseudobonds, 3050 residues, 3 models selected 
    5500 
    5501 > select clear
    5502 
    5503 > turn y 2 180
    5504 
    5505 > wait 180
    5506 
    5507 > turn y 2 180
    5508 
    5509 > wait 180
    5510 
    5511 > turn y 2 180
    5512 
    5513 > wait 180
    5514 
    5515 > turn y 2 180
    5516 
    5517 > wait 180
    5518 
    5519 > turn y 2 180
    5520 
    5521 > wait 180
    5522 
    5523 > select /I:32@O6
    5524 
    5525 1 atom, 1 residue, 1 model selected 
    5526 
    5527 > turn y 2 180 centerOn sel ; wait 180
    5528 
    5529 Expected a keyword 
    5530 
    5531 > turn y 2 180 centerOn sel ; wait 180
    5532 
    5533 Expected a keyword 
    5534 
    5535 > turn y 2 180 center sel
    5536 
    5537 > wait 180
    5538 
    5539 > select clear
    5540 
    5541 > turn y 2 180 center sel ; wait 180
    5542 
    5543 Invalid "center" argument: Center argument no objects specified 
    5544 
    5545 > select /I:31@O6
    5546 
    5547 1 atom, 1 residue, 1 model selected 
    5548 
    5549 > turn y 2 180 center sel
    5550 
    5551 > wait 180
    5552 
    5553 > turn y 2 180 center (#1/I:31 | #1/H:24) ; wait 180
    5554 
    5555 Invalid "center" argument: Center argument no objects specified 
    5556 
    5557 > select clear
    5558 
    5559 > turn y 2 180 center (#1/I:31 | #1/H:24) ; wait 180
    5560 
    5561 Invalid "center" argument: Center argument no objects specified 
    5562 
    5563 > turn y 2 180 center #1/I:31 ; wait 180
    5564 
    5565 Invalid "center" argument: Center argument no objects specified 
    5566 
    5567 > turn y 2 180 models #1/I:31
    5568 
    5569 > wait 180
    5570 
    5571 > turn y 2 180 models #1/I:31
    5572 
    5573 > wait 180
    5574 
    5575 > turn y 2 180 models #1/I:31
    5576 
    5577 > turn y 2 180 models #1 center #1/I:31
    5578 
    5579 Invalid "center" argument: Center argument no objects specified 
    5580 
    5581 > select clear
    5582 
    5583 > select /I:31@O6
    5584 
    5585 1 atom, 1 residue, 1 model selected 
    5586 
    5587 > select clear
    5588 
    5589 > turn y 2 180 models #1 center #1/I:31@O6
    5590 
    5591 Invalid "center" argument: Center argument no objects specified 
    5592 
    5593 > turn y 2 180 center #1/I:31@O6
    5594 
    5595 Invalid "center" argument: Center argument no objects specified 
    5596 
    5597 > select /I:31@O6
    5598 
    5599 1 atom, 1 residue, 1 model selected 
    5600 
    5601 > turn y 2 180 center /I:31@O6
    5602 
    5603 > select clear
    5604 
    5605 > turn y 2 180 center /I:31@O6
    5606 
    5607 > turn y 1 360 center /I:31@O6
    5608 
    5609 > wait 360
    5610 
    5611 > turn y 1 360 center /I:31@O6
    5612 
    5613 > wait 360
    5614 
    5615 > movie record supersample 3
    5616 
    5617 > turn y 2 180 center /I:31@O6
    5618 
    5619 > wait 180
    5620 
    5621 > movie encode "/Users/jtbauer/Library/CloudStorage/OneDrive-
    5622 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/figures for
    5623 > posterpub/Orc4-Cdc6-binding-region-54bpOriC.mp4"
    5624 
    5625 Movie saved to /Users/jtbauer/.../figures for posterpub/Orc4-Cdc6-binding-
    5626 region-54bpOriC.mp4 
    5627  
    5628 
    5629 > turn y 2 180 center /I:31@O6
    5630 
    5631 > wait 180
    5632 
    5633 > turn y 2 180 center /I:31@O6
    5634 
    5635 > wait 180
    5636 
    5637 > turn y 2 180 center /I:31@O6
    5638 
    5639 > wait 180
    5640 
    5641 > turn y 2 180 center /I:31@O6
    5642 
    5643 > wait 180
    5644 
    5645 > turn y 2 180 center /I:31@O6
    5646 
    5647 > wait 180
    5648 
    5649 > turn y 2 180 center /I:31@O6
    5650 
    5651 > wait 180
    5652 
    5653 > turn y 2 180 center /I:31@O6
    5654 
    5655 > wait 180
    5656 
    5657 > turn y 2 180 center /I:31@O6
    5658 
    5659 > wait 180
    5660 
    5661 > turn y 2 180 center /I:31@O6
    5662 
    5663 > wait 180
    5664 
    5665 > movie record supersample 3
    5666 
    5667 > turn y 2 180 center /I:31@O6
    5668 
    5669 > wait 180
    5670 
    5671 > movie encode "/Users/jtbauer/Library/CloudStorage/OneDrive-
    5672 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/figures for
    5673 > posterpub/Orc4-Cdc6-binding-region-54bpOriC-camera2.mp4"
    5674 
    5675 Movie saved to /Users/jtbauer/.../figures for posterpub/Orc4-Cdc6-binding-
    5676 region-54bpOriC-camera2.mp4 
    5677  
    5678 
    5679 > show cartoons
    5680 
    5681 > transparency 0 cartoons
    5682 
    5683 > modelfix
    5684 
    5685 Changed 25299 atom styles 
    5686 23699 atoms, 24145 bonds, 9 pseudobonds, 2970 residues, 2 models selected 
    5687 
    5688 > select nucleic
    5689 
    5690 1476 atoms, 1654 bonds, 72 residues, 1 model selected 
    5691 
    5692 > ui tool show "Add Hydrogens"
    5693 
    5694 > addh #!2
    5695 
    5696 Summary of feedback from adding hydrogens to
    5697 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2 
    5698 --- 
    5699 warnings | Not adding hydrogens to /H DG 8 P because it is missing heavy-atom bond partners 
    5700 Not adding hydrogens to /I DG 13 P because it is missing heavy-atom bond
    5701 partners 
    5702 notes | Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain A determined from SEQRES records 
    5703 Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain B determined
    5704 from SEQRES records 
    5705 No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain
    5706 C; guessing termini instead 
    5707 No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain
    5708 D; guessing termini instead 
    5709 No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain
    5710 E; guessing termini instead 
    5711 No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain
    5712 F; guessing termini instead 
    5713 No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain
    5714 G; guessing termini instead 
    5715 Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain H determined
    5716 from SEQRES records 
    5717 Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain I determined
    5718 from SEQRES records 
    5719 Chain-initial residues that are actual N termini: /A PRO 299, /B PRO 106, /C
    5720 THR 6, /D VAL 34, /E MET 1, /F PRO 179, /G PRO 93, /C THR 6, /C ASN 72, /D VAL
    5721 34, /D GLN 127, /D LEU 296, /D PHE 436, /E MET 1, /E ASP 319, /F PRO 179, /F
    5722 GLY 316, /G PRO 93, /G ALA 213, /G THR 386, /G VAL 439 
    5723 Chain-initial residues that are not actual N termini: /C ASN 72, /D GLN 127,
    5724 /D LEU 296, /D PHE 436, /E ASP 319, /F GLY 316, /G ALA 213, /G THR 386, /G VAL
    5725 439 
    5726 Chain-final residues that are actual C termini: /A LEU 718, /B LEU 507, /C LEU
    5727 685, /D ARG 511, /C ARG 29, /C LEU 685, /D SER 123, /D MET 285, /D LEU 420, /D
    5728 ARG 511, /E MET 300, /E ASN 464, /F THR 307, /F LYS 349, /G GLY 207, /G HIS
    5729 335, /G ASN 434, /G LYS 602 
    5730 Chain-final residues that are not actual C termini: /C ARG 29, /D SER 123, /D
    5731 MET 285, /D LEU 420, /E ASN 464, /E MET 300, /F LYS 349, /F THR 307, /G LYS
    5732 602, /G GLY 207, /G HIS 335, /G ASN 434 
    5733 Chain-initial residues that are not actual 5' termini: /I DG 13 
    5734 Missing OXT added to C-terminal residue /B LEU 507 
    5735 Missing OXT added to C-terminal residue /C ARG 29 
    5736 Missing OXT added to C-terminal residue /D SER 123 
    5737 Missing OXT added to C-terminal residue /D MET 285 
    5738 Missing OXT added to C-terminal residue /D LEU 420 
    5739 8 messages similar to the above omitted 
    5740 3052 hydrogen bonds 
    5741 Adding 'H' to /C ASN 72 
    5742 Adding 'H' to /D GLN 127 
    5743 Adding 'H' to /D LEU 296 
    5744 Adding 'H' to /D PHE 436 
    5745 Adding 'H' to /E ASP 319 
    5746 4 messages similar to the above omitted 
    5747 24712 hydrogens added 
    5748  
    5749 
    5750 > ui tool show H-Bonds
    5751 
    5752 > hbonds sel restrict #2/A,B,C,D,E,F,G twoColors true intraRes false reveal
    5753 > true log true
    5754    
    5755    
    5756     Finding intermodel H-bonds
    5757     Finding intramodel H-bonds
    5758     Constraints relaxed by 0.4 angstroms and 20 degrees
    5759     Models used:
    5760         2 ylODC_54bpOriC061_rev30_PostPhenix.pdb
    5761    
    5762     61 H-bonds
    5763     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    5764     /A ARG 301 NE   /I DC 47 OP1  /A ARG 301 HE    3.042  2.096
    5765     /A ARG 301 NH1  /H DT 10 O2   /A ARG 301 HH12  2.780  1.937
    5766     /A ARG 301 NH1  /H DC 11 O4'  /A ARG 301 HH11  2.808  1.918
    5767     /A ARG 301 NH2  /I DT 46 O2   /A ARG 301 HH22  3.419  2.726
    5768     /A ARG 301 NH2  /I DC 47 OP1  /A ARG 301 HH21  3.241  2.383
    5769     /A PHE 303 N    /H DC 13 OP1  /A PHE 303 H     2.683  1.713
    5770     /A LYS 305 NZ   /H DA 14 OP1  /A LYS 305 HZ1   3.005  2.074
    5771     /A ASN 435 ND2  /H DC 13 OP2  /A ASN 435 HD22  2.896  1.911
    5772     /A ASN 436 ND2  /H DC 13 OP2  /A ASN 436 HD22  3.172  2.251
    5773     /B LYS 148 NZ   /I DG 19 OP1  /B LYS 148 HZ3   2.880  2.062
    5774     /B ARG 150 NH1  /H DG 35 O6   /B ARG 150 HH12  3.317  2.492
    5775     /B ARG 150 NH1  /I DG 19 O6   /B ARG 150 HH12  3.200  2.518
    5776     /B ARG 150 NH2  /H DG 35 O6   /B ARG 150 HH22  2.932  1.954
    5777     /B GLY 153 N    /H DT 34 OP2  /B GLY 153 H     2.955  1.965
    5778     /B LYS 248 NZ   /I DA 37 O3'  /B LYS 248 HZ1   3.058  2.307
    5779     /B LYS 279 N    /I DA 39 OP1  /B LYS 279 H     3.012  2.176
    5780     /B ASP 280 N    /I DA 39 OP1  /B ASP 280 H     3.419  2.439
    5781     /C LYS 188 NZ   /H DT 18 OP1  /C LYS 188 HZ1   2.597  1.602
    5782     /C ARG 219 N    /I DT 41 OP1  /C ARG 219 H     2.860  1.859
    5783     /C ARG 219 NH1  /I DT 40 OP1  /C ARG 219 HH11  2.808  2.044
    5784     /C ARG 220 NH1  /H DT 16 O2   /C ARG 220 HH11  3.328  2.600
    5785     /C ARG 220 NH1  /I DT 40 O2   /C ARG 220 HH11  3.062  2.380
    5786     /C TYR 223 OH   /H DA 17 O3'  /C TYR 223 HH    2.926  2.064
    5787     /C TYR 607 OH   /H DC 32 OP2  /C TYR 607 HH    3.278  2.327
    5788     /C ARG 672 N    /H DC 32 OP1  /C ARG 672 H     2.895  1.905
    5789     /C ARG 672 NH1  /I DT 25 O2   /C ARG 672 HH12  2.707  1.845
    5790     /C ARG 672 NH2  /I DT 25 O2   /C ARG 672 HH22  3.408  2.771
    5791     /C LYS 673 NZ   /H DA 33 OP1  /C LYS 673 HZ1   2.886  1.972
    5792     /D LYS 168 NZ   /H DA 14 N3   /D LYS 168 HZ1   2.838  1.847
    5793     /D SER 169 OG   /H DA 15 OP2  /D SER 169 HG    2.801  1.842
    5794     /D ILE 170 N    /H DA 15 OP2  /D ILE 170 H     3.077  2.202
    5795     /D SER 463 OG   /I DG 30 OP1  /D SER 463 HG    2.493  1.565
    5796     /D LYS 465 NZ   /I DG 31 O6   /D LYS 465 HZ1   2.363  1.498
    5797     /D LYS 465 NZ   /I DG 32 O6   /D LYS 465 HZ2   2.546  1.684
    5798     /E ARG 76 NH1   /H DA 17 OP1  /E ARG 76 HH11   3.235  2.257
    5799     /E ARG 340 NE   /I DG 19 O5'  /E ARG 340 HE    3.009  2.192
    5800     /E ARG 340 NE   /I DG 19 OP2  /E ARG 340 HE    2.873  1.974
    5801     /E ARG 340 NH2  /I DG 19 OP2  /E ARG 340 HH21  3.300  2.551
    5802     /E TYR 341 OH   /I DC 20 OP1  /E TYR 341 HH    2.940  2.219
    5803     /E ARG 357 NH1  /I DT 16 O2   /E ARG 357 HH12  2.784  1.882
    5804     /E ARG 357 NH2  /I DT 16 O2   /E ARG 357 HH22  2.882  2.025
    5805     /E ARG 357 NH2  /I DT 16 O4'  /E ARG 357 HH22  3.135  2.386
    5806     /E GLU 358 N    /H DG 41 OP1  /E GLU 358 H     2.888  1.905
    5807     /E THR 359 OG1  /I DG 19 OP1  /E THR 359 HG1   2.802  2.243
    5808     /E ARG 362 N    /I DG 19 O3'  /E ARG 362 H     3.350  2.344
    5809     /E ARG 362 NH1  /I DT 18 O2   /E ARG 362 HH12  2.975  2.081
    5810     /E ARG 362 NH1  /I DG 19 O4'  /E ARG 362 HH11  3.022  2.183
    5811     /E ARG 362 NH2  /H DT 38 O2   /E ARG 362 HH22  2.881  2.130
    5812     /E LYS 363 N    /I DC 20 OP2  /E LYS 363 H     3.408  2.442
    5813     /E LYS 363 NZ   /I DA 21 OP1  /E LYS 363 HZ1   2.944  1.968
    5814     /G GLY 546 N    /H DA 27 OP1  /G GLY 546 H     2.915  2.028
    5815     /G LYS 547 NZ   /I DG 32 OP1  /G LYS 547 HZ1   2.552  1.558
    5816     /G LYS 548 NZ   /I DT 29 O2   /G LYS 548 HZ3   3.197  2.248
    5817     /G ASN 553 N    /I DG 32 OP2  /G ASN 553 H     2.957  2.079
    5818     /G ARG 557 NH1  /I DG 34 O6   /G ARG 557 HH12  2.913  1.906
    5819     /G ARG 557 NH2  /I DG 34 N7   /G ARG 557 HH22  2.372  1.443
    5820     /G GLY 561 N    /H DT 16 OP2  /G GLY 561 H     2.846  2.111
    5821     /G THR 563 OG1  /H DT 16 OP1  /G THR 563 HG1   3.027  2.078
    5822     /G ALA 565 N    /H DA 17 OP2  /G ALA 565 H     2.576  1.574
    5823     /G ARG 574 NH2  /I DG 32 OP1  /G ARG 574 HH21  3.076  2.128
    5824     /G LYS 581 NZ   /H DA 26 OP2  /G LYS 581 HZ1   3.143  2.140
    5825    
    5826 
    5827  
    5828 61 hydrogen bonds found 
    5829 21 strict hydrogen bonds found 
    5830 
    5831 > split #2
    5832 
    5833 Split ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) into 9 models 
    5834 Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb A #2.1 
    5835 --- 
    5836 Chain | Description 
    5837 A | No description available 
    5838  
    5839 Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb B #2.2 
    5840 --- 
    5841 Chain | Description 
    5842 B | No description available 
    5843  
    5844 Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb C #2.3 
    5845 --- 
    5846 Chain | Description 
    5847 C | No description available 
    5848  
    5849 Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb D #2.4 
    5850 --- 
    5851 Chain | Description 
    5852 D | No description available 
    5853  
    5854 Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb E #2.5 
    5855 --- 
    5856 Chain | Description 
    5857 E | No description available 
    5858  
    5859 Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb F #2.6 
    5860 --- 
    5861 Chain | Description 
    5862 F | No description available 
    5863  
    5864 Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb G #2.7 
    5865 --- 
    5866 Chain | Description 
    5867 G | No description available 
    5868  
    5869 Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb H #2.8 
    5870 --- 
    5871 Chain | Description 
    5872 H | No description available 
    5873  
    5874 Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb I #2.9 
    5875 --- 
    5876 Chain | Description 
    5877 I | No description available 
    5878  
    5879 
    5880 > select add #2.8
    5881 
    5882 1170 atoms, 1262 bonds, 37 residues, 1 model selected 
    5883 
    5884 > select add #2.9
    5885 
    5886 2291 atoms, 2469 bonds, 72 residues, 2 models selected 
    5887 
    5888 > hbonds sel restrict #2/A,B,C,D,E,F,G twoColors true intraRes false reveal
    5889 > true log true
    5890    
    5891    
    5892     Finding intermodel H-bonds
    5893     Finding intramodel H-bonds
    5894     Constraints relaxed by 0.4 angstroms and 20 degrees
    5895     Models used:
    5896         2.7 ylODC_54bpOriC061_rev30_PostPhenix.pdb G
    5897         2.9 ylODC_54bpOriC061_rev30_PostPhenix.pdb I
    5898         2.8 ylODC_54bpOriC061_rev30_PostPhenix.pdb H
    5899         2.1 ylODC_54bpOriC061_rev30_PostPhenix.pdb A
    5900         2.2 ylODC_54bpOriC061_rev30_PostPhenix.pdb B
    5901         2.3 ylODC_54bpOriC061_rev30_PostPhenix.pdb C
    5902         2.4 ylODC_54bpOriC061_rev30_PostPhenix.pdb D
    5903         2.5 ylODC_54bpOriC061_rev30_PostPhenix.pdb E
    5904         2.6 ylODC_54bpOriC061_rev30_PostPhenix.pdb F
    5905    
    5906     0 H-bonds
    5907     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    5908    
    5909 
    5910  
    5911 0 hydrogen bonds found 
    5912 0 strict hydrogen bonds found 
    5913 
    5914 > close #2
    5915 
    5916 > open "/Users/jtbauer/Library/CloudStorage/OneDrive-
    5917 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    5918 > structures/PDBs/ylODC_54bp-
    5919 > oriC061_complete/ylODC_54bpOriC061_rev30_PostPhenix.pdb" format pdb
    5920 
    5921 Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb #1 
    5922 --- 
    5923 Chain | Description 
    5924 A | No description available 
    5925 B | No description available 
    5926 C | No description available 
    5927 D | No description available 
    5928 E | No description available 
    5929 F | No description available 
    5930 G | No description available 
    5931 H | No description available 
    5932 I | No description available 
    5933  
    5934 
    5935 > modelfix
    5936 
    5937 Changed 25299 atom styles 
    5938 23699 atoms, 24145 bonds, 9 pseudobonds, 2970 residues, 2 models selected 
    5939 
    5940 > select nucleic
    5941 
    5942 1476 atoms, 1654 bonds, 72 residues, 1 model selected 
    5943 
    5944 > hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
    5945 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    5946 > structures/PDBs/ylODC_54bp-oriC061_complete/hbond-generation2" restrict
    5947 > #2/A,B,C,D,E,F,G twoColors true intraRes false reveal true log true
    5948 
    5949 'restrict' atom specifier selects no atoms 
    5950 
    5951 > ui tool show "Add Hydrogens"
    5952 
    5953 > addh #!1
    5954 
    5955 Summary of feedback from adding hydrogens to
    5956 ylODC_54bpOriC061_rev30_PostPhenix.pdb #1 
    5957 --- 
    5958 warnings | Not adding hydrogens to /H DG 8 P because it is missing heavy-atom bond partners 
    5959 Not adding hydrogens to /I DG 13 P because it is missing heavy-atom bond
    5960 partners 
    5961 notes | Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#1) chain A determined from SEQRES records 
    5962 Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#1) chain B determined
    5963 from SEQRES records 
    5964 No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#1) chain
    5965 C; guessing termini instead 
    5966 No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#1) chain
    5967 D; guessing termini instead 
    5968 No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#1) chain
    5969 E; guessing termini instead 
    5970 No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#1) chain
    5971 F; guessing termini instead 
    5972 No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#1) chain
    5973 G; guessing termini instead 
    5974 Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#1) chain H determined
    5975 from SEQRES records 
    5976 Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#1) chain I determined
    5977 from SEQRES records 
    5978 Chain-initial residues that are actual N termini: /A PRO 299, /B PRO 106, /C
    5979 THR 6, /D VAL 34, /E MET 1, /F PRO 179, /G PRO 93, /C THR 6, /C ASN 72, /D VAL
    5980 34, /D GLN 127, /D LEU 296, /D PHE 436, /E MET 1, /E ASP 319, /F PRO 179, /F
    5981 GLY 316, /G PRO 93, /G ALA 213, /G THR 386, /G VAL 439 
    5982 Chain-initial residues that are not actual N termini: /C ASN 72, /D GLN 127,
    5983 /D LEU 296, /D PHE 436, /E ASP 319, /F GLY 316, /G ALA 213, /G THR 386, /G VAL
    5984 439 
    5985 Chain-final residues that are actual C termini: /A LEU 718, /B LEU 507, /C LEU
    5986 685, /D ARG 511, /C ARG 29, /C LEU 685, /D SER 123, /D MET 285, /D LEU 420, /D
    5987 ARG 511, /E MET 300, /E ASN 464, /F THR 307, /F LYS 349, /G GLY 207, /G HIS
    5988 335, /G ASN 434, /G LYS 602 
    5989 Chain-final residues that are not actual C termini: /C ARG 29, /D SER 123, /D
    5990 MET 285, /D LEU 420, /E ASN 464, /E MET 300, /F LYS 349, /F THR 307, /G LYS
    5991 602, /G GLY 207, /G HIS 335, /G ASN 434 
    5992 Chain-initial residues that are not actual 5' termini: /I DG 13 
    5993 Missing OXT added to C-terminal residue /B LEU 507 
    5994 Missing OXT added to C-terminal residue /C ARG 29 
    5995 Missing OXT added to C-terminal residue /D SER 123 
    5996 Missing OXT added to C-terminal residue /D MET 285 
    5997 Missing OXT added to C-terminal residue /D LEU 420 
    5998 8 messages similar to the above omitted 
    5999 3052 hydrogen bonds 
    6000 Adding 'H' to /C ASN 72 
    6001 Adding 'H' to /D GLN 127 
    6002 Adding 'H' to /D LEU 296 
    6003 Adding 'H' to /D PHE 436 
    6004 Adding 'H' to /E ASP 319 
    6005 4 messages similar to the above omitted 
    6006 24712 hydrogens added 
    6007  
    6008 
    6009 > hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
    6010 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    6011 > structures/PDBs/ylODC_54bp-oriC061_complete/hbond-generation2" restrict
    6012 > #1/A,B,C,D,E,F,G twoColors true intraRes false reveal true log true
    6013    
    6014    
    6015     Finding intermodel H-bonds
    6016     Finding intramodel H-bonds
    6017     Constraints relaxed by 0.4 angstroms and 20 degrees
    6018     Models used:
    6019         1 ylODC_54bpOriC061_rev30_PostPhenix.pdb
    6020    
    6021     61 H-bonds
    6022     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    6023     /A ARG 301 NE   /I DC 47 OP1  /A ARG 301 HE    3.042  2.096
    6024     /A ARG 301 NH1  /H DT 10 O2   /A ARG 301 HH12  2.780  1.937
    6025     /A ARG 301 NH1  /H DC 11 O4'  /A ARG 301 HH11  2.808  1.918
    6026     /A ARG 301 NH2  /I DT 46 O2   /A ARG 301 HH22  3.419  2.726
    6027     /A ARG 301 NH2  /I DC 47 OP1  /A ARG 301 HH21  3.241  2.383
    6028     /A PHE 303 N    /H DC 13 OP1  /A PHE 303 H     2.683  1.713
    6029     /A LYS 305 NZ   /H DA 14 OP1  /A LYS 305 HZ1   3.005  2.074
    6030     /A ASN 435 ND2  /H DC 13 OP2  /A ASN 435 HD22  2.896  1.911
    6031     /A ASN 436 ND2  /H DC 13 OP2  /A ASN 436 HD22  3.172  2.251
    6032     /B LYS 148 NZ   /I DG 19 OP1  /B LYS 148 HZ3   2.880  2.062
    6033     /B ARG 150 NH1  /H DG 35 O6   /B ARG 150 HH12  3.317  2.492
    6034     /B ARG 150 NH1  /I DG 19 O6   /B ARG 150 HH12  3.200  2.518
    6035     /B ARG 150 NH2  /H DG 35 O6   /B ARG 150 HH22  2.932  1.954
    6036     /B GLY 153 N    /H DT 34 OP2  /B GLY 153 H     2.955  1.965
    6037     /B LYS 248 NZ   /I DA 37 O3'  /B LYS 248 HZ1   3.058  2.307
    6038     /B LYS 279 N    /I DA 39 OP1  /B LYS 279 H     3.012  2.176
    6039     /B ASP 280 N    /I DA 39 OP1  /B ASP 280 H     3.419  2.439
    6040     /C LYS 188 NZ   /H DT 18 OP1  /C LYS 188 HZ1   2.597  1.602
    6041     /C ARG 219 N    /I DT 41 OP1  /C ARG 219 H     2.860  1.859
    6042     /C ARG 219 NH1  /I DT 40 OP1  /C ARG 219 HH11  2.808  2.044
    6043     /C ARG 220 NH1  /H DT 16 O2   /C ARG 220 HH11  3.328  2.600
    6044     /C ARG 220 NH1  /I DT 40 O2   /C ARG 220 HH11  3.062  2.380
    6045     /C TYR 223 OH   /H DA 17 O3'  /C TYR 223 HH    2.926  2.064
    6046     /C TYR 607 OH   /H DC 32 OP2  /C TYR 607 HH    3.278  2.327
    6047     /C ARG 672 N    /H DC 32 OP1  /C ARG 672 H     2.895  1.905
    6048     /C ARG 672 NH1  /I DT 25 O2   /C ARG 672 HH12  2.707  1.845
    6049     /C ARG 672 NH2  /I DT 25 O2   /C ARG 672 HH22  3.408  2.771
    6050     /C LYS 673 NZ   /H DA 33 OP1  /C LYS 673 HZ1   2.886  1.972
    6051     /D LYS 168 NZ   /H DA 14 N3   /D LYS 168 HZ1   2.838  1.847
    6052     /D SER 169 OG   /H DA 15 OP2  /D SER 169 HG    2.801  1.842
    6053     /D ILE 170 N    /H DA 15 OP2  /D ILE 170 H     3.077  2.202
    6054     /D SER 463 OG   /I DG 30 OP1  /D SER 463 HG    2.493  1.565
    6055     /D LYS 465 NZ   /I DG 31 O6   /D LYS 465 HZ1   2.363  1.498
    6056     /D LYS 465 NZ   /I DG 32 O6   /D LYS 465 HZ2   2.546  1.684
    6057     /E ARG 76 NH1   /H DA 17 OP1  /E ARG 76 HH11   3.235  2.257
    6058     /E ARG 340 NE   /I DG 19 O5'  /E ARG 340 HE    3.009  2.192
    6059     /E ARG 340 NE   /I DG 19 OP2  /E ARG 340 HE    2.873  1.974
    6060     /E ARG 340 NH2  /I DG 19 OP2  /E ARG 340 HH21  3.300  2.551
    6061     /E TYR 341 OH   /I DC 20 OP1  /E TYR 341 HH    2.940  2.219
    6062     /E ARG 357 NH1  /I DT 16 O2   /E ARG 357 HH12  2.784  1.882
    6063     /E ARG 357 NH2  /I DT 16 O2   /E ARG 357 HH22  2.882  2.025
    6064     /E ARG 357 NH2  /I DT 16 O4'  /E ARG 357 HH22  3.135  2.386
    6065     /E GLU 358 N    /H DG 41 OP1  /E GLU 358 H     2.888  1.905
    6066     /E THR 359 OG1  /I DG 19 OP1  /E THR 359 HG1   2.802  2.243
    6067     /E ARG 362 N    /I DG 19 O3'  /E ARG 362 H     3.350  2.344
    6068     /E ARG 362 NH1  /I DT 18 O2   /E ARG 362 HH12  2.975  2.081
    6069     /E ARG 362 NH1  /I DG 19 O4'  /E ARG 362 HH11  3.022  2.183
    6070     /E ARG 362 NH2  /H DT 38 O2   /E ARG 362 HH22  2.881  2.130
    6071     /E LYS 363 N    /I DC 20 OP2  /E LYS 363 H     3.408  2.442
    6072     /E LYS 363 NZ   /I DA 21 OP1  /E LYS 363 HZ1   2.944  1.968
    6073     /G GLY 546 N    /H DA 27 OP1  /G GLY 546 H     2.915  2.028
    6074     /G LYS 547 NZ   /I DG 32 OP1  /G LYS 547 HZ1   2.552  1.558
    6075     /G LYS 548 NZ   /I DT 29 O2   /G LYS 548 HZ3   3.197  2.248
    6076     /G ASN 553 N    /I DG 32 OP2  /G ASN 553 H     2.957  2.079
    6077     /G ARG 557 NH1  /I DG 34 O6   /G ARG 557 HH12  2.913  1.906
    6078     /G ARG 557 NH2  /I DG 34 N7   /G ARG 557 HH22  2.372  1.443
    6079     /G GLY 561 N    /H DT 16 OP2  /G GLY 561 H     2.846  2.111
    6080     /G THR 563 OG1  /H DT 16 OP1  /G THR 563 HG1   3.027  2.078
    6081     /G ALA 565 N    /H DA 17 OP2  /G ALA 565 H     2.576  1.574
    6082     /G ARG 574 NH2  /I DG 32 OP1  /G ARG 574 HH21  3.076  2.128
    6083     /G LYS 581 NZ   /H DA 26 OP2  /G LYS 581 HZ1   3.143  2.140
    6084    
    6085 
    6086  
    6087 61 hydrogen bonds found 
    6088 21 strict hydrogen bonds found 
    6089 
    6090 > hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
    6091 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    6092 > structures/PDBs/ylODC_54bp-oriC061_complete/hbond-generation2_relaxed40"
    6093 > restrict #1/A,B,C,D,E,F,G angleSlop 40.0 twoColors true intraRes false
    6094 > reveal true log true
    6095    
    6096    
    6097     Finding intermodel H-bonds
    6098     Finding intramodel H-bonds
    6099     Constraints relaxed by 0.4 angstroms and 40 degrees
    6100     Models used:
    6101         1 ylODC_54bpOriC061_rev30_PostPhenix.pdb
    6102    
    6103     74 H-bonds
    6104     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    6105     /A ARG 301 NE   /I DC 47 OP1  /A ARG 301 HE    3.042  2.096
    6106     /A ARG 301 NH1  /H DT 10 O2   /A ARG 301 HH12  2.780  1.937
    6107     /A ARG 301 NH1  /H DC 11 O4'  /A ARG 301 HH11  2.808  1.918
    6108     /A ARG 301 NH2  /I DT 46 O2   /A ARG 301 HH22  3.419  2.726
    6109     /A ARG 301 NH2  /I DC 47 OP1  /A ARG 301 HH21  3.241  2.383
    6110     /A PHE 303 N    /H DC 13 OP1  /A PHE 303 H     2.683  1.713
    6111     /A LYS 305 NZ   /H DA 14 OP1  /A LYS 305 HZ1   3.005  2.074
    6112     /A ASN 435 ND2  /H DC 13 OP2  /A ASN 435 HD22  2.896  1.911
    6113     /A ASN 436 ND2  /H DC 13 OP2  /A ASN 436 HD22  3.172  2.251
    6114     /B LYS 148 NZ   /I DG 19 OP1  /B LYS 148 HZ3   2.880  2.062
    6115     /B ARG 150 NH1  /H DG 35 O6   /B ARG 150 HH12  3.317  2.492
    6116     /B ARG 150 NH1  /I DG 19 O6   /B ARG 150 HH12  3.200  2.518
    6117     /B ARG 150 NH2  /H DG 35 O6   /B ARG 150 HH22  2.932  1.954
    6118     /B GLY 153 N    /H DT 34 OP2  /B GLY 153 H     2.955  1.965
    6119     /B LYS 248 NZ   /I DA 37 O3'  /B LYS 248 HZ1   3.058  2.307
    6120     /B LYS 279 N    /I DA 39 OP1  /B LYS 279 H     3.012  2.176
    6121     /B ASP 280 N    /I DA 39 OP1  /B ASP 280 H     3.419  2.439
    6122     /C LYS 188 NZ   /H DT 18 OP1  /C LYS 188 HZ1   2.597  1.602
    6123     /C ARG 219 N    /I DT 41 OP1  /C ARG 219 H     2.860  1.859
    6124     /C ARG 219 NH1  /I DT 40 OP1  /C ARG 219 HH11  2.808  2.044
    6125     /C ARG 220 NH1  /H DA 15 N3   /C ARG 220 HH12  3.522  2.929
    6126     /C ARG 220 NH1  /H DT 16 O2   /C ARG 220 HH11  3.328  2.600
    6127     /C ARG 220 NH1  /I DT 40 O2   /C ARG 220 HH11  3.062  2.380
    6128     /C TYR 223 OH   /H DA 17 O3'  /C TYR 223 HH    2.926  2.064
    6129     /C TYR 607 OH   /H DC 32 OP2  /C TYR 607 HH    3.278  2.327
    6130     /C LYS 671 N    /H DC 32 OP1  /C LYS 671 H     2.864  2.159
    6131     /C ARG 672 N    /H DC 32 OP1  /C ARG 672 H     2.895  1.905
    6132     /C ARG 672 NH1  /I DT 25 O2   /C ARG 672 HH12  2.707  1.845
    6133     /C ARG 672 NH2  /I DT 25 O2   /C ARG 672 HH22  3.408  2.771
    6134     /C LYS 673 NZ   /H DA 33 OP1  /C LYS 673 HZ1   2.886  1.972
    6135     /D LYS 168 NZ   /H DA 14 N3   /D LYS 168 HZ1   2.838  1.847
    6136     /D SER 169 OG   /H DA 14 O3'  /D SER 169 HG    3.382  2.801
    6137     /D SER 169 OG   /H DA 15 OP2  /D SER 169 HG    2.801  1.842
    6138     /D ILE 170 N    /H DA 15 OP2  /D ILE 170 H     3.077  2.202
    6139     /D SER 463 OG   /I DG 30 OP1  /D SER 463 HG    2.493  1.565
    6140     /D LYS 465 NZ   /I DG 31 N7   /D LYS 465 HZ1   3.444  2.853
    6141     /D LYS 465 NZ   /I DG 31 O6   /D LYS 465 HZ1   2.363  1.498
    6142     /D LYS 465 NZ   /I DG 32 O6   /D LYS 465 HZ2   2.546  1.684
    6143     /E ARG 76 NH1   /H DA 17 OP1  /E ARG 76 HH11   3.235  2.257
    6144     /E ARG 340 NE   /I DG 19 O5'  /E ARG 340 HE    3.009  2.192
    6145     /E ARG 340 NE   /I DG 19 OP2  /E ARG 340 HE    2.873  1.974
    6146     /E ARG 340 NH2  /I DG 19 OP2  /E ARG 340 HH21  3.300  2.551
    6147     /E TYR 341 OH   /I DC 20 OP1  /E TYR 341 HH    2.940  2.219
    6148     /E ARG 357 NH1  /I DT 16 O2   /E ARG 357 HH12  2.784  1.882
    6149     /E ARG 357 NH2  /I DT 16 O2   /E ARG 357 HH22  2.882  2.025
    6150     /E ARG 357 NH2  /I DT 16 O4'  /E ARG 357 HH22  3.135  2.386
    6151     /E GLU 358 N    /H DG 41 OP1  /E GLU 358 H     2.888  1.905
    6152     /E THR 359 OG1  /I DG 19 OP1  /E THR 359 HG1   2.802  2.243
    6153     /E ARG 362 N    /I DG 19 O3'  /E ARG 362 H     3.350  2.344
    6154     /E ARG 362 NH1  /I DT 18 O2   /E ARG 362 HH12  2.975  2.081
    6155     /E ARG 362 NH1  /I DG 19 O4'  /E ARG 362 HH11  3.022  2.183
    6156     /E ARG 362 NH2  /H DT 38 O2   /E ARG 362 HH22  2.881  2.130
    6157     /E ARG 362 NH2  /H DA 39 O4'  /E ARG 362 HH21  3.366  2.779
    6158     /E LYS 363 N    /I DC 20 OP2  /E LYS 363 H     3.408  2.442
    6159     /E LYS 363 NZ   /I DA 21 OP1  /E LYS 363 HZ1   2.944  1.968
    6160     /G GLY 543 N    /H DA 26 OP1  /G GLY 543 H     2.943  2.343
    6161     /G GLY 546 N    /H DA 27 OP1  /G GLY 546 H     2.915  2.028
    6162     /G LYS 547 NZ   /I DG 31 O3'  /G LYS 547 HZ2   2.870  2.326
    6163     /G LYS 547 NZ   /I DG 32 OP1  /G LYS 547 HZ1   2.552  1.558
    6164     /G LYS 548 NZ   /H DA 27 N3   /G LYS 548 HZ1   2.902  2.236
    6165     /G LYS 548 NZ   /H DG 28 O4'  /G LYS 548 HZ2   2.987  2.212
    6166     /G LYS 548 NZ   /I DT 29 O2   /G LYS 548 HZ3   3.197  2.248
    6167     /G ASN 553 N    /I DG 32 OP2  /G ASN 553 H     2.957  2.079
    6168     /G ARG 557 NH1  /I DG 34 O6   /G ARG 557 HH12  2.913  1.906
    6169     /G ARG 557 NH2  /I DG 34 N7   /G ARG 557 HH22  2.372  1.443
    6170     /G LYS 560 NZ   /H DA 15 OP1  /G LYS 560 HZ3   3.180  2.601
    6171     /G GLY 561 N    /H DT 16 OP1  /G GLY 561 H     3.390  2.598
    6172     /G GLY 561 N    /H DT 16 OP2  /G GLY 561 H     2.846  2.111
    6173     /G THR 563 N    /H DT 16 OP1  /G THR 563 H     2.931  2.306
    6174     /G THR 563 OG1  /H DT 16 OP1  /G THR 563 HG1   3.027  2.078
    6175     /G ALA 565 N    /H DA 17 OP2  /G ALA 565 H     2.576  1.574
    6176     /G ARG 574 NH2  /I DG 32 OP1  /G ARG 574 HH21  3.076  2.128
    6177     /G LYS 581 NZ   /H DA 26 O5'  /G LYS 581 HZ1   3.367  2.792
    6178     /G LYS 581 NZ   /H DA 26 OP2  /G LYS 581 HZ1   3.143  2.140
    6179    
    6180 
    6181  
    6182 74 hydrogen bonds found 
    6183 21 strict hydrogen bonds found 
    6184 
    6185 > hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
    6186 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    6187 > structures/PDBs/ylODC_54bp-oriC061_complete/hbond-generation2_relaxed40"
    6188 > restrict #1/A,B,C,D,E,F,G angleSlop 40.0 twoColors true intraRes false
    6189 > select true reveal true log true
    6190    
    6191    
    6192     Finding intermodel H-bonds
    6193     Finding intramodel H-bonds
    6194     Constraints relaxed by 0.4 angstroms and 40 degrees
    6195     Models used:
    6196         1 ylODC_54bpOriC061_rev30_PostPhenix.pdb
    6197    
    6198     74 H-bonds
    6199     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    6200     /A ARG 301 NE   /I DC 47 OP1  /A ARG 301 HE    3.042  2.096
    6201     /A ARG 301 NH1  /H DT 10 O2   /A ARG 301 HH12  2.780  1.937
    6202     /A ARG 301 NH1  /H DC 11 O4'  /A ARG 301 HH11  2.808  1.918
    6203     /A ARG 301 NH2  /I DT 46 O2   /A ARG 301 HH22  3.419  2.726
    6204     /A ARG 301 NH2  /I DC 47 OP1  /A ARG 301 HH21  3.241  2.383
    6205     /A PHE 303 N    /H DC 13 OP1  /A PHE 303 H     2.683  1.713
    6206     /A LYS 305 NZ   /H DA 14 OP1  /A LYS 305 HZ1   3.005  2.074
    6207     /A ASN 435 ND2  /H DC 13 OP2  /A ASN 435 HD22  2.896  1.911
    6208     /A ASN 436 ND2  /H DC 13 OP2  /A ASN 436 HD22  3.172  2.251
    6209     /B LYS 148 NZ   /I DG 19 OP1  /B LYS 148 HZ3   2.880  2.062
    6210     /B ARG 150 NH1  /H DG 35 O6   /B ARG 150 HH12  3.317  2.492
    6211     /B ARG 150 NH1  /I DG 19 O6   /B ARG 150 HH12  3.200  2.518
    6212     /B ARG 150 NH2  /H DG 35 O6   /B ARG 150 HH22  2.932  1.954
    6213     /B GLY 153 N    /H DT 34 OP2  /B GLY 153 H     2.955  1.965
    6214     /B LYS 248 NZ   /I DA 37 O3'  /B LYS 248 HZ1   3.058  2.307
    6215     /B LYS 279 N    /I DA 39 OP1  /B LYS 279 H     3.012  2.176
    6216     /B ASP 280 N    /I DA 39 OP1  /B ASP 280 H     3.419  2.439
    6217     /C LYS 188 NZ   /H DT 18 OP1  /C LYS 188 HZ1   2.597  1.602
    6218     /C ARG 219 N    /I DT 41 OP1  /C ARG 219 H     2.860  1.859
    6219     /C ARG 219 NH1  /I DT 40 OP1  /C ARG 219 HH11  2.808  2.044
    6220     /C ARG 220 NH1  /H DA 15 N3   /C ARG 220 HH12  3.522  2.929
    6221     /C ARG 220 NH1  /H DT 16 O2   /C ARG 220 HH11  3.328  2.600
    6222     /C ARG 220 NH1  /I DT 40 O2   /C ARG 220 HH11  3.062  2.380
    6223     /C TYR 223 OH   /H DA 17 O3'  /C TYR 223 HH    2.926  2.064
    6224     /C TYR 607 OH   /H DC 32 OP2  /C TYR 607 HH    3.278  2.327
    6225     /C LYS 671 N    /H DC 32 OP1  /C LYS 671 H     2.864  2.159
    6226     /C ARG 672 N    /H DC 32 OP1  /C ARG 672 H     2.895  1.905
    6227     /C ARG 672 NH1  /I DT 25 O2   /C ARG 672 HH12  2.707  1.845
    6228     /C ARG 672 NH2  /I DT 25 O2   /C ARG 672 HH22  3.408  2.771
    6229     /C LYS 673 NZ   /H DA 33 OP1  /C LYS 673 HZ1   2.886  1.972
    6230     /D LYS 168 NZ   /H DA 14 N3   /D LYS 168 HZ1   2.838  1.847
    6231     /D SER 169 OG   /H DA 14 O3'  /D SER 169 HG    3.382  2.801
    6232     /D SER 169 OG   /H DA 15 OP2  /D SER 169 HG    2.801  1.842
    6233     /D ILE 170 N    /H DA 15 OP2  /D ILE 170 H     3.077  2.202
    6234     /D SER 463 OG   /I DG 30 OP1  /D SER 463 HG    2.493  1.565
    6235     /D LYS 465 NZ   /I DG 31 N7   /D LYS 465 HZ1   3.444  2.853
    6236     /D LYS 465 NZ   /I DG 31 O6   /D LYS 465 HZ1   2.363  1.498
    6237     /D LYS 465 NZ   /I DG 32 O6   /D LYS 465 HZ2   2.546  1.684
    6238     /E ARG 76 NH1   /H DA 17 OP1  /E ARG 76 HH11   3.235  2.257
    6239     /E ARG 340 NE   /I DG 19 O5'  /E ARG 340 HE    3.009  2.192
    6240     /E ARG 340 NE   /I DG 19 OP2  /E ARG 340 HE    2.873  1.974
    6241     /E ARG 340 NH2  /I DG 19 OP2  /E ARG 340 HH21  3.300  2.551
    6242     /E TYR 341 OH   /I DC 20 OP1  /E TYR 341 HH    2.940  2.219
    6243     /E ARG 357 NH1  /I DT 16 O2   /E ARG 357 HH12  2.784  1.882
    6244     /E ARG 357 NH2  /I DT 16 O2   /E ARG 357 HH22  2.882  2.025
    6245     /E ARG 357 NH2  /I DT 16 O4'  /E ARG 357 HH22  3.135  2.386
    6246     /E GLU 358 N    /H DG 41 OP1  /E GLU 358 H     2.888  1.905
    6247     /E THR 359 OG1  /I DG 19 OP1  /E THR 359 HG1   2.802  2.243
    6248     /E ARG 362 N    /I DG 19 O3'  /E ARG 362 H     3.350  2.344
    6249     /E ARG 362 NH1  /I DT 18 O2   /E ARG 362 HH12  2.975  2.081
    6250     /E ARG 362 NH1  /I DG 19 O4'  /E ARG 362 HH11  3.022  2.183
    6251     /E ARG 362 NH2  /H DT 38 O2   /E ARG 362 HH22  2.881  2.130
    6252     /E ARG 362 NH2  /H DA 39 O4'  /E ARG 362 HH21  3.366  2.779
    6253     /E LYS 363 N    /I DC 20 OP2  /E LYS 363 H     3.408  2.442
    6254     /E LYS 363 NZ   /I DA 21 OP1  /E LYS 363 HZ1   2.944  1.968
    6255     /G GLY 543 N    /H DA 26 OP1  /G GLY 543 H     2.943  2.343
    6256     /G GLY 546 N    /H DA 27 OP1  /G GLY 546 H     2.915  2.028
    6257     /G LYS 547 NZ   /I DG 31 O3'  /G LYS 547 HZ2   2.870  2.326
    6258     /G LYS 547 NZ   /I DG 32 OP1  /G LYS 547 HZ1   2.552  1.558
    6259     /G LYS 548 NZ   /H DA 27 N3   /G LYS 548 HZ1   2.902  2.236
    6260     /G LYS 548 NZ   /H DG 28 O4'  /G LYS 548 HZ2   2.987  2.212
    6261     /G LYS 548 NZ   /I DT 29 O2   /G LYS 548 HZ3   3.197  2.248
    6262     /G ASN 553 N    /I DG 32 OP2  /G ASN 553 H     2.957  2.079
    6263     /G ARG 557 NH1  /I DG 34 O6   /G ARG 557 HH12  2.913  1.906
    6264     /G ARG 557 NH2  /I DG 34 N7   /G ARG 557 HH22  2.372  1.443
    6265     /G LYS 560 NZ   /H DA 15 OP1  /G LYS 560 HZ3   3.180  2.601
    6266     /G GLY 561 N    /H DT 16 OP1  /G GLY 561 H     3.390  2.598
    6267     /G GLY 561 N    /H DT 16 OP2  /G GLY 561 H     2.846  2.111
    6268     /G THR 563 N    /H DT 16 OP1  /G THR 563 H     2.931  2.306
    6269     /G THR 563 OG1  /H DT 16 OP1  /G THR 563 HG1   3.027  2.078
    6270     /G ALA 565 N    /H DA 17 OP2  /G ALA 565 H     2.576  1.574
    6271     /G ARG 574 NH2  /I DG 32 OP1  /G ARG 574 HH21  3.076  2.128
    6272     /G LYS 581 NZ   /H DA 26 O5'  /G LYS 581 HZ1   3.367  2.792
    6273     /G LYS 581 NZ   /H DA 26 OP2  /G LYS 581 HZ1   3.143  2.140
    6274    
    6275 
    6276  
    6277 74 hydrogen bonds found 
    6278 21 strict hydrogen bonds found 
    6279 
    6280 > select up
    6281 
    6282 1950 atoms, 1998 bonds, 79 residues, 1 model selected 
    6283 
    6284 > show sel atoms
    6285 
    6286 > select clear
    6287 
    6288 > select ~nucleic
    6289 
    6290 47733 atoms, 48183 bonds, 11 pseudobonds, 2978 residues, 3 models selected 
    6291 
    6292 > hide sel cartoons
    6293 
    6294 > select clear
    6295 
    6296 > save "/Users/jtbauer/Library/CloudStorage/OneDrive-
    6297 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    6298 > structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver30.cxs"
    6299 
    6300 > select /G:548@NZ
    6301 
    6302 1 atom, 1 residue, 1 model selected 
    6303 
    6304 > select /I:29@N3
    6305 
    6306 1 atom, 1 residue, 1 model selected 
    6307 
    6308 > select /I:30
    6309 
    6310 33 atoms, 35 bonds, 1 residue, 1 model selected 
    6311 
    6312 > select /I:29
    6313 
    6314 32 atoms, 33 bonds, 1 residue, 1 model selected 
    6315 
    6316 > select /H:26
    6317 
    6318 32 atoms, 34 bonds, 1 residue, 1 model selected 
    6319 
    6320 > ui tool show "Renumber Residues"
    6321 
    6322 > renumber /H start -7
    6323 
    6324 37 residues renumbered 
    6325 
    6326 > select /H:12
    6327 
    6328 32 atoms, 34 bonds, 1 residue, 1 model selected 
    6329 
    6330 > select /H:11
    6331 
    6332 32 atoms, 34 bonds, 1 residue, 1 model selected 
    6333 
    6334 > renumber /H start -16
    6335 
    6336 37 residues renumbered 
    6337 
    6338 > renumber /H start -16
    6339 
    6340 0 residues renumbered 
    6341 
    6342 > renumber /H start -16
    6343 
    6344 0 residues renumbered 
    6345 
    6346 > select /H:3
    6347 
    6348 32 atoms, 34 bonds, 1 residue, 1 model selected 
    6349 
    6350 > select /H:2
    6351 
    6352 32 atoms, 34 bonds, 1 residue, 1 model selected 
    6353 
    6354 > renumber /H start -18
    6355 
    6356 37 residues renumbered 
    6357 
    6358 > select /H:0
    6359 
    6360 32 atoms, 34 bonds, 1 residue, 1 model selected 
    6361 
    6362 > save "/Users/jtbauer/Library/CloudStorage/OneDrive-
    6363 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    6364 > structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver30.cxs"
    6365 
    6366 > select /I:29
    6367 
    6368 32 atoms, 33 bonds, 1 residue, 1 model selected 
    6369 
    6370 > ui tool show "Renumber Residues"
    6371 
    6372 > renumber /I start -15
    6373 
    6374 35 residues renumbered 
    6375 
    6376 > select /I:1
    6377 
    6378 32 atoms, 33 bonds, 1 residue, 1 model selected 
    6379 
    6380 > renumber /I start -16
    6381 
    6382 35 residues renumbered 
    6383 
    6384 > renumber /I start -16
    6385 
    6386 0 residues renumbered 
    6387 
    6388 > select clear
    6389 
    6390 > save "/Users/jtbauer/Library/CloudStorage/OneDrive-
    6391 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    6392 > structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver30.cxs"
    6393 
    6394 > hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
    6395 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    6396 > structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver30" restrict
    6397 > #1/A,B,C,D,E,F,G angleSlop 40.0 twoColors true intraRes false select true
    6398 > reveal true log true
    6399 
    6400 Atom specifier selects no atoms 
    6401 
    6402 > select nucleic
    6403 
    6404 2291 atoms, 2469 bonds, 72 residues, 1 model selected 
    6405 
    6406 > hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
    6407 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    6408 > structures/PDBs/ylODC_54bp-oriC061_complete/hbond-generation2_relaxed40"
    6409 > restrict #1/A,B,C,D,E,F,G angleSlop 40.0 twoColors true intraRes false
    6410 > select true reveal true log true
    6411    
    6412    
    6413     Finding intermodel H-bonds
    6414     Finding intramodel H-bonds
    6415     Constraints relaxed by 0.4 angstroms and 40 degrees
    6416     Models used:
    6417         1 ylODC_54bpOriC061_rev30_PostPhenix.pdb
    6418    
    6419     74 H-bonds
    6420     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    6421     /A ARG 301 NE   /I DC 18 OP1   /A ARG 301 HE    3.042  2.096
    6422     /A ARG 301 NH1  /H DT -16 O2   /A ARG 301 HH12  2.780  1.937
    6423     /A ARG 301 NH1  /H DC -15 O4'  /A ARG 301 HH11  2.808  1.918
    6424     /A ARG 301 NH2  /I DT 17 O2    /A ARG 301 HH22  3.419  2.726
    6425     /A ARG 301 NH2  /I DC 18 OP1   /A ARG 301 HH21  3.241  2.383
    6426     /A PHE 303 N    /H DC -13 OP1  /A PHE 303 H     2.683  1.713
    6427     /A LYS 305 NZ   /H DA -12 OP1  /A LYS 305 HZ1   3.005  2.074
    6428     /A ASN 435 ND2  /H DC -13 OP2  /A ASN 435 HD22  2.896  1.911
    6429     /A ASN 436 ND2  /H DC -13 OP2  /A ASN 436 HD22  3.172  2.251
    6430     /B LYS 148 NZ   /I DG -10 OP1  /B LYS 148 HZ3   2.880  2.062
    6431     /B ARG 150 NH1  /H DG 9 O6     /B ARG 150 HH12  3.317  2.492
    6432     /B ARG 150 NH1  /I DG -10 O6   /B ARG 150 HH12  3.200  2.518
    6433     /B ARG 150 NH2  /H DG 9 O6     /B ARG 150 HH22  2.932  1.954
    6434     /B GLY 153 N    /H DT 8 OP2    /B GLY 153 H     2.955  1.965
    6435     /B LYS 248 NZ   /I DA 8 O3'    /B LYS 248 HZ1   3.058  2.307
    6436     /B LYS 279 N    /I DA 10 OP1   /B LYS 279 H     3.012  2.176
    6437     /B ASP 280 N    /I DA 10 OP1   /B ASP 280 H     3.419  2.439
    6438     /C LYS 188 NZ   /H DT -8 OP1   /C LYS 188 HZ1   2.597  1.602
    6439     /C ARG 219 N    /I DT 12 OP1   /C ARG 219 H     2.860  1.859
    6440     /C ARG 219 NH1  /I DT 11 OP1   /C ARG 219 HH11  2.808  2.044
    6441     /C ARG 220 NH1  /H DA -11 N3   /C ARG 220 HH12  3.522  2.929
    6442     /C ARG 220 NH1  /H DT -10 O2   /C ARG 220 HH11  3.328  2.600
    6443     /C ARG 220 NH1  /I DT 11 O2    /C ARG 220 HH11  3.062  2.380
    6444     /C TYR 223 OH   /H DA -9 O3'   /C TYR 223 HH    2.926  2.064
    6445     /C TYR 607 OH   /H DC 6 OP2    /C TYR 607 HH    3.278  2.327
    6446     /C LYS 671 N    /H DC 6 OP1    /C LYS 671 H     2.864  2.159
    6447     /C ARG 672 N    /H DC 6 OP1    /C ARG 672 H     2.895  1.905
    6448     /C ARG 672 NH1  /I DT -4 O2    /C ARG 672 HH12  2.707  1.845
    6449     /C ARG 672 NH2  /I DT -4 O2    /C ARG 672 HH22  3.408  2.771
    6450     /C LYS 673 NZ   /H DA 7 OP1    /C LYS 673 HZ1   2.886  1.972
    6451     /D LYS 168 NZ   /H DA -12 N3   /D LYS 168 HZ1   2.838  1.847
    6452     /D SER 169 OG   /H DA -12 O3'  /D SER 169 HG    3.382  2.801
    6453     /D SER 169 OG   /H DA -11 OP2  /D SER 169 HG    2.801  1.842
    6454     /D ILE 170 N    /H DA -11 OP2  /D ILE 170 H     3.077  2.202
    6455     /D SER 463 OG   /I DG 1 OP1    /D SER 463 HG    2.493  1.565
    6456     /D LYS 465 NZ   /I DG 2 N7     /D LYS 465 HZ1   3.444  2.853
    6457     /D LYS 465 NZ   /I DG 2 O6     /D LYS 465 HZ1   2.363  1.498
    6458     /D LYS 465 NZ   /I DG 3 O6     /D LYS 465 HZ2   2.546  1.684
    6459     /E ARG 76 NH1   /H DA -9 OP1   /E ARG 76 HH11   3.235  2.257
    6460     /E ARG 340 NE   /I DG -10 O5'  /E ARG 340 HE    3.009  2.192
    6461     /E ARG 340 NE   /I DG -10 OP2  /E ARG 340 HE    2.873  1.974
    6462     /E ARG 340 NH2  /I DG -10 OP2  /E ARG 340 HH21  3.300  2.551
    6463     /E TYR 341 OH   /I DC -9 OP1   /E TYR 341 HH    2.940  2.219
    6464     /E ARG 357 NH1  /I DT -13 O2   /E ARG 357 HH12  2.784  1.882
    6465     /E ARG 357 NH2  /I DT -13 O2   /E ARG 357 HH22  2.882  2.025
    6466     /E ARG 357 NH2  /I DT -13 O4'  /E ARG 357 HH22  3.135  2.386
    6467     /E GLU 358 N    /H DG 15 OP1   /E GLU 358 H     2.888  1.905
    6468     /E THR 359 OG1  /I DG -10 OP1  /E THR 359 HG1   2.802  2.243
    6469     /E ARG 362 N    /I DG -10 O3'  /E ARG 362 H     3.350  2.344
    6470     /E ARG 362 NH1  /I DT -11 O2   /E ARG 362 HH12  2.975  2.081
    6471     /E ARG 362 NH1  /I DG -10 O4'  /E ARG 362 HH11  3.022  2.183
    6472     /E ARG 362 NH2  /H DT 12 O2    /E ARG 362 HH22  2.881  2.130
    6473     /E ARG 362 NH2  /H DA 13 O4'   /E ARG 362 HH21  3.366  2.779
    6474     /E LYS 363 N    /I DC -9 OP2   /E LYS 363 H     3.408  2.442
    6475     /E LYS 363 NZ   /I DA -8 OP1   /E LYS 363 HZ1   2.944  1.968
    6476     /G GLY 543 N    /H DA 0 OP1    /G GLY 543 H     2.943  2.343
    6477     /G GLY 546 N    /H DA 1 OP1    /G GLY 546 H     2.915  2.028
    6478     /G LYS 547 NZ   /I DG 2 O3'    /G LYS 547 HZ2   2.870  2.326
    6479     /G LYS 547 NZ   /I DG 3 OP1    /G LYS 547 HZ1   2.552  1.558
    6480     /G LYS 548 NZ   /H DA 1 N3     /G LYS 548 HZ1   2.902  2.236
    6481     /G LYS 548 NZ   /H DG 2 O4'    /G LYS 548 HZ2   2.987  2.212
    6482     /G LYS 548 NZ   /I DT 0 O2     /G LYS 548 HZ3   3.197  2.248
    6483     /G ASN 553 N    /I DG 3 OP2    /G ASN 553 H     2.957  2.079
    6484     /G ARG 557 NH1  /I DG 5 O6     /G ARG 557 HH12  2.913  1.906
    6485     /G ARG 557 NH2  /I DG 5 N7     /G ARG 557 HH22  2.372  1.443
    6486     /G LYS 560 NZ   /H DA -11 OP1  /G LYS 560 HZ3   3.180  2.601
    6487     /G GLY 561 N    /H DT -10 OP1  /G GLY 561 H     3.390  2.598
    6488     /G GLY 561 N    /H DT -10 OP2  /G GLY 561 H     2.846  2.111
    6489     /G THR 563 N    /H DT -10 OP1  /G THR 563 H     2.931  2.306
    6490     /G THR 563 OG1  /H DT -10 OP1  /G THR 563 HG1   3.027  2.078
    6491     /G ALA 565 N    /H DA -9 OP2   /G ALA 565 H     2.576  1.574
    6492     /G ARG 574 NH2  /I DG 3 OP1    /G ARG 574 HH21  3.076  2.128
    6493     /G LYS 581 NZ   /H DA 0 O5'    /G LYS 581 HZ1   3.367  2.792
    6494     /G LYS 581 NZ   /H DA 0 OP2    /G LYS 581 HZ1   3.143  2.140
    6495    
    6496 
    6497  
    6498 74 hydrogen bonds found 
    6499 21 strict hydrogen bonds found 
    6500 
    6501 > show sel atoms
    6502 
    6503 > select clear
    6504 
    6505 > ui tool show "Change Chain IDs"
    6506 
    6507 > changechains H main
    6508 
    6509 Proposed chain ID change would produce multiple residues with the samechain-
    6510 ID/number/insertion-code combo (main/299/) 
    6511 
    6512 > changechains H main
    6513 
    6514 Proposed chain ID change would produce multiple residues with the samechain-
    6515 ID/number/insertion-code combo (main/299/) 
    6516 
    6517 > changechains I opp
    6518 
    6519 No residues specified 
    6520 
    6521 > changechains I opp
    6522 
    6523 No residues specified 
    6524 
    6525 > changechains H main
    6526 
    6527 Proposed chain ID change would produce multiple residues with the samechain-
    6528 ID/number/insertion-code combo (main/299/) 
    6529 
    6530 > select /H
    6531 
    6532 1170 atoms, 1262 bonds, 37 residues, 1 model selected 
    6533 
    6534 > changechains sel main
    6535 
    6536 Chain IDs of 37 residues changed 
    6537 
    6538 > select /I
    6539 
    6540 1121 atoms, 1207 bonds, 35 residues, 1 model selected 
    6541 
    6542 > changechains sel opp
    6543 
    6544 Chain IDs of 35 residues changed 
    6545 
    6546 > select clear
    6547 
    6548 > ui tool show H-Bonds
    6549 
    6550 > hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
    6551 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    6552 > structures/PDBs/ylODC_54bp-oriC061_complete/hbond-generation2_relaxed40"
    6553 > restrict #1/A,B,C,D,E,F,G angleSlop 40.0 twoColors true intraRes false
    6554 > reveal true log true
    6555 
    6556 Atom specifier selects no atoms 
    6557 
    6558 > select nucleic
    6559 
    6560 2291 atoms, 2469 bonds, 72 residues, 1 model selected 
    6561 
    6562 > hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
    6563 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    6564 > structures/PDBs/ylODC_54bp-oriC061_complete/hbond-generation2_relaxed40"
    6565 > restrict #1/A,B,C,D,E,F,G angleSlop 40.0 twoColors true intraRes false
    6566 > reveal true log true
    6567    
    6568    
    6569     Finding intermodel H-bonds
    6570     Finding intramodel H-bonds
    6571     Constraints relaxed by 0.4 angstroms and 40 degrees
    6572     Models used:
    6573         1 ylODC_54bpOriC061_rev30_PostPhenix.pdb
    6574    
    6575     74 H-bonds
    6576     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    6577     /A ARG 301 NE   /opp DC 18 OP1    /A ARG 301 HE    3.042  2.096
    6578     /A ARG 301 NH1  /main DT -16 O2   /A ARG 301 HH12  2.780  1.937
    6579     /A ARG 301 NH1  /main DC -15 O4'  /A ARG 301 HH11  2.808  1.918
    6580     /A ARG 301 NH2  /opp DT 17 O2     /A ARG 301 HH22  3.419  2.726
    6581     /A ARG 301 NH2  /opp DC 18 OP1    /A ARG 301 HH21  3.241  2.383
    6582     /A PHE 303 N    /main DC -13 OP1  /A PHE 303 H     2.683  1.713
    6583     /A LYS 305 NZ   /main DA -12 OP1  /A LYS 305 HZ1   3.005  2.074
    6584     /A ASN 435 ND2  /main DC -13 OP2  /A ASN 435 HD22  2.896  1.911
    6585     /A ASN 436 ND2  /main DC -13 OP2  /A ASN 436 HD22  3.172  2.251
    6586     /B LYS 148 NZ   /opp DG -10 OP1   /B LYS 148 HZ3   2.880  2.062
    6587     /B ARG 150 NH1  /main DG 9 O6     /B ARG 150 HH12  3.317  2.492
    6588     /B ARG 150 NH1  /opp DG -10 O6    /B ARG 150 HH12  3.200  2.518
    6589     /B ARG 150 NH2  /main DG 9 O6     /B ARG 150 HH22  2.932  1.954
    6590     /B GLY 153 N    /main DT 8 OP2    /B GLY 153 H     2.955  1.965
    6591     /B LYS 248 NZ   /opp DA 8 O3'     /B LYS 248 HZ1   3.058  2.307
    6592     /B LYS 279 N    /opp DA 10 OP1    /B LYS 279 H     3.012  2.176
    6593     /B ASP 280 N    /opp DA 10 OP1    /B ASP 280 H     3.419  2.439
    6594     /C LYS 188 NZ   /main DT -8 OP1   /C LYS 188 HZ1   2.597  1.602
    6595     /C ARG 219 N    /opp DT 12 OP1    /C ARG 219 H     2.860  1.859
    6596     /C ARG 219 NH1  /opp DT 11 OP1    /C ARG 219 HH11  2.808  2.044
    6597     /C ARG 220 NH1  /main DA -11 N3   /C ARG 220 HH12  3.522  2.929
    6598     /C ARG 220 NH1  /main DT -10 O2   /C ARG 220 HH11  3.328  2.600
    6599     /C ARG 220 NH1  /opp DT 11 O2     /C ARG 220 HH11  3.062  2.380
    6600     /C TYR 223 OH   /main DA -9 O3'   /C TYR 223 HH    2.926  2.064
    6601     /C TYR 607 OH   /main DC 6 OP2    /C TYR 607 HH    3.278  2.327
    6602     /C LYS 671 N    /main DC 6 OP1    /C LYS 671 H     2.864  2.159
    6603     /C ARG 672 N    /main DC 6 OP1    /C ARG 672 H     2.895  1.905
    6604     /C ARG 672 NH1  /opp DT -4 O2     /C ARG 672 HH12  2.707  1.845
    6605     /C ARG 672 NH2  /opp DT -4 O2     /C ARG 672 HH22  3.408  2.771
    6606     /C LYS 673 NZ   /main DA 7 OP1    /C LYS 673 HZ1   2.886  1.972
    6607     /D LYS 168 NZ   /main DA -12 N3   /D LYS 168 HZ1   2.838  1.847
    6608     /D SER 169 OG   /main DA -12 O3'  /D SER 169 HG    3.382  2.801
    6609     /D SER 169 OG   /main DA -11 OP2  /D SER 169 HG    2.801  1.842
    6610     /D ILE 170 N    /main DA -11 OP2  /D ILE 170 H     3.077  2.202
    6611     /D SER 463 OG   /opp DG 1 OP1     /D SER 463 HG    2.493  1.565
    6612     /D LYS 465 NZ   /opp DG 2 N7      /D LYS 465 HZ1   3.444  2.853
    6613     /D LYS 465 NZ   /opp DG 2 O6      /D LYS 465 HZ1   2.363  1.498
    6614     /D LYS 465 NZ   /opp DG 3 O6      /D LYS 465 HZ2   2.546  1.684
    6615     /E ARG 76 NH1   /main DA -9 OP1   /E ARG 76 HH11   3.235  2.257
    6616     /E ARG 340 NE   /opp DG -10 O5'   /E ARG 340 HE    3.009  2.192
    6617     /E ARG 340 NE   /opp DG -10 OP2   /E ARG 340 HE    2.873  1.974
    6618     /E ARG 340 NH2  /opp DG -10 OP2   /E ARG 340 HH21  3.300  2.551
    6619     /E TYR 341 OH   /opp DC -9 OP1    /E TYR 341 HH    2.940  2.219
    6620     /E ARG 357 NH1  /opp DT -13 O2    /E ARG 357 HH12  2.784  1.882
    6621     /E ARG 357 NH2  /opp DT -13 O2    /E ARG 357 HH22  2.882  2.025
    6622     /E ARG 357 NH2  /opp DT -13 O4'   /E ARG 357 HH22  3.135  2.386
    6623     /E GLU 358 N    /main DG 15 OP1   /E GLU 358 H     2.888  1.905
    6624     /E THR 359 OG1  /opp DG -10 OP1   /E THR 359 HG1   2.802  2.243
    6625     /E ARG 362 N    /opp DG -10 O3'   /E ARG 362 H     3.350  2.344
    6626     /E ARG 362 NH1  /opp DT -11 O2    /E ARG 362 HH12  2.975  2.081
    6627     /E ARG 362 NH1  /opp DG -10 O4'   /E ARG 362 HH11  3.022  2.183
    6628     /E ARG 362 NH2  /main DT 12 O2    /E ARG 362 HH22  2.881  2.130
    6629     /E ARG 362 NH2  /main DA 13 O4'   /E ARG 362 HH21  3.366  2.779
    6630     /E LYS 363 N    /opp DC -9 OP2    /E LYS 363 H     3.408  2.442
    6631     /E LYS 363 NZ   /opp DA -8 OP1    /E LYS 363 HZ1   2.944  1.968
    6632     /G GLY 543 N    /main DA 0 OP1    /G GLY 543 H     2.943  2.343
    6633     /G GLY 546 N    /main DA 1 OP1    /G GLY 546 H     2.915  2.028
    6634     /G LYS 547 NZ   /opp DG 2 O3'     /G LYS 547 HZ2   2.870  2.326
    6635     /G LYS 547 NZ   /opp DG 3 OP1     /G LYS 547 HZ1   2.552  1.558
    6636     /G LYS 548 NZ   /main DA 1 N3     /G LYS 548 HZ1   2.902  2.236
    6637     /G LYS 548 NZ   /main DG 2 O4'    /G LYS 548 HZ2   2.987  2.212
    6638     /G LYS 548 NZ   /opp DT 0 O2      /G LYS 548 HZ3   3.197  2.248
    6639     /G ASN 553 N    /opp DG 3 OP2     /G ASN 553 H     2.957  2.079
    6640     /G ARG 557 NH1  /opp DG 5 O6      /G ARG 557 HH12  2.913  1.906
    6641     /G ARG 557 NH2  /opp DG 5 N7      /G ARG 557 HH22  2.372  1.443
    6642     /G LYS 560 NZ   /main DA -11 OP1  /G LYS 560 HZ3   3.180  2.601
    6643     /G GLY 561 N    /main DT -10 OP1  /G GLY 561 H     3.390  2.598
    6644     /G GLY 561 N    /main DT -10 OP2  /G GLY 561 H     2.846  2.111
    6645     /G THR 563 N    /main DT -10 OP1  /G THR 563 H     2.931  2.306
    6646     /G THR 563 OG1  /main DT -10 OP1  /G THR 563 HG1   3.027  2.078
    6647     /G ALA 565 N    /main DA -9 OP2   /G ALA 565 H     2.576  1.574
    6648     /G ARG 574 NH2  /opp DG 3 OP1     /G ARG 574 HH21  3.076  2.128
    6649     /G LYS 581 NZ   /main DA 0 O5'    /G LYS 581 HZ1   3.367  2.792
    6650     /G LYS 581 NZ   /main DA 0 OP2    /G LYS 581 HZ1   3.143  2.140
    6651    
    6652 
    6653  
    6654 74 hydrogen bonds found 
    6655 21 strict hydrogen bonds found 
    6656 
    6657 > select clear
    6658 
    6659 > save "/Users/jtbauer/Library/CloudStorage/OneDrive-
    6660 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    6661 > structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver30.cxs"
    6662 
    6663 > select /main:-13
    6664 
    6665 30 atoms, 31 bonds, 1 residue, 1 model selected 
    6666 
    6667 > hide sel cartoons
    6668 
    6669 > show sel cartoons
    6670 
    6671 > select /A:436@ND2
    6672 
    6673 1 atom, 1 residue, 1 model selected 
    6674 
    6675 > select /main:-12
    6676 
    6677 32 atoms, 34 bonds, 1 residue, 1 model selected 
    6678 
    6679 > select /main:-10
    6680 
    6681 32 atoms, 33 bonds, 1 residue, 1 model selected 
    6682 
    6683 > hide sel cartoons
    6684 
    6685 > show sel cartoons
    6686 
    6687 > select /main:-11
    6688 
    6689 32 atoms, 34 bonds, 1 residue, 1 model selected 
    6690 
    6691 > hide sel cartoons
    6692 
    6693 > show sel cartoons
    6694 
    6695 > select /main:-10
    6696 
    6697 32 atoms, 33 bonds, 1 residue, 1 model selected 
    6698 
    6699 > select clear
    6700 
    6701 > select /main:-9
    6702 
    6703 32 atoms, 34 bonds, 1 residue, 1 model selected 
    6704 
    6705 > select /main:-9
    6706 
    6707 32 atoms, 34 bonds, 1 residue, 1 model selected 
    6708 
    6709 > hide sel cartoons
    6710 
    6711 > show sel cartoons
    6712 
    6713 > select /main:-8
    6714 
    6715 32 atoms, 33 bonds, 1 residue, 1 model selected 
    6716 
    6717 > select /main:-9
    6718 
    6719 32 atoms, 34 bonds, 1 residue, 1 model selected 
    6720 
    6721 > hide sel cartoons
    6722 
    6723 > show sel cartoons
    6724 
    6725 > hide sel cartoons
    6726 
    6727 > select /main:-8
    6728 
    6729 32 atoms, 33 bonds, 1 residue, 1 model selected 
    6730 
    6731 > hide sel cartoons
    6732 
    6733 > show sel cartoons
    6734 
    6735 > select /main:-9@C3'
    6736 
    6737 1 atom, 1 residue, 1 model selected 
    6738 
    6739 > select down
    6740 
    6741 1 atom, 1 residue, 1 model selected 
    6742 
    6743 > select up
    6744 
    6745 32 atoms, 34 bonds, 1 residue, 1 model selected 
    6746 
    6747 > show sel cartoons
    6748 
    6749 > select clear
    6750 
    6751 > select /main:0
    6752 
    6753 32 atoms, 34 bonds, 1 residue, 1 model selected 
    6754 
    6755 > select /main:0
    6756 
    6757 32 atoms, 34 bonds, 1 residue, 1 model selected 
    6758 
    6759 > hide sel cartoons
    6760 
    6761 > show sel cartoons
    6762 
    6763 > select /main:1
    6764 
    6765 32 atoms, 34 bonds, 1 residue, 1 model selected 
    6766 
    6767 > select /main:6
    6768 
    6769 30 atoms, 31 bonds, 1 residue, 1 model selected 
    6770 
    6771 > hide sel cartoons
    6772 
    6773 > select nucleic
    6774 
    6775 2291 atoms, 2469 bonds, 72 residues, 1 model selected 
    6776 
    6777 > hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
    6778 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    6779 > structures/PDBs/ylODC_54bp-oriC061_complete/hbond-generation2" dashes 6
    6780 > restrict #1/A,B,C,D,E,F,G twoColors true intraRes false reveal true
    6781 > retainCurrent true log true
    6782    
    6783    
    6784     Finding intermodel H-bonds
    6785     Finding intramodel H-bonds
    6786     Constraints relaxed by 0.4 angstroms and 20 degrees
    6787     Models used:
    6788         1 ylODC_54bpOriC061_rev30_PostPhenix.pdb
    6789    
    6790     61 H-bonds
    6791     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    6792     /A ARG 301 NE   /opp DC 18 OP1    /A ARG 301 HE    3.042  2.096
    6793     /A ARG 301 NH1  /main DT -16 O2   /A ARG 301 HH12  2.780  1.937
    6794     /A ARG 301 NH1  /main DC -15 O4'  /A ARG 301 HH11  2.808  1.918
    6795     /A ARG 301 NH2  /opp DT 17 O2     /A ARG 301 HH22  3.419  2.726
    6796     /A ARG 301 NH2  /opp DC 18 OP1    /A ARG 301 HH21  3.241  2.383
    6797     /A PHE 303 N    /main DC -13 OP1  /A PHE 303 H     2.683  1.713
    6798     /A LYS 305 NZ   /main DA -12 OP1  /A LYS 305 HZ1   3.005  2.074
    6799     /A ASN 435 ND2  /main DC -13 OP2  /A ASN 435 HD22  2.896  1.911
    6800     /A ASN 436 ND2  /main DC -13 OP2  /A ASN 436 HD22  3.172  2.251
    6801     /B LYS 148 NZ   /opp DG -10 OP1   /B LYS 148 HZ3   2.880  2.062
    6802     /B ARG 150 NH1  /main DG 9 O6     /B ARG 150 HH12  3.317  2.492
    6803     /B ARG 150 NH1  /opp DG -10 O6    /B ARG 150 HH12  3.200  2.518
    6804     /B ARG 150 NH2  /main DG 9 O6     /B ARG 150 HH22  2.932  1.954
    6805     /B GLY 153 N    /main DT 8 OP2    /B GLY 153 H     2.955  1.965
    6806     /B LYS 248 NZ   /opp DA 8 O3'     /B LYS 248 HZ1   3.058  2.307
    6807     /B LYS 279 N    /opp DA 10 OP1    /B LYS 279 H     3.012  2.176
    6808     /B ASP 280 N    /opp DA 10 OP1    /B ASP 280 H     3.419  2.439
    6809     /C LYS 188 NZ   /main DT -8 OP1   /C LYS 188 HZ1   2.597  1.602
    6810     /C ARG 219 N    /opp DT 12 OP1    /C ARG 219 H     2.860  1.859
    6811     /C ARG 219 NH1  /opp DT 11 OP1    /C ARG 219 HH11  2.808  2.044
    6812     /C ARG 220 NH1  /main DT -10 O2   /C ARG 220 HH11  3.328  2.600
    6813     /C ARG 220 NH1  /opp DT 11 O2     /C ARG 220 HH11  3.062  2.380
    6814     /C TYR 223 OH   /main DA -9 O3'   /C TYR 223 HH    2.926  2.064
    6815     /C TYR 607 OH   /main DC 6 OP2    /C TYR 607 HH    3.278  2.327
    6816     /C ARG 672 N    /main DC 6 OP1    /C ARG 672 H     2.895  1.905
    6817     /C ARG 672 NH1  /opp DT -4 O2     /C ARG 672 HH12  2.707  1.845
    6818     /C ARG 672 NH2  /opp DT -4 O2     /C ARG 672 HH22  3.408  2.771
    6819     /C LYS 673 NZ   /main DA 7 OP1    /C LYS 673 HZ1   2.886  1.972
    6820     /D LYS 168 NZ   /main DA -12 N3   /D LYS 168 HZ1   2.838  1.847
    6821     /D SER 169 OG   /main DA -11 OP2  /D SER 169 HG    2.801  1.842
    6822     /D ILE 170 N    /main DA -11 OP2  /D ILE 170 H     3.077  2.202
    6823     /D SER 463 OG   /opp DG 1 OP1     /D SER 463 HG    2.493  1.565
    6824     /D LYS 465 NZ   /opp DG 2 O6      /D LYS 465 HZ1   2.363  1.498
    6825     /D LYS 465 NZ   /opp DG 3 O6      /D LYS 465 HZ2   2.546  1.684
    6826     /E ARG 76 NH1   /main DA -9 OP1   /E ARG 76 HH11   3.235  2.257
    6827     /E ARG 340 NE   /opp DG -10 O5'   /E ARG 340 HE    3.009  2.192
    6828     /E ARG 340 NE   /opp DG -10 OP2   /E ARG 340 HE    2.873  1.974
    6829     /E ARG 340 NH2  /opp DG -10 OP2   /E ARG 340 HH21  3.300  2.551
    6830     /E TYR 341 OH   /opp DC -9 OP1    /E TYR 341 HH    2.940  2.219
    6831     /E ARG 357 NH1  /opp DT -13 O2    /E ARG 357 HH12  2.784  1.882
    6832     /E ARG 357 NH2  /opp DT -13 O2    /E ARG 357 HH22  2.882  2.025
    6833     /E ARG 357 NH2  /opp DT -13 O4'   /E ARG 357 HH22  3.135  2.386
    6834     /E GLU 358 N    /main DG 15 OP1   /E GLU 358 H     2.888  1.905
    6835     /E THR 359 OG1  /opp DG -10 OP1   /E THR 359 HG1   2.802  2.243
    6836     /E ARG 362 N    /opp DG -10 O3'   /E ARG 362 H     3.350  2.344
    6837     /E ARG 362 NH1  /opp DT -11 O2    /E ARG 362 HH12  2.975  2.081
    6838     /E ARG 362 NH1  /opp DG -10 O4'   /E ARG 362 HH11  3.022  2.183
    6839     /E ARG 362 NH2  /main DT 12 O2    /E ARG 362 HH22  2.881  2.130
    6840     /E LYS 363 N    /opp DC -9 OP2    /E LYS 363 H     3.408  2.442
    6841     /E LYS 363 NZ   /opp DA -8 OP1    /E LYS 363 HZ1   2.944  1.968
    6842     /G GLY 546 N    /main DA 1 OP1    /G GLY 546 H     2.915  2.028
    6843     /G LYS 547 NZ   /opp DG 3 OP1     /G LYS 547 HZ1   2.552  1.558
    6844     /G LYS 548 NZ   /opp DT 0 O2      /G LYS 548 HZ3   3.197  2.248
    6845     /G ASN 553 N    /opp DG 3 OP2     /G ASN 553 H     2.957  2.079
    6846     /G ARG 557 NH1  /opp DG 5 O6      /G ARG 557 HH12  2.913  1.906
    6847     /G ARG 557 NH2  /opp DG 5 N7      /G ARG 557 HH22  2.372  1.443
    6848     /G GLY 561 N    /main DT -10 OP2  /G GLY 561 H     2.846  2.111
    6849     /G THR 563 OG1  /main DT -10 OP1  /G THR 563 HG1   3.027  2.078
    6850     /G ALA 565 N    /main DA -9 OP2   /G ALA 565 H     2.576  1.574
    6851     /G ARG 574 NH2  /opp DG 3 OP1     /G ARG 574 HH21  3.076  2.128
    6852     /G LYS 581 NZ   /main DA 0 OP2    /G LYS 581 HZ1   3.143  2.140
    6853    
    6854 
    6855  
    6856 61 hydrogen bonds found 
    6857 21 strict hydrogen bonds found 
    6858 
    6859 > ui tool show H-Bonds
    6860 
    6861 > hbonds sel dashes 6 restrict #1/A,B,C,D,E,F,G twoColors true intraRes false
    6862 > select true reveal true retainCurrent true log true
    6863    
    6864    
    6865     Finding intermodel H-bonds
    6866     Finding intramodel H-bonds
    6867     Constraints relaxed by 0.4 angstroms and 20 degrees
    6868     Models used:
    6869         1 ylODC_54bpOriC061_rev30_PostPhenix.pdb
    6870    
    6871     61 H-bonds
    6872     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    6873     /A ARG 301 NE   /opp DC 18 OP1    /A ARG 301 HE    3.042  2.096
    6874     /A ARG 301 NH1  /main DT -16 O2   /A ARG 301 HH12  2.780  1.937
    6875     /A ARG 301 NH1  /main DC -15 O4'  /A ARG 301 HH11  2.808  1.918
    6876     /A ARG 301 NH2  /opp DT 17 O2     /A ARG 301 HH22  3.419  2.726
    6877     /A ARG 301 NH2  /opp DC 18 OP1    /A ARG 301 HH21  3.241  2.383
    6878     /A PHE 303 N    /main DC -13 OP1  /A PHE 303 H     2.683  1.713
    6879     /A LYS 305 NZ   /main DA -12 OP1  /A LYS 305 HZ1   3.005  2.074
    6880     /A ASN 435 ND2  /main DC -13 OP2  /A ASN 435 HD22  2.896  1.911
    6881     /A ASN 436 ND2  /main DC -13 OP2  /A ASN 436 HD22  3.172  2.251
    6882     /B LYS 148 NZ   /opp DG -10 OP1   /B LYS 148 HZ3   2.880  2.062
    6883     /B ARG 150 NH1  /main DG 9 O6     /B ARG 150 HH12  3.317  2.492
    6884     /B ARG 150 NH1  /opp DG -10 O6    /B ARG 150 HH12  3.200  2.518
    6885     /B ARG 150 NH2  /main DG 9 O6     /B ARG 150 HH22  2.932  1.954
    6886     /B GLY 153 N    /main DT 8 OP2    /B GLY 153 H     2.955  1.965
    6887     /B LYS 248 NZ   /opp DA 8 O3'     /B LYS 248 HZ1   3.058  2.307
    6888     /B LYS 279 N    /opp DA 10 OP1    /B LYS 279 H     3.012  2.176
    6889     /B ASP 280 N    /opp DA 10 OP1    /B ASP 280 H     3.419  2.439
    6890     /C LYS 188 NZ   /main DT -8 OP1   /C LYS 188 HZ1   2.597  1.602
    6891     /C ARG 219 N    /opp DT 12 OP1    /C ARG 219 H     2.860  1.859
    6892     /C ARG 219 NH1  /opp DT 11 OP1    /C ARG 219 HH11  2.808  2.044
    6893     /C ARG 220 NH1  /main DT -10 O2   /C ARG 220 HH11  3.328  2.600
    6894     /C ARG 220 NH1  /opp DT 11 O2     /C ARG 220 HH11  3.062  2.380
    6895     /C TYR 223 OH   /main DA -9 O3'   /C TYR 223 HH    2.926  2.064
    6896     /C TYR 607 OH   /main DC 6 OP2    /C TYR 607 HH    3.278  2.327
    6897     /C ARG 672 N    /main DC 6 OP1    /C ARG 672 H     2.895  1.905
    6898     /C ARG 672 NH1  /opp DT -4 O2     /C ARG 672 HH12  2.707  1.845
    6899     /C ARG 672 NH2  /opp DT -4 O2     /C ARG 672 HH22  3.408  2.771
    6900     /C LYS 673 NZ   /main DA 7 OP1    /C LYS 673 HZ1   2.886  1.972
    6901     /D LYS 168 NZ   /main DA -12 N3   /D LYS 168 HZ1   2.838  1.847
    6902     /D SER 169 OG   /main DA -11 OP2  /D SER 169 HG    2.801  1.842
    6903     /D ILE 170 N    /main DA -11 OP2  /D ILE 170 H     3.077  2.202
    6904     /D SER 463 OG   /opp DG 1 OP1     /D SER 463 HG    2.493  1.565
    6905     /D LYS 465 NZ   /opp DG 2 O6      /D LYS 465 HZ1   2.363  1.498
    6906     /D LYS 465 NZ   /opp DG 3 O6      /D LYS 465 HZ2   2.546  1.684
    6907     /E ARG 76 NH1   /main DA -9 OP1   /E ARG 76 HH11   3.235  2.257
    6908     /E ARG 340 NE   /opp DG -10 O5'   /E ARG 340 HE    3.009  2.192
    6909     /E ARG 340 NE   /opp DG -10 OP2   /E ARG 340 HE    2.873  1.974
    6910     /E ARG 340 NH2  /opp DG -10 OP2   /E ARG 340 HH21  3.300  2.551
    6911     /E TYR 341 OH   /opp DC -9 OP1    /E TYR 341 HH    2.940  2.219
    6912     /E ARG 357 NH1  /opp DT -13 O2    /E ARG 357 HH12  2.784  1.882
    6913     /E ARG 357 NH2  /opp DT -13 O2    /E ARG 357 HH22  2.882  2.025
    6914     /E ARG 357 NH2  /opp DT -13 O4'   /E ARG 357 HH22  3.135  2.386
    6915     /E GLU 358 N    /main DG 15 OP1   /E GLU 358 H     2.888  1.905
    6916     /E THR 359 OG1  /opp DG -10 OP1   /E THR 359 HG1   2.802  2.243
    6917     /E ARG 362 N    /opp DG -10 O3'   /E ARG 362 H     3.350  2.344
    6918     /E ARG 362 NH1  /opp DT -11 O2    /E ARG 362 HH12  2.975  2.081
    6919     /E ARG 362 NH1  /opp DG -10 O4'   /E ARG 362 HH11  3.022  2.183
    6920     /E ARG 362 NH2  /main DT 12 O2    /E ARG 362 HH22  2.881  2.130
    6921     /E LYS 363 N    /opp DC -9 OP2    /E LYS 363 H     3.408  2.442
    6922     /E LYS 363 NZ   /opp DA -8 OP1    /E LYS 363 HZ1   2.944  1.968
    6923     /G GLY 546 N    /main DA 1 OP1    /G GLY 546 H     2.915  2.028
    6924     /G LYS 547 NZ   /opp DG 3 OP1     /G LYS 547 HZ1   2.552  1.558
    6925     /G LYS 548 NZ   /opp DT 0 O2      /G LYS 548 HZ3   3.197  2.248
    6926     /G ASN 553 N    /opp DG 3 OP2     /G ASN 553 H     2.957  2.079
    6927     /G ARG 557 NH1  /opp DG 5 O6      /G ARG 557 HH12  2.913  1.906
    6928     /G ARG 557 NH2  /opp DG 5 N7      /G ARG 557 HH22  2.372  1.443
    6929     /G GLY 561 N    /main DT -10 OP2  /G GLY 561 H     2.846  2.111
    6930     /G THR 563 OG1  /main DT -10 OP1  /G THR 563 HG1   3.027  2.078
    6931     /G ALA 565 N    /main DA -9 OP2   /G ALA 565 H     2.576  1.574
    6932     /G ARG 574 NH2  /opp DG 3 OP1     /G ARG 574 HH21  3.076  2.128
    6933     /G LYS 581 NZ   /main DA 0 OP2    /G LYS 581 HZ1   3.143  2.140
    6934    
    6935 
    6936  
    6937 61 hydrogen bonds found 
    6938 21 strict hydrogen bonds found 
    6939 
    6940 > select nucleic
    6941 
    6942 2291 atoms, 2469 bonds, 72 residues, 1 model selected 
    6943 
    6944 > hbonds sel dashes 6 restrict #1/A,B,C,D,E,F,G twoColors true slopColor
    6945 > #00f900 intraRes false select true reveal true retainCurrent true log true
    6946    
    6947    
    6948     Finding intermodel H-bonds
    6949     Finding intramodel H-bonds
    6950     Constraints relaxed by 0.4 angstroms and 20 degrees
    6951     Models used:
    6952         1 ylODC_54bpOriC061_rev30_PostPhenix.pdb
    6953    
    6954     61 H-bonds
    6955     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    6956     /A ARG 301 NE   /opp DC 18 OP1    /A ARG 301 HE    3.042  2.096
    6957     /A ARG 301 NH1  /main DT -16 O2   /A ARG 301 HH12  2.780  1.937
    6958     /A ARG 301 NH1  /main DC -15 O4'  /A ARG 301 HH11  2.808  1.918
    6959     /A ARG 301 NH2  /opp DT 17 O2     /A ARG 301 HH22  3.419  2.726
    6960     /A ARG 301 NH2  /opp DC 18 OP1    /A ARG 301 HH21  3.241  2.383
    6961     /A PHE 303 N    /main DC -13 OP1  /A PHE 303 H     2.683  1.713
    6962     /A LYS 305 NZ   /main DA -12 OP1  /A LYS 305 HZ1   3.005  2.074
    6963     /A ASN 435 ND2  /main DC -13 OP2  /A ASN 435 HD22  2.896  1.911
    6964     /A ASN 436 ND2  /main DC -13 OP2  /A ASN 436 HD22  3.172  2.251
    6965     /B LYS 148 NZ   /opp DG -10 OP1   /B LYS 148 HZ3   2.880  2.062
    6966     /B ARG 150 NH1  /main DG 9 O6     /B ARG 150 HH12  3.317  2.492
    6967     /B ARG 150 NH1  /opp DG -10 O6    /B ARG 150 HH12  3.200  2.518
    6968     /B ARG 150 NH2  /main DG 9 O6     /B ARG 150 HH22  2.932  1.954
    6969     /B GLY 153 N    /main DT 8 OP2    /B GLY 153 H     2.955  1.965
    6970     /B LYS 248 NZ   /opp DA 8 O3'     /B LYS 248 HZ1   3.058  2.307
    6971     /B LYS 279 N    /opp DA 10 OP1    /B LYS 279 H     3.012  2.176
    6972     /B ASP 280 N    /opp DA 10 OP1    /B ASP 280 H     3.419  2.439
    6973     /C LYS 188 NZ   /main DT -8 OP1   /C LYS 188 HZ1   2.597  1.602
    6974     /C ARG 219 N    /opp DT 12 OP1    /C ARG 219 H     2.860  1.859
    6975     /C ARG 219 NH1  /opp DT 11 OP1    /C ARG 219 HH11  2.808  2.044
    6976     /C ARG 220 NH1  /main DT -10 O2   /C ARG 220 HH11  3.328  2.600
    6977     /C ARG 220 NH1  /opp DT 11 O2     /C ARG 220 HH11  3.062  2.380
    6978     /C TYR 223 OH   /main DA -9 O3'   /C TYR 223 HH    2.926  2.064
    6979     /C TYR 607 OH   /main DC 6 OP2    /C TYR 607 HH    3.278  2.327
    6980     /C ARG 672 N    /main DC 6 OP1    /C ARG 672 H     2.895  1.905
    6981     /C ARG 672 NH1  /opp DT -4 O2     /C ARG 672 HH12  2.707  1.845
    6982     /C ARG 672 NH2  /opp DT -4 O2     /C ARG 672 HH22  3.408  2.771
    6983     /C LYS 673 NZ   /main DA 7 OP1    /C LYS 673 HZ1   2.886  1.972
    6984     /D LYS 168 NZ   /main DA -12 N3   /D LYS 168 HZ1   2.838  1.847
    6985     /D SER 169 OG   /main DA -11 OP2  /D SER 169 HG    2.801  1.842
    6986     /D ILE 170 N    /main DA -11 OP2  /D ILE 170 H     3.077  2.202
    6987     /D SER 463 OG   /opp DG 1 OP1     /D SER 463 HG    2.493  1.565
    6988     /D LYS 465 NZ   /opp DG 2 O6      /D LYS 465 HZ1   2.363  1.498
    6989     /D LYS 465 NZ   /opp DG 3 O6      /D LYS 465 HZ2   2.546  1.684
    6990     /E ARG 76 NH1   /main DA -9 OP1   /E ARG 76 HH11   3.235  2.257
    6991     /E ARG 340 NE   /opp DG -10 O5'   /E ARG 340 HE    3.009  2.192
    6992     /E ARG 340 NE   /opp DG -10 OP2   /E ARG 340 HE    2.873  1.974
    6993     /E ARG 340 NH2  /opp DG -10 OP2   /E ARG 340 HH21  3.300  2.551
    6994     /E TYR 341 OH   /opp DC -9 OP1    /E TYR 341 HH    2.940  2.219
    6995     /E ARG 357 NH1  /opp DT -13 O2    /E ARG 357 HH12  2.784  1.882
    6996     /E ARG 357 NH2  /opp DT -13 O2    /E ARG 357 HH22  2.882  2.025
    6997     /E ARG 357 NH2  /opp DT -13 O4'   /E ARG 357 HH22  3.135  2.386
    6998     /E GLU 358 N    /main DG 15 OP1   /E GLU 358 H     2.888  1.905
    6999     /E THR 359 OG1  /opp DG -10 OP1   /E THR 359 HG1   2.802  2.243
    7000     /E ARG 362 N    /opp DG -10 O3'   /E ARG 362 H     3.350  2.344
    7001     /E ARG 362 NH1  /opp DT -11 O2    /E ARG 362 HH12  2.975  2.081
    7002     /E ARG 362 NH1  /opp DG -10 O4'   /E ARG 362 HH11  3.022  2.183
    7003     /E ARG 362 NH2  /main DT 12 O2    /E ARG 362 HH22  2.881  2.130
    7004     /E LYS 363 N    /opp DC -9 OP2    /E LYS 363 H     3.408  2.442
    7005     /E LYS 363 NZ   /opp DA -8 OP1    /E LYS 363 HZ1   2.944  1.968
    7006     /G GLY 546 N    /main DA 1 OP1    /G GLY 546 H     2.915  2.028
    7007     /G LYS 547 NZ   /opp DG 3 OP1     /G LYS 547 HZ1   2.552  1.558
    7008     /G LYS 548 NZ   /opp DT 0 O2      /G LYS 548 HZ3   3.197  2.248
    7009     /G ASN 553 N    /opp DG 3 OP2     /G ASN 553 H     2.957  2.079
    7010     /G ARG 557 NH1  /opp DG 5 O6      /G ARG 557 HH12  2.913  1.906
    7011     /G ARG 557 NH2  /opp DG 5 N7      /G ARG 557 HH22  2.372  1.443
    7012     /G GLY 561 N    /main DT -10 OP2  /G GLY 561 H     2.846  2.111
    7013     /G THR 563 OG1  /main DT -10 OP1  /G THR 563 HG1   3.027  2.078
    7014     /G ALA 565 N    /main DA -9 OP2   /G ALA 565 H     2.576  1.574
    7015     /G ARG 574 NH2  /opp DG 3 OP1     /G ARG 574 HH21  3.076  2.128
    7016     /G LYS 581 NZ   /main DA 0 OP2    /G LYS 581 HZ1   3.143  2.140
    7017    
    7018 
    7019  
    7020 61 hydrogen bonds found 
    7021 21 strict hydrogen bonds found 
    7022 
    7023 > select clear
    7024 
    7025 > select /main:7
    7026 
    7027 32 atoms, 34 bonds, 1 residue, 1 model selected 
    7028 
    7029 > hide sel cartoons
    7030 
    7031 > show sel cartoons
    7032 
    7033 > select /main:8
    7034 
    7035 32 atoms, 33 bonds, 1 residue, 1 model selected 
    7036 
    7037 > hide sel cartoons
    7038 
    7039 > show sel cartoons
    7040 
    7041 > select clear
    7042 
    7043 > select /main:12@C2
    7044 
    7045 1 atom, 1 residue, 1 model selected 
    7046 
    7047 > select /main:15
    7048 
    7049 33 atoms, 35 bonds, 1 residue, 1 model selected 
    7050 
    7051 > select clear
    7052 
    7053 > select /opp:17
    7054 
    7055 32 atoms, 33 bonds, 1 residue, 1 model selected 
    7056 
    7057 > select /opp:18
    7058 
    7059 31 atoms, 32 bonds, 1 residue, 1 model selected 
    7060 
    7061 > select /opp:18
    7062 
    7063 31 atoms, 32 bonds, 1 residue, 1 model selected 
    7064 
    7065 > select /opp:17
    7066 
    7067 32 atoms, 33 bonds, 1 residue, 1 model selected 
    7068 
    7069 > select /opp:18
    7070 
    7071 31 atoms, 32 bonds, 1 residue, 1 model selected 
    7072 
    7073 > hide sel cartoons
    7074 
    7075 > show sel cartoons
    7076 
    7077 > hide sel cartoons
    7078 
    7079 > select /opp:11
    7080 
    7081 32 atoms, 33 bonds, 1 residue, 1 model selected 
    7082 
    7083 > hide sel cartoons
    7084 
    7085 > show sel cartoons
    7086 
    7087 > select clear
    7088 
    7089 > select /opp:12
    7090 
    7091 32 atoms, 33 bonds, 1 residue, 1 model selected 
    7092 
    7093 > hide sel cartoons
    7094 
    7095 > show sel cartoons
    7096 
    7097 > select /opp:10
    7098 
    7099 32 atoms, 34 bonds, 1 residue, 1 model selected 
    7100 
    7101 > hide sel cartoons
    7102 
    7103 > select /opp:9
    7104 
    7105 32 atoms, 33 bonds, 1 residue, 1 model selected 
    7106 
    7107 > hide sel cartoons
    7108 
    7109 > show sel cartoons
    7110 
    7111 > select /opp:8
    7112 
    7113 32 atoms, 34 bonds, 1 residue, 1 model selected 
    7114 
    7115 > hide sel cartoons
    7116 
    7117 > select /opp:9
    7118 
    7119 32 atoms, 33 bonds, 1 residue, 1 model selected 
    7120 
    7121 > select /opp:1
    7122 
    7123 33 atoms, 35 bonds, 1 residue, 1 model selected 
    7124 
    7125 > hide sel cartoons
    7126 
    7127 > show sel cartoons
    7128 
    7129 > select /opp:0
    7130 
    7131 32 atoms, 33 bonds, 1 residue, 1 model selected 
    7132 
    7133 > select /opp:-2
    7134 
    7135 30 atoms, 31 bonds, 1 residue, 1 model selected 
    7136 
    7137 > select /opp:-4
    7138 
    7139 32 atoms, 33 bonds, 1 residue, 1 model selected 
    7140 
    7141 > select /opp:-8
    7142 
    7143 32 atoms, 34 bonds, 1 residue, 1 model selected 
    7144 
    7145 > select /opp:-9
    7146 
    7147 30 atoms, 31 bonds, 1 residue, 1 model selected 
    7148 
    7149 > hide sel cartoons
    7150 
    7151 > show sel cartoons
    7152 
    7153 > select /E:363@N
    7154 
    7155 1 atom, 1 residue, 1 model selected 
    7156 
    7157 > select /opp:-9
    7158 
    7159 30 atoms, 31 bonds, 1 residue, 1 model selected 
    7160 
    7161 > select /E:362@N
    7162 
    7163 1 atom, 1 residue, 1 model selected 
    7164 
    7165 > select /opp:-9
    7166 
    7167 30 atoms, 31 bonds, 1 residue, 1 model selected 
    7168 
    7169 > hide sel cartoons
    7170 
    7171 > select /opp:-11
    7172 
    7173 32 atoms, 33 bonds, 1 residue, 1 model selected 
    7174 
    7175 > hide sel cartoons
    7176 
    7177 > select /opp:-10
    7178 
    7179 33 atoms, 35 bonds, 1 residue, 1 model selected 
    7180 
    7181 > select /E:357@N
    7182 
    7183 1 atom, 1 residue, 1 model selected 
    7184 
    7185 > select /E:356
    7186 
    7187 24 atoms, 23 bonds, 1 residue, 1 model selected 
    7188 
    7189 > show sel atoms
    7190 
    7191 > open "/Users/jtbauer/Library/CloudStorage/OneDrive-
    7192 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    7193 > structures/PDBs/ylODC_54bp-
    7194 > oriC061_complete/ylODC_54bpOriC061_rev31_PostPhenix.pdb"
    7195 
    7196 Chain information for ylODC_54bpOriC061_rev31_PostPhenix.pdb #2 
    7197 --- 
    7198 Chain | Description 
    7199 A | No description available 
    7200 B | No description available 
    7201 C | No description available 
    7202 D | No description available 
    7203 E | No description available 
    7204 F | No description available 
    7205 G | No description available 
    7206 H | No description available 
    7207 I | No description available 
    7208  
    7209 
    7210 > modelfix
    7211 
    7212 Changed 75323 atom styles 
    7213 71260 atoms, 72152 bonds, 18 pseudobonds, 5940 residues, 4 models selected 
    7214 
    7215 > close #1
    7216 
    7217 > select nucleic
    7218 
    7219 1476 atoms, 1654 bonds, 72 residues, 1 model selected 
    7220 
    7221 > hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
    7222 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    7223 > structures/PDBs/ylODC_54bp-oriC061_complete/hbond-
    7224 > generation2_ver31_relaxed40" dashes 6 restrict #2/A,B,C,D,E,F,G angleSlop
    7225 > 40.0 twoColors true slopColor #ff9300 intraRes false select true reveal true
    7226 > retainCurrent true log true
    7227    
    7228    
    7229     Finding intermodel H-bonds
    7230     Finding intramodel H-bonds
    7231     Constraints relaxed by 0.4 angstroms and 40 degrees
    7232     Models used:
    7233         2 ylODC_54bpOriC061_rev31_PostPhenix.pdb
    7234    
    7235     78 H-bonds
    7236     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    7237     /A ARG 301 NE   /I DC 47 OP1  no hydrogen  3.042  N/A
    7238     /A ARG 301 NH1  /H DT 10 O2   no hydrogen  2.780  N/A
    7239     /A ARG 301 NH1  /H DC 11 O4'  no hydrogen  2.808  N/A
    7240     /A ARG 301 NH2  /I DT 46 O2   no hydrogen  3.419  N/A
    7241     /A ARG 301 NH2  /I DC 47 OP1  no hydrogen  3.241  N/A
    7242     /A PHE 303 N    /H DC 13 OP1  no hydrogen  2.683  N/A
    7243     /A LYS 305 NZ   /H DA 14 OP1  no hydrogen  3.005  N/A
    7244     /A ASN 435 ND2  /H DC 13 OP2  no hydrogen  2.896  N/A
    7245     /A ASN 436 ND2  /H DC 13 OP2  no hydrogen  3.172  N/A
    7246     /B LYS 148 NZ   /I DG 19 OP1  no hydrogen  2.880  N/A
    7247     /B ARG 150 NH1  /H DG 35 O6   no hydrogen  3.317  N/A
    7248     /B ARG 150 NH1  /I DG 19 O6   no hydrogen  3.200  N/A
    7249     /B ARG 150 NH2  /H DG 35 O6   no hydrogen  2.932  N/A
    7250     /B GLY 153 N    /H DT 34 OP2  no hydrogen  2.955  N/A
    7251     /B LYS 248 NZ   /I DA 37 O3'  no hydrogen  3.058  N/A
    7252     /B LYS 279 N    /I DA 39 OP1  no hydrogen  3.012  N/A
    7253     /B ASP 280 N    /I DA 39 OP1  no hydrogen  3.419  N/A
    7254     /C LYS 188 NZ   /H DT 18 OP1  no hydrogen  2.597  N/A
    7255     /C ARG 219 N    /I DT 41 OP1  no hydrogen  2.860  N/A
    7256     /C ARG 219 NH1  /I DT 40 OP1  no hydrogen  2.808  N/A
    7257     /C ARG 220 NH1  /H DA 15 N3   no hydrogen  3.522  N/A
    7258     /C ARG 220 NH1  /H DT 16 O2   no hydrogen  3.328  N/A
    7259     /C ARG 220 NH1  /I DT 40 O2   no hydrogen  3.062  N/A
    7260     /C TYR 223 OH   /H DA 17 O3'  no hydrogen  2.926  N/A
    7261     /C TYR 223 OH   /H DT 18 OP1  no hydrogen  2.834  N/A
    7262     /C TYR 607 OH   /H DC 32 OP2  no hydrogen  3.278  N/A
    7263     /C LYS 671 N    /H DC 32 OP1  no hydrogen  2.864  N/A
    7264     /C ARG 672 N    /H DC 32 OP1  no hydrogen  2.895  N/A
    7265     /C ARG 672 NH1  /I DT 25 O2   no hydrogen  2.707  N/A
    7266     /C ARG 672 NH2  /I DT 25 O2   no hydrogen  3.408  N/A
    7267     /C LYS 673 NZ   /H DA 33 OP1  no hydrogen  2.886  N/A
    7268     /D LYS 168 NZ   /H DA 14 N3   no hydrogen  2.838  N/A
    7269     /D SER 169 OG   /H DA 14 O3'  no hydrogen  3.382  N/A
    7270     /D SER 169 OG   /H DA 15 OP2  no hydrogen  2.801  N/A
    7271     /D ILE 170 N    /H DA 15 OP2  no hydrogen  3.077  N/A
    7272     /D SER 463 OG   /I DG 30 OP1  no hydrogen  2.493  N/A
    7273     /D LYS 465 NZ   /I DG 31 N7   no hydrogen  3.444  N/A
    7274     /D LYS 465 NZ   /I DG 31 O6   no hydrogen  2.363  N/A
    7275     /D LYS 465 NZ   /I DG 32 O6   no hydrogen  2.546  N/A
    7276     /E ARG 76 NH1   /H DA 17 OP1  no hydrogen  3.235  N/A
    7277     /E ARG 340 NE   /I DG 19 O5'  no hydrogen  3.009  N/A
    7278     /E ARG 340 NE   /I DG 19 OP2  no hydrogen  2.873  N/A
    7279     /E ARG 340 NH2  /I DG 19 OP2  no hydrogen  3.300  N/A
    7280     /E TYR 341 OH   /I DG 19 O3'  no hydrogen  3.180  N/A
    7281     /E TYR 341 OH   /I DC 20 OP1  no hydrogen  2.940  N/A
    7282     /E ARG 356 NH1  /I DT 18 OP2  no hydrogen  2.602  N/A
    7283     /E ARG 357 NH1  /I DT 16 O2   no hydrogen  2.784  N/A
    7284     /E ARG 357 NH2  /I DT 16 O2   no hydrogen  2.882  N/A
    7285     /E ARG 357 NH2  /I DT 16 O4'  no hydrogen  3.135  N/A
    7286     /E GLU 358 N    /H DG 41 OP1  no hydrogen  2.888  N/A
    7287     /E THR 359 OG1  /I DG 19 OP1  no hydrogen  2.802  N/A
    7288     /E ARG 362 N    /I DG 19 O3'  no hydrogen  3.350  N/A
    7289     /E ARG 362 NH1  /I DT 18 O2   no hydrogen  2.975  N/A
    7290     /E ARG 362 NH1  /I DG 19 O4'  no hydrogen  3.022  N/A
    7291     /E ARG 362 NH2  /H DT 38 O2   no hydrogen  2.881  N/A
    7292     /E ARG 362 NH2  /H DA 39 O4'  no hydrogen  3.366  N/A
    7293     /E LYS 363 N    /I DC 20 OP2  no hydrogen  3.408  N/A
    7294     /E LYS 363 NZ   /I DA 21 OP1  no hydrogen  2.944  N/A
    7295     /G GLY 543 N    /H DA 26 OP1  no hydrogen  2.943  N/A
    7296     /G GLY 546 N    /H DA 27 OP1  no hydrogen  2.915  N/A
    7297     /G LYS 547 NZ   /I DG 31 O3'  no hydrogen  2.870  N/A
    7298     /G LYS 547 NZ   /I DG 32 OP1  no hydrogen  2.552  N/A
    7299     /G LYS 548 NZ   /H DA 27 N3   no hydrogen  2.902  N/A
    7300     /G LYS 548 NZ   /H DG 28 O4'  no hydrogen  2.987  N/A
    7301     /G LYS 548 NZ   /I DT 29 O2   no hydrogen  3.197  N/A
    7302     /G ASN 553 N    /I DG 32 OP2  no hydrogen  2.957  N/A
    7303     /G ARG 557 NH1  /I DG 34 O6   no hydrogen  2.913  N/A
    7304     /G ARG 557 NH1  /I DT 35 O4   no hydrogen  3.519  N/A
    7305     /G ARG 557 NH2  /I DG 34 N7   no hydrogen  2.372  N/A
    7306     /G LYS 560 NZ   /H DA 15 OP1  no hydrogen  3.180  N/A
    7307     /G GLY 561 N    /H DT 16 OP2  no hydrogen  2.846  N/A
    7308     /G THR 563 N    /H DT 16 OP1  no hydrogen  2.931  N/A
    7309     /G THR 563 OG1  /H DA 15 O3'  no hydrogen  2.798  N/A
    7310     /G THR 563 OG1  /H DT 16 OP1  no hydrogen  3.027  N/A
    7311     /G ALA 565 N    /H DA 17 OP2  no hydrogen  2.576  N/A
    7312     /G ARG 574 NH2  /I DG 32 OP1  no hydrogen  3.076  N/A
    7313     /G LYS 581 NZ   /H DA 26 O5'  no hydrogen  3.367  N/A
    7314     /G LYS 581 NZ   /H DA 26 OP2  no hydrogen  3.143  N/A
    7315    
    7316 
    7317  
    7318 78 hydrogen bonds found 
    7319 25 strict hydrogen bonds found 
    7320 
    7321 > select up
    7322 
    7323 1142 atoms, 1192 bonds, 81 residues, 1 model selected 
    7324 
    7325 > show sel atoms
    7326 
    7327 > ui tool show H-Bonds
    7328 
    7329 > ui tool show "Add Hydrogens"
    7330 
    7331 > addh #!2
    7332 
    7333 Summary of feedback from adding hydrogens to
    7334 ylODC_54bpOriC061_rev31_PostPhenix.pdb #2 
    7335 --- 
    7336 warnings | Not adding hydrogens to /H DG 8 P because it is missing heavy-atom bond partners 
    7337 Not adding hydrogens to /I DG 13 P because it is missing heavy-atom bond
    7338 partners 
    7339 notes | Termini for ylODC_54bpOriC061_rev31_PostPhenix.pdb (#2) chain A determined from SEQRES records 
    7340 Termini for ylODC_54bpOriC061_rev31_PostPhenix.pdb (#2) chain B determined
    7341 from SEQRES records 
    7342 No usable SEQRES records for ylODC_54bpOriC061_rev31_PostPhenix.pdb (#2) chain
    7343 C; guessing termini instead 
    7344 No usable SEQRES records for ylODC_54bpOriC061_rev31_PostPhenix.pdb (#2) chain
    7345 D; guessing termini instead 
    7346 No usable SEQRES records for ylODC_54bpOriC061_rev31_PostPhenix.pdb (#2) chain
    7347 E; guessing termini instead 
    7348 No usable SEQRES records for ylODC_54bpOriC061_rev31_PostPhenix.pdb (#2) chain
    7349 F; guessing termini instead 
    7350 No usable SEQRES records for ylODC_54bpOriC061_rev31_PostPhenix.pdb (#2) chain
    7351 G; guessing termini instead 
    7352 Termini for ylODC_54bpOriC061_rev31_PostPhenix.pdb (#2) chain H determined
    7353 from SEQRES records 
    7354 Termini for ylODC_54bpOriC061_rev31_PostPhenix.pdb (#2) chain I determined
    7355 from SEQRES records 
    7356 Chain-initial residues that are actual N termini: /A PRO 299, /B PRO 106, /C
    7357 THR 6, /D VAL 34, /E MET 1, /F PRO 179, /G PRO 93, /C THR 6, /C ASN 72, /D VAL
    7358 34, /D GLN 127, /D LEU 296, /D PHE 436, /E MET 1, /E ASP 319, /F PRO 179, /F
    7359 GLY 316, /G PRO 93, /G ALA 213, /G THR 386, /G VAL 439 
    7360 Chain-initial residues that are not actual N termini: /C ASN 72, /D GLN 127,
    7361 /D LEU 296, /D PHE 436, /E ASP 319, /F GLY 316, /G ALA 213, /G THR 386, /G VAL
    7362 439 
    7363 Chain-final residues that are actual C termini: /A LEU 718, /B LEU 507, /C LEU
    7364 685, /D ARG 511, /C ARG 29, /C LEU 685, /D SER 123, /D MET 285, /D LEU 420, /D
    7365 ARG 511, /E MET 300, /E ASN 464, /F THR 307, /F LYS 349, /G GLY 207, /G HIS
    7366 335, /G ASN 434, /G LYS 602 
    7367 Chain-final residues that are not actual C termini: /C ARG 29, /D SER 123, /D
    7368 MET 285, /D LEU 420, /E ASN 464, /E MET 300, /F LYS 349, /F THR 307, /G LYS
    7369 602, /G GLY 207, /G HIS 335, /G ASN 434 
    7370 Chain-initial residues that are not actual 5' termini: /I DG 13 
    7371 Missing OXT added to C-terminal residue /B LEU 507 
    7372 Missing OXT added to C-terminal residue /C ARG 29 
    7373 Missing OXT added to C-terminal residue /D SER 123 
    7374 Missing OXT added to C-terminal residue /D MET 285 
    7375 Missing OXT added to C-terminal residue /D LEU 420 
    7376 8 messages similar to the above omitted 
    7377 3054 hydrogen bonds 
    7378 Adding 'H' to /C ASN 72 
    7379 Adding 'H' to /D GLN 127 
    7380 Adding 'H' to /D LEU 296 
    7381 Adding 'H' to /D PHE 436 
    7382 Adding 'H' to /E ASP 319 
    7383 4 messages similar to the above omitted 
    7384 24712 hydrogens added 
    7385  
    7386 
    7387 > hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
    7388 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    7389 > structures/PDBs/ylODC_54bp-oriC061_complete/hbond-
    7390 > generation2_ver31_relaxed40" restrict #2/A,B,C,D,E,F,G angleSlop 40.0
    7391 > twoColors true slopColor #ff9300 intraRes false select true reveal true log
    7392 > true
    7393    
    7394    
    7395     Finding intermodel H-bonds
    7396     Finding intramodel H-bonds
    7397     Constraints relaxed by 0.4 angstroms and 40 degrees
    7398     Models used:
    7399         2 ylODC_54bpOriC061_rev31_PostPhenix.pdb
    7400    
    7401     139 H-bonds
    7402     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    7403     /A LYS 300 NZ   /A ASN 436 OD1  /A LYS 300 HZ1   3.118  2.399
    7404     /A ARG 301 NE   /I DC 47 OP1    /A ARG 301 HE    3.042  2.096
    7405     /A ARG 301 NH1  /H DT 10 O2     /A ARG 301 HH12  2.780  1.937
    7406     /A ARG 301 NH1  /H DC 11 O4'    /A ARG 301 HH11  2.808  1.918
    7407     /A ARG 301 NH2  /I DT 46 O2     /A ARG 301 HH22  3.419  2.726
    7408     /A ARG 301 NH2  /I DC 47 OP1    /A ARG 301 HH21  3.241  2.383
    7409     /A PHE 303 N    /H DC 13 OP1    /A PHE 303 H     2.683  1.713
    7410     /A LYS 305 N    /A ARG 431 O    /A LYS 305 H     2.798  1.912
    7411     /A LYS 305 NZ   /A GLU 421 OE1  /A LYS 305 HZ2   3.041  2.143
    7412     /A LYS 305 NZ   /H DA 14 OP1    /A LYS 305 HZ1   3.005  2.074
    7413     /A ASN 435 ND2  /A ASN 436 OD1  /A ASN 435 HD21  3.103  2.697
    7414     /A ASN 435 ND2  /H DC 13 OP2    /A ASN 435 HD22  2.896  1.911
    7415     /A ASN 436 ND2  /H DC 13 OP2    /A ASN 436 HD22  3.172  2.251
    7416     /A LYS 439 N    /A ASN 435 O    /A LYS 439 H     3.001  2.009
    7417     /A LEU 440 N    /A ASN 436 O    /A LEU 440 H     2.894  1.926
    7418     /A ARG 696 NH2  /G GLY 546 O    /A ARG 696 HH21  3.117  2.584
    7419     /B LYS 148 N    /B PHE 144 O    /B LYS 148 H     2.920  2.035
    7420     /B LYS 148 NZ   /E ARG 340 O    /B LYS 148 HZ1   2.840  1.919
    7421     /B LYS 148 NZ   /I DG 19 OP1    /B LYS 148 HZ3   2.880  2.062
    7422     /B ARG 150 NH1  /H DG 35 O6     /B ARG 150 HH12  3.317  2.492
    7423     /B ARG 150 NH1  /I DG 19 O6     /B ARG 150 HH12  3.200  2.518
    7424     /B ARG 150 NH2  /H DG 35 O6     /B ARG 150 HH22  2.932  1.954
    7425     /B GLY 153 N    /H DT 34 OP2    /B GLY 153 H     2.955  1.965
    7426     /B LYS 248 NZ   /I DA 37 O3'    /B LYS 248 HZ1   3.058  2.307
    7427     /B ASN 252 N    /B LYS 248 O    /B ASN 252 H     2.859  1.943
    7428     /B ASN 252 ND2  /B LYS 248 O    /B ASN 252 HD21  2.823  2.421
    7429     /B LYS 279 N    /I DA 39 OP1    /B LYS 279 H     3.012  2.176
    7430     /B LYS 279 NZ   /B ASN 275 O    /B LYS 279 HZ1   3.083  2.418
    7431     /B ASP 280 N    /I DA 39 OP1    /B ASP 280 H     3.419  2.439
    7432     /B ASP 282 N    /B ASP 280 OD1  /B ASP 282 H     3.192  2.326
    7433     /B LEU 284 N    /B ASP 280 O    /B LEU 284 H     2.837  1.850
    7434     /C LYS 188 N    /C SER 186 OG   /C LYS 188 H     3.325  2.447
    7435     /C LYS 188 NZ   /H DT 18 OP1    /C LYS 188 HZ1   2.597  1.602
    7436     /C LYS 192 N    /C LYS 188 O    /C LYS 192 H     2.878  1.920
    7437     /C ARG 219 N    /I DT 41 OP1    /C ARG 219 H     2.860  1.859
    7438     /C ARG 219 NE   /C GLU 212 OE1  /C ARG 219 HE    3.259  2.637
    7439     /C ARG 219 NE   /C GLU 212 OE2  /C ARG 219 HE    2.841  2.024
    7440     /C ARG 219 NH1  /I DT 40 OP1    /C ARG 219 HH11  2.808  2.044
    7441     /C ARG 219 NH2  /C GLU 212 OE1  /C ARG 219 HH21  2.795  2.099
    7442     /C ARG 220 N    /C ASP 218 OD1  /C ARG 220 H     2.980  2.018
    7443     /C ARG 220 NE   /C ASP 218 OD1  /C ARG 220 HE    2.810  1.851
    7444     /C ARG 220 NH1  /H DA 15 N3     /C ARG 220 HH12  3.522  2.929
    7445     /C ARG 220 NH1  /H DT 16 O2     /C ARG 220 HH11  3.328  2.600
    7446     /C ARG 220 NH1  /I DT 40 O2     /C ARG 220 HH11  3.062  2.380
    7447     /C ARG 220 NH2  /C ASP 218 OD2  /C ARG 220 HH21  2.856  1.862
    7448     /C LYS 222 N    /C ARG 219 O    /C LYS 222 H     3.430  2.524
    7449     /C TYR 223 OH   /H DA 17 O3'    /C TYR 223 HH    2.926  2.064
    7450     /C TYR 607 OH   /H DC 32 OP2    /C TYR 607 HH    3.278  2.327
    7451     /C THR 670 OG1  /C LYS 673 O    /C THR 670 HG1   2.628  1.854
    7452     /C LYS 671 N    /H DC 32 OP1    /C LYS 671 H     2.864  2.159
    7453     /C ARG 672 N    /H DC 32 OP1    /C ARG 672 H     2.895  1.905
    7454     /C ARG 672 NH1  /I DT 25 O2     /C ARG 672 HH12  2.707  1.845
    7455     /C ARG 672 NH2  /I DT 25 O2     /C ARG 672 HH22  3.408  2.771
    7456     /C LYS 673 NZ   /B ARG 152 O    /C LYS 673 HZ3   3.238  2.551
    7457     /C LYS 673 NZ   /H DA 33 OP1    /C LYS 673 HZ1   2.886  1.972
    7458     /C SER 676 N    /C LYS 673 O    /C SER 676 H     3.091  2.178
    7459     /D LYS 144 NZ   /G LYS 560 O    /D LYS 144 HZ1   3.005  2.080
    7460     /D ARG 148 NE   /G GLY 561 O    /D ARG 148 HE    3.310  2.528
    7461     /D ARG 148 NH1  /D LYS 168 O    /D ARG 148 HH12  2.488  1.669
    7462     /D ARG 148 NH2  /D LYS 168 O    /D ARG 148 HH22  2.570  1.792
    7463     /D ARG 148 NH2  /G GLY 561 O    /D ARG 148 HH21  2.721  1.730
    7464     /D LYS 168 NZ   /H DA 14 N3     /D LYS 168 HZ1   2.838  1.847
    7465     /D SER 169 N    /D ASN 167 OD1  /D SER 169 H     3.368  2.513
    7466     /D SER 169 OG   /H DA 14 O3'    /D SER 169 HG    3.382  2.801
    7467     /D SER 169 OG   /H DA 15 OP2    /D SER 169 HG    2.801  1.842
    7468     /D ILE 170 N    /H DA 15 OP2    /D ILE 170 H     3.077  2.202
    7469     /D THR 173 N    /D SER 169 O    /D THR 173 H     2.884  1.953
    7470     /D THR 173 OG1  /D SER 169 O    /D THR 173 HG1   2.830  1.908
    7471     /D LEU 174 N    /D ILE 170 O    /D LEU 174 H     2.877  1.880
    7472     /D SER 463 OG   /I DG 30 OP1    /D SER 463 HG    2.493  1.565
    7473     /D LYS 465 NZ   /I DG 31 N7     /D LYS 465 HZ1   3.444  2.853
    7474     /D LYS 465 NZ   /I DG 31 O6     /D LYS 465 HZ1   2.363  1.498
    7475     /D LYS 465 NZ   /I DG 32 O6     /D LYS 465 HZ2   2.546  1.684
    7476     /D ARG 466 N    /D SER 463 O    /D ARG 466 H     2.968  2.378
    7477     /D ARG 466 N    /D SER 463 OG   /D ARG 466 H     3.160  2.176
    7478     /D VAL 467 N    /D SER 463 O    /D VAL 467 H     2.848  1.922
    7479     /D ALA 468 N    /D LYS 465 O    /D ALA 468 H     3.107  2.545
    7480     /D LYS 469 N    /D LYS 465 O    /D LYS 469 H     3.084  2.242
    7481     /E ARG 76 NE    /E GLN 80 OE1   /E ARG 76 HE     2.849  1.855
    7482     /E ARG 76 NH1   /H DA 17 OP1    /E ARG 76 HH11   3.235  2.257
    7483     /E ARG 76 NH2   /C ASP 218 OD2  /E ARG 76 HH22   3.505  2.561
    7484     /E ARG 76 NH2   /E GLN 80 OE1   /E ARG 76 HH21   3.522  2.773
    7485     /E GLN 80 N     /E ARG 76 O     /E GLN 80 H      2.915  1.931
    7486     /E ARG 340 NE   /I DG 19 O5'    /E ARG 340 HE    3.009  2.192
    7487     /E ARG 340 NE   /I DG 19 OP2    /E ARG 340 HE    2.873  1.974
    7488     /E ARG 340 NH2  /I DG 19 OP2    /E ARG 340 HH21  3.300  2.551
    7489     /E TYR 341 N    /E PRO 338 O    /E TYR 341 H     3.454  2.618
    7490     /E TYR 341 OH   /I DC 20 OP1    /E TYR 341 HH    2.940  2.219
    7491     /E ARG 344 N    /E TYR 341 O    /E ARG 344 H     2.933  2.330
    7492     /E ARG 344 NH1  /E THR 359 O    /E ARG 344 HH11  3.312  2.421
    7493     /E PHE 345 N    /E TYR 341 O    /E PHE 345 H     3.133  2.333
    7494     /E LYS 350 NZ   /E GLU 358 OE2  /E LYS 350 HZ1   2.768  1.940
    7495     /E ARG 356 NE   /B ASP 145 OD1  /E ARG 356 HE    2.892  2.039
    7496     /E ARG 356 NH1  /I DT 18 OP2    /E ARG 356 HH11  2.602  1.912
    7497     /E ARG 356 NH2  /B ASP 145 O    /E ARG 356 HH21  2.568  1.841
    7498     /E ARG 356 NH2  /B ASP 145 OD1  /E ARG 356 HH21  3.006  2.208
    7499     /E ARG 356 NH2  /B THR 149 OG1  /E ARG 356 HH22  3.252  2.468
    7500     /E ARG 357 NH1  /I DT 16 O2     /E ARG 357 HH12  2.784  1.882
    7501     /E ARG 357 NH2  /I DT 16 O2     /E ARG 357 HH22  2.882  2.025
    7502     /E ARG 357 NH2  /I DT 16 O4'    /E ARG 357 HH22  3.135  2.386
    7503     /E GLU 358 N    /H DG 41 OP1    /E GLU 358 H     2.888  1.905
    7504     /E THR 359 N    /E ARG 357 O    /E THR 359 H     3.010  2.141
    7505     /E THR 359 OG1  /I DG 19 OP1    /E THR 359 HG1   2.802  2.243
    7506     /E ARG 362 N    /I DG 19 O3'    /E ARG 362 H     3.350  2.344
    7507     /E ARG 362 NH1  /I DT 18 O2     /E ARG 362 HH12  2.975  2.081
    7508     /E ARG 362 NH1  /I DG 19 O4'    /E ARG 362 HH11  3.022  2.183
    7509     /E ARG 362 NH2  /H DT 38 O2     /E ARG 362 HH22  2.881  2.130
    7510     /E ARG 362 NH2  /H DA 39 O4'    /E ARG 362 HH21  3.366  2.779
    7511     /E LYS 363 N    /I DC 20 OP2    /E LYS 363 H     3.408  2.442
    7512     /E LYS 363 NZ   /I DA 21 OP1    /E LYS 363 HZ1   2.944  1.968
    7513     /G THR 542 N    /G LYS 581 O    /G THR 542 H     2.775  1.833
    7514     /G THR 542 OG1  /G LYS 581 O    /G THR 542 HG1   3.224  2.270
    7515     /G GLY 543 N    /H DA 26 OP1    /G GLY 543 H     2.943  2.343
    7516     /G CYS 545 SG   /G GLY 543 O    /G CYS 545 HG    3.840  2.525
    7517     /G GLY 546 N    /H DA 27 OP1    /G GLY 546 H     2.915  2.028
    7518     /G LYS 547 NZ   /I DG 31 O3'    /G LYS 547 HZ2   2.870  2.326
    7519     /G LYS 547 NZ   /I DG 32 OP1    /G LYS 547 HZ1   2.552  1.558
    7520     /G LYS 548 NZ   /H DA 27 N3     /G LYS 548 HZ1   2.902  2.236
    7521     /G LYS 548 NZ   /H DG 28 O4'    /G LYS 548 HZ2   2.987  2.212
    7522     /G LYS 548 NZ   /I DT 29 O2     /G LYS 548 HZ3   3.197  2.248
    7523     /G ASN 553 N    /I DG 32 OP2    /G ASN 553 H     2.957  2.079
    7524     /G ASN 553 ND2  /G GLY 572 O    /G ASN 553 HD22  2.832  2.022
    7525     /G ARG 557 NH1  /I DG 34 O6     /G ARG 557 HH12  2.913  1.906
    7526     /G ARG 557 NH2  /I DG 34 N7     /G ARG 557 HH22  2.372  1.443
    7527     /G LYS 560 NZ   /H DA 15 OP1    /G LYS 560 HZ3   3.180  2.601
    7528     /G GLY 561 N    /H DT 16 OP1    /G GLY 561 H     3.390  2.598
    7529     /G GLY 561 N    /H DT 16 OP2    /G GLY 561 H     2.846  2.111
    7530     /G THR 563 N    /H DT 16 OP1    /G THR 563 H     2.931  2.306
    7531     /G THR 563 OG1  /H DT 16 OP1    /G THR 563 HG1   3.027  2.078
    7532     /G ALA 565 N    /H DA 17 OP2    /G ALA 565 H     2.576  1.574
    7533     /G VAL 570 N    /G ASN 553 O    /G VAL 570 H     3.200  2.301
    7534     /G TYR 571 N    /G ASN 553 OD1  /G TYR 571 H     3.237  2.453
    7535     /G ARG 574 NH2  /G GLY 551 O    /G ARG 574 HH22  2.887  1.879
    7536     /G ARG 574 NH2  /I DG 32 OP1    /G ARG 574 HH21  3.076  2.128
    7537     /G ASP 576 N    /G ARG 574 O    /G ASP 576 H     2.809  1.912
    7538     /G LYS 581 N    /G THR 542 O    /G LYS 581 H     3.429  2.627
    7539     /G LYS 581 N    /G GLY 543 O    /G LYS 581 H     3.308  2.380
    7540     /G LYS 581 NZ   /H DA 26 O5'    /G LYS 581 HZ1   3.367  2.792
    7541     /G LYS 581 NZ   /H DA 26 OP2    /G LYS 581 HZ1   3.143  2.140
    7542    
    7543 
    7544  
    7545 139 hydrogen bonds found 
    7546 44 strict hydrogen bonds found 
    7547 
    7548 > select up
    7549 
    7550 2686 atoms, 2716 bonds, 122 residues, 1 model selected 
    7551 
    7552 > show sel atoms
    7553 
    7554 > select nucleic
    7555 
    7556 2291 atoms, 2469 bonds, 72 residues, 1 model selected 
    7557 
    7558 > hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
    7559 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    7560 > structures/PDBs/ylODC_54bp-oriC061_complete/hbond-
    7561 > generation2_ver31_relaxed40" restrict #2/A,B,C,D,E,F,G angleSlop 40.0
    7562 > twoColors true slopColor #ff9300 intraRes false select true reveal true log
    7563 > true
    7564    
    7565    
    7566     Finding intermodel H-bonds
    7567     Finding intramodel H-bonds
    7568     Constraints relaxed by 0.4 angstroms and 40 degrees
    7569     Models used:
    7570         2 ylODC_54bpOriC061_rev31_PostPhenix.pdb
    7571    
    7572     75 H-bonds
    7573     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    7574     /A ARG 301 NE   /I DC 47 OP1  /A ARG 301 HE    3.042  2.096
    7575     /A ARG 301 NH1  /H DT 10 O2   /A ARG 301 HH12  2.780  1.937
    7576     /A ARG 301 NH1  /H DC 11 O4'  /A ARG 301 HH11  2.808  1.918
    7577     /A ARG 301 NH2  /I DT 46 O2   /A ARG 301 HH22  3.419  2.726
    7578     /A ARG 301 NH2  /I DC 47 OP1  /A ARG 301 HH21  3.241  2.383
    7579     /A PHE 303 N    /H DC 13 OP1  /A PHE 303 H     2.683  1.713
    7580     /A LYS 305 NZ   /H DA 14 OP1  /A LYS 305 HZ1   3.005  2.074
    7581     /A ASN 435 ND2  /H DC 13 OP2  /A ASN 435 HD22  2.896  1.911
    7582     /A ASN 436 ND2  /H DC 13 OP2  /A ASN 436 HD22  3.172  2.251
    7583     /B LYS 148 NZ   /I DG 19 OP1  /B LYS 148 HZ3   2.880  2.062
    7584     /B ARG 150 NH1  /H DG 35 O6   /B ARG 150 HH12  3.317  2.492
    7585     /B ARG 150 NH1  /I DG 19 O6   /B ARG 150 HH12  3.200  2.518
    7586     /B ARG 150 NH2  /H DG 35 O6   /B ARG 150 HH22  2.932  1.954
    7587     /B GLY 153 N    /H DT 34 OP2  /B GLY 153 H     2.955  1.965
    7588     /B LYS 248 NZ   /I DA 37 O3'  /B LYS 248 HZ1   3.058  2.307
    7589     /B LYS 279 N    /I DA 39 OP1  /B LYS 279 H     3.012  2.176
    7590     /B ASP 280 N    /I DA 39 OP1  /B ASP 280 H     3.419  2.439
    7591     /C LYS 188 NZ   /H DT 18 OP1  /C LYS 188 HZ1   2.597  1.602
    7592     /C ARG 219 N    /I DT 41 OP1  /C ARG 219 H     2.860  1.859
    7593     /C ARG 219 NH1  /I DT 40 OP1  /C ARG 219 HH11  2.808  2.044
    7594     /C ARG 220 NH1  /H DA 15 N3   /C ARG 220 HH12  3.522  2.929
    7595     /C ARG 220 NH1  /H DT 16 O2   /C ARG 220 HH11  3.328  2.600
    7596     /C ARG 220 NH1  /I DT 40 O2   /C ARG 220 HH11  3.062  2.380
    7597     /C TYR 223 OH   /H DA 17 O3'  /C TYR 223 HH    2.926  2.064
    7598     /C TYR 607 OH   /H DC 32 OP2  /C TYR 607 HH    3.278  2.327
    7599     /C LYS 671 N    /H DC 32 OP1  /C LYS 671 H     2.864  2.159
    7600     /C ARG 672 N    /H DC 32 OP1  /C ARG 672 H     2.895  1.905
    7601     /C ARG 672 NH1  /I DT 25 O2   /C ARG 672 HH12  2.707  1.845
    7602     /C ARG 672 NH2  /I DT 25 O2   /C ARG 672 HH22  3.408  2.771
    7603     /C LYS 673 NZ   /H DA 33 OP1  /C LYS 673 HZ1   2.886  1.972
    7604     /D LYS 168 NZ   /H DA 14 N3   /D LYS 168 HZ1   2.838  1.847
    7605     /D SER 169 OG   /H DA 14 O3'  /D SER 169 HG    3.382  2.801
    7606     /D SER 169 OG   /H DA 15 OP2  /D SER 169 HG    2.801  1.842
    7607     /D ILE 170 N    /H DA 15 OP2  /D ILE 170 H     3.077  2.202
    7608     /D SER 463 OG   /I DG 30 OP1  /D SER 463 HG    2.493  1.565
    7609     /D LYS 465 NZ   /I DG 31 N7   /D LYS 465 HZ1   3.444  2.853
    7610     /D LYS 465 NZ   /I DG 31 O6   /D LYS 465 HZ1   2.363  1.498
    7611     /D LYS 465 NZ   /I DG 32 O6   /D LYS 465 HZ2   2.546  1.684
    7612     /E ARG 76 NH1   /H DA 17 OP1  /E ARG 76 HH11   3.235  2.257
    7613     /E ARG 340 NE   /I DG 19 O5'  /E ARG 340 HE    3.009  2.192
    7614     /E ARG 340 NE   /I DG 19 OP2  /E ARG 340 HE    2.873  1.974
    7615     /E ARG 340 NH2  /I DG 19 OP2  /E ARG 340 HH21  3.300  2.551
    7616     /E TYR 341 OH   /I DC 20 OP1  /E TYR 341 HH    2.940  2.219
    7617     /E ARG 356 NH1  /I DT 18 OP2  /E ARG 356 HH11  2.602  1.912
    7618     /E ARG 357 NH1  /I DT 16 O2   /E ARG 357 HH12  2.784  1.882
    7619     /E ARG 357 NH2  /I DT 16 O2   /E ARG 357 HH22  2.882  2.025
    7620     /E ARG 357 NH2  /I DT 16 O4'  /E ARG 357 HH22  3.135  2.386
    7621     /E GLU 358 N    /H DG 41 OP1  /E GLU 358 H     2.888  1.905
    7622     /E THR 359 OG1  /I DG 19 OP1  /E THR 359 HG1   2.802  2.243
    7623     /E ARG 362 N    /I DG 19 O3'  /E ARG 362 H     3.350  2.344
    7624     /E ARG 362 NH1  /I DT 18 O2   /E ARG 362 HH12  2.975  2.081
    7625     /E ARG 362 NH1  /I DG 19 O4'  /E ARG 362 HH11  3.022  2.183
    7626     /E ARG 362 NH2  /H DT 38 O2   /E ARG 362 HH22  2.881  2.130
    7627     /E ARG 362 NH2  /H DA 39 O4'  /E ARG 362 HH21  3.366  2.779
    7628     /E LYS 363 N    /I DC 20 OP2  /E LYS 363 H     3.408  2.442
    7629     /E LYS 363 NZ   /I DA 21 OP1  /E LYS 363 HZ1   2.944  1.968
    7630     /G GLY 543 N    /H DA 26 OP1  /G GLY 543 H     2.943  2.343
    7631     /G GLY 546 N    /H DA 27 OP1  /G GLY 546 H     2.915  2.028
    7632     /G LYS 547 NZ   /I DG 31 O3'  /G LYS 547 HZ2   2.870  2.326
    7633     /G LYS 547 NZ   /I DG 32 OP1  /G LYS 547 HZ1   2.552  1.558
    7634     /G LYS 548 NZ   /H DA 27 N3   /G LYS 548 HZ1   2.902  2.236
    7635     /G LYS 548 NZ   /H DG 28 O4'  /G LYS 548 HZ2   2.987  2.212
    7636     /G LYS 548 NZ   /I DT 29 O2   /G LYS 548 HZ3   3.197  2.248
    7637     /G ASN 553 N    /I DG 32 OP2  /G ASN 553 H     2.957  2.079
    7638     /G ARG 557 NH1  /I DG 34 O6   /G ARG 557 HH12  2.913  1.906
    7639     /G ARG 557 NH2  /I DG 34 N7   /G ARG 557 HH22  2.372  1.443
    7640     /G LYS 560 NZ   /H DA 15 OP1  /G LYS 560 HZ3   3.180  2.601
    7641     /G GLY 561 N    /H DT 16 OP1  /G GLY 561 H     3.390  2.598
    7642     /G GLY 561 N    /H DT 16 OP2  /G GLY 561 H     2.846  2.111
    7643     /G THR 563 N    /H DT 16 OP1  /G THR 563 H     2.931  2.306
    7644     /G THR 563 OG1  /H DT 16 OP1  /G THR 563 HG1   3.027  2.078
    7645     /G ALA 565 N    /H DA 17 OP2  /G ALA 565 H     2.576  1.574
    7646     /G ARG 574 NH2  /I DG 32 OP1  /G ARG 574 HH21  3.076  2.128
    7647     /G LYS 581 NZ   /H DA 26 O5'  /G LYS 581 HZ1   3.367  2.792
    7648     /G LYS 581 NZ   /H DA 26 OP2  /G LYS 581 HZ1   3.143  2.140
    7649    
    7650 
    7651  
    7652 75 hydrogen bonds found 
    7653 21 strict hydrogen bonds found 
    7654 
    7655 > select up
    7656 
    7657 1974 atoms, 2022 bonds, 80 residues, 1 model selected 
    7658 
    7659 > show sel atoms
    7660 
    7661 > select clear
    7662 
    7663 > select nucleic
    7664 
    7665 2291 atoms, 2469 bonds, 72 residues, 1 model selected 
    7666 
    7667 > hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
    7668 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    7669 > structures/PDBs/ylODC_54bp-oriC061_complete/hbond-generation2_ver31" dashes
    7670 > 6 restrict #2/A,B,C,D,E,F,G twoColors true slopColor #00f900 intraRes false
    7671 > select true reveal true retainCurrent true log true
    7672    
    7673    
    7674     Finding intermodel H-bonds
    7675     Finding intramodel H-bonds
    7676     Constraints relaxed by 0.4 angstroms and 20 degrees
    7677     Models used:
    7678         2 ylODC_54bpOriC061_rev31_PostPhenix.pdb
    7679    
    7680     61 H-bonds
    7681     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    7682     /A ARG 301 NE   /I DC 47 OP1  /A ARG 301 HE    3.042  2.096
    7683     /A ARG 301 NH1  /H DT 10 O2   /A ARG 301 HH12  2.780  1.937
    7684     /A ARG 301 NH1  /H DC 11 O4'  /A ARG 301 HH11  2.808  1.918
    7685     /A ARG 301 NH2  /I DT 46 O2   /A ARG 301 HH22  3.419  2.726
    7686     /A ARG 301 NH2  /I DC 47 OP1  /A ARG 301 HH21  3.241  2.383
    7687     /A PHE 303 N    /H DC 13 OP1  /A PHE 303 H     2.683  1.713
    7688     /A LYS 305 NZ   /H DA 14 OP1  /A LYS 305 HZ1   3.005  2.074
    7689     /A ASN 435 ND2  /H DC 13 OP2  /A ASN 435 HD22  2.896  1.911
    7690     /A ASN 436 ND2  /H DC 13 OP2  /A ASN 436 HD22  3.172  2.251
    7691     /B LYS 148 NZ   /I DG 19 OP1  /B LYS 148 HZ3   2.880  2.062
    7692     /B ARG 150 NH1  /H DG 35 O6   /B ARG 150 HH12  3.317  2.492
    7693     /B ARG 150 NH1  /I DG 19 O6   /B ARG 150 HH12  3.200  2.518
    7694     /B ARG 150 NH2  /H DG 35 O6   /B ARG 150 HH22  2.932  1.954
    7695     /B GLY 153 N    /H DT 34 OP2  /B GLY 153 H     2.955  1.965
    7696     /B LYS 248 NZ   /I DA 37 O3'  /B LYS 248 HZ1   3.058  2.307
    7697     /B LYS 279 N    /I DA 39 OP1  /B LYS 279 H     3.012  2.176
    7698     /B ASP 280 N    /I DA 39 OP1  /B ASP 280 H     3.419  2.439
    7699     /C LYS 188 NZ   /H DT 18 OP1  /C LYS 188 HZ1   2.597  1.602
    7700     /C ARG 219 N    /I DT 41 OP1  /C ARG 219 H     2.860  1.859
    7701     /C ARG 219 NH1  /I DT 40 OP1  /C ARG 219 HH11  2.808  2.044
    7702     /C ARG 220 NH1  /H DT 16 O2   /C ARG 220 HH11  3.328  2.600
    7703     /C ARG 220 NH1  /I DT 40 O2   /C ARG 220 HH11  3.062  2.380
    7704     /C TYR 223 OH   /H DA 17 O3'  /C TYR 223 HH    2.926  2.064
    7705     /C TYR 607 OH   /H DC 32 OP2  /C TYR 607 HH    3.278  2.327
    7706     /C ARG 672 N    /H DC 32 OP1  /C ARG 672 H     2.895  1.905
    7707     /C ARG 672 NH1  /I DT 25 O2   /C ARG 672 HH12  2.707  1.845
    7708     /C ARG 672 NH2  /I DT 25 O2   /C ARG 672 HH22  3.408  2.771
    7709     /C LYS 673 NZ   /H DA 33 OP1  /C LYS 673 HZ1   2.886  1.972
    7710     /D LYS 168 NZ   /H DA 14 N3   /D LYS 168 HZ1   2.838  1.847
    7711     /D SER 169 OG   /H DA 15 OP2  /D SER 169 HG    2.801  1.842
    7712     /D ILE 170 N    /H DA 15 OP2  /D ILE 170 H     3.077  2.202
    7713     /D SER 463 OG   /I DG 30 OP1  /D SER 463 HG    2.493  1.565
    7714     /D LYS 465 NZ   /I DG 31 O6   /D LYS 465 HZ1   2.363  1.498
    7715     /D LYS 465 NZ   /I DG 32 O6   /D LYS 465 HZ2   2.546  1.684
    7716     /E ARG 76 NH1   /H DA 17 OP1  /E ARG 76 HH11   3.235  2.257
    7717     /E ARG 340 NE   /I DG 19 O5'  /E ARG 340 HE    3.009  2.192
    7718     /E ARG 340 NE   /I DG 19 OP2  /E ARG 340 HE    2.873  1.974
    7719     /E ARG 340 NH2  /I DG 19 OP2  /E ARG 340 HH21  3.300  2.551
    7720     /E TYR 341 OH   /I DC 20 OP1  /E TYR 341 HH    2.940  2.219
    7721     /E ARG 357 NH1  /I DT 16 O2   /E ARG 357 HH12  2.784  1.882
    7722     /E ARG 357 NH2  /I DT 16 O2   /E ARG 357 HH22  2.882  2.025
    7723     /E ARG 357 NH2  /I DT 16 O4'  /E ARG 357 HH22  3.135  2.386
    7724     /E GLU 358 N    /H DG 41 OP1  /E GLU 358 H     2.888  1.905
    7725     /E THR 359 OG1  /I DG 19 OP1  /E THR 359 HG1   2.802  2.243
    7726     /E ARG 362 N    /I DG 19 O3'  /E ARG 362 H     3.350  2.344
    7727     /E ARG 362 NH1  /I DT 18 O2   /E ARG 362 HH12  2.975  2.081
    7728     /E ARG 362 NH1  /I DG 19 O4'  /E ARG 362 HH11  3.022  2.183
    7729     /E ARG 362 NH2  /H DT 38 O2   /E ARG 362 HH22  2.881  2.130
    7730     /E LYS 363 N    /I DC 20 OP2  /E LYS 363 H     3.408  2.442
    7731     /E LYS 363 NZ   /I DA 21 OP1  /E LYS 363 HZ1   2.944  1.968
    7732     /G GLY 546 N    /H DA 27 OP1  /G GLY 546 H     2.915  2.028
    7733     /G LYS 547 NZ   /I DG 32 OP1  /G LYS 547 HZ1   2.552  1.558
    7734     /G LYS 548 NZ   /I DT 29 O2   /G LYS 548 HZ3   3.197  2.248
    7735     /G ASN 553 N    /I DG 32 OP2  /G ASN 553 H     2.957  2.079
    7736     /G ARG 557 NH1  /I DG 34 O6   /G ARG 557 HH12  2.913  1.906
    7737     /G ARG 557 NH2  /I DG 34 N7   /G ARG 557 HH22  2.372  1.443
    7738     /G GLY 561 N    /H DT 16 OP2  /G GLY 561 H     2.846  2.111
    7739     /G THR 563 OG1  /H DT 16 OP1  /G THR 563 HG1   3.027  2.078
    7740     /G ALA 565 N    /H DA 17 OP2  /G ALA 565 H     2.576  1.574
    7741     /G ARG 574 NH2  /I DG 32 OP1  /G ARG 574 HH21  3.076  2.128
    7742     /G LYS 581 NZ   /H DA 26 OP2  /G LYS 581 HZ1   3.143  2.140
    7743    
    7744 
    7745  
    7746 61 hydrogen bonds found 
    7747 21 strict hydrogen bonds found 
    7748 
    7749 > select clear
    7750 
    7751 > select ~sel & ##selected
    7752 
    7753 Nothing selected 
    7754 
    7755 > select ~nucleic
    7756 
    7757 47733 atoms, 48183 bonds, 11 pseudobonds, 2978 residues, 3 models selected 
    7758 
    7759 > hide sel cartoons
    7760 
    7761 > select clear
    7762 
    7763 > save "/Users/jtbauer/Library/CloudStorage/OneDrive-
    7764 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    7765 > structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver31.cxs"
    7766 
    7767 > select /I:18
    7768 
    7769 32 atoms, 33 bonds, 1 residue, 1 model selected 
    7770 
    7771 > hide sel cartoons
    7772 
    7773 > show sel cartoons
    7774 
    7775 > select /I:16
    7776 
    7777 32 atoms, 33 bonds, 1 residue, 1 model selected 
    7778 
    7779 > hide sel atoms
    7780 
    7781 > select clear
    7782 
    7783 > hide atoms
    7784 
    7785 > select nucleic
    7786 
    7787 2291 atoms, 2469 bonds, 72 residues, 1 model selected 
    7788 
    7789 > hbonds sel dashes 6 restrict #2/A,B,C,D,E,F,G angleSlop 40.0 twoColors true
    7790 > slopColor #ff9300 intraRes false select true reveal true retainCurrent true
    7791 > log true
    7792    
    7793    
    7794     Finding intermodel H-bonds
    7795     Finding intramodel H-bonds
    7796     Constraints relaxed by 0.4 angstroms and 40 degrees
    7797     Models used:
    7798         2 ylODC_54bpOriC061_rev31_PostPhenix.pdb
    7799    
    7800     75 H-bonds
    7801     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    7802     /A ARG 301 NE   /I DC 47 OP1  /A ARG 301 HE    3.042  2.096
    7803     /A ARG 301 NH1  /H DT 10 O2   /A ARG 301 HH12  2.780  1.937
    7804     /A ARG 301 NH1  /H DC 11 O4'  /A ARG 301 HH11  2.808  1.918
    7805     /A ARG 301 NH2  /I DT 46 O2   /A ARG 301 HH22  3.419  2.726
    7806     /A ARG 301 NH2  /I DC 47 OP1  /A ARG 301 HH21  3.241  2.383
    7807     /A PHE 303 N    /H DC 13 OP1  /A PHE 303 H     2.683  1.713
    7808     /A LYS 305 NZ   /H DA 14 OP1  /A LYS 305 HZ1   3.005  2.074
    7809     /A ASN 435 ND2  /H DC 13 OP2  /A ASN 435 HD22  2.896  1.911
    7810     /A ASN 436 ND2  /H DC 13 OP2  /A ASN 436 HD22  3.172  2.251
    7811     /B LYS 148 NZ   /I DG 19 OP1  /B LYS 148 HZ3   2.880  2.062
    7812     /B ARG 150 NH1  /H DG 35 O6   /B ARG 150 HH12  3.317  2.492
    7813     /B ARG 150 NH1  /I DG 19 O6   /B ARG 150 HH12  3.200  2.518
    7814     /B ARG 150 NH2  /H DG 35 O6   /B ARG 150 HH22  2.932  1.954
    7815     /B GLY 153 N    /H DT 34 OP2  /B GLY 153 H     2.955  1.965
    7816     /B LYS 248 NZ   /I DA 37 O3'  /B LYS 248 HZ1   3.058  2.307
    7817     /B LYS 279 N    /I DA 39 OP1  /B LYS 279 H     3.012  2.176
    7818     /B ASP 280 N    /I DA 39 OP1  /B ASP 280 H     3.419  2.439
    7819     /C LYS 188 NZ   /H DT 18 OP1  /C LYS 188 HZ1   2.597  1.602
    7820     /C ARG 219 N    /I DT 41 OP1  /C ARG 219 H     2.860  1.859
    7821     /C ARG 219 NH1  /I DT 40 OP1  /C ARG 219 HH11  2.808  2.044
    7822     /C ARG 220 NH1  /H DA 15 N3   /C ARG 220 HH12  3.522  2.929
    7823     /C ARG 220 NH1  /H DT 16 O2   /C ARG 220 HH11  3.328  2.600
    7824     /C ARG 220 NH1  /I DT 40 O2   /C ARG 220 HH11  3.062  2.380
    7825     /C TYR 223 OH   /H DA 17 O3'  /C TYR 223 HH    2.926  2.064
    7826     /C TYR 607 OH   /H DC 32 OP2  /C TYR 607 HH    3.278  2.327
    7827     /C LYS 671 N    /H DC 32 OP1  /C LYS 671 H     2.864  2.159
    7828     /C ARG 672 N    /H DC 32 OP1  /C ARG 672 H     2.895  1.905
    7829     /C ARG 672 NH1  /I DT 25 O2   /C ARG 672 HH12  2.707  1.845
    7830     /C ARG 672 NH2  /I DT 25 O2   /C ARG 672 HH22  3.408  2.771
    7831     /C LYS 673 NZ   /H DA 33 OP1  /C LYS 673 HZ1   2.886  1.972
    7832     /D LYS 168 NZ   /H DA 14 N3   /D LYS 168 HZ1   2.838  1.847
    7833     /D SER 169 OG   /H DA 14 O3'  /D SER 169 HG    3.382  2.801
    7834     /D SER 169 OG   /H DA 15 OP2  /D SER 169 HG    2.801  1.842
    7835     /D ILE 170 N    /H DA 15 OP2  /D ILE 170 H     3.077  2.202
    7836     /D SER 463 OG   /I DG 30 OP1  /D SER 463 HG    2.493  1.565
    7837     /D LYS 465 NZ   /I DG 31 N7   /D LYS 465 HZ1   3.444  2.853
    7838     /D LYS 465 NZ   /I DG 31 O6   /D LYS 465 HZ1   2.363  1.498
    7839     /D LYS 465 NZ   /I DG 32 O6   /D LYS 465 HZ2   2.546  1.684
    7840     /E ARG 76 NH1   /H DA 17 OP1  /E ARG 76 HH11   3.235  2.257
    7841     /E ARG 340 NE   /I DG 19 O5'  /E ARG 340 HE    3.009  2.192
    7842     /E ARG 340 NE   /I DG 19 OP2  /E ARG 340 HE    2.873  1.974
    7843     /E ARG 340 NH2  /I DG 19 OP2  /E ARG 340 HH21  3.300  2.551
    7844     /E TYR 341 OH   /I DC 20 OP1  /E TYR 341 HH    2.940  2.219
    7845     /E ARG 356 NH1  /I DT 18 OP2  /E ARG 356 HH11  2.602  1.912
    7846     /E ARG 357 NH1  /I DT 16 O2   /E ARG 357 HH12  2.784  1.882
    7847     /E ARG 357 NH2  /I DT 16 O2   /E ARG 357 HH22  2.882  2.025
    7848     /E ARG 357 NH2  /I DT 16 O4'  /E ARG 357 HH22  3.135  2.386
    7849     /E GLU 358 N    /H DG 41 OP1  /E GLU 358 H     2.888  1.905
    7850     /E THR 359 OG1  /I DG 19 OP1  /E THR 359 HG1   2.802  2.243
    7851     /E ARG 362 N    /I DG 19 O3'  /E ARG 362 H     3.350  2.344
    7852     /E ARG 362 NH1  /I DT 18 O2   /E ARG 362 HH12  2.975  2.081
    7853     /E ARG 362 NH1  /I DG 19 O4'  /E ARG 362 HH11  3.022  2.183
    7854     /E ARG 362 NH2  /H DT 38 O2   /E ARG 362 HH22  2.881  2.130
    7855     /E ARG 362 NH2  /H DA 39 O4'  /E ARG 362 HH21  3.366  2.779
    7856     /E LYS 363 N    /I DC 20 OP2  /E LYS 363 H     3.408  2.442
    7857     /E LYS 363 NZ   /I DA 21 OP1  /E LYS 363 HZ1   2.944  1.968
    7858     /G GLY 543 N    /H DA 26 OP1  /G GLY 543 H     2.943  2.343
    7859     /G GLY 546 N    /H DA 27 OP1  /G GLY 546 H     2.915  2.028
    7860     /G LYS 547 NZ   /I DG 31 O3'  /G LYS 547 HZ2   2.870  2.326
    7861     /G LYS 547 NZ   /I DG 32 OP1  /G LYS 547 HZ1   2.552  1.558
    7862     /G LYS 548 NZ   /H DA 27 N3   /G LYS 548 HZ1   2.902  2.236
    7863     /G LYS 548 NZ   /H DG 28 O4'  /G LYS 548 HZ2   2.987  2.212
    7864     /G LYS 548 NZ   /I DT 29 O2   /G LYS 548 HZ3   3.197  2.248
    7865     /G ASN 553 N    /I DG 32 OP2  /G ASN 553 H     2.957  2.079
    7866     /G ARG 557 NH1  /I DG 34 O6   /G ARG 557 HH12  2.913  1.906
    7867     /G ARG 557 NH2  /I DG 34 N7   /G ARG 557 HH22  2.372  1.443
    7868     /G LYS 560 NZ   /H DA 15 OP1  /G LYS 560 HZ3   3.180  2.601
    7869     /G GLY 561 N    /H DT 16 OP1  /G GLY 561 H     3.390  2.598
    7870     /G GLY 561 N    /H DT 16 OP2  /G GLY 561 H     2.846  2.111
    7871     /G THR 563 N    /H DT 16 OP1  /G THR 563 H     2.931  2.306
    7872     /G THR 563 OG1  /H DT 16 OP1  /G THR 563 HG1   3.027  2.078
    7873     /G ALA 565 N    /H DA 17 OP2  /G ALA 565 H     2.576  1.574
    7874     /G ARG 574 NH2  /I DG 32 OP1  /G ARG 574 HH21  3.076  2.128
    7875     /G LYS 581 NZ   /H DA 26 O5'  /G LYS 581 HZ1   3.367  2.792
    7876     /G LYS 581 NZ   /H DA 26 OP2  /G LYS 581 HZ1   3.143  2.140
    7877    
    7878 
    7879  
    7880 75 hydrogen bonds found 
    7881 21 strict hydrogen bonds found 
    7882 
    7883 > select up
    7884 
    7885 1974 atoms, 2022 bonds, 80 residues, 1 model selected 
    7886 
    7887 > show sel atoms
    7888 
    7889 > select nucleic
    7890 
    7891 2291 atoms, 2469 bonds, 72 residues, 1 model selected 
    7892 
    7893 > show sel atoms
    7894 
    7895 > hbonds sel dashes 6 restrict #2/A,B,C,D,E,F,G twoColors true slopColor
    7896 > #00f900 intraRes false select true reveal true retainCurrent true log true
    7897    
    7898    
    7899     Finding intermodel H-bonds
    7900     Finding intramodel H-bonds
    7901     Constraints relaxed by 0.4 angstroms and 20 degrees
    7902     Models used:
    7903         2 ylODC_54bpOriC061_rev31_PostPhenix.pdb
    7904    
    7905     61 H-bonds
    7906     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    7907     /A ARG 301 NE   /I DC 47 OP1  /A ARG 301 HE    3.042  2.096
    7908     /A ARG 301 NH1  /H DT 10 O2   /A ARG 301 HH12  2.780  1.937
    7909     /A ARG 301 NH1  /H DC 11 O4'  /A ARG 301 HH11  2.808  1.918
    7910     /A ARG 301 NH2  /I DT 46 O2   /A ARG 301 HH22  3.419  2.726
    7911     /A ARG 301 NH2  /I DC 47 OP1  /A ARG 301 HH21  3.241  2.383
    7912     /A PHE 303 N    /H DC 13 OP1  /A PHE 303 H     2.683  1.713
    7913     /A LYS 305 NZ   /H DA 14 OP1  /A LYS 305 HZ1   3.005  2.074
    7914     /A ASN 435 ND2  /H DC 13 OP2  /A ASN 435 HD22  2.896  1.911
    7915     /A ASN 436 ND2  /H DC 13 OP2  /A ASN 436 HD22  3.172  2.251
    7916     /B LYS 148 NZ   /I DG 19 OP1  /B LYS 148 HZ3   2.880  2.062
    7917     /B ARG 150 NH1  /H DG 35 O6   /B ARG 150 HH12  3.317  2.492
    7918     /B ARG 150 NH1  /I DG 19 O6   /B ARG 150 HH12  3.200  2.518
    7919     /B ARG 150 NH2  /H DG 35 O6   /B ARG 150 HH22  2.932  1.954
    7920     /B GLY 153 N    /H DT 34 OP2  /B GLY 153 H     2.955  1.965
    7921     /B LYS 248 NZ   /I DA 37 O3'  /B LYS 248 HZ1   3.058  2.307
    7922     /B LYS 279 N    /I DA 39 OP1  /B LYS 279 H     3.012  2.176
    7923     /B ASP 280 N    /I DA 39 OP1  /B ASP 280 H     3.419  2.439
    7924     /C LYS 188 NZ   /H DT 18 OP1  /C LYS 188 HZ1   2.597  1.602
    7925     /C ARG 219 N    /I DT 41 OP1  /C ARG 219 H     2.860  1.859
    7926     /C ARG 219 NH1  /I DT 40 OP1  /C ARG 219 HH11  2.808  2.044
    7927     /C ARG 220 NH1  /H DT 16 O2   /C ARG 220 HH11  3.328  2.600
    7928     /C ARG 220 NH1  /I DT 40 O2   /C ARG 220 HH11  3.062  2.380
    7929     /C TYR 223 OH   /H DA 17 O3'  /C TYR 223 HH    2.926  2.064
    7930     /C TYR 607 OH   /H DC 32 OP2  /C TYR 607 HH    3.278  2.327
    7931     /C ARG 672 N    /H DC 32 OP1  /C ARG 672 H     2.895  1.905
    7932     /C ARG 672 NH1  /I DT 25 O2   /C ARG 672 HH12  2.707  1.845
    7933     /C ARG 672 NH2  /I DT 25 O2   /C ARG 672 HH22  3.408  2.771
    7934     /C LYS 673 NZ   /H DA 33 OP1  /C LYS 673 HZ1   2.886  1.972
    7935     /D LYS 168 NZ   /H DA 14 N3   /D LYS 168 HZ1   2.838  1.847
    7936     /D SER 169 OG   /H DA 15 OP2  /D SER 169 HG    2.801  1.842
    7937     /D ILE 170 N    /H DA 15 OP2  /D ILE 170 H     3.077  2.202
    7938     /D SER 463 OG   /I DG 30 OP1  /D SER 463 HG    2.493  1.565
    7939     /D LYS 465 NZ   /I DG 31 O6   /D LYS 465 HZ1   2.363  1.498
    7940     /D LYS 465 NZ   /I DG 32 O6   /D LYS 465 HZ2   2.546  1.684
    7941     /E ARG 76 NH1   /H DA 17 OP1  /E ARG 76 HH11   3.235  2.257
    7942     /E ARG 340 NE   /I DG 19 O5'  /E ARG 340 HE    3.009  2.192
    7943     /E ARG 340 NE   /I DG 19 OP2  /E ARG 340 HE    2.873  1.974
    7944     /E ARG 340 NH2  /I DG 19 OP2  /E ARG 340 HH21  3.300  2.551
    7945     /E TYR 341 OH   /I DC 20 OP1  /E TYR 341 HH    2.940  2.219
    7946     /E ARG 357 NH1  /I DT 16 O2   /E ARG 357 HH12  2.784  1.882
    7947     /E ARG 357 NH2  /I DT 16 O2   /E ARG 357 HH22  2.882  2.025
    7948     /E ARG 357 NH2  /I DT 16 O4'  /E ARG 357 HH22  3.135  2.386
    7949     /E GLU 358 N    /H DG 41 OP1  /E GLU 358 H     2.888  1.905
    7950     /E THR 359 OG1  /I DG 19 OP1  /E THR 359 HG1   2.802  2.243
    7951     /E ARG 362 N    /I DG 19 O3'  /E ARG 362 H     3.350  2.344
    7952     /E ARG 362 NH1  /I DT 18 O2   /E ARG 362 HH12  2.975  2.081
    7953     /E ARG 362 NH1  /I DG 19 O4'  /E ARG 362 HH11  3.022  2.183
    7954     /E ARG 362 NH2  /H DT 38 O2   /E ARG 362 HH22  2.881  2.130
    7955     /E LYS 363 N    /I DC 20 OP2  /E LYS 363 H     3.408  2.442
    7956     /E LYS 363 NZ   /I DA 21 OP1  /E LYS 363 HZ1   2.944  1.968
    7957     /G GLY 546 N    /H DA 27 OP1  /G GLY 546 H     2.915  2.028
    7958     /G LYS 547 NZ   /I DG 32 OP1  /G LYS 547 HZ1   2.552  1.558
    7959     /G LYS 548 NZ   /I DT 29 O2   /G LYS 548 HZ3   3.197  2.248
    7960     /G ASN 553 N    /I DG 32 OP2  /G ASN 553 H     2.957  2.079
    7961     /G ARG 557 NH1  /I DG 34 O6   /G ARG 557 HH12  2.913  1.906
    7962     /G ARG 557 NH2  /I DG 34 N7   /G ARG 557 HH22  2.372  1.443
    7963     /G GLY 561 N    /H DT 16 OP2  /G GLY 561 H     2.846  2.111
    7964     /G THR 563 OG1  /H DT 16 OP1  /G THR 563 HG1   3.027  2.078
    7965     /G ALA 565 N    /H DA 17 OP2  /G ALA 565 H     2.576  1.574
    7966     /G ARG 574 NH2  /I DG 32 OP1  /G ARG 574 HH21  3.076  2.128
    7967     /G LYS 581 NZ   /H DA 26 OP2  /G LYS 581 HZ1   3.143  2.140
    7968    
    7969 
    7970  
    7971 61 hydrogen bonds found 
    7972 21 strict hydrogen bonds found 
    7973 
    7974 > select clear
    7975 
    7976 > save "/Users/jtbauer/Library/CloudStorage/OneDrive-
    7977 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    7978 > structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver31.cxs"
    7979 
    7980 > select /I:17
    7981 
    7982 32 atoms, 34 bonds, 1 residue, 1 model selected 
    7983 
    7984 > select clear
    7985 
    7986 > select /H:26
    7987 
    7988 32 atoms, 34 bonds, 1 residue, 1 model selected 
    7989 
    7990 > ui tool show "Renumber Residues"
    7991 
    7992 > renumber /H start -16
    7993 
    7994 37 residues renumbered 
    7995 
    7996 > renumber /H start -18
    7997 
    7998 37 residues renumbered 
    7999 
    8000 > renumber /I start -16
    8001 
    8002 35 residues renumbered 
    8003 
    8004 > select /I
    8005 
    8006 1121 atoms, 1207 bonds, 35 residues, 1 model selected 
    8007 
    8008 > ui tool show "Change Chain IDs"
    8009 
    8010 > changechains sel opp
    8011 
    8012 Chain IDs of 35 residues changed 
    8013 
    8014 > select /H
    8015 
    8016 1170 atoms, 1262 bonds, 37 residues, 1 model selected 
    8017 
    8018 > ui tool show "Change Chain IDs"
    8019 
    8020 > changechains sel main
    8021 
    8022 Chain IDs of 37 residues changed 
    8023 
    8024 > select clear
    8025 
    8026 > save "/Users/jtbauer/Library/CloudStorage/OneDrive-
    8027 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    8028 > structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver31.cxs"
    8029 
    8030 > select /opp:-13
    8031 
    8032 32 atoms, 33 bonds, 1 residue, 1 model selected 
    8033 
    8034 > select clear
    8035 
    8036 > close #2
    8037 
    8038 > open "/Users/jtbauer/Library/CloudStorage/OneDrive-
    8039 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    8040 > structures/PDBs/ylODC_oriA006_complete/ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb"
    8041 
    8042 Chain information for ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb #1 
    8043 --- 
    8044 Chain | Description 
    8045 A | No description available 
    8046 B | No description available 
    8047 C | No description available 
    8048 D | No description available 
    8049 E | No description available 
    8050 F | No description available 
    8051 G | No description available 
    8052 H | No description available 
    8053 I | No description available 
    8054  
    8055 
    8056 > modelfix
    8057 
    8058 Changed 24882 atom styles 
    8059 23363 atoms, 23801 bonds, 15 pseudobonds, 2924 residues, 2 models selected 
    8060 
    8061 > select ~nucleic
    8062 
    8063 23491 atoms, 23933 bonds, 16 pseudobonds, 2932 residues, 3 models selected 
    8064 
    8065 > hide sel cartoons
    8066 
    8067 > select nucleic
    8068 
    8069 1391 atoms, 1559 bonds, 68 residues, 1 model selected 
    8070 
    8071 > hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
    8072 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    8073 > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_generation_ver20_relaxed40"
    8074 > dashes 6 restrict #1/A,B,C,D,E,F,G angleSlop 40.0 twoColors true slopColor
    8075 > #ff9300 intraRes false select true reveal true retainCurrent true log true
    8076    
    8077    
    8078     Finding intermodel H-bonds
    8079     Finding intramodel H-bonds
    8080     Constraints relaxed by 0.4 angstroms and 40 degrees
    8081     Models used:
    8082         1 ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb
    8083    
    8084     50 H-bonds
    8085     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    8086     /A GLN 306 NE2  /I DG 53 O3'  no hydrogen  3.342  N/A
    8087     /A ASN 436 ND2  /H DA 10 OP1  no hydrogen  2.810  N/A
    8088     /B LYS 148 NZ   /I DA 28 OP1  no hydrogen  3.208  N/A
    8089     /B LYS 279 N    /I DA 48 OP1  no hydrogen  3.110  N/A
    8090     /C LYS 188 NZ   /H DC 15 OP1  no hydrogen  3.176  N/A
    8091     /C ARG 219 NH1  /I DT 49 OP2  no hydrogen  3.015  N/A
    8092     /C ARG 220 NH1  /H DT 13 O2   no hydrogen  3.388  N/A
    8093     /C ARG 220 NH1  /I DT 49 O2   no hydrogen  3.296  N/A
    8094     /C TYR 223 OH   /H DC 15 OP1  no hydrogen  2.762  N/A
    8095     /C TYR 607 OH   /H DC 29 OP2  no hydrogen  3.098  N/A
    8096     /C ARG 672 N    /H DC 29 OP1  no hydrogen  3.388  N/A
    8097     /C ARG 672 NH1  /I DT 34 O2   no hydrogen  2.806  N/A
    8098     /C ARG 672 NH2  /I DT 34 O2   no hydrogen  2.902  N/A
    8099     /C ARG 672 NH2  /I DT 34 O4'  no hydrogen  3.185  N/A
    8100     /C LYS 673 NZ   /H DT 30 OP1  no hydrogen  3.030  N/A
    8101     /D LYS 168 NZ   /H DT 11 O2   no hydrogen  2.564  N/A
    8102     /D SER 169 OG   /H DA 12 OP1  no hydrogen  3.284  N/A
    8103     /D SER 463 OG   /I DT 39 OP2  no hydrogen  2.803  N/A
    8104     /D LYS 465 NZ   /I DG 40 N7   no hydrogen  3.514  N/A
    8105     /D LYS 465 NZ   /I DG 40 O6   no hydrogen  3.045  N/A
    8106     /D LYS 465 NZ   /I DG 41 O6   no hydrogen  3.189  N/A
    8107     /E ARG 76 NH1   /H DG 14 OP1  no hydrogen  2.908  N/A
    8108     /E ARG 340 NH1  /I DA 28 OP2  no hydrogen  3.135  N/A
    8109     /E ARG 356 NH1  /I DT 27 OP2  no hydrogen  2.946  N/A
    8110     /E ARG 357 N    /I DT 27 OP1  no hydrogen  3.073  N/A
    8111     /E ARG 357 NH1  /I DT 25 O2   no hydrogen  2.761  N/A
    8112     /E ARG 357 NH2  /I DT 25 O2   no hydrogen  2.690  N/A
    8113     /E GLU 358 N    /H DG 38 OP1  no hydrogen  3.275  N/A
    8114     /E THR 359 OG1  /I DA 28 OP1  no hydrogen  2.552  N/A
    8115     /E ARG 362 N    /I DG 29 OP2  no hydrogen  2.892  N/A
    8116     /E ARG 362 NH1  /H DC 35 O4'  no hydrogen  3.369  N/A
    8117     /E ARG 362 NH2  /H DC 35 O2   no hydrogen  3.076  N/A
    8118     /E ARG 362 NH2  /H DA 36 O4'  no hydrogen  3.065  N/A
    8119     /E LYS 363 N    /I DG 29 OP2  no hydrogen  3.221  N/A
    8120     /E LYS 363 NZ   /I DG 30 OP1  no hydrogen  2.954  N/A
    8121     /E LYS 363 NZ   /I DG 30 OP2  no hydrogen  2.890  N/A
    8122     /G THR 542 OG1  /H DA 23 OP1  no hydrogen  3.290  N/A
    8123     /G LYS 547 NZ   /I DG 41 OP1  no hydrogen  3.303  N/A
    8124     /G LYS 548 NZ   /H DT 24 O2   no hydrogen  2.747  N/A
    8125     /G LYS 548 NZ   /H DC 25 O4'  no hydrogen  2.889  N/A
    8126     /G LYS 548 NZ   /I DT 38 O2   no hydrogen  3.045  N/A
    8127     /G ASN 553 N    /I DG 41 OP2  no hydrogen  3.220  N/A
    8128     /G ARG 557 NH1  /I DG 44 N7   no hydrogen  3.403  N/A
    8129     /G ARG 557 NH1  /I DG 44 O6   no hydrogen  2.566  N/A
    8130     /G ARG 557 NH2  /I DG 44 N7   no hydrogen  3.082  N/A
    8131     /G LYS 560 NZ   /H DA 12 OP2  no hydrogen  2.981  N/A
    8132     /G GLY 561 N    /H DT 13 OP1  no hydrogen  2.977  N/A
    8133     /G THR 563 N    /H DT 13 OP2  no hydrogen  3.051  N/A
    8134     /G GLY 564 N    /H DT 13 OP2  no hydrogen  2.948  N/A
    8135     /G ALA 565 N    /H DG 14 OP2  no hydrogen  3.032  N/A
    8136    
    8137 
    8138  
    8139 50 hydrogen bonds found 
    8140 13 strict hydrogen bonds found 
    8141 
    8142 > ui tool show "Add Hydrogens"
    8143 
    8144 > addh #!1
    8145 
    8146 Summary of feedback from adding hydrogens to
    8147 ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb #1 
    8148 --- 
    8149 warning | Not adding hydrogens to /I DA 22 P because it is missing heavy-atom bond partners 
    8150 notes | No usable SEQRES records for ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb (#1) chain A; guessing termini instead 
    8151 No usable SEQRES records for ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb (#1)
    8152 chain B; guessing termini instead 
    8153 No usable SEQRES records for ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb (#1)
    8154 chain C; guessing termini instead 
    8155 No usable SEQRES records for ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb (#1)
    8156 chain D; guessing termini instead 
    8157 No usable SEQRES records for ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb (#1)
    8158 chain E; guessing termini instead 
    8159 4 messages similar to the above omitted 
    8160 Chain-initial residues that are actual N termini: /A PRO 299, /B PRO 106, /C
    8161 THR 6, /D PRO 33, /E MET 1, /F PRO 179, /G PRO 93 
    8162 Chain-initial residues that are not actual N termini: /B VAL 396, /B VAL 444,
    8163 /B LYS 489, /C ASN 72, /D ASN 128, /D GLY 162, /D LEU 296, /D PHE 436, /E GLU
    8164 217, /E ASP 319, /F SER 313, /G ALA 213, /G THR 386, /G VAL 439, /G ASN 461 
    8165 Chain-final residues that are actual C termini: /A LEU 718, /C LEU 685 
    8166 Chain-final residues that are not actual C termini: /B GLU 504, /B GLU 386, /B
    8167 HIS 420, /B VAL 479, /C ARG 29, /D ARG 510, /D SER 123, /D LEU 159, /D MET
    8168 285, /D LEU 420, /E ASN 464, /E ALA 210, /E LEU 304, /F GLN 351, /F THR 307,
    8169 /G LEU 604, /G GLY 207, /G HIS 335, /G GLN 433, /G PHE 457 
    8170 2714 hydrogen bonds 
    8171 Adding 'H' to /B VAL 396 
    8172 Adding 'H' to /B VAL 444 
    8173 Adding 'H' to /B LYS 489 
    8174 Adding 'H' to /C ASN 72 
    8175 Adding 'H' to /D ASN 128 
    8176 10 messages similar to the above omitted 
    8177 /B GLU 504 is not terminus, removing H atom from 'C' 
    8178 /D ARG 510 is not terminus, removing H atom from 'C' 
    8179 /E ASN 464 is not terminus, removing H atom from 'C' 
    8180 /F GLN 351 is not terminus, removing H atom from 'C' 
    8181 /G LEU 604 is not terminus, removing H atom from 'C' 
    8182 24328 hydrogens added 
    8183  
    8184 
    8185 > select clear
    8186 
    8187 > select nucleic
    8188 
    8189 2158 atoms, 2326 bonds, 68 residues, 1 model selected 
    8190 
    8191 > ui tool show H-Bonds
    8192 
    8193 > hbonds sel dashes 6 restrict #1/A,B,C,D,E,F,G angleSlop 40.0 twoColors true
    8194 > slopColor #ff9300 intraRes false select true reveal true retainCurrent true
    8195 > log true
    8196    
    8197    
    8198     Finding intermodel H-bonds
    8199     Finding intramodel H-bonds
    8200     Constraints relaxed by 0.4 angstroms and 40 degrees
    8201     Models used:
    8202         1 ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb
    8203    
    8204     49 H-bonds
    8205     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    8206     /A GLN 306 NE2  /I DG 53 O3'  /A GLN 306 HE22  3.342  2.769
    8207     /A ASN 436 ND2  /H DA 10 OP1  /A ASN 436 HD22  2.810  1.833
    8208     /B LYS 148 NZ   /I DA 28 OP1  /B LYS 148 HZ3   3.208  2.369
    8209     /B LYS 279 N    /I DA 48 OP1  /B LYS 279 H     3.110  2.192
    8210     /C LYS 188 NZ   /H DC 15 OP1  /C LYS 188 HZ1   3.176  2.193
    8211     /C ARG 219 NH1  /I DT 49 OP2  /C ARG 219 HH11  3.015  2.053
    8212     /C ARG 220 NH1  /H DT 13 O2   /C ARG 220 HH11  3.388  2.481
    8213     /C ARG 220 NH1  /I DT 49 O2   /C ARG 220 HH11  3.296  2.935
    8214     /C TYR 223 OH   /H DC 15 OP1  /C TYR 223 HH    2.762  1.806
    8215     /C TYR 607 OH   /H DC 29 OP2  /C TYR 607 HH    3.098  2.200
    8216     /C ARG 672 N    /H DC 29 OP1  /C ARG 672 H     3.388  2.439
    8217     /C ARG 672 NH1  /I DT 34 O2   /C ARG 672 HH12  2.806  1.902
    8218     /C ARG 672 NH2  /I DT 34 O2   /C ARG 672 HH22  2.902  2.042
    8219     /C ARG 672 NH2  /I DT 34 O4'  /C ARG 672 HH22  3.185  2.472
    8220     /C LYS 673 NZ   /H DT 30 OP1  /C LYS 673 HZ1   3.030  2.116
    8221     /D LYS 168 NZ   /H DT 11 O2   /D LYS 168 HZ1   2.564  2.050
    8222     /D SER 169 OG   /H DA 12 OP1  /D SER 169 HG    3.284  2.325
    8223     /D SER 463 OG   /I DT 39 OP2  /D SER 463 HG    2.803  1.844
    8224     /D LYS 465 NZ   /I DG 40 N7   /D LYS 465 HZ1   3.514  2.654
    8225     /D LYS 465 NZ   /I DG 40 O6   /D LYS 465 HZ1   3.045  2.260
    8226     /D LYS 465 NZ   /I DG 41 O6   /D LYS 465 HZ2   3.189  2.368
    8227     /E ARG 76 NH1   /H DG 14 OP1  /E ARG 76 HH11   2.908  2.005
    8228     /E ARG 340 NH1  /I DA 28 OP2  /E ARG 340 HH11  3.135  2.272
    8229     /E ARG 356 NH1  /I DT 27 OP2  /E ARG 356 HH11  2.946  2.163
    8230     /E ARG 357 N    /I DT 27 OP1  /E ARG 357 H     3.073  2.081
    8231     /E ARG 357 NH1  /I DT 25 O2   /E ARG 357 HH12  2.761  1.945
    8232     /E ARG 357 NH2  /I DT 25 O2   /E ARG 357 HH22  2.690  1.846
    8233     /E GLU 358 N    /H DG 38 OP1  /E GLU 358 H     3.275  2.276
    8234     /E THR 359 OG1  /I DA 28 OP1  /E THR 359 HG1   2.552  1.830
    8235     /E ARG 362 N    /I DG 29 OP2  /E ARG 362 H     2.892  2.000
    8236     /E ARG 362 NH1  /H DC 35 O4'  /E ARG 362 HH12  3.369  2.780
    8237     /E ARG 362 NH2  /H DC 35 O2   /E ARG 362 HH22  3.076  2.066
    8238     /E ARG 362 NH2  /H DA 36 O4'  /E ARG 362 HH21  3.065  2.496
    8239     /E LYS 363 N    /I DG 29 OP2  /E LYS 363 H     3.221  2.221
    8240     /E LYS 363 NZ   /I DG 30 OP1  /E LYS 363 HZ3   2.954  2.284
    8241     /E LYS 363 NZ   /I DG 30 OP2  /E LYS 363 HZ1   2.890  1.985
    8242     /G GLY 546 N    /H DT 24 OP1  /G GLY 546 H     3.276  2.580
    8243     /G LYS 547 NZ   /I DG 41 OP1  /G LYS 547 HZ1   3.303  2.294
    8244     /G LYS 548 NZ   /H DT 24 O2   /G LYS 548 HZ1   2.747  2.031
    8245     /G LYS 548 NZ   /H DC 25 O4'  /G LYS 548 HZ2   2.889  2.196
    8246     /G LYS 548 NZ   /I DT 38 O2   /G LYS 548 HZ3   3.045  2.142
    8247     /G ASN 553 N    /I DG 41 OP2  /G ASN 553 H     3.220  2.217
    8248     /G ARG 557 NH1  /I DG 44 N7   /G ARG 557 HH12  3.403  2.708
    8249     /G ARG 557 NH1  /I DG 44 O6   /G ARG 557 HH12  2.566  1.988
    8250     /G ARG 557 NH2  /I DG 44 N7   /G ARG 557 HH22  3.082  2.292
    8251     /G LYS 560 NZ   /H DA 12 OP2  /G LYS 560 HZ1   2.981  2.268
    8252     /G GLY 561 N    /H DT 13 OP1  /G GLY 561 H     2.977  2.057
    8253     /G THR 563 N    /H DT 13 OP2  /G THR 563 H     3.051  2.249
    8254     /G ALA 565 N    /H DG 14 OP2  /G ALA 565 H     3.032  2.059
    8255    
    8256 
    8257  
    8258 49 hydrogen bonds found 
    8259 8 strict hydrogen bonds found 
    8260 
    8261 > select clear
    8262 
    8263 > hide atoms
    8264 
    8265 > select nucleic
    8266 
    8267 2158 atoms, 2326 bonds, 68 residues, 1 model selected 
    8268 
    8269 > show sel atoms
    8270 
    8271 > hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
    8272 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    8273 > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_generation_ver20_relaxed40"
    8274 > restrict #1/A,B,C,D,E,F,G angleSlop 40.0 twoColors true slopColor #ff9300
    8275 > intraRes false select true reveal true log true
    8276    
    8277    
    8278     Finding intermodel H-bonds
    8279     Finding intramodel H-bonds
    8280     Constraints relaxed by 0.4 angstroms and 40 degrees
    8281     Models used:
    8282         1 ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb
    8283    
    8284     49 H-bonds
    8285     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    8286     /A GLN 306 NE2  /I DG 53 O3'  /A GLN 306 HE22  3.342  2.769
    8287     /A ASN 436 ND2  /H DA 10 OP1  /A ASN 436 HD22  2.810  1.833
    8288     /B LYS 148 NZ   /I DA 28 OP1  /B LYS 148 HZ3   3.208  2.369
    8289     /B LYS 279 N    /I DA 48 OP1  /B LYS 279 H     3.110  2.192
    8290     /C LYS 188 NZ   /H DC 15 OP1  /C LYS 188 HZ1   3.176  2.193
    8291     /C ARG 219 NH1  /I DT 49 OP2  /C ARG 219 HH11  3.015  2.053
    8292     /C ARG 220 NH1  /H DT 13 O2   /C ARG 220 HH11  3.388  2.481
    8293     /C ARG 220 NH1  /I DT 49 O2   /C ARG 220 HH11  3.296  2.935
    8294     /C TYR 223 OH   /H DC 15 OP1  /C TYR 223 HH    2.762  1.806
    8295     /C TYR 607 OH   /H DC 29 OP2  /C TYR 607 HH    3.098  2.200
    8296     /C ARG 672 N    /H DC 29 OP1  /C ARG 672 H     3.388  2.439
    8297     /C ARG 672 NH1  /I DT 34 O2   /C ARG 672 HH12  2.806  1.902
    8298     /C ARG 672 NH2  /I DT 34 O2   /C ARG 672 HH22  2.902  2.042
    8299     /C ARG 672 NH2  /I DT 34 O4'  /C ARG 672 HH22  3.185  2.472
    8300     /C LYS 673 NZ   /H DT 30 OP1  /C LYS 673 HZ1   3.030  2.116
    8301     /D LYS 168 NZ   /H DT 11 O2   /D LYS 168 HZ1   2.564  2.050
    8302     /D SER 169 OG   /H DA 12 OP1  /D SER 169 HG    3.284  2.325
    8303     /D SER 463 OG   /I DT 39 OP2  /D SER 463 HG    2.803  1.844
    8304     /D LYS 465 NZ   /I DG 40 N7   /D LYS 465 HZ1   3.514  2.654
    8305     /D LYS 465 NZ   /I DG 40 O6   /D LYS 465 HZ1   3.045  2.260
    8306     /D LYS 465 NZ   /I DG 41 O6   /D LYS 465 HZ2   3.189  2.368
    8307     /E ARG 76 NH1   /H DG 14 OP1  /E ARG 76 HH11   2.908  2.005
    8308     /E ARG 340 NH1  /I DA 28 OP2  /E ARG 340 HH11  3.135  2.272
    8309     /E ARG 356 NH1  /I DT 27 OP2  /E ARG 356 HH11  2.946  2.163
    8310     /E ARG 357 N    /I DT 27 OP1  /E ARG 357 H     3.073  2.081
    8311     /E ARG 357 NH1  /I DT 25 O2   /E ARG 357 HH12  2.761  1.945
    8312     /E ARG 357 NH2  /I DT 25 O2   /E ARG 357 HH22  2.690  1.846
    8313     /E GLU 358 N    /H DG 38 OP1  /E GLU 358 H     3.275  2.276
    8314     /E THR 359 OG1  /I DA 28 OP1  /E THR 359 HG1   2.552  1.830
    8315     /E ARG 362 N    /I DG 29 OP2  /E ARG 362 H     2.892  2.000
    8316     /E ARG 362 NH1  /H DC 35 O4'  /E ARG 362 HH12  3.369  2.780
    8317     /E ARG 362 NH2  /H DC 35 O2   /E ARG 362 HH22  3.076  2.066
    8318     /E ARG 362 NH2  /H DA 36 O4'  /E ARG 362 HH21  3.065  2.496
    8319     /E LYS 363 N    /I DG 29 OP2  /E LYS 363 H     3.221  2.221
    8320     /E LYS 363 NZ   /I DG 30 OP1  /E LYS 363 HZ3   2.954  2.284
    8321     /E LYS 363 NZ   /I DG 30 OP2  /E LYS 363 HZ1   2.890  1.985
    8322     /G GLY 546 N    /H DT 24 OP1  /G GLY 546 H     3.276  2.580
    8323     /G LYS 547 NZ   /I DG 41 OP1  /G LYS 547 HZ1   3.303  2.294
    8324     /G LYS 548 NZ   /H DT 24 O2   /G LYS 548 HZ1   2.747  2.031
    8325     /G LYS 548 NZ   /H DC 25 O4'  /G LYS 548 HZ2   2.889  2.196
    8326     /G LYS 548 NZ   /I DT 38 O2   /G LYS 548 HZ3   3.045  2.142
    8327     /G ASN 553 N    /I DG 41 OP2  /G ASN 553 H     3.220  2.217
    8328     /G ARG 557 NH1  /I DG 44 N7   /G ARG 557 HH12  3.403  2.708
    8329     /G ARG 557 NH1  /I DG 44 O6   /G ARG 557 HH12  2.566  1.988
    8330     /G ARG 557 NH2  /I DG 44 N7   /G ARG 557 HH22  3.082  2.292
    8331     /G LYS 560 NZ   /H DA 12 OP2  /G LYS 560 HZ1   2.981  2.268
    8332     /G GLY 561 N    /H DT 13 OP1  /G GLY 561 H     2.977  2.057
    8333     /G THR 563 N    /H DT 13 OP2  /G THR 563 H     3.051  2.249
    8334     /G ALA 565 N    /H DG 14 OP2  /G ALA 565 H     3.032  2.059
    8335    
    8336 
    8337  
    8338 49 hydrogen bonds found 
    8339 8 strict hydrogen bonds found 
    8340 
    8341 > select up
    8342 
    8343 1476 atoms, 1511 bonds, 59 residues, 1 model selected 
    8344 
    8345 > show sel atoms
    8346 
    8347 > select nucleic
    8348 
    8349 2158 atoms, 2326 bonds, 68 residues, 1 model selected 
    8350 
    8351 > select nucleic
    8352 
    8353 2158 atoms, 2326 bonds, 68 residues, 1 model selected 
    8354 
    8355 > hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
    8356 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    8357 > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_generation_ver20" dashes 6
    8358 > restrict #1/A,B,C,D,E,F,G twoColors true slopColor #00f900 intraRes false
    8359 > select true reveal true retainCurrent true log true
    8360    
    8361    
    8362     Finding intermodel H-bonds
    8363     Finding intramodel H-bonds
    8364     Constraints relaxed by 0.4 angstroms and 20 degrees
    8365     Models used:
    8366         1 ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb
    8367    
    8368     39 H-bonds
    8369     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    8370     /A ASN 436 ND2  /H DA 10 OP1  /A ASN 436 HD22  2.810  1.833
    8371     /B LYS 148 NZ   /I DA 28 OP1  /B LYS 148 HZ3   3.208  2.369
    8372     /B LYS 279 N    /I DA 48 OP1  /B LYS 279 H     3.110  2.192
    8373     /C LYS 188 NZ   /H DC 15 OP1  /C LYS 188 HZ1   3.176  2.193
    8374     /C ARG 219 NH1  /I DT 49 OP2  /C ARG 219 HH11  3.015  2.053
    8375     /C ARG 220 NH1  /H DT 13 O2   /C ARG 220 HH11  3.388  2.481
    8376     /C TYR 223 OH   /H DC 15 OP1  /C TYR 223 HH    2.762  1.806
    8377     /C TYR 607 OH   /H DC 29 OP2  /C TYR 607 HH    3.098  2.200
    8378     /C ARG 672 N    /H DC 29 OP1  /C ARG 672 H     3.388  2.439
    8379     /C ARG 672 NH1  /I DT 34 O2   /C ARG 672 HH12  2.806  1.902
    8380     /C ARG 672 NH2  /I DT 34 O2   /C ARG 672 HH22  2.902  2.042
    8381     /C ARG 672 NH2  /I DT 34 O4'  /C ARG 672 HH22  3.185  2.472
    8382     /C LYS 673 NZ   /H DT 30 OP1  /C LYS 673 HZ1   3.030  2.116
    8383     /D SER 169 OG   /H DA 12 OP1  /D SER 169 HG    3.284  2.325
    8384     /D SER 463 OG   /I DT 39 OP2  /D SER 463 HG    2.803  1.844
    8385     /D LYS 465 NZ   /I DG 40 N7   /D LYS 465 HZ1   3.514  2.654
    8386     /D LYS 465 NZ   /I DG 40 O6   /D LYS 465 HZ1   3.045  2.260
    8387     /D LYS 465 NZ   /I DG 41 O6   /D LYS 465 HZ2   3.189  2.368
    8388     /E ARG 76 NH1   /H DG 14 OP1  /E ARG 76 HH11   2.908  2.005
    8389     /E ARG 340 NH1  /I DA 28 OP2  /E ARG 340 HH11  3.135  2.272
    8390     /E ARG 356 NH1  /I DT 27 OP2  /E ARG 356 HH11  2.946  2.163
    8391     /E ARG 357 N    /I DT 27 OP1  /E ARG 357 H     3.073  2.081
    8392     /E ARG 357 NH1  /I DT 25 O2   /E ARG 357 HH12  2.761  1.945
    8393     /E ARG 357 NH2  /I DT 25 O2   /E ARG 357 HH22  2.690  1.846
    8394     /E GLU 358 N    /H DG 38 OP1  /E GLU 358 H     3.275  2.276
    8395     /E THR 359 OG1  /I DA 28 OP1  /E THR 359 HG1   2.552  1.830
    8396     /E ARG 362 N    /I DG 29 OP2  /E ARG 362 H     2.892  2.000
    8397     /E ARG 362 NH2  /H DC 35 O2   /E ARG 362 HH22  3.076  2.066
    8398     /E LYS 363 N    /I DG 29 OP2  /E LYS 363 H     3.221  2.221
    8399     /E LYS 363 NZ   /I DG 30 OP2  /E LYS 363 HZ1   2.890  1.985
    8400     /G LYS 547 NZ   /I DG 41 OP1  /G LYS 547 HZ1   3.303  2.294
    8401     /G LYS 548 NZ   /H DT 24 O2   /G LYS 548 HZ1   2.747  2.031
    8402     /G LYS 548 NZ   /I DT 38 O2   /G LYS 548 HZ3   3.045  2.142
    8403     /G ASN 553 N    /I DG 41 OP2  /G ASN 553 H     3.220  2.217
    8404     /G ARG 557 NH1  /I DG 44 N7   /G ARG 557 HH12  3.403  2.708
    8405     /G ARG 557 NH2  /I DG 44 N7   /G ARG 557 HH22  3.082  2.292
    8406     /G GLY 561 N    /H DT 13 OP1  /G GLY 561 H     2.977  2.057
    8407     /G THR 563 N    /H DT 13 OP2  /G THR 563 H     3.051  2.249
    8408     /G ALA 565 N    /H DG 14 OP2  /G ALA 565 H     3.032  2.059
    8409    
    8410 
    8411  
    8412 39 hydrogen bonds found 
    8413 8 strict hydrogen bonds found 
    8414 
    8415 > select clear
    8416 
    8417 > select /I:38
    8418 
    8419 32 atoms, 33 bonds, 1 residue, 1 model selected 
    8420 
    8421 > select /H:23
    8422 
    8423 32 atoms, 34 bonds, 1 residue, 1 model selected 
    8424 
    8425 > ui tool show "Renumber Residues"
    8426 
    8427 > renumber /H start -18
    8428 
    8429 34 residues renumbered 
    8430 
    8431 > renumber /H start -17
    8432 
    8433 34 residues renumbered 
    8434 
    8435 > select /I:39
    8436 
    8437 32 atoms, 33 bonds, 1 residue, 1 model selected 
    8438 
    8439 > select /I:38
    8440 
    8441 32 atoms, 33 bonds, 1 residue, 1 model selected 
    8442 
    8443 > renumber /I start -16
    8444 
    8445 34 residues renumbered 
    8446 
    8447 > select /H
    8448 
    8449 1060 atoms, 1139 bonds, 34 residues, 1 model selected 
    8450 
    8451 > ui tool show "Change Chain IDs"
    8452 
    8453 > changechains sel main
    8454 
    8455 Chain IDs of 34 residues changed 
    8456 
    8457 > select /I
    8458 
    8459 1098 atoms, 1187 bonds, 34 residues, 1 model selected 
    8460 
    8461 > changechains sel opp
    8462 
    8463 Chain IDs of 34 residues changed 
    8464 
    8465 > select clear
    8466 
    8467 > select nucleic
    8468 
    8469 2158 atoms, 2326 bonds, 68 residues, 1 model selected 
    8470 
    8471 > hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
    8472 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    8473 > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_generation_ver20_relaxed40"
    8474 > dashes 6 restrict #1/A,B,C,D,E,F,G angleSlop 40.0 twoColors true slopColor
    8475 > #ff9300 intraRes false select true reveal true retainCurrent true log true
    8476    
    8477    
    8478     Finding intermodel H-bonds
    8479     Finding intramodel H-bonds
    8480     Constraints relaxed by 0.4 angstroms and 40 degrees
    8481     Models used:
    8482         1 ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb
    8483    
    8484     49 H-bonds
    8485     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    8486     /A GLN 306 NE2  /opp DG 15 O3'    /A GLN 306 HE22  3.342  2.769
    8487     /A ASN 436 ND2  /main DA -13 OP1  /A ASN 436 HD22  2.810  1.833
    8488     /B LYS 148 NZ   /opp DA -10 OP1   /B LYS 148 HZ3   3.208  2.369
    8489     /B LYS 279 N    /opp DA 10 OP1    /B LYS 279 H     3.110  2.192
    8490     /C LYS 188 NZ   /main DC -8 OP1   /C LYS 188 HZ1   3.176  2.193
    8491     /C ARG 219 NH1  /opp DT 11 OP2    /C ARG 219 HH11  3.015  2.053
    8492     /C ARG 220 NH1  /main DT -10 O2   /C ARG 220 HH11  3.388  2.481
    8493     /C ARG 220 NH1  /opp DT 11 O2     /C ARG 220 HH11  3.296  2.935
    8494     /C TYR 223 OH   /main DC -8 OP1   /C TYR 223 HH    2.762  1.806
    8495     /C TYR 607 OH   /main DC 6 OP2    /C TYR 607 HH    3.098  2.200
    8496     /C ARG 672 N    /main DC 6 OP1    /C ARG 672 H     3.388  2.439
    8497     /C ARG 672 NH1  /opp DT -4 O2     /C ARG 672 HH12  2.806  1.902
    8498     /C ARG 672 NH2  /opp DT -4 O2     /C ARG 672 HH22  2.902  2.042
    8499     /C ARG 672 NH2  /opp DT -4 O4'    /C ARG 672 HH22  3.185  2.472
    8500     /C LYS 673 NZ   /main DT 7 OP1    /C LYS 673 HZ1   3.030  2.116
    8501     /D LYS 168 NZ   /main DT -12 O2   /D LYS 168 HZ1   2.564  2.050
    8502     /D SER 169 OG   /main DA -11 OP1  /D SER 169 HG    3.284  2.325
    8503     /D SER 463 OG   /opp DT 1 OP2     /D SER 463 HG    2.803  1.844
    8504     /D LYS 465 NZ   /opp DG 2 N7      /D LYS 465 HZ1   3.514  2.654
    8505     /D LYS 465 NZ   /opp DG 2 O6      /D LYS 465 HZ1   3.045  2.260
    8506     /D LYS 465 NZ   /opp DG 3 O6      /D LYS 465 HZ2   3.189  2.368
    8507     /E ARG 76 NH1   /main DG -9 OP1   /E ARG 76 HH11   2.908  2.005
    8508     /E ARG 340 NH1  /opp DA -10 OP2   /E ARG 340 HH11  3.135  2.272
    8509     /E ARG 356 NH1  /opp DT -11 OP2   /E ARG 356 HH11  2.946  2.163
    8510     /E ARG 357 N    /opp DT -11 OP1   /E ARG 357 H     3.073  2.081
    8511     /E ARG 357 NH1  /opp DT -13 O2    /E ARG 357 HH12  2.761  1.945
    8512     /E ARG 357 NH2  /opp DT -13 O2    /E ARG 357 HH22  2.690  1.846
    8513     /E GLU 358 N    /main DG 15 OP1   /E GLU 358 H     3.275  2.276
    8514     /E THR 359 OG1  /opp DA -10 OP1   /E THR 359 HG1   2.552  1.830
    8515     /E ARG 362 N    /opp DG -9 OP2    /E ARG 362 H     2.892  2.000
    8516     /E ARG 362 NH1  /main DC 12 O4'   /E ARG 362 HH12  3.369  2.780
    8517     /E ARG 362 NH2  /main DC 12 O2    /E ARG 362 HH22  3.076  2.066
    8518     /E ARG 362 NH2  /main DA 13 O4'   /E ARG 362 HH21  3.065  2.496
    8519     /E LYS 363 N    /opp DG -9 OP2    /E LYS 363 H     3.221  2.221
    8520     /E LYS 363 NZ   /opp DG -8 OP1    /E LYS 363 HZ3   2.954  2.284
    8521     /E LYS 363 NZ   /opp DG -8 OP2    /E LYS 363 HZ1   2.890  1.985
    8522     /G GLY 546 N    /main DT 1 OP1    /G GLY 546 H     3.276  2.580
    8523     /G LYS 547 NZ   /opp DG 3 OP1     /G LYS 547 HZ1   3.303  2.294
    8524     /G LYS 548 NZ   /main DT 1 O2     /G LYS 548 HZ1   2.747  2.031
    8525     /G LYS 548 NZ   /main DC 2 O4'    /G LYS 548 HZ2   2.889  2.196
    8526     /G LYS 548 NZ   /opp DT 0 O2      /G LYS 548 HZ3   3.045  2.142
    8527     /G ASN 553 N    /opp DG 3 OP2     /G ASN 553 H     3.220  2.217
    8528     /G ARG 557 NH1  /opp DG 6 N7      /G ARG 557 HH12  3.403  2.708
    8529     /G ARG 557 NH1  /opp DG 6 O6      /G ARG 557 HH12  2.566  1.988
    8530     /G ARG 557 NH2  /opp DG 6 N7      /G ARG 557 HH22  3.082  2.292
    8531     /G LYS 560 NZ   /main DA -11 OP2  /G LYS 560 HZ1   2.981  2.268
    8532     /G GLY 561 N    /main DT -10 OP1  /G GLY 561 H     2.977  2.057
    8533     /G THR 563 N    /main DT -10 OP2  /G THR 563 H     3.051  2.249
    8534     /G ALA 565 N    /main DG -9 OP2   /G ALA 565 H     3.032  2.059
    8535    
    8536 
    8537  
    8538 49 hydrogen bonds found 
    8539 8 strict hydrogen bonds found 
    8540 
    8541 > select nucleic
    8542 
    8543 2158 atoms, 2326 bonds, 68 residues, 1 model selected 
    8544 
    8545 > hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
    8546 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    8547 > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_generation_ver20" dashes 6
    8548 > restrict #1/A,B,C,D,E,F,G twoColors true slopColor #00f900 intraRes false
    8549 > select true reveal true retainCurrent true log true
    8550    
    8551    
    8552     Finding intermodel H-bonds
    8553     Finding intramodel H-bonds
    8554     Constraints relaxed by 0.4 angstroms and 20 degrees
    8555     Models used:
    8556         1 ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb
    8557    
    8558     39 H-bonds
    8559     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    8560     /A ASN 436 ND2  /main DA -13 OP1  /A ASN 436 HD22  2.810  1.833
    8561     /B LYS 148 NZ   /opp DA -10 OP1   /B LYS 148 HZ3   3.208  2.369
    8562     /B LYS 279 N    /opp DA 10 OP1    /B LYS 279 H     3.110  2.192
    8563     /C LYS 188 NZ   /main DC -8 OP1   /C LYS 188 HZ1   3.176  2.193
    8564     /C ARG 219 NH1  /opp DT 11 OP2    /C ARG 219 HH11  3.015  2.053
    8565     /C ARG 220 NH1  /main DT -10 O2   /C ARG 220 HH11  3.388  2.481
    8566     /C TYR 223 OH   /main DC -8 OP1   /C TYR 223 HH    2.762  1.806
    8567     /C TYR 607 OH   /main DC 6 OP2    /C TYR 607 HH    3.098  2.200
    8568     /C ARG 672 N    /main DC 6 OP1    /C ARG 672 H     3.388  2.439
    8569     /C ARG 672 NH1  /opp DT -4 O2     /C ARG 672 HH12  2.806  1.902
    8570     /C ARG 672 NH2  /opp DT -4 O2     /C ARG 672 HH22  2.902  2.042
    8571     /C ARG 672 NH2  /opp DT -4 O4'    /C ARG 672 HH22  3.185  2.472
    8572     /C LYS 673 NZ   /main DT 7 OP1    /C LYS 673 HZ1   3.030  2.116
    8573     /D SER 169 OG   /main DA -11 OP1  /D SER 169 HG    3.284  2.325
    8574     /D SER 463 OG   /opp DT 1 OP2     /D SER 463 HG    2.803  1.844
    8575     /D LYS 465 NZ   /opp DG 2 N7      /D LYS 465 HZ1   3.514  2.654
    8576     /D LYS 465 NZ   /opp DG 2 O6      /D LYS 465 HZ1   3.045  2.260
    8577     /D LYS 465 NZ   /opp DG 3 O6      /D LYS 465 HZ2   3.189  2.368
    8578     /E ARG 76 NH1   /main DG -9 OP1   /E ARG 76 HH11   2.908  2.005
    8579     /E ARG 340 NH1  /opp DA -10 OP2   /E ARG 340 HH11  3.135  2.272
    8580     /E ARG 356 NH1  /opp DT -11 OP2   /E ARG 356 HH11  2.946  2.163
    8581     /E ARG 357 N    /opp DT -11 OP1   /E ARG 357 H     3.073  2.081
    8582     /E ARG 357 NH1  /opp DT -13 O2    /E ARG 357 HH12  2.761  1.945
    8583     /E ARG 357 NH2  /opp DT -13 O2    /E ARG 357 HH22  2.690  1.846
    8584     /E GLU 358 N    /main DG 15 OP1   /E GLU 358 H     3.275  2.276
    8585     /E THR 359 OG1  /opp DA -10 OP1   /E THR 359 HG1   2.552  1.830
    8586     /E ARG 362 N    /opp DG -9 OP2    /E ARG 362 H     2.892  2.000
    8587     /E ARG 362 NH2  /main DC 12 O2    /E ARG 362 HH22  3.076  2.066
    8588     /E LYS 363 N    /opp DG -9 OP2    /E LYS 363 H     3.221  2.221
    8589     /E LYS 363 NZ   /opp DG -8 OP2    /E LYS 363 HZ1   2.890  1.985
    8590     /G LYS 547 NZ   /opp DG 3 OP1     /G LYS 547 HZ1   3.303  2.294
    8591     /G LYS 548 NZ   /main DT 1 O2     /G LYS 548 HZ1   2.747  2.031
    8592     /G LYS 548 NZ   /opp DT 0 O2      /G LYS 548 HZ3   3.045  2.142
    8593     /G ASN 553 N    /opp DG 3 OP2     /G ASN 553 H     3.220  2.217
    8594     /G ARG 557 NH1  /opp DG 6 N7      /G ARG 557 HH12  3.403  2.708
    8595     /G ARG 557 NH2  /opp DG 6 N7      /G ARG 557 HH22  3.082  2.292
    8596     /G GLY 561 N    /main DT -10 OP1  /G GLY 561 H     2.977  2.057
    8597     /G THR 563 N    /main DT -10 OP2  /G THR 563 H     3.051  2.249
    8598     /G ALA 565 N    /main DG -9 OP2   /G ALA 565 H     3.032  2.059
    8599    
    8600 
    8601  
    8602 39 hydrogen bonds found 
    8603 8 strict hydrogen bonds found 
    8604 
    8605 > select clear
    8606 
    8607 > save "/Users/jtbauer/Library/CloudStorage/OneDrive-
    8608 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    8609 > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_ver20.cxs"
    8610 
    8611 > select /A:303
    8612 
    8613 20 atoms, 20 bonds, 1 residue, 1 model selected 
    8614 
    8615 > show sel atoms
    8616 
    8617 > select /main:-13
    8618 
    8619 32 atoms, 34 bonds, 1 residue, 1 model selected 
    8620 
    8621 > hide sel cartoons
    8622 
    8623 > select nucleic
    8624 
    8625 2158 atoms, 2326 bonds, 68 residues, 1 model selected 
    8626 
    8627 > hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
    8628 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    8629 > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_generation_ver20_relaxed40"
    8630 > dashes 6 restrict #1/A,B,C,D,E,F,G distSlop 0.5 angleSlop 40.0 twoColors
    8631 > true slopColor #ff9300 intraRes false select true reveal true retainCurrent
    8632 > true log true
    8633    
    8634    
    8635     Finding intermodel H-bonds
    8636     Finding intramodel H-bonds
    8637     Constraints relaxed by 0.5 angstroms and 40 degrees
    8638     Models used:
    8639         1 ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb
    8640    
    8641     53 H-bonds
    8642     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    8643     /A GLN 306 NE2  /opp DG 15 O3'    /A GLN 306 HE22  3.342  2.769
    8644     /A ASN 436 ND2  /main DA -13 OP1  /A ASN 436 HD22  2.810  1.833
    8645     /B LYS 148 NZ   /opp DA -10 OP1   /B LYS 148 HZ3   3.208  2.369
    8646     /B LYS 279 N    /opp DA 10 OP1    /B LYS 279 H     3.110  2.192
    8647     /C LYS 188 NZ   /main DC -8 OP1   /C LYS 188 HZ1   3.176  2.193
    8648     /C ARG 219 N    /opp DA 12 OP1    /C ARG 219 H     3.467  2.499
    8649     /C ARG 219 NH1  /opp DT 11 OP2    /C ARG 219 HH11  3.015  2.053
    8650     /C ARG 220 NH1  /main DT -10 O2   /C ARG 220 HH11  3.388  2.481
    8651     /C ARG 220 NH1  /opp DT 11 O2     /C ARG 220 HH11  3.296  2.935
    8652     /C TYR 223 OH   /main DG -9 O3'   /C TYR 223 HH    3.522  2.887
    8653     /C TYR 223 OH   /main DC -8 OP1   /C TYR 223 HH    2.762  1.806
    8654     /C TYR 607 OH   /main DC 6 OP2    /C TYR 607 HH    3.098  2.200
    8655     /C LYS 671 N    /main DC 6 OP1    /C LYS 671 H     3.429  2.701
    8656     /C ARG 672 N    /main DC 6 OP1    /C ARG 672 H     3.388  2.439
    8657     /C ARG 672 NH1  /opp DT -4 O2     /C ARG 672 HH12  2.806  1.902
    8658     /C ARG 672 NH2  /opp DT -4 O2     /C ARG 672 HH22  2.902  2.042
    8659     /C ARG 672 NH2  /opp DT -4 O4'    /C ARG 672 HH22  3.185  2.472
    8660     /C LYS 673 NZ   /main DT 7 OP1    /C LYS 673 HZ1   3.030  2.116
    8661     /D LYS 168 NZ   /main DT -12 O2   /D LYS 168 HZ1   2.564  2.050
    8662     /D SER 169 OG   /main DA -11 OP1  /D SER 169 HG    3.284  2.325
    8663     /D SER 463 OG   /opp DT 1 OP2     /D SER 463 HG    2.803  1.844
    8664     /D LYS 465 NZ   /opp DG 2 N7      /D LYS 465 HZ1   3.514  2.654
    8665     /D LYS 465 NZ   /opp DG 2 O6      /D LYS 465 HZ1   3.045  2.260
    8666     /D LYS 465 NZ   /opp DG 3 O6      /D LYS 465 HZ2   3.189  2.368
    8667     /E ARG 76 NH1   /main DG -9 OP1   /E ARG 76 HH11   2.908  2.005
    8668     /E ARG 340 NH1  /opp DA -10 OP2   /E ARG 340 HH11  3.135  2.272
    8669     /E ARG 356 NH1  /opp DT -11 OP2   /E ARG 356 HH11  2.946  2.163
    8670     /E ARG 357 N    /opp DT -11 OP1   /E ARG 357 H     3.073  2.081
    8671     /E ARG 357 NH1  /opp DT -13 O2    /E ARG 357 HH12  2.761  1.945
    8672     /E ARG 357 NH2  /opp DT -13 O2    /E ARG 357 HH22  2.690  1.846
    8673     /E GLU 358 N    /main DG 15 OP1   /E GLU 358 H     3.275  2.276
    8674     /E THR 359 OG1  /opp DA -10 OP1   /E THR 359 HG1   2.552  1.830
    8675     /E ARG 362 N    /opp DA -10 O3'   /E ARG 362 H     3.515  2.618
    8676     /E ARG 362 N    /opp DG -9 OP2    /E ARG 362 H     2.892  2.000
    8677     /E ARG 362 NH1  /main DC 12 O4'   /E ARG 362 HH12  3.369  2.780
    8678     /E ARG 362 NH2  /main DC 12 O2    /E ARG 362 HH22  3.076  2.066
    8679     /E ARG 362 NH2  /main DA 13 O4'   /E ARG 362 HH21  3.065  2.496
    8680     /E LYS 363 N    /opp DG -9 OP2    /E LYS 363 H     3.221  2.221
    8681     /E LYS 363 NZ   /opp DG -8 OP1    /E LYS 363 HZ3   2.954  2.284
    8682     /E LYS 363 NZ   /opp DG -8 OP2    /E LYS 363 HZ1   2.890  1.985
    8683     /G GLY 546 N    /main DT 1 OP1    /G GLY 546 H     3.276  2.580
    8684     /G LYS 547 NZ   /opp DG 3 OP1     /G LYS 547 HZ1   3.303  2.294
    8685     /G LYS 548 NZ   /main DT 1 O2     /G LYS 548 HZ1   2.747  2.031
    8686     /G LYS 548 NZ   /main DC 2 O4'    /G LYS 548 HZ2   2.889  2.196
    8687     /G LYS 548 NZ   /opp DT 0 O2      /G LYS 548 HZ3   3.045  2.142
    8688     /G ASN 553 N    /opp DG 3 OP2     /G ASN 553 H     3.220  2.217
    8689     /G ARG 557 NH1  /opp DG 6 N7      /G ARG 557 HH12  3.403  2.708
    8690     /G ARG 557 NH1  /opp DG 6 O6      /G ARG 557 HH12  2.566  1.988
    8691     /G ARG 557 NH2  /opp DG 6 N7      /G ARG 557 HH22  3.082  2.292
    8692     /G LYS 560 NZ   /main DA -11 OP2  /G LYS 560 HZ1   2.981  2.268
    8693     /G GLY 561 N    /main DT -10 OP1  /G GLY 561 H     2.977  2.057
    8694     /G THR 563 N    /main DT -10 OP2  /G THR 563 H     3.051  2.249
    8695     /G ALA 565 N    /main DG -9 OP2   /G ALA 565 H     3.032  2.059
    8696    
    8697 
    8698  
    8699 53 hydrogen bonds found 
    8700 8 strict hydrogen bonds found 
    8701 
    8702 > select up
    8703 
    8704 1530 atoms, 1568 bonds, 61 residues, 1 model selected 
    8705 
    8706 > show sel atoms
    8707 
    8708 > select clear
    8709 
    8710 > select nucleic
    8711 
    8712 2158 atoms, 2326 bonds, 68 residues, 1 model selected 
    8713 
    8714 > hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
    8715 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    8716 > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_generation_ver20" dashes 6
    8717 > restrict #1/A,B,C,D,E,F,G distSlop 0.5 twoColors true slopColor #00f900
    8718 > intraRes false select true reveal true retainCurrent true log true
    8719    
    8720    
    8721     Finding intermodel H-bonds
    8722     Finding intramodel H-bonds
    8723     Constraints relaxed by 0.5 angstroms and 20 degrees
    8724     Models used:
    8725         1 ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb
    8726    
    8727     42 H-bonds
    8728     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    8729     /A ASN 436 ND2  /main DA -13 OP1  /A ASN 436 HD22  2.810  1.833
    8730     /B LYS 148 NZ   /opp DA -10 OP1   /B LYS 148 HZ3   3.208  2.369
    8731     /B LYS 279 N    /opp DA 10 OP1    /B LYS 279 H     3.110  2.192
    8732     /C LYS 188 NZ   /main DC -8 OP1   /C LYS 188 HZ1   3.176  2.193
    8733     /C ARG 219 N    /opp DA 12 OP1    /C ARG 219 H     3.467  2.499
    8734     /C ARG 219 NH1  /opp DT 11 OP2    /C ARG 219 HH11  3.015  2.053
    8735     /C ARG 220 NH1  /main DT -10 O2   /C ARG 220 HH11  3.388  2.481
    8736     /C TYR 223 OH   /main DC -8 OP1   /C TYR 223 HH    2.762  1.806
    8737     /C TYR 607 OH   /main DC 6 OP2    /C TYR 607 HH    3.098  2.200
    8738     /C LYS 671 N    /main DC 6 OP1    /C LYS 671 H     3.429  2.701
    8739     /C ARG 672 N    /main DC 6 OP1    /C ARG 672 H     3.388  2.439
    8740     /C ARG 672 NH1  /opp DT -4 O2     /C ARG 672 HH12  2.806  1.902
    8741     /C ARG 672 NH2  /opp DT -4 O2     /C ARG 672 HH22  2.902  2.042
    8742     /C ARG 672 NH2  /opp DT -4 O4'    /C ARG 672 HH22  3.185  2.472
    8743     /C LYS 673 NZ   /main DT 7 OP1    /C LYS 673 HZ1   3.030  2.116
    8744     /D SER 169 OG   /main DA -11 OP1  /D SER 169 HG    3.284  2.325
    8745     /D SER 463 OG   /opp DT 1 OP2     /D SER 463 HG    2.803  1.844
    8746     /D LYS 465 NZ   /opp DG 2 N7      /D LYS 465 HZ1   3.514  2.654
    8747     /D LYS 465 NZ   /opp DG 2 O6      /D LYS 465 HZ1   3.045  2.260
    8748     /D LYS 465 NZ   /opp DG 3 O6      /D LYS 465 HZ2   3.189  2.368
    8749     /E ARG 76 NH1   /main DG -9 OP1   /E ARG 76 HH11   2.908  2.005
    8750     /E ARG 340 NH1  /opp DA -10 OP2   /E ARG 340 HH11  3.135  2.272
    8751     /E ARG 356 NH1  /opp DT -11 OP2   /E ARG 356 HH11  2.946  2.163
    8752     /E ARG 357 N    /opp DT -11 OP1   /E ARG 357 H     3.073  2.081
    8753     /E ARG 357 NH1  /opp DT -13 O2    /E ARG 357 HH12  2.761  1.945
    8754     /E ARG 357 NH2  /opp DT -13 O2    /E ARG 357 HH22  2.690  1.846
    8755     /E GLU 358 N    /main DG 15 OP1   /E GLU 358 H     3.275  2.276
    8756     /E THR 359 OG1  /opp DA -10 OP1   /E THR 359 HG1   2.552  1.830
    8757     /E ARG 362 N    /opp DA -10 O3'   /E ARG 362 H     3.515  2.618
    8758     /E ARG 362 N    /opp DG -9 OP2    /E ARG 362 H     2.892  2.000
    8759     /E ARG 362 NH2  /main DC 12 O2    /E ARG 362 HH22  3.076  2.066
    8760     /E LYS 363 N    /opp DG -9 OP2    /E LYS 363 H     3.221  2.221
    8761     /E LYS 363 NZ   /opp DG -8 OP2    /E LYS 363 HZ1   2.890  1.985
    8762     /G LYS 547 NZ   /opp DG 3 OP1     /G LYS 547 HZ1   3.303  2.294
    8763     /G LYS 548 NZ   /main DT 1 O2     /G LYS 548 HZ1   2.747  2.031
    8764     /G LYS 548 NZ   /opp DT 0 O2      /G LYS 548 HZ3   3.045  2.142
    8765     /G ASN 553 N    /opp DG 3 OP2     /G ASN 553 H     3.220  2.217
    8766     /G ARG 557 NH1  /opp DG 6 N7      /G ARG 557 HH12  3.403  2.708
    8767     /G ARG 557 NH2  /opp DG 6 N7      /G ARG 557 HH22  3.082  2.292
    8768     /G GLY 561 N    /main DT -10 OP1  /G GLY 561 H     2.977  2.057
    8769     /G THR 563 N    /main DT -10 OP2  /G THR 563 H     3.051  2.249
    8770     /G ALA 565 N    /main DG -9 OP2   /G ALA 565 H     3.032  2.059
    8771    
    8772 
    8773  
    8774 42 hydrogen bonds found 
    8775 8 strict hydrogen bonds found 
    8776 
    8777 > select up
    8778 
    8779 1335 atoms, 1364 bonds, 53 residues, 1 model selected 
    8780 
    8781 > show sel atoms
    8782 
    8783 > select clear
    8784 
    8785 > select /A:436-436
    8786 
    8787 14 atoms, 13 bonds, 1 residue, 1 model selected 
    8788 
    8789 > show sel atoms
    8790 
    8791 > select /A:435-436
    8792 
    8793 28 atoms, 27 bonds, 2 residues, 1 model selected 
    8794 
    8795 > show sel atoms
    8796 
    8797 > select nucleic
    8798 
    8799 2158 atoms, 2326 bonds, 68 residues, 1 model selected 
    8800 
    8801 > select clear
    8802 
    8803 > show cartoons
    8804 
    8805 > select nucleic
    8806 
    8807 2158 atoms, 2326 bonds, 68 residues, 1 model selected 
    8808 
    8809 > hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
    8810 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    8811 > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_generation_ver20_relaxed40"
    8812 > dashes 6 restrict #1/A,B,C,D,E,F,G distSlop 0.5 angleSlop 40.0 twoColors
    8813 > true slopColor #ff9300 intraRes false select true reveal true retainCurrent
    8814 > true log true
    8815    
    8816    
    8817     Finding intermodel H-bonds
    8818     Finding intramodel H-bonds
    8819     Constraints relaxed by 0.5 angstroms and 40 degrees
    8820     Models used:
    8821         1 ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb
    8822    
    8823     53 H-bonds
    8824     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    8825     /A GLN 306 NE2  /opp DG 15 O3'    /A GLN 306 HE22  3.342  2.769
    8826     /A ASN 436 ND2  /main DA -13 OP1  /A ASN 436 HD22  2.810  1.833
    8827     /B LYS 148 NZ   /opp DA -10 OP1   /B LYS 148 HZ3   3.208  2.369
    8828     /B LYS 279 N    /opp DA 10 OP1    /B LYS 279 H     3.110  2.192
    8829     /C LYS 188 NZ   /main DC -8 OP1   /C LYS 188 HZ1   3.176  2.193
    8830     /C ARG 219 N    /opp DA 12 OP1    /C ARG 219 H     3.467  2.499
    8831     /C ARG 219 NH1  /opp DT 11 OP2    /C ARG 219 HH11  3.015  2.053
    8832     /C ARG 220 NH1  /main DT -10 O2   /C ARG 220 HH11  3.388  2.481
    8833     /C ARG 220 NH1  /opp DT 11 O2     /C ARG 220 HH11  3.296  2.935
    8834     /C TYR 223 OH   /main DG -9 O3'   /C TYR 223 HH    3.522  2.887
    8835     /C TYR 223 OH   /main DC -8 OP1   /C TYR 223 HH    2.762  1.806
    8836     /C TYR 607 OH   /main DC 6 OP2    /C TYR 607 HH    3.098  2.200
    8837     /C LYS 671 N    /main DC 6 OP1    /C LYS 671 H     3.429  2.701
    8838     /C ARG 672 N    /main DC 6 OP1    /C ARG 672 H     3.388  2.439
    8839     /C ARG 672 NH1  /opp DT -4 O2     /C ARG 672 HH12  2.806  1.902
    8840     /C ARG 672 NH2  /opp DT -4 O2     /C ARG 672 HH22  2.902  2.042
    8841     /C ARG 672 NH2  /opp DT -4 O4'    /C ARG 672 HH22  3.185  2.472
    8842     /C LYS 673 NZ   /main DT 7 OP1    /C LYS 673 HZ1   3.030  2.116
    8843     /D LYS 168 NZ   /main DT -12 O2   /D LYS 168 HZ1   2.564  2.050
    8844     /D SER 169 OG   /main DA -11 OP1  /D SER 169 HG    3.284  2.325
    8845     /D SER 463 OG   /opp DT 1 OP2     /D SER 463 HG    2.803  1.844
    8846     /D LYS 465 NZ   /opp DG 2 N7      /D LYS 465 HZ1   3.514  2.654
    8847     /D LYS 465 NZ   /opp DG 2 O6      /D LYS 465 HZ1   3.045  2.260
    8848     /D LYS 465 NZ   /opp DG 3 O6      /D LYS 465 HZ2   3.189  2.368
    8849     /E ARG 76 NH1   /main DG -9 OP1   /E ARG 76 HH11   2.908  2.005
    8850     /E ARG 340 NH1  /opp DA -10 OP2   /E ARG 340 HH11  3.135  2.272
    8851     /E ARG 356 NH1  /opp DT -11 OP2   /E ARG 356 HH11  2.946  2.163
    8852     /E ARG 357 N    /opp DT -11 OP1   /E ARG 357 H     3.073  2.081
    8853     /E ARG 357 NH1  /opp DT -13 O2    /E ARG 357 HH12  2.761  1.945
    8854     /E ARG 357 NH2  /opp DT -13 O2    /E ARG 357 HH22  2.690  1.846
    8855     /E GLU 358 N    /main DG 15 OP1   /E GLU 358 H     3.275  2.276
    8856     /E THR 359 OG1  /opp DA -10 OP1   /E THR 359 HG1   2.552  1.830
    8857     /E ARG 362 N    /opp DA -10 O3'   /E ARG 362 H     3.515  2.618
    8858     /E ARG 362 N    /opp DG -9 OP2    /E ARG 362 H     2.892  2.000
    8859     /E ARG 362 NH1  /main DC 12 O4'   /E ARG 362 HH12  3.369  2.780
    8860     /E ARG 362 NH2  /main DC 12 O2    /E ARG 362 HH22  3.076  2.066
    8861     /E ARG 362 NH2  /main DA 13 O4'   /E ARG 362 HH21  3.065  2.496
    8862     /E LYS 363 N    /opp DG -9 OP2    /E LYS 363 H     3.221  2.221
    8863     /E LYS 363 NZ   /opp DG -8 OP1    /E LYS 363 HZ3   2.954  2.284
    8864     /E LYS 363 NZ   /opp DG -8 OP2    /E LYS 363 HZ1   2.890  1.985
    8865     /G GLY 546 N    /main DT 1 OP1    /G GLY 546 H     3.276  2.580
    8866     /G LYS 547 NZ   /opp DG 3 OP1     /G LYS 547 HZ1   3.303  2.294
    8867     /G LYS 548 NZ   /main DT 1 O2     /G LYS 548 HZ1   2.747  2.031
    8868     /G LYS 548 NZ   /main DC 2 O4'    /G LYS 548 HZ2   2.889  2.196
    8869     /G LYS 548 NZ   /opp DT 0 O2      /G LYS 548 HZ3   3.045  2.142
    8870     /G ASN 553 N    /opp DG 3 OP2     /G ASN 553 H     3.220  2.217
    8871     /G ARG 557 NH1  /opp DG 6 N7      /G ARG 557 HH12  3.403  2.708
    8872     /G ARG 557 NH1  /opp DG 6 O6      /G ARG 557 HH12  2.566  1.988
    8873     /G ARG 557 NH2  /opp DG 6 N7      /G ARG 557 HH22  3.082  2.292
    8874     /G LYS 560 NZ   /main DA -11 OP2  /G LYS 560 HZ1   2.981  2.268
    8875     /G GLY 561 N    /main DT -10 OP1  /G GLY 561 H     2.977  2.057
    8876     /G THR 563 N    /main DT -10 OP2  /G THR 563 H     3.051  2.249
    8877     /G ALA 565 N    /main DG -9 OP2   /G ALA 565 H     3.032  2.059
    8878    
    8879 
    8880  
    8881 53 hydrogen bonds found 
    8882 8 strict hydrogen bonds found 
    8883 
    8884 > select clear
    8885 
    8886 > select ~nucleic
    8887 
    8888 47052 atoms, 47494 bonds, 16 pseudobonds, 2932 residues, 3 models selected 
    8889 
    8890 > hide sel cartoons
    8891 
    8892 > select clear
    8893 
    8894 > select /main:-13
    8895 
    8896 32 atoms, 34 bonds, 1 residue, 1 model selected 
    8897 
    8898 > hide sel atoms
    8899 
    8900 > show sel atoms
    8901 
    8902 > hide sel cartoons
    8903 
    8904 > select /A:301,306,303,435,436,305
    8905 
    8906 111 atoms, 108 bonds, 6 residues, 1 model selected 
    8907 
    8908 > show sel atoms
    8909 
    8910 > select /B:279,280,248,153,150,148
    8911 
    8912 109 atoms, 104 bonds, 6 residues, 1 model selected 
    8913 
    8914 > show sel atoms
    8915 
    8916 > select /C:219,220,223,188,671-673
    8917 
    8918 159 atoms, 156 bonds, 7 residues, 1 model selected 
    8919 
    8920 > show sel atoms
    8921 
    8922 > select clear
    8923 
    8924 > select /D:168,169,465,463
    8925 
    8926 66 atoms, 63 bonds, 4 residues, 1 model selected 
    8927 
    8928 > show sel atoms
    8929 
    8930 > select clear
    8931 
    8932 > select /E:76,341,363,359,362,340,356,357,358
    8933 
    8934 192 atoms, 189 bonds, 9 residues, 1 model selected 
    8935 
    8936 > show sel atoms
    8937 
    8938 > select clear
    8939 
    8940 > select /G:560,561,563,565,557,547,548,543,581,546
    8941 
    8942 157 atoms, 150 bonds, 10 residues, 1 model selected 
    8943 
    8944 > show sel atoms
    8945 
    8946 > select clear
    8947 
    8948 > select /main:-1
    8949 
    8950 32 atoms, 34 bonds, 1 residue, 1 model selected 
    8951 
    8952 > hide sel cartoons
    8953 
    8954 > show sel cartoons
    8955 
    8956 > select /main:0
    8957 
    8958 32 atoms, 34 bonds, 1 residue, 1 model selected 
    8959 
    8960 > hide sel cartoons
    8961 
    8962 > select /main:-1
    8963 
    8964 32 atoms, 34 bonds, 1 residue, 1 model selected 
    8965 
    8966 > hide sel cartoons
    8967 
    8968 > select clear
    8969 
    8970 Drag select of 2 atoms, 2 bonds 
    8971 
    8972 > select clear
    8973 
    8974 > select /A:305@NZ
    8975 
    8976 1 atom, 1 residue, 1 model selected 
    8977 
    8978 > select /main:-12
    8979 
    8980 32 atoms, 33 bonds, 1 residue, 1 model selected 
    8981 
    8982 > hide sel cartoons
    8983 
    8984 > select /main:-13@C3'
    8985 
    8986 1 atom, 1 residue, 1 model selected 
    8987 
    8988 > show sel cartoons
    8989 
    8990 > select clear
    8991 
    8992 > select /main:-11
    8993 
    8994 32 atoms, 34 bonds, 1 residue, 1 model selected 
    8995 
    8996 > select nucleic
    8997 
    8998 2158 atoms, 2326 bonds, 68 residues, 1 model selected 
    8999 
    9000 > hbonds sel saveFile "/Users/jtbauer/Library/CloudStorage/OneDrive-
    9001 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    9002 > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_generation_ver20" dashes 6
    9003 > restrict #1/A,B,C,D,E,F,G distSlop 0.5 twoColors true slopColor #00f900
    9004 > intraRes false select true reveal true retainCurrent true log true
    9005    
    9006    
    9007     Finding intermodel H-bonds
    9008     Finding intramodel H-bonds
    9009     Constraints relaxed by 0.5 angstroms and 20 degrees
    9010     Models used:
    9011         1 ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb
    9012    
    9013     42 H-bonds
    9014     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    9015     /A ASN 436 ND2  /main DA -13 OP1  /A ASN 436 HD22  2.810  1.833
    9016     /B LYS 148 NZ   /opp DA -10 OP1   /B LYS 148 HZ3   3.208  2.369
    9017     /B LYS 279 N    /opp DA 10 OP1    /B LYS 279 H     3.110  2.192
    9018     /C LYS 188 NZ   /main DC -8 OP1   /C LYS 188 HZ1   3.176  2.193
    9019     /C ARG 219 N    /opp DA 12 OP1    /C ARG 219 H     3.467  2.499
    9020     /C ARG 219 NH1  /opp DT 11 OP2    /C ARG 219 HH11  3.015  2.053
    9021     /C ARG 220 NH1  /main DT -10 O2   /C ARG 220 HH11  3.388  2.481
    9022     /C TYR 223 OH   /main DC -8 OP1   /C TYR 223 HH    2.762  1.806
    9023     /C TYR 607 OH   /main DC 6 OP2    /C TYR 607 HH    3.098  2.200
    9024     /C LYS 671 N    /main DC 6 OP1    /C LYS 671 H     3.429  2.701
    9025     /C ARG 672 N    /main DC 6 OP1    /C ARG 672 H     3.388  2.439
    9026     /C ARG 672 NH1  /opp DT -4 O2     /C ARG 672 HH12  2.806  1.902
    9027     /C ARG 672 NH2  /opp DT -4 O2     /C ARG 672 HH22  2.902  2.042
    9028     /C ARG 672 NH2  /opp DT -4 O4'    /C ARG 672 HH22  3.185  2.472
    9029     /C LYS 673 NZ   /main DT 7 OP1    /C LYS 673 HZ1   3.030  2.116
    9030     /D SER 169 OG   /main DA -11 OP1  /D SER 169 HG    3.284  2.325
    9031     /D SER 463 OG   /opp DT 1 OP2     /D SER 463 HG    2.803  1.844
    9032     /D LYS 465 NZ   /opp DG 2 N7      /D LYS 465 HZ1   3.514  2.654
    9033     /D LYS 465 NZ   /opp DG 2 O6      /D LYS 465 HZ1   3.045  2.260
    9034     /D LYS 465 NZ   /opp DG 3 O6      /D LYS 465 HZ2   3.189  2.368
    9035     /E ARG 76 NH1   /main DG -9 OP1   /E ARG 76 HH11   2.908  2.005
    9036     /E ARG 340 NH1  /opp DA -10 OP2   /E ARG 340 HH11  3.135  2.272
    9037     /E ARG 356 NH1  /opp DT -11 OP2   /E ARG 356 HH11  2.946  2.163
    9038     /E ARG 357 N    /opp DT -11 OP1   /E ARG 357 H     3.073  2.081
    9039     /E ARG 357 NH1  /opp DT -13 O2    /E ARG 357 HH12  2.761  1.945
    9040     /E ARG 357 NH2  /opp DT -13 O2    /E ARG 357 HH22  2.690  1.846
    9041     /E GLU 358 N    /main DG 15 OP1   /E GLU 358 H     3.275  2.276
    9042     /E THR 359 OG1  /opp DA -10 OP1   /E THR 359 HG1   2.552  1.830
    9043     /E ARG 362 N    /opp DA -10 O3'   /E ARG 362 H     3.515  2.618
    9044     /E ARG 362 N    /opp DG -9 OP2    /E ARG 362 H     2.892  2.000
    9045     /E ARG 362 NH2  /main DC 12 O2    /E ARG 362 HH22  3.076  2.066
    9046     /E LYS 363 N    /opp DG -9 OP2    /E LYS 363 H     3.221  2.221
    9047     /E LYS 363 NZ   /opp DG -8 OP2    /E LYS 363 HZ1   2.890  1.985
    9048     /G LYS 547 NZ   /opp DG 3 OP1     /G LYS 547 HZ1   3.303  2.294
    9049     /G LYS 548 NZ   /main DT 1 O2     /G LYS 548 HZ1   2.747  2.031
    9050     /G LYS 548 NZ   /opp DT 0 O2      /G LYS 548 HZ3   3.045  2.142
    9051     /G ASN 553 N    /opp DG 3 OP2     /G ASN 553 H     3.220  2.217
    9052     /G ARG 557 NH1  /opp DG 6 N7      /G ARG 557 HH12  3.403  2.708
    9053     /G ARG 557 NH2  /opp DG 6 N7      /G ARG 557 HH22  3.082  2.292
    9054     /G GLY 561 N    /main DT -10 OP1  /G GLY 561 H     2.977  2.057
    9055     /G THR 563 N    /main DT -10 OP2  /G THR 563 H     3.051  2.249
    9056     /G ALA 565 N    /main DG -9 OP2   /G ALA 565 H     3.032  2.059
    9057    
    9058 
    9059  
    9060 42 hydrogen bonds found 
    9061 8 strict hydrogen bonds found 
    9062 
    9063 > select clear
    9064 
    9065 > select /main:-9
    9066 
    9067 33 atoms, 35 bonds, 1 residue, 1 model selected 
    9068 
    9069 > select /main:-8
    9070 
    9071 30 atoms, 31 bonds, 1 residue, 1 model selected 
    9072 
    9073 > open "/Users/jtbauer/Library/CloudStorage/OneDrive-
    9074 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    9075 > structures/PDBs/ylODC_oriA006_complete/ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb"
    9076 
    9077 Chain information for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2 
    9078 --- 
    9079 Chain | Description 
    9080 A | No description available 
    9081 B | No description available 
    9082 C | No description available 
    9083 D | No description available 
    9084 E | No description available 
    9085 F | No description available 
    9086 G | No description available 
    9087 H | No description available 
    9088 I | No description available 
    9089  
    9090 
    9091 > select #2
    9092 
    9093 24882 atoms, 25492 bonds, 16 pseudobonds, 3000 residues, 3 models selected 
    9094 
    9095 > show sel atoms
    9096 
    9097 > show sel cartoons
    9098 
    9099 > style sel stick
    9100 
    9101 Changed 24882 atom styles 
    9102 
    9103 > newcolor #2/A #2/B #2/C #2/D #2/E #2/F #2/G #2/H #2/I
    9104 
    9105 > color sel byhetero
    9106 
    9107 > hide sel atoms
    9108 
    9109 > select clear
    9110 
    9111 > select #2 & nucleic
    9112 
    9113 1391 atoms, 1559 bonds, 68 residues, 1 model selected 
    9114 
    9115 > hbonds sel dashes 6 restrict #2/A,B,C,D,E,F,G distSlop 0.5 twoColors true
    9116 > slopColor #00f900 intraRes false select true reveal true retainCurrent true
    9117 > log true
    9118    
    9119    
    9120     Finding intermodel H-bonds
    9121     Finding intramodel H-bonds
    9122     Constraints relaxed by 0.5 angstroms and 20 degrees
    9123     Models used:
    9124         2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb
    9125    
    9126     46 H-bonds
    9127     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    9128     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A ASN 436 ND2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 10 OP1  no hydrogen  2.810  N/A
    9129     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 148 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP1  no hydrogen  3.208  N/A
    9130     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 279 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 48 OP1  no hydrogen  3.110  N/A
    9131     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 188 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 15 OP1  no hydrogen  3.176  N/A
    9132     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 50 OP1  no hydrogen  3.467  N/A
    9133     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 49 OP2  no hydrogen  3.015  N/A
    9134     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 220 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 O2   no hydrogen  3.388  N/A
    9135     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 223 OH   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 15 OP1  no hydrogen  2.762  N/A
    9136     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 607 OH   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 29 OP2  no hydrogen  3.098  N/A
    9137     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 29 OP1  no hydrogen  3.388  N/A
    9138     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O2   no hydrogen  2.806  N/A
    9139     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O2   no hydrogen  2.902  N/A
    9140     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O4'  no hydrogen  3.185  N/A
    9141     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 673 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 30 OP1  no hydrogen  3.030  N/A
    9142     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 168 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 11 O2   no hydrogen  2.564  N/A
    9143     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 169 OG   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 12 OP1  no hydrogen  3.284  N/A
    9144     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 463 OG   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 39 OP2  no hydrogen  2.803  N/A
    9145     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 40 N7   no hydrogen  3.514  N/A
    9146     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 40 O6   no hydrogen  3.045  N/A
    9147     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 O6   no hydrogen  3.189  N/A
    9148     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 76 NH1   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 14 OP1  no hydrogen  2.908  N/A
    9149     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 340 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP2  no hydrogen  3.135  N/A
    9150     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 356 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 27 OP2  no hydrogen  2.946  N/A
    9151     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 27 OP1  no hydrogen  3.073  N/A
    9152     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 25 O2   no hydrogen  2.761  N/A
    9153     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 NH2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 25 O2   no hydrogen  2.690  N/A
    9154     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E GLU 358 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 38 OP1  no hydrogen  3.275  N/A
    9155     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E THR 359 OG1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP1  no hydrogen  2.552  N/A
    9156     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 O3'  no hydrogen  3.515  N/A
    9157     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 29 OP2  no hydrogen  2.892  N/A
    9158     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 NH2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 35 O2   no hydrogen  3.076  N/A
    9159     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 29 OP2  no hydrogen  3.221  N/A
    9160     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 30 OP2  no hydrogen  2.890  N/A
    9161     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G THR 542 OG1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 23 OP1  no hydrogen  3.290  N/A
    9162     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 546 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 24 OP1  no hydrogen  3.276  N/A
    9163     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 547 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 OP1  no hydrogen  3.303  N/A
    9164     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 24 O2   no hydrogen  2.747  N/A
    9165     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 25 O4'  no hydrogen  2.889  N/A
    9166     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 38 O2   no hydrogen  3.045  N/A
    9167     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ASN 553 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 OP2  no hydrogen  3.220  N/A
    9168     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 44 N7   no hydrogen  3.403  N/A
    9169     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 NH2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 44 N7   no hydrogen  3.082  N/A
    9170     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 560 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 12 OP2  no hydrogen  2.981  N/A
    9171     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 561 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 OP1  no hydrogen  2.977  N/A
    9172     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G THR 563 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 OP2  no hydrogen  3.051  N/A
    9173     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ALA 565 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 14 OP2  no hydrogen  3.032  N/A
    9174    
    9175 
    9176  
    9177 46 hydrogen bonds found 
    9178 13 strict hydrogen bonds found 
    9179 
    9180 > select up
    9181 
    9182 840 atoms, 876 bonds, 59 residues, 1 model selected 
    9183 
    9184 > show sel atoms
    9185 
    9186 > select #2 & ~nucleic
    9187 
    9188 23491 atoms, 23933 bonds, 16 pseudobonds, 2932 residues, 3 models selected 
    9189 
    9190 > hide sel cartoons
    9191 
    9192 > select clear
    9193 
    9194 > hide #!1 models
    9195 
    9196 > show #!1 models
    9197 
    9198 > hide #!1 models
    9199 
    9200 > show #!1 models
    9201 
    9202 > hide #!1 models
    9203 
    9204 > show #!1 models
    9205 
    9206 > select #2 & nucleic
    9207 
    9208 1391 atoms, 1559 bonds, 68 residues, 1 model selected 
    9209 
    9210 > hbonds sel dashes 6 restrict #2/A,B,C,D,E,F,G distSlop 0.5 angleSlop 40.0
    9211 > twoColors true slopColor #ff9300 intraRes false select true reveal true
    9212 > retainCurrent true log true
    9213    
    9214    
    9215     Finding intermodel H-bonds
    9216     Finding intramodel H-bonds
    9217     Constraints relaxed by 0.5 angstroms and 40 degrees
    9218     Models used:
    9219         2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb
    9220    
    9221     55 H-bonds
    9222     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    9223     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A ARG 301 NH2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 54 N3   no hydrogen  3.290  N/A
    9224     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A GLN 306 NE2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 53 O3'  no hydrogen  3.342  N/A
    9225     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A ASN 436 ND2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 10 OP1  no hydrogen  2.810  N/A
    9226     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 148 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP1  no hydrogen  3.208  N/A
    9227     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 279 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 48 OP1  no hydrogen  3.110  N/A
    9228     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 188 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 15 OP1  no hydrogen  3.176  N/A
    9229     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 50 OP1  no hydrogen  3.467  N/A
    9230     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 49 OP2  no hydrogen  3.015  N/A
    9231     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 220 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 O2   no hydrogen  3.388  N/A
    9232     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 220 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 49 O2   no hydrogen  3.296  N/A
    9233     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 223 OH   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 14 O3'  no hydrogen  3.522  N/A
    9234     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 223 OH   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 15 OP1  no hydrogen  2.762  N/A
    9235     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 607 OH   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 29 OP2  no hydrogen  3.098  N/A
    9236     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 29 OP1  no hydrogen  3.388  N/A
    9237     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O2   no hydrogen  2.806  N/A
    9238     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O2   no hydrogen  2.902  N/A
    9239     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O4'  no hydrogen  3.185  N/A
    9240     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 673 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 30 OP1  no hydrogen  3.030  N/A
    9241     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 168 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 11 O2   no hydrogen  2.564  N/A
    9242     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 169 OG   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 12 OP1  no hydrogen  3.284  N/A
    9243     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 463 OG   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 39 OP2  no hydrogen  2.803  N/A
    9244     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 40 N7   no hydrogen  3.514  N/A
    9245     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 40 O6   no hydrogen  3.045  N/A
    9246     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 O6   no hydrogen  3.189  N/A
    9247     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 76 NH1   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 14 OP1  no hydrogen  2.908  N/A
    9248     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 340 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP2  no hydrogen  3.135  N/A
    9249     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 356 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 27 OP2  no hydrogen  2.946  N/A
    9250     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 27 OP1  no hydrogen  3.073  N/A
    9251     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 25 O2   no hydrogen  2.761  N/A
    9252     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 NH2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 25 O2   no hydrogen  2.690  N/A
    9253     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E GLU 358 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 38 OP1  no hydrogen  3.275  N/A
    9254     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E THR 359 OG1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP1  no hydrogen  2.552  N/A
    9255     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 O3'  no hydrogen  3.515  N/A
    9256     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 29 OP2  no hydrogen  2.892  N/A
    9257     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 35 O4'  no hydrogen  3.369  N/A
    9258     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 NH2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 35 O2   no hydrogen  3.076  N/A
    9259     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 NH2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 36 O4'  no hydrogen  3.065  N/A
    9260     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 29 OP2  no hydrogen  3.221  N/A
    9261     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 30 OP1  no hydrogen  2.954  N/A
    9262     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 30 OP2  no hydrogen  2.890  N/A
    9263     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G THR 542 OG1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 23 OP1  no hydrogen  3.290  N/A
    9264     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 546 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 24 OP1  no hydrogen  3.276  N/A
    9265     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 547 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 OP1  no hydrogen  3.303  N/A
    9266     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 24 O2   no hydrogen  2.747  N/A
    9267     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 25 O4'  no hydrogen  2.889  N/A
    9268     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 38 O2   no hydrogen  3.045  N/A
    9269     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ASN 553 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 OP2  no hydrogen  3.220  N/A
    9270     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 44 N7   no hydrogen  3.403  N/A
    9271     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 44 O6   no hydrogen  2.566  N/A
    9272     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 NH2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 44 N7   no hydrogen  3.082  N/A
    9273     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 560 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 12 OP2  no hydrogen  2.981  N/A
    9274     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 561 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 OP1  no hydrogen  2.977  N/A
    9275     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G THR 563 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 OP2  no hydrogen  3.051  N/A
    9276     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 564 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 OP2  no hydrogen  2.948  N/A
    9277     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ALA 565 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 14 OP2  no hydrogen  3.032  N/A
    9278    
    9279 
    9280  
    9281 55 hydrogen bonds found 
    9282 13 strict hydrogen bonds found 
    9283 
    9284 > select up
    9285 
    9286 929 atoms, 972 bonds, 65 residues, 1 model selected 
    9287 
    9288 > show sel atoms
    9289 
    9290 > select clear
    9291 
    9292 > ui tool show "Add Hydrogens"
    9293 
    9294 > addh #!2
    9295 
    9296 Summary of feedback from adding hydrogens to
    9297 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2 
    9298 --- 
    9299 warning | Not adding hydrogens to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 22 P because it is missing heavy-atom bond partners 
    9300 notes | No usable SEQRES records for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb (#2) chain A; guessing termini instead 
    9301 No usable SEQRES records for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb (#2)
    9302 chain B; guessing termini instead 
    9303 No usable SEQRES records for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb (#2)
    9304 chain C; guessing termini instead 
    9305 No usable SEQRES records for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb (#2)
    9306 chain D; guessing termini instead 
    9307 No usable SEQRES records for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb (#2)
    9308 chain E; guessing termini instead 
    9309 4 messages similar to the above omitted 
    9310 Chain-initial residues that are actual N termini:
    9311 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A PRO 299,
    9312 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B PRO 106,
    9313 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C THR 6,
    9314 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D PRO 33,
    9315 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E MET 1,
    9316 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/F PRO 179,
    9317 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G PRO 93 
    9318 Chain-initial residues that are not actual N termini:
    9319 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B VAL 396,
    9320 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B VAL 444,
    9321 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 489,
    9322 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ASN 72,
    9323 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D ASN 128,
    9324 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D GLY 162,
    9325 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LEU 296,
    9326 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D PHE 436,
    9327 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E GLU 217,
    9328 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ASP 319,
    9329 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/F SER 313,
    9330 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ALA 213,
    9331 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G THR 386,
    9332 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G VAL 439,
    9333 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ASN 461 
    9334 Chain-final residues that are actual C termini:
    9335 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A LEU 718,
    9336 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LEU 685 
    9337 Chain-final residues that are not actual C termini:
    9338 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B GLU 504,
    9339 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B GLU 386,
    9340 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B HIS 420,
    9341 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B VAL 479,
    9342 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 29,
    9343 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D ARG 510,
    9344 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 123,
    9345 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LEU 159,
    9346 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D MET 285,
    9347 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LEU 420,
    9348 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ASN 464,
    9349 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ALA 210,
    9350 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LEU 304,
    9351 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/F GLN 351,
    9352 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/F THR 307,
    9353 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LEU 604,
    9354 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 207,
    9355 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G HIS 335,
    9356 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLN 433,
    9357 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G PHE 457 
    9358 2714 hydrogen bonds 
    9359 Adding 'H' to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B VAL 396 
    9360 Adding 'H' to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B VAL 444 
    9361 Adding 'H' to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 489 
    9362 Adding 'H' to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ASN 72 
    9363 Adding 'H' to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D ASN 128 
    9364 10 messages similar to the above omitted 
    9365 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B GLU 504 is not terminus,
    9366 removing H atom from 'C' 
    9367 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D ARG 510 is not terminus,
    9368 removing H atom from 'C' 
    9369 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ASN 464 is not terminus,
    9370 removing H atom from 'C' 
    9371 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/F GLN 351 is not terminus,
    9372 removing H atom from 'C' 
    9373 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LEU 604 is not terminus,
    9374 removing H atom from 'C' 
    9375 24328 hydrogens added 
    9376  
    9377 
    9378 > select #2 & nucleic
    9379 
    9380 2158 atoms, 2326 bonds, 68 residues, 1 model selected 
    9381 
    9382 > hbonds sel dashes 6 restrict #2/A,B,C,D,E,F,G distSlop 0.5 angleSlop 40.0
    9383 > twoColors true slopColor #ff9300 intraRes false select true reveal true
    9384 > retainCurrent true log true
    9385    
    9386    
    9387     Finding intermodel H-bonds
    9388     Finding intramodel H-bonds
    9389     Constraints relaxed by 0.5 angstroms and 40 degrees
    9390     Models used:
    9391         2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb
    9392    
    9393     54 H-bonds
    9394     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    9395     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A ARG 301 NH2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 54 N3   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A ARG 301 HH22  3.290  2.710
    9396     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A GLN 306 NE2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 53 O3'  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A GLN 306 HE22  3.342  2.769
    9397     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A ASN 436 ND2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 10 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A ASN 436 HD22  2.810  1.833
    9398     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 148 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 148 HZ3   3.208  2.369
    9399     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 279 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 48 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 279 H     3.110  2.192
    9400     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 188 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 15 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 188 HZ1   3.176  2.193
    9401     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 50 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 H     3.467  2.499
    9402     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 49 OP2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 HH11  3.015  2.053
    9403     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 220 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 O2   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 220 HH11  3.388  2.481
    9404     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 220 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 49 O2   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 220 HH11  3.296  2.935
    9405     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 223 OH   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 14 O3'  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 223 HH    3.522  2.887
    9406     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 223 OH   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 15 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 223 HH    2.762  1.806
    9407     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 607 OH   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 29 OP2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 607 HH    3.098  2.200
    9408     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 671 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 29 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 671 H     3.429  2.701
    9409     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 29 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 H     3.388  2.439
    9410     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O2   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 HH12  2.806  1.902
    9411     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O2   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 HH22  2.902  2.042
    9412     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O4'  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 HH22  3.185  2.472
    9413     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 673 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 30 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 673 HZ1   3.030  2.116
    9414     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 168 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 11 O2   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 168 HZ1   2.564  2.050
    9415     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 169 OG   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 12 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 169 HG    3.284  2.325
    9416     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 463 OG   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 39 OP2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 463 HG    2.803  1.844
    9417     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 40 N7   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 HZ1   3.514  2.654
    9418     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 40 O6   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 HZ1   3.045  2.260
    9419     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 O6   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 HZ2   3.189  2.368
    9420     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 76 NH1   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 14 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 76 HH11   2.908  2.005
    9421     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 340 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 340 HH11  3.135  2.272
    9422     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 356 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 27 OP2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 356 HH11  2.946  2.163
    9423     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 27 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 H     3.073  2.081
    9424     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 25 O2   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 HH12  2.761  1.945
    9425     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 NH2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 25 O2   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 HH22  2.690  1.846
    9426     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E GLU 358 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 38 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E GLU 358 H     3.275  2.276
    9427     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E THR 359 OG1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E THR 359 HG1   2.552  1.830
    9428     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 O3'  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 H     3.515  2.618
    9429     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 29 OP2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 H     2.892  2.000
    9430     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 35 O4'  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 HH12  3.369  2.780
    9431     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 NH2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 35 O2   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 HH22  3.076  2.066
    9432     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 NH2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 36 O4'  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 HH21  3.065  2.496
    9433     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 29 OP2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 H     3.221  2.221
    9434     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 30 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 HZ3   2.954  2.284
    9435     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 30 OP2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 HZ1   2.890  1.985
    9436     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 546 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 24 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 546 H     3.276  2.580
    9437     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 547 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 547 HZ1   3.303  2.294
    9438     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 24 O2   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 HZ1   2.747  2.031
    9439     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 25 O4'  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 HZ2   2.889  2.196
    9440     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 38 O2   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 HZ3   3.045  2.142
    9441     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ASN 553 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 OP2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ASN 553 H     3.220  2.217
    9442     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 44 N7   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 HH12  3.403  2.708
    9443     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 44 O6   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 HH12  2.566  1.988
    9444     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 NH2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 44 N7   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 HH22  3.082  2.292
    9445     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 560 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 12 OP2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 560 HZ1   2.981  2.268
    9446     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 561 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 561 H     2.977  2.057
    9447     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G THR 563 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 OP2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G THR 563 H     3.051  2.249
    9448     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ALA 565 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 14 OP2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ALA 565 H     3.032  2.059
    9449    
    9450 
    9451  
    9452 54 hydrogen bonds found 
    9453 8 strict hydrogen bonds found 
    9454 
    9455 > hide #!1 models
    9456 
    9457 > show #!1 models
    9458 
    9459 > hide #!1 models
    9460 
    9461 > select #2 & nucleic
    9462 
    9463 2158 atoms, 2326 bonds, 68 residues, 1 model selected 
    9464 
    9465 > show sel atoms
    9466 
    9467 > select clear
    9468 
    9469 > select #2 & nucleic
    9470 
    9471 2158 atoms, 2326 bonds, 68 residues, 1 model selected 
    9472 
    9473 > hbonds sel dashes 6 restrict #2/A,B,C,D,E,F,G distSlop 0.5 twoColors true
    9474 > slopColor #00f900 intraRes false select true reveal true retainCurrent true
    9475 > log true
    9476    
    9477    
    9478     Finding intermodel H-bonds
    9479     Finding intramodel H-bonds
    9480     Constraints relaxed by 0.5 angstroms and 20 degrees
    9481     Models used:
    9482         2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb
    9483    
    9484     42 H-bonds
    9485     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    9486     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A ASN 436 ND2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 10 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A ASN 436 HD22  2.810  1.833
    9487     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 148 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 148 HZ3   3.208  2.369
    9488     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 279 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 48 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 279 H     3.110  2.192
    9489     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 188 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 15 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 188 HZ1   3.176  2.193
    9490     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 50 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 H     3.467  2.499
    9491     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 49 OP2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 HH11  3.015  2.053
    9492     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 220 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 O2   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 220 HH11  3.388  2.481
    9493     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 223 OH   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 15 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 223 HH    2.762  1.806
    9494     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 607 OH   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 29 OP2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 607 HH    3.098  2.200
    9495     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 671 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 29 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 671 H     3.429  2.701
    9496     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 29 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 H     3.388  2.439
    9497     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O2   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 HH12  2.806  1.902
    9498     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O2   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 HH22  2.902  2.042
    9499     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O4'  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 HH22  3.185  2.472
    9500     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 673 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 30 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 673 HZ1   3.030  2.116
    9501     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 169 OG   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 12 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 169 HG    3.284  2.325
    9502     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 463 OG   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 39 OP2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 463 HG    2.803  1.844
    9503     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 40 N7   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 HZ1   3.514  2.654
    9504     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 40 O6   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 HZ1   3.045  2.260
    9505     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 O6   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 HZ2   3.189  2.368
    9506     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 76 NH1   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 14 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 76 HH11   2.908  2.005
    9507     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 340 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 340 HH11  3.135  2.272
    9508     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 356 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 27 OP2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 356 HH11  2.946  2.163
    9509     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 27 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 H     3.073  2.081
    9510     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 25 O2   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 HH12  2.761  1.945
    9511     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 NH2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 25 O2   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 HH22  2.690  1.846
    9512     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E GLU 358 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 38 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E GLU 358 H     3.275  2.276
    9513     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E THR 359 OG1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E THR 359 HG1   2.552  1.830
    9514     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 O3'  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 H     3.515  2.618
    9515     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 29 OP2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 H     2.892  2.000
    9516     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 NH2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 35 O2   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 HH22  3.076  2.066
    9517     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 29 OP2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 H     3.221  2.221
    9518     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 30 OP2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 HZ1   2.890  1.985
    9519     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 547 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 547 HZ1   3.303  2.294
    9520     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 24 O2   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 HZ1   2.747  2.031
    9521     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 NZ   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 38 O2   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 HZ3   3.045  2.142
    9522     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ASN 553 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 OP2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ASN 553 H     3.220  2.217
    9523     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 NH1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 44 N7   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 HH12  3.403  2.708
    9524     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 NH2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 44 N7   ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 HH22  3.082  2.292
    9525     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 561 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 OP1  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 561 H     2.977  2.057
    9526     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G THR 563 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 OP2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G THR 563 H     3.051  2.249
    9527     ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ALA 565 N    ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 14 OP2  ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ALA 565 H     3.032  2.059
    9528    
    9529 
    9530  
    9531 42 hydrogen bonds found 
    9532 8 strict hydrogen bonds found 
    9533 
    9534 > select clear
    9535 
    9536 > select #2/A:301@HH12
    9537 
    9538 1 atom, 1 residue, 1 model selected 
    9539 
    9540 > show #!1 models
    9541 
    9542 > hide #!2 models
    9543 
    9544 > show #!2 models
    9545 
    9546 > hide #!2 models
    9547 
    9548 > show #!2 models
    9549 
    9550 > hide #!2 models
    9551 
    9552 > show #!2 models
    9553 
    9554 > hide #!2 models
    9555 
    9556 > show #!2 models
    9557 
    9558 > hide #!1 models
    9559 
    9560 > show #!1 models
    9561 
    9562 > hide #!1 models
    9563 
    9564 > show #!1 models
    9565 
    9566 > hide #!2 models
    9567 
    9568 > show #!2 models
    9569 
    9570 > hide #!2 models
    9571 
    9572 > show #!2 models
    9573 
    9574 > hide #!2 models
    9575 
    9576 > show #!2 models
    9577 
    9578 > hide #!1 models
    9579 
    9580 > show #!1 models
    9581 
    9582 > hide #!1 models
    9583 
    9584 > show #!1 models
    9585 
    9586 > hide #!1 models
    9587 
    9588 > show #!1 models
    9589 
    9590 > hide #!1 models
    9591 
    9592 > show #!1 models
    9593 
    9594 > hide #!1 models
    9595 
    9596 > show #!1 models
    9597 
    9598 > hide #!1 models
    9599 
    9600 > show #!1 models
    9601 
    9602 > hide #!1 models
    9603 
    9604 > show #!1 models
    9605 
    9606 > hide #!1 models
    9607 
    9608 > show #!1 models
    9609 
    9610 > hide #!2 models
    9611 
    9612 > select #1/opp:16
    9613 
    9614 33 atoms, 35 bonds, 1 residue, 1 model selected 
    9615 
    9616 > select #1/D:168@NZ
    9617 
    9618 1 atom, 1 residue, 1 model selected 
    9619 
    9620 > undo
    9621 
    9622 > show #!2 models
    9623 
    9624 > hide #!2 models
    9625 
    9626 > show #!2 models
    9627 
    9628 > hide #!2 models
    9629 
    9630 > show #!2 models
    9631 
    9632 > hide #!2 models
    9633 
    9634 > show #!2 models
    9635 
    9636 > hide #!2 models
    9637 
    9638 > show #!2 models
    9639 
    9640 > hide #!2 models
    9641 
    9642 > show #!2 models
    9643 
    9644 > hide #!2 models
    9645 
    9646 > select #1/main:-10
    9647 
    9648 32 atoms, 33 bonds, 1 residue, 1 model selected 
    9649 
    9650 > select #1/main:-11
    9651 
    9652 32 atoms, 34 bonds, 1 residue, 1 model selected 
    9653 
    9654 > hide sel cartoons
    9655 
    9656 > show sel cartoons
    9657 
    9658 > select clear
    9659 
    9660 > select #1/main:-9
    9661 
    9662 33 atoms, 35 bonds, 1 residue, 1 model selected 
    9663 
    9664 > select #1/main:-8
    9665 
    9666 30 atoms, 31 bonds, 1 residue, 1 model selected 
    9667 
    9668 > show #!2 models
    9669 
    9670 > hide #!2 models
    9671 
    9672 > show #!2 models
    9673 
    9674 > hide #!2 models
    9675 
    9676 > select #1/B:280@CA
    9677 
    9678 1 atom, 1 residue, 1 model selected 
    9679 
    9680 > select #1/opp:9
    9681 
    9682 30 atoms, 31 bonds, 1 residue, 1 model selected 
    9683 
    9684 > select #1/opp:10
    9685 
    9686 32 atoms, 34 bonds, 1 residue, 1 model selected 
    9687 
    9688 > hide sel cartoons
    9689 
    9690 > show #!2 models
    9691 
    9692 > hide #!1 models
    9693 
    9694 > hide #!2 models
    9695 
    9696 > show #!1 models
    9697 
    9698 > open "/Users/jtbauer/Library/CloudStorage/OneDrive-
    9699 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    9700 > structures/PDBs/ylODC_oriA006_complete/ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb"
    9701 
    9702 Chain information for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3 
    9703 --- 
    9704 Chain | Description 
    9705 A | No description available 
    9706 B | No description available 
    9707 C | No description available 
    9708 D | No description available 
    9709 E | No description available 
    9710 F | No description available 
    9711 G | No description available 
    9712 H | No description available 
    9713 I | No description available 
    9714  
    9715 
    9716 > hide #3
    9717 
    9718 > show #3/B:248
    9719 
    9720 > style sel stick
    9721 
    9722 Changed 32 atom styles 
    9723 
    9724 > style sel stick
    9725 
    9726 Changed 32 atom styles 
    9727 
    9728 > style sel stick
    9729 
    9730 Changed 32 atom styles 
    9731 
    9732 > select clear
    9733 
    9734 > select add #3
    9735 
    9736 24882 atoms, 25492 bonds, 16 pseudobonds, 3000 residues, 3 models selected 
    9737 
    9738 > style sel stick
    9739 
    9740 Changed 24882 atom styles 
    9741 
    9742 > color sel byhetero
    9743 
    9744 > select #1/opp:9
    9745 
    9746 30 atoms, 31 bonds, 1 residue, 1 model selected 
    9747 
    9748 > select #3/B:248@CE
    9749 
    9750 1 atom, 1 residue, 1 model selected 
    9751 
    9752 > select up
    9753 
    9754 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9755 
    9756 > hbonds sel dashes 6 restrict #3/H,I distSlop 0.5 angleSlop 40.0 twoColors
    9757 > true slopColor #00f900 intraRes false select true reveal true retainCurrent
    9758 > true log true
    9759    
    9760    
    9761     Finding intermodel H-bonds
    9762     Finding intramodel H-bonds
    9763     Constraints relaxed by 0.5 angstroms and 40 degrees
    9764     Models used:
    9765         3 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb
    9766    
    9767     0 H-bonds
    9768     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    9769    
    9770 
    9771  
    9772 0 hydrogen bonds found 
    9773 0 strict hydrogen bonds found 
    9774 
    9775 > select #3/B:248@CE
    9776 
    9777 1 atom, 1 residue, 1 model selected 
    9778 
    9779 > select up
    9780 
    9781 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9782 
    9783 > hbonds sel dashes 6 restrict #3/H,I distSlop 0.5 angleSlop 40.0 twoColors
    9784 > true slopColor #00f900 intraRes false select true reveal true retainCurrent
    9785 > true log true
    9786    
    9787    
    9788     Finding intermodel H-bonds
    9789     Finding intramodel H-bonds
    9790     Constraints relaxed by 0.5 angstroms and 40 degrees
    9791     Models used:
    9792         3 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb
    9793    
    9794     0 H-bonds
    9795     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    9796    
    9797 
    9798  
    9799 0 hydrogen bonds found 
    9800 0 strict hydrogen bonds found 
    9801 
    9802 > select #1/opp:9
    9803 
    9804 30 atoms, 31 bonds, 1 residue, 1 model selected 
    9805 
    9806 > hide sel cartoons
    9807 
    9808 > select #3/B:248@CE
    9809 
    9810 1 atom, 1 residue, 1 model selected 
    9811 
    9812 > select up
    9813 
    9814 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9815 
    9816 > ui tool show "Add Hydrogens"
    9817 
    9818 > addh #!3
    9819 
    9820 Summary of feedback from adding hydrogens to
    9821 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3 
    9822 --- 
    9823 warning | Not adding hydrogens to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/I DA 22 P because it is missing heavy-atom bond partners 
    9824 notes | No usable SEQRES records for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb (#3) chain A; guessing termini instead 
    9825 No usable SEQRES records for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb (#3)
    9826 chain B; guessing termini instead 
    9827 No usable SEQRES records for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb (#3)
    9828 chain C; guessing termini instead 
    9829 No usable SEQRES records for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb (#3)
    9830 chain D; guessing termini instead 
    9831 No usable SEQRES records for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb (#3)
    9832 chain E; guessing termini instead 
    9833 4 messages similar to the above omitted 
    9834 Chain-initial residues that are actual N termini:
    9835 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/A PRO 299,
    9836 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B PRO 106,
    9837 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/C THR 6,
    9838 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D PRO 33,
    9839 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/E MET 1,
    9840 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/F PRO 179,
    9841 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G PRO 93 
    9842 Chain-initial residues that are not actual N termini:
    9843 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B VAL 396,
    9844 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B VAL 444,
    9845 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B LYS 489,
    9846 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/C ASN 72,
    9847 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D ASN 128,
    9848 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D GLY 162,
    9849 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D LEU 296,
    9850 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D PHE 436,
    9851 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/E GLU 217,
    9852 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/E ASP 319,
    9853 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/F SER 313,
    9854 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G ALA 213,
    9855 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G THR 386,
    9856 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G VAL 439,
    9857 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G ASN 461 
    9858 Chain-final residues that are actual C termini:
    9859 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/A LEU 718,
    9860 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/C LEU 685 
    9861 Chain-final residues that are not actual C termini:
    9862 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B GLU 504,
    9863 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B GLU 386,
    9864 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B HIS 420,
    9865 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B VAL 479,
    9866 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/C ARG 29,
    9867 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D ARG 510,
    9868 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D SER 123,
    9869 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D LEU 159,
    9870 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D MET 285,
    9871 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D LEU 420,
    9872 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/E ASN 464,
    9873 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/E ALA 210,
    9874 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/E LEU 304,
    9875 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/F GLN 351,
    9876 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/F THR 307,
    9877 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G LEU 604,
    9878 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G GLY 207,
    9879 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G HIS 335,
    9880 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G GLN 433,
    9881 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G PHE 457 
    9882 2713 hydrogen bonds 
    9883 Adding 'H' to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B VAL 396 
    9884 Adding 'H' to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B VAL 444 
    9885 Adding 'H' to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B LYS 489 
    9886 Adding 'H' to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/C ASN 72 
    9887 Adding 'H' to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D ASN 128 
    9888 10 messages similar to the above omitted 
    9889 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B GLU 504 is not terminus,
    9890 removing H atom from 'C' 
    9891 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D ARG 510 is not terminus,
    9892 removing H atom from 'C' 
    9893 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/E ASN 464 is not terminus,
    9894 removing H atom from 'C' 
    9895 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/F GLN 351 is not terminus,
    9896 removing H atom from 'C' 
    9897 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G LEU 604 is not terminus,
    9898 removing H atom from 'C' 
    9899 24328 hydrogens added 
    9900  
    9901 
    9902 > select #3/B:248@HZ2
    9903 
    9904 1 atom, 1 residue, 1 model selected 
    9905 
    9906 > close #3
    9907 
    9908 > select #1/B:279@N
    9909 
    9910 1 atom, 1 residue, 1 model selected 
    9911 
    9912 > select #1/opp:10@P
    9913 
    9914 1 atom, 1 residue, 1 model selected 
    9915 
    9916 > save "/Users/jtbauer/Library/CloudStorage/OneDrive-
    9917 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    9918 > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_ver20-21.cxs"
    9919 
    9920 > open "/Users/jtbauer/Library/CloudStorage/OneDrive-
    9921 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    9922 > structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver31.cxs"
    9923 
    9924 opened ChimeraX session 
    9925 
    9926 > select /opp:3
    9927 
    9928 33 atoms, 35 bonds, 1 residue, 1 model selected 
    9929 
    9930 > hide sel cartoons
    9931 
    9932 > show sel cartoons
    9933 
    9934 > open "/Users/jtbauer/Library/CloudStorage/OneDrive-
    9935 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    9936 > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_ver20-21.cxs" format
    9937 > session
    9938 
    9939 opened ChimeraX session 
    9940 
    9941 > select /G:574
    9942 
    9943 48 atoms, 46 bonds, 2 residues, 2 models selected 
    9944 
    9945 > show sel & #!1 atoms
    9946 
    9947 > select #1/opp:3
    9948 
    9949 33 atoms, 35 bonds, 1 residue, 1 model selected 
    9950 
    9951 > hide sel cartoons
    9952 
    9953 > select #1/G:543@N
    9954 
    9955 1 atom, 1 residue, 1 model selected 
    9956 
    9957 > show #!2 models
    9958 
    9959 > hide #!1 models
    9960 
    9961 > select #2/H:23
    9962 
    9963 32 atoms, 34 bonds, 1 residue, 1 model selected 
    9964 
    9965 > hide sel cartoons
    9966 
    9967 > select #2/G:542@OG1
    9968 
    9969 1 atom, 1 residue, 1 model selected 
    9970 
    9971 > hide #!2 models
    9972 
    9973 > open "/Users/jtbauer/Library/CloudStorage/OneDrive-
    9974 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    9975 > structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver31.cxs"
    9976 
    9977 opened ChimeraX session 
    9978 
    9979 > select /G:542
    9980 
    9981 14 atoms, 13 bonds, 1 residue, 1 model selected 
    9982 
    9983 > show sel atoms
    9984 
    9985 > select /main:-1
    9986 
    9987 30 atoms, 31 bonds, 1 residue, 1 model selected 
    9988 
    9989 > select /main:0
    9990 
    9991 32 atoms, 34 bonds, 1 residue, 1 model selected 
    9992 
    9993 > hide sel cartoons
    9994 
    9995 > open "/Users/jtbauer/Library/CloudStorage/OneDrive-
    9996 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    9997 > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_ver20.cxs" format session
    9998 
    9999 opened ChimeraX session 
    10000 
    10001 > open "/Users/jtbauer/Library/CloudStorage/OneDrive-
    10002 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    10003 > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_ver20-21.cxs" format
    10004 > session
    10005 
    10006 opened ChimeraX session 
    10007 
    10008 > show #!2 models
    10009 
    10010 > hide #!1 models
    10011 
    10012 > select /G:542
    10013 
    10014 28 atoms, 26 bonds, 2 residues, 2 models selected 
    10015 
    10016 > show sel & #!2 atoms
    10017 
    10018 > select /G:543
    10019 
    10020 14 atoms, 12 bonds, 2 residues, 2 models selected 
    10021 
    10022 > show sel & #!2 atoms
    10023 
    10024 > select clear
    10025 
    10026 > select #2/H:22
    10027 
    10028 32 atoms, 34 bonds, 1 residue, 1 model selected 
    10029 
    10030 > show sel cartoons
    10031 
    10032 > hide sel cartoons
    10033 
    10034 > show sel cartoons
    10035 
    10036 > select #2/H:23
    10037 
    10038 32 atoms, 34 bonds, 1 residue, 1 model selected 
    10039 
    10040 > hide sel cartoons
    10041 
    10042 > show sel cartoons
    10043 
    10044 > show #!1 models
    10045 
    10046 > hide #!2 models
    10047 
    10048 > open "/Users/jtbauer/Library/CloudStorage/OneDrive-
    10049 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    10050 > structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver31.cxs" format
    10051 > session
    10052 
    10053 opened ChimeraX session 
    10054 
    10055 > select /main:0
    10056 
    10057 32 atoms, 34 bonds, 1 residue, 1 model selected 
    10058 
    10059 > hide sel cartoons
    10060 
    10061 > open "/Users/jtbauer/Library/CloudStorage/OneDrive-
    10062 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    10063 > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_ver20-21.cxs" format
    10064 > session
    10065 
    10066 opened ChimeraX session 
    10067 
    10068 > select #1/G:581@NZ
    10069 
    10070 1 atom, 1 residue, 1 model selected 
    10071 
    10072 > select add #1/main:0@OP2
    10073 
    10074 2 atoms, 2 residues, 1 model selected 
    10075 
    10076 > ui tool show Distances
    10077 
    10078 > distance #1/G:581@NZ #1/main:0@OP2
    10079 
    10080 Distance between ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb #1/G LYS 581 NZ
    10081 and /main DA 0 OP2: 5.033Å 
    10082 
    10083 > select #1/G:581@NZ
    10084 
    10085 1 atom, 1 residue, 1 model selected 
    10086 
    10087 > select add #1/main:0@OP1
    10088 
    10089 2 atoms, 2 residues, 1 model selected 
    10090 
    10091 > distance #1/G:581@NZ #1/main:0@OP1
    10092 
    10093 Distance between ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb #1/G LYS 581 NZ
    10094 and /main DA 0 OP1: 4.742Å 
    10095 
    10096 > ~distance #1/G:581@NZ #1/main:0@OP1
    10097 
    10098 > ~distance #1/G:581@NZ #1/main:0@OP2
    10099 
    10100 > show #!2 models
    10101 
    10102 > hide #!2 models
    10103 
    10104 > select add #1
    10105 
    10106 49210 atoms, 49820 bonds, 69 pseudobonds, 3000 residues, 4 models selected 
    10107 
    10108 > select subtract #1
    10109 
    10110 Nothing selected 
    10111 
    10112 > open "/Users/jtbauer/Library/CloudStorage/OneDrive-
    10113 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    10114 > structures/PDBs/ylODC_oriA006_complete/ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb"
    10115 
    10116 Chain information for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3 
    10117 --- 
    10118 Chain | Description 
    10119 A | No description available 
    10120 B | No description available 
    10121 C | No description available 
    10122 D | No description available 
    10123 E | No description available 
    10124 F | No description available 
    10125 G | No description available 
    10126 H | No description available 
    10127 I | No description available 
    10128  
    10129 
    10130 > hide #3
    10131 
    10132 > select /G:548
    10133 
    10134 53 atoms, 50 bonds, 3 residues, 3 models selected 
    10135 
    10136 > select /G:581
    10137 
    10138 53 atoms, 50 bonds, 3 residues, 3 models selected 
    10139 
    10140 > show sel & #!1,3 atoms
    10141 
    10142 > style sel & #!1,3 stick
    10143 
    10144 Changed 31 atom styles 
    10145 
    10146 > select #3/G:581@NZ
    10147 
    10148 1 atom, 1 residue, 1 model selected 
    10149 
    10150 > select add #1/main:0@OP1
    10151 
    10152 2 atoms, 2 residues, 2 models selected 
    10153 
    10154 > distance #3/G:581@NZ #1/main:0@OP1
    10155 
    10156 Distance between ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G LYS 581 NZ
    10157 and ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb #1/main DA 0 OP1: 4.358Å 
    10158 
    10159 > select #3/G:581@NZ
    10160 
    10161 1 atom, 1 residue, 1 model selected 
    10162 
    10163 > select add #1/main:0@OP2
    10164 
    10165 2 atoms, 2 residues, 2 models selected 
    10166 
    10167 > distance #3/G:581@NZ #1/main:0@OP2
    10168 
    10169 Distance between ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G LYS 581 NZ
    10170 and ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb #1/main DA 0 OP2: 4.621Å 
    10171 
    10172 > ~distance #3/G:581@NZ #1/main:0@OP2
    10173 
    10174 > ~distance #3/G:581@NZ #1/main:0@OP1
    10175 
    10176 > close #3
    10177 
    10178 > select #1/main:6
    10179 
    10180 30 atoms, 31 bonds, 1 residue, 1 model selected 
    10181 
    10182 > select #1/main:7
    10183 
    10184 32 atoms, 33 bonds, 1 residue, 1 model selected 
    10185 
    10186 > open "/Users/jtbauer/Library/CloudStorage/OneDrive-
    10187 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    10188 > structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver31.cxs" format
    10189 > session
    10190 
    10191 opened ChimeraX session 
    10192 
    10193 > select /main:6
    10194 
    10195 30 atoms, 31 bonds, 1 residue, 1 model selected 
    10196 
    10197 > open "/Users/jtbauer/Library/CloudStorage/OneDrive-
    10198 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    10199 > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_ver20-21.cxs" format
    10200 > session
    10201 
    10202 opened ChimeraX session 
    10203 
    10204 > select #1/main:7
    10205 
    10206 32 atoms, 33 bonds, 1 residue, 1 model selected 
    10207 
    10208 > select #1/B:153@CA
    10209 
    10210 1 atom, 1 residue, 1 model selected 
    10211 
    10212 > select #1/main:8
    10213 
    10214 30 atoms, 31 bonds, 1 residue, 1 model selected 
    10215 
    10216 > show sel atoms
    10217 
    10218 > hide sel cartoons
    10219 
    10220 > select #1/B:153@N
    10221 
    10222 1 atom, 1 residue, 1 model selected 
    10223 
    10224 > select add #1/main:8@OP1
    10225 
    10226 2 atoms, 2 residues, 1 model selected 
    10227 
    10228 > select #1/main:7
    10229 
    10230 32 atoms, 33 bonds, 1 residue, 1 model selected 
    10231 
    10232 > hide sel cartoons
    10233 
    10234 > select #1/B:153@H
    10235 
    10236 1 atom, 1 residue, 1 model selected 
    10237 
    10238 > select add #1/main:8@OP1
    10239 
    10240 2 atoms, 2 residues, 1 model selected 
    10241 
    10242 > select #1/B:153@N
    10243 
    10244 1 atom, 1 residue, 1 model selected 
    10245 
    10246 > select add #1/main:8@OP1
    10247 
    10248 2 atoms, 2 residues, 1 model selected 
    10249 
    10250 > ui tool show Distances
    10251 
    10252 > distance #1/B:153@N #1/main:8@OP1
    10253 
    10254 Distance between ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb #1/B GLY 153 N
    10255 and /main DC 8 OP1: 3.580Å 
    10256 
    10257 > ~distance #1/B:153@N #1/main:8@OP1
    10258 
    10259 > select clear
    10260 
    10261 > show #!2 models
    10262 
    10263 > hide #!1 models
    10264 
    10265 > show #!1 models
    10266 
    10267 > hide #!2 models
    10268 
    10269 > select #1/B:148@NZ
    10270 
    10271 1 atom, 1 residue, 1 model selected 
    10272 
    10273 > select #1/opp:-10
    10274 
    10275 32 atoms, 34 bonds, 1 residue, 1 model selected 
    10276 
    10277 > select #1/opp:-9
    10278 
    10279 33 atoms, 35 bonds, 1 residue, 1 model selected 
    10280 
    10281 > hide sel cartoons
    10282 
    10283 > select #1/opp:-10
    10284 
    10285 32 atoms, 34 bonds, 1 residue, 1 model selected 
    10286 
    10287 > select #1/opp:-11
    10288 
    10289 32 atoms, 33 bonds, 1 residue, 1 model selected 
    10290 
    10291 > select #1/opp:-10
    10292 
    10293 32 atoms, 34 bonds, 1 residue, 1 model selected 
    10294 
    10295 > hide sel cartoons
    10296 
    10297 > select #1/E:358@N
    10298 
    10299 1 atom, 1 residue, 1 model selected 
    10300 
    10301 > select #1/main:-13
    10302 
    10303 32 atoms, 34 bonds, 1 residue, 1 model selected 
    10304 
    10305 > open "/Users/jtbauer/Library/CloudStorage/OneDrive-
    10306 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    10307 > structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver31.cxs" format
    10308 > session
    10309 
    10310 opened ChimeraX session 
    10311 
    10312 > select /main:-14
    10313 
    10314 30 atoms, 31 bonds, 1 residue, 1 model selected 
    10315 
    10316 > select /main:-13
    10317 
    10318 30 atoms, 31 bonds, 1 residue, 1 model selected 
    10319 
    10320 > select /opp:18
    10321 
    10322 31 atoms, 32 bonds, 1 residue, 1 model selected 
    10323 
    10324 > open "/Users/jtbauer/Library/CloudStorage/OneDrive-
    10325 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    10326 > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_ver20-21.cxs" format
    10327 > session
    10328 
    10329 opened ChimeraX session 
    10330 
    10331 > close
    10332 
    10333 > open /Users/jtbauer/Library/CloudStorage/OneDrive-
    10334 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/7jk3-dmODC_GCrich.pdb
    10335 
    10336 7jk3-dmODC_GCrich.pdb title: 
    10337 Structure of drosophila orc bound to GC-rich DNA and CDC6 [more info...] 
    10338  
    10339 Chain information for 7jk3-dmODC_GCrich.pdb #1 
    10340 --- 
    10341 Chain | Description | UniProt 
    10342 A | DMORC1 | ORC1_DROME 440-924 
    10343 B | DMORC2 | ORC2_DROME 1-618 
    10344 C | origin recognition complex subunit 3 | Q7K2L1_DROME 1-721 
    10345 D | ORC4 | Q9W102_DROME 1-459 
    10346 E | ORC5 | ORC5_DROME 1-460 
    10347 F | ORC6 | ORC6_DROME 1-257 
    10348 G | CDC6 | Q9VSM9_DROME 242-662 
    10349 H | DNA (33-mer) |   
    10350 I | DNA (33-mer) |   
    10351  
    10352 Non-standard residues in 7jk3-dmODC_GCrich.pdb #1 
    10353 --- 
    10354 ATP — adenosine-5'-triphosphate 
    10355 MG — magnesium ion 
    10356  
    10357 
    10358 > modelfix
    10359 
    10360 Changed 21661 atom styles 
    10361 20180 atoms, 20524 bonds, 18 pseudobonds, 2528 residues, 2 models selected 
    10362 
    10363 > close #1
    10364 
    10365 > open /Users/jtbauer/Library/CloudStorage/OneDrive-
    10366 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/hsORC1-6_CDC6_60bpDNA.pdb
    10367 > format pdb
    10368 
    10369 Chain information for hsORC1-6_CDC6_60bpDNA.pdb #1 
    10370 --- 
    10371 Chain | Description 
    10372 A | No description available 
    10373 B | No description available 
    10374 C | No description available 
    10375 D | No description available 
    10376 E | No description available 
    10377 F | No description available 
    10378 G | No description available 
    10379 H | No description available 
    10380 I | No description available 
    10381  
    10382 
    10383 > modelfix
    10384 
    10385 Changed 21416 atom styles 
    10386 20099 atoms, 20484 bonds, 13 pseudobonds, 2485 residues, 2 models selected 
    10387 Computing secondary structure 
    10388 
    10389 > open /Users/jtbauer/Library/CloudStorage/OneDrive-
    10390 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/7jk3-dmODC_GCrich.pdb format
    10391 > pdb
    10392 
    10393 7jk3-dmODC_GCrich.pdb title: 
    10394 Structure of drosophila orc bound to GC-rich DNA and CDC6 [more info...] 
    10395  
    10396 Chain information for 7jk3-dmODC_GCrich.pdb #2 
    10397 --- 
    10398 Chain | Description | UniProt 
    10399 A | DMORC1 | ORC1_DROME 440-924 
    10400 B | DMORC2 | ORC2_DROME 1-618 
    10401 C | origin recognition complex subunit 3 | Q7K2L1_DROME 1-721 
    10402 D | ORC4 | Q9W102_DROME 1-459 
    10403 E | ORC5 | ORC5_DROME 1-460 
    10404 F | ORC6 | ORC6_DROME 1-257 
    10405 G | CDC6 | Q9VSM9_DROME 242-662 
    10406 H | DNA (33-mer) |   
    10407 I | DNA (33-mer) |   
    10408  
    10409 Non-standard residues in 7jk3-dmODC_GCrich.pdb #2 
    10410 --- 
    10411 ATP — adenosine-5'-triphosphate 
    10412 MG — magnesium ion 
    10413  
    10414 
    10415 > modelfix
    10416 
    10417 Changed 43077 atom styles 
    10418 40279 atoms, 41008 bonds, 31 pseudobonds, 5013 residues, 4 models selected 
    10419 
    10420 > matchmaker #2 to #1
    10421 
    10422 Computing secondary structure 
    10423 Parameters 
    10424 --- 
    10425 Chain pairing | bb 
    10426 Alignment algorithm | Needleman-Wunsch 
    10427 Similarity matrix | BLOSUM-62 
    10428 SS fraction | 0.3 
    10429 Gap open (HH/SS/other) | 18/18/6 
    10430 Gap extend | 1 
    10431 SS matrix |  |  | H | S | O 
    10432 ---|---|---|--- 
    10433 H | 6 | -9 | -6 
    10434 S |  | 6 | -6 
    10435 O |  |  | 4 
    10436 Iteration cutoff | 2 
    10437  
    10438 Matchmaker hsORC1-6_CDC6_60bpDNA.pdb, chain C (#1) with 7jk3-dmODC_GCrich.pdb,
    10439 chain C (#2), sequence alignment score = 1256.2 
    10440 RMSD between 288 pruned atom pairs is 1.187 angstroms; (across all 575 pairs:
    10441 4.218) 
    10442  
    10443 
    10444 > select #2/G:623
    10445 
    10446 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10447 
    10448 > show sel atoms
    10449 
    10450 > hide sel atoms
    10451 
    10452 > select clear
    10453 
    10454 > select #2/C:181
    10455 
    10456 6 atoms, 5 bonds, 1 residue, 1 model selected 
    10457 
    10458 > hide #!2 models
    10459 
    10460 > hide #!1 models
    10461 
    10462 > show #!1 models
    10463 
    10464 > select add #2
    10465 
    10466 21661 atoms, 22172 bonds, 30 pseudobonds, 2602 residues, 3 models selected 
    10467 
    10468 > select subtract #2
    10469 
    10470 Nothing selected 
    10471 
    10472 > show #!2 models
    10473 
    10474 > hide #!1 models
    10475 
    10476 > select #2/C:711
    10477 
    10478 11 atoms, 10 bonds, 1 residue, 1 model selected 
    10479 
    10480 > show sel atoms
    10481 
    10482 > select #2/C:712
    10483 
    10484 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10485 
    10486 > show sel atoms
    10487 
    10488 > select #2/C:710
    10489 
    10490 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10491 
    10492 > show #!1 models
    10493 
    10494 > hide #!2 models
    10495 
    10496 > show #!2 models
    10497 
    10498 > select clear
    10499 
    10500 > matchmaker #2/D to #1/D
    10501 
    10502 Computing secondary structure 
    10503 Parameters 
    10504 --- 
    10505 Chain pairing | bb 
    10506 Alignment algorithm | Needleman-Wunsch 
    10507 Similarity matrix | BLOSUM-62 
    10508 SS fraction | 0.3 
    10509 Gap open (HH/SS/other) | 18/18/6 
    10510 Gap extend | 1 
    10511 SS matrix |  |  | H | S | O 
    10512 ---|---|---|--- 
    10513 H | 6 | -9 | -6 
    10514 S |  | 6 | -6 
    10515 O |  |  | 4 
    10516 Iteration cutoff | 2 
    10517  
    10518 Matchmaker hsORC1-6_CDC6_60bpDNA.pdb, chain D (#1) with 7jk3-dmODC_GCrich.pdb,
    10519 chain D (#2), sequence alignment score = 1104.3 
    10520 RMSD between 338 pruned atom pairs is 0.924 angstroms; (across all 410 pairs:
    10521 2.005) 
    10522  
    10523 
    10524 > select #2/D:410
    10525 
    10526 7 atoms, 6 bonds, 1 residue, 1 model selected 
    10527 
    10528 > matchmaker #2/E to #1/E
    10529 
    10530 Computing secondary structure 
    10531 Parameters 
    10532 --- 
    10533 Chain pairing | bb 
    10534 Alignment algorithm | Needleman-Wunsch 
    10535 Similarity matrix | BLOSUM-62 
    10536 SS fraction | 0.3 
    10537 Gap open (HH/SS/other) | 18/18/6 
    10538 Gap extend | 1 
    10539 SS matrix |  |  | H | S | O 
    10540 ---|---|---|--- 
    10541 H | 6 | -9 | -6 
    10542 S |  | 6 | -6 
    10543 O |  |  | 4 
    10544 Iteration cutoff | 2 
    10545  
    10546 Matchmaker hsORC1-6_CDC6_60bpDNA.pdb, chain E (#1) with 7jk3-dmODC_GCrich.pdb,
    10547 chain E (#2), sequence alignment score = 853.4 
    10548 RMSD between 290 pruned atom pairs is 1.201 angstroms; (across all 363 pairs:
    10549 2.631) 
    10550  
    10551 
    10552 > select clear
    10553 
    10554 > open /Users/jtbauer/Library/CloudStorage/OneDrive-
    10555 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/7mca-assembly1.cif format
    10556 > mmcif
    10557 
    10558 7mca-assembly1.cif title: 
    10559 Structure of the S. cerevisiae origin recognition complex bound to the
    10560 replication initiator Cdc6 and the ARS1 origin DNA. [more info...] 
    10561  
    10562 Chain information for 7mca-assembly1.cif #3 
    10563 --- 
    10564 Chain | Description 
    10565 A | Origin recognition complex subunit 1 
    10566 B | Origin recognition complex subunit 2 
    10567 C | Origin recognition complex subunit 3 
    10568 D | Origin recognition complex subunit 4 
    10569 E | Origin recognition complex subunit 5 
    10570 F | Origin recognition complex subunit 6 
    10571 G | DNA (85-MER) 
    10572 H | DNA (85-MER) 
    10573 I | Cell division control protein 6 
    10574  
    10575 Non-standard residues in 7mca-assembly1.cif #3 
    10576 --- 
    10577 AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
    10578 5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate);
    10579 adenosine-5'-diphosphate monothiophosphate) 
    10580 MG — magnesium ion 
    10581  
    10582 
    10583 > modelfix
    10584 
    10585 Changed 67769 atom styles 
    10586 62793 atoms, 63953 bonds, 45 pseudobonds, 7773 residues, 6 models selected 
    10587 
    10588 > newcolor #3/A #3/B #3/C #3/D #3/E #3/F #3/I #3/G #3/H
    10589 
    10590 > matchmaker /A to #1/A
    10591 
    10592 Must use different reference and match structures 
    10593 
    10594 > matchmaker #2-3/A to #1/A
    10595 
    10596 Computing secondary structure 
    10597 Parameters 
    10598 --- 
    10599 Chain pairing | bb 
    10600 Alignment algorithm | Needleman-Wunsch 
    10601 Similarity matrix | BLOSUM-62 
    10602 SS fraction | 0.3 
    10603 Gap open (HH/SS/other) | 18/18/6 
    10604 Gap extend | 1 
    10605 SS matrix |  |  | H | S | O 
    10606 ---|---|---|--- 
    10607 H | 6 | -9 | -6 
    10608 S |  | 6 | -6 
    10609 O |  |  | 4 
    10610 Iteration cutoff | 2 
    10611  
    10612 Matchmaker hsORC1-6_CDC6_60bpDNA.pdb, chain A (#1) with 7jk3-dmODC_GCrich.pdb,
    10613 chain A (#2), sequence alignment score = 1245.5 
    10614 RMSD between 341 pruned atom pairs is 0.995 angstroms; (across all 383 pairs:
    10615 1.387) 
    10616  
    10617 Matchmaker hsORC1-6_CDC6_60bpDNA.pdb, chain A (#1) with 7mca-assembly1.cif,
    10618 chain A (#3), sequence alignment score = 707.9 
    10619 RMSD between 295 pruned atom pairs is 1.089 angstroms; (across all 368 pairs:
    10620 4.720) 
    10621  
    10622 
    10623 > matchmaker #2-3/B to #1/B
    10624 
    10625 Computing secondary structure 
    10626 Parameters 
    10627 --- 
    10628 Chain pairing | bb 
    10629 Alignment algorithm | Needleman-Wunsch 
    10630 Similarity matrix | BLOSUM-62 
    10631 SS fraction | 0.3 
    10632 Gap open (HH/SS/other) | 18/18/6 
    10633 Gap extend | 1 
    10634 SS matrix |  |  | H | S | O 
    10635 ---|---|---|--- 
    10636 H | 6 | -9 | -6 
    10637 S |  | 6 | -6 
    10638 O |  |  | 4 
    10639 Iteration cutoff | 2 
    10640  
    10641 Matchmaker hsORC1-6_CDC6_60bpDNA.pdb, chain B (#1) with 7jk3-dmODC_GCrich.pdb,
    10642 chain B (#2), sequence alignment score = 879.5 
    10643 RMSD between 201 pruned atom pairs is 1.032 angstroms; (across all 272 pairs:
    10644 2.378) 
    10645  
    10646 Matchmaker hsORC1-6_CDC6_60bpDNA.pdb, chain B (#1) with 7mca-assembly1.cif,
    10647 chain B (#3), sequence alignment score = 458.2 
    10648 RMSD between 130 pruned atom pairs is 0.873 angstroms; (across all 193 pairs:
    10649 3.624) 
    10650  
    10651 
    10652 > hide #!2 models
    10653 
    10654 > hide #!1 models
    10655 
    10656 > select #3/C:178
    10657 
    10658 8 atoms, 7 bonds, 1 residue, 1 model selected 
    10659 
    10660 > select #3/C:159
    10661 
    10662 10 atoms, 10 bonds, 1 residue, 1 model selected 
    10663 
    10664 > select add #3
    10665 
    10666 24692 atoms, 25375 bonds, 14 pseudobonds, 2868 residues, 2 models selected 
    10667 
    10668 > hide #!3 models
    10669 
    10670 > select subtract #3
    10671 
    10672 Nothing selected 
    10673 
    10674 > open "/Users/jtbauer/Library/CloudStorage/OneDrive-
    10675 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    10676 > structures/PDBs/ylODC_54bp-
    10677 > oriC061_complete/ylODC_54bpOriC061_rev31_PostPhenix.pdb"
    10678 
    10679 Chain information for ylODC_54bpOriC061_rev31_PostPhenix.pdb #4 
    10680 --- 
    10681 Chain | Description 
    10682 A | No description available 
    10683 B | No description available 
    10684 C | No description available 
    10685 D | No description available 
    10686 E | No description available 
    10687 F | No description available 
    10688 G | No description available 
    10689 H | No description available 
    10690 I | No description available 
    10691  
    10692 
    10693 > modelfix
    10694 
    10695 Changed 93068 atom styles 
    10696 86492 atoms, 88098 bonds, 54 pseudobonds, 10743 residues, 8 models selected 
    10697 
    10698 > newcolor #3/A #3/B #3/C #3/D #3/E #3/F #3/I #3/G #3/H
    10699 
    10700 > matchmaker #1-3/A to #4
    10701 
    10702 Computing secondary structure 
    10703 Parameters 
    10704 --- 
    10705 Chain pairing | bb 
    10706 Alignment algorithm | Needleman-Wunsch 
    10707 Similarity matrix | BLOSUM-62 
    10708 SS fraction | 0.3 
    10709 Gap open (HH/SS/other) | 18/18/6 
    10710 Gap extend | 1 
    10711 SS matrix |  |  | H | S | O 
    10712 ---|---|---|--- 
    10713 H | 6 | -9 | -6 
    10714 S |  | 6 | -6 
    10715 O |  |  | 4 
    10716 Iteration cutoff | 2 
    10717  
    10718 Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain A (#4) with
    10719 hsORC1-6_CDC6_60bpDNA.pdb, chain A (#1), sequence alignment score = 965.4 
    10720 RMSD between 213 pruned atom pairs is 1.228 angstroms; (across all 381 pairs:
    10721 3.152) 
    10722  
    10723 Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain A (#4) with
    10724 7jk3-dmODC_GCrich.pdb, chain A (#2), sequence alignment score = 962.2 
    10725 RMSD between 250 pruned atom pairs is 1.152 angstroms; (across all 383 pairs:
    10726 6.101) 
    10727  
    10728 Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain A (#4) with 7mca-
    10729 assembly1.cif, chain A (#3), sequence alignment score = 943 
    10730 RMSD between 228 pruned atom pairs is 1.005 angstroms; (across all 394 pairs:
    10731 5.169) 
    10732  
    10733 
    10734 > show #!3 models
    10735 
    10736 > show #!2 models
    10737 
    10738 > show #!1 models
    10739 
    10740 > matchmaker #1-3/A to #4/A
    10741 
    10742 Computing secondary structure 
    10743 Parameters 
    10744 --- 
    10745 Chain pairing | bb 
    10746 Alignment algorithm | Needleman-Wunsch 
    10747 Similarity matrix | BLOSUM-62 
    10748 SS fraction | 0.3 
    10749 Gap open (HH/SS/other) | 18/18/6 
    10750 Gap extend | 1 
    10751 SS matrix |  |  | H | S | O 
    10752 ---|---|---|--- 
    10753 H | 6 | -9 | -6 
    10754 S |  | 6 | -6 
    10755 O |  |  | 4 
    10756 Iteration cutoff | 2 
    10757  
    10758 Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain A (#4) with
    10759 hsORC1-6_CDC6_60bpDNA.pdb, chain A (#1), sequence alignment score = 965.4 
    10760 RMSD between 213 pruned atom pairs is 1.228 angstroms; (across all 381 pairs:
    10761 3.152) 
    10762  
    10763 Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain A (#4) with
    10764 7jk3-dmODC_GCrich.pdb, chain A (#2), sequence alignment score = 962.2 
    10765 RMSD between 250 pruned atom pairs is 1.152 angstroms; (across all 383 pairs:
    10766 6.101) 
    10767  
    10768 Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain A (#4) with 7mca-
    10769 assembly1.cif, chain A (#3), sequence alignment score = 943 
    10770 RMSD between 228 pruned atom pairs is 1.005 angstroms; (across all 394 pairs:
    10771 5.169) 
    10772  
    10773 
    10774 > matchmaker #1-3/B to #4/B
    10775 
    10776 Computing secondary structure 
    10777 Parameters 
    10778 --- 
    10779 Chain pairing | bb 
    10780 Alignment algorithm | Needleman-Wunsch 
    10781 Similarity matrix | BLOSUM-62 
    10782 SS fraction | 0.3 
    10783 Gap open (HH/SS/other) | 18/18/6 
    10784 Gap extend | 1 
    10785 SS matrix |  |  | H | S | O 
    10786 ---|---|---|--- 
    10787 H | 6 | -9 | -6 
    10788 S |  | 6 | -6 
    10789 O |  |  | 4 
    10790 Iteration cutoff | 2 
    10791  
    10792 Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain B (#4) with
    10793 hsORC1-6_CDC6_60bpDNA.pdb, chain B (#1), sequence alignment score = 635.5 
    10794 RMSD between 137 pruned atom pairs is 1.099 angstroms; (across all 304 pairs:
    10795 5.531) 
    10796  
    10797 Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain B (#4) with
    10798 7jk3-dmODC_GCrich.pdb, chain B (#2), sequence alignment score = 558 
    10799 RMSD between 135 pruned atom pairs is 0.988 angstroms; (across all 284 pairs:
    10800 5.027) 
    10801  
    10802 Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain B (#4) with 7mca-
    10803 assembly1.cif, chain B (#3), sequence alignment score = 609.7 
    10804 RMSD between 153 pruned atom pairs is 1.065 angstroms; (across all 237 pairs:
    10805 4.405) 
    10806  
    10807 
    10808 > select #3/B:396
    10809 
    10810 14 atoms, 15 bonds, 1 residue, 1 model selected 
    10811 
    10812 > hide #!2 models
    10813 
    10814 > hide #!3 models
    10815 
    10816 > hide #!4 models
    10817 
    10818 > select #1/B:367
    10819 
    10820 11 atoms, 10 bonds, 1 residue, 1 model selected 
    10821 
    10822 > show sel atoms
    10823 
    10824 > select #1/B:365
    10825 
    10826 7 atoms, 6 bonds, 1 residue, 1 model selected 
    10827 
    10828 > show sel atoms
    10829 
    10830 > hide sel atoms
    10831 
    10832 > select #1/B:367@CA
    10833 
    10834 1 atom, 1 residue, 1 model selected 
    10835 
    10836 > hide sel atoms
    10837 
    10838 > select #1/B:367
    10839 
    10840 11 atoms, 10 bonds, 1 residue, 1 model selected 
    10841 
    10842 > hide sel atoms
    10843 
    10844 > select #1/C:177
    10845 
    10846 7 atoms, 6 bonds, 1 residue, 1 model selected 
    10847 
    10848 > select clear
    10849 
    10850 > show #!4 models
    10851 
    10852 > hide #!1 models
    10853 
    10854 > select #4/B:150
    10855 
    10856 11 atoms, 10 bonds, 1 residue, 1 model selected 
    10857 
    10858 > show sel atoms
    10859 
    10860 > select clear
    10861 
    10862 > show #!3 models
    10863 
    10864 > show #!2 models
    10865 
    10866 > show #!1 models
    10867 
    10868 > select #3/B:255
    10869 
    10870 7 atoms, 6 bonds, 1 residue, 1 model selected 
    10871 
    10872 > select #3/B:254
    10873 
    10874 11 atoms, 10 bonds, 1 residue, 1 model selected 
    10875 
    10876 > show sel atoms
    10877 
    10878 > hide #!4 models
    10879 
    10880 > hide #!2 models
    10881 
    10882 > hide #!1 models
    10883 
    10884 > select clear
    10885 
    10886 > color #!3 byhetero
    10887 
    10888 > show #!4 models
    10889 
    10890 > matchmaker #1-3/E to #4/E
    10891 
    10892 Computing secondary structure 
    10893 Parameters 
    10894 --- 
    10895 Chain pairing | bb 
    10896 Alignment algorithm | Needleman-Wunsch 
    10897 Similarity matrix | BLOSUM-62 
    10898 SS fraction | 0.3 
    10899 Gap open (HH/SS/other) | 18/18/6 
    10900 Gap extend | 1 
    10901 SS matrix |  |  | H | S | O 
    10902 ---|---|---|--- 
    10903 H | 6 | -9 | -6 
    10904 S |  | 6 | -6 
    10905 O |  |  | 4 
    10906 Iteration cutoff | 2 
    10907  
    10908 Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain E (#4) with
    10909 hsORC1-6_CDC6_60bpDNA.pdb, chain E (#1), sequence alignment score = 675 
    10910 RMSD between 179 pruned atom pairs is 1.291 angstroms; (across all 379 pairs:
    10911 4.186) 
    10912  
    10913 Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain E (#4) with
    10914 7jk3-dmODC_GCrich.pdb, chain E (#2), sequence alignment score = 567.4 
    10915 RMSD between 149 pruned atom pairs is 1.290 angstroms; (across all 374 pairs:
    10916 4.652) 
    10917  
    10918 Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain E (#4) with 7mca-
    10919 assembly1.cif, chain E (#3), sequence alignment score = 646.2 
    10920 RMSD between 174 pruned atom pairs is 1.399 angstroms; (across all 417 pairs:
    10921 4.188) 
    10922  
    10923 
    10924 > hide #!4 models
    10925 
    10926 > select #3/E:366
    10927 
    10928 11 atoms, 10 bonds, 1 residue, 1 model selected 
    10929 
    10930 > show sel atoms
    10931 
    10932 > select #3/E:363
    10933 
    10934 12 atoms, 12 bonds, 1 residue, 1 model selected 
    10935 
    10936 > select #3/E:360
    10937 
    10938 11 atoms, 10 bonds, 1 residue, 1 model selected 
    10939 
    10940 > show sel atoms
    10941 
    10942 > show #!4 models
    10943 
    10944 > matchmaker #1-3/E to #4/E:307-end
    10945 
    10946 Computing secondary structure 
    10947 Parameters 
    10948 --- 
    10949 Chain pairing | bb 
    10950 Alignment algorithm | Needleman-Wunsch 
    10951 Similarity matrix | BLOSUM-62 
    10952 SS fraction | 0.3 
    10953 Gap open (HH/SS/other) | 18/18/6 
    10954 Gap extend | 1 
    10955 SS matrix |  |  | H | S | O 
    10956 ---|---|---|--- 
    10957 H | 6 | -9 | -6 
    10958 S |  | 6 | -6 
    10959 O |  |  | 4 
    10960 Iteration cutoff | 2 
    10961  
    10962 Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain E (#4) with
    10963 hsORC1-6_CDC6_60bpDNA.pdb, chain E (#1), sequence alignment score = 281.2 
    10964 RMSD between 99 pruned atom pairs is 0.965 angstroms; (across all 120 pairs:
    10965 3.490) 
    10966  
    10967 Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain E (#4) with
    10968 7jk3-dmODC_GCrich.pdb, chain E (#2), sequence alignment score = 198.4 
    10969 RMSD between 96 pruned atom pairs is 1.015 angstroms; (across all 110 pairs:
    10970 1.673) 
    10971  
    10972 Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain E (#4) with 7mca-
    10973 assembly1.cif, chain E (#3), sequence alignment score = 312.4 
    10974 RMSD between 101 pruned atom pairs is 0.945 angstroms; (across all 138 pairs:
    10975 3.466) 
    10976  
    10977 
    10978 > select #4/E:362
    10979 
    10980 11 atoms, 10 bonds, 1 residue, 1 model selected 
    10981 
    10982 > show sel atoms
    10983 
    10984 > select #4/E:359
    10985 
    10986 7 atoms, 6 bonds, 1 residue, 1 model selected 
    10987 
    10988 > select #4/E:357
    10989 
    10990 11 atoms, 10 bonds, 1 residue, 1 model selected 
    10991 
    10992 > show sel atoms
    10993 
    10994 > select #4/E:354
    10995 
    10996 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10997 
    10998 > hide #!3 models
    10999 
    11000 > select #4/E:355
    11001 
    11002 4 atoms, 3 bonds, 1 residue, 1 model selected 
    11003 
    11004 > select #4/E:354
    11005 
    11006 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11007 
    11008 > show #!3 models
    11009 
    11010 > hide #!4 models
    11011 
    11012 > select #3/E:363
    11013 
    11014 12 atoms, 12 bonds, 1 residue, 1 model selected 
    11015 
    11016 > show sel atoms
    11017 
    11018 > select #3/E:358
    11019 
    11020 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11021 
    11022 > select #3/E:439
    11023 
    11024 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11025 
    11026 > show sel atoms
    11027 
    11028 > select #3/A:369
    11029 
    11030 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11031 
    11032 > show sel atoms
    11033 
    11034 > select #3/A:367
    11035 
    11036 11 atoms, 10 bonds, 1 residue, 1 model selected 
    11037 
    11038 > show sel atoms
    11039 
    11040 > select #3/A:365
    11041 
    11042 7 atoms, 6 bonds, 1 residue, 1 model selected 
    11043 
    11044 > show sel atoms
    11045 
    11046 > show #!4 models
    11047 
    11048 > hide #!3 models
    11049 
    11050 > hide #!4 models
    11051 
    11052 > show #!3 models
    11053 
    11054 > close #3
    11055 
    11056 > close
    11057 
    11058 > open "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11059 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11060 > structures/intermediate
    11061 > results/cryosparc_P370_J407_component_000/J407_component_000_frame_024.mrc"
    11062 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11063 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11064 > structures/intermediate
    11065 > results/cryosparc_P370_J407_component_000/J407_component_000_frame_023.mrc"
    11066 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11067 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11068 > structures/intermediate
    11069 > results/cryosparc_P370_J407_component_000/J407_component_000_frame_022.mrc"
    11070 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11071 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11072 > structures/intermediate
    11073 > results/cryosparc_P370_J407_component_000/J407_component_000_frame_021.mrc"
    11074 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11075 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11076 > structures/intermediate
    11077 > results/cryosparc_P370_J407_component_000/J407_component_000_frame_020.mrc"
    11078 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11079 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11080 > structures/intermediate
    11081 > results/cryosparc_P370_J407_component_000/J407_component_000_frame_019.mrc"
    11082 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11083 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11084 > structures/intermediate
    11085 > results/cryosparc_P370_J407_component_000/J407_component_000_frame_018.mrc"
    11086 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11087 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11088 > structures/intermediate
    11089 > results/cryosparc_P370_J407_component_000/J407_component_000_frame_017.mrc"
    11090 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11091 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11092 > structures/intermediate
    11093 > results/cryosparc_P370_J407_component_000/J407_component_000_frame_016.mrc"
    11094 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11095 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11096 > structures/intermediate
    11097 > results/cryosparc_P370_J407_component_000/J407_component_000_frame_015.mrc"
    11098 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11099 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11100 > structures/intermediate
    11101 > results/cryosparc_P370_J407_component_000/J407_component_000_frame_014.mrc"
    11102 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11103 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11104 > structures/intermediate
    11105 > results/cryosparc_P370_J407_component_000/J407_component_000_frame_013.mrc"
    11106 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11107 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11108 > structures/intermediate
    11109 > results/cryosparc_P370_J407_component_000/J407_component_000_frame_012.mrc"
    11110 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11111 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11112 > structures/intermediate
    11113 > results/cryosparc_P370_J407_component_000/J407_component_000_frame_011.mrc"
    11114 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11115 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11116 > structures/intermediate
    11117 > results/cryosparc_P370_J407_component_000/J407_component_000_frame_010.mrc"
    11118 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11119 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11120 > structures/intermediate
    11121 > results/cryosparc_P370_J407_component_000/J407_component_000_frame_009.mrc"
    11122 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11123 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11124 > structures/intermediate
    11125 > results/cryosparc_P370_J407_component_000/J407_component_000_frame_008.mrc"
    11126 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11127 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11128 > structures/intermediate
    11129 > results/cryosparc_P370_J407_component_000/J407_component_000_frame_007.mrc"
    11130 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11131 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11132 > structures/intermediate
    11133 > results/cryosparc_P370_J407_component_000/J407_component_000_frame_006.mrc"
    11134 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11135 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11136 > structures/intermediate
    11137 > results/cryosparc_P370_J407_component_000/J407_component_000_frame_005.mrc"
    11138 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11139 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11140 > structures/intermediate
    11141 > results/cryosparc_P370_J407_component_000/J407_component_000_frame_004.mrc"
    11142 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11143 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11144 > structures/intermediate
    11145 > results/cryosparc_P370_J407_component_000/J407_component_000_frame_003.mrc"
    11146 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11147 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11148 > structures/intermediate
    11149 > results/cryosparc_P370_J407_component_000/J407_component_000_frame_002.mrc"
    11150 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11151 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11152 > structures/intermediate
    11153 > results/cryosparc_P370_J407_component_000/J407_component_000_frame_001.mrc"
    11154 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11155 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11156 > structures/intermediate
    11157 > results/cryosparc_P370_J407_component_000/J407_component_000_frame_000.mrc"
    11158 
    11159 Opened J407_component_000_frame_024.mrc as #1.1, grid size 440,440,440, pixel
    11160 0.827, shown at level 0.0246, step 2, values float32 
    11161 Opened J407_component_000_frame_023.mrc as #1.2, grid size 440,440,440, pixel
    11162 0.827, shown at level 0.0247, step 2, values float32 
    11163 Opened J407_component_000_frame_022.mrc as #1.3, grid size 440,440,440, pixel
    11164 0.827, shown at level 0.0246, step 2, values float32 
    11165 Opened J407_component_000_frame_021.mrc as #1.4, grid size 440,440,440, pixel
    11166 0.827, shown at level 0.0248, step 2, values float32 
    11167 Opened J407_component_000_frame_020.mrc as #1.5, grid size 440,440,440, pixel
    11168 0.827, shown at level 0.025, step 2, values float32 
    11169 Opened J407_component_000_frame_019.mrc as #1.6, grid size 440,440,440, pixel
    11170 0.827, shown at level 0.0253, step 2, values float32 
    11171 Opened J407_component_000_frame_018.mrc as #1.7, grid size 440,440,440, pixel
    11172 0.827, shown at level 0.0256, step 2, values float32 
    11173 Opened J407_component_000_frame_017.mrc as #1.8, grid size 440,440,440, pixel
    11174 0.827, shown at level 0.0259, step 2, values float32 
    11175 Opened J407_component_000_frame_016.mrc as #1.9, grid size 440,440,440, pixel
    11176 0.827, shown at level 0.0262, step 2, values float32 
    11177 Opened J407_component_000_frame_015.mrc as #1.10, grid size 440,440,440, pixel
    11178 0.827, shown at level 0.0265, step 2, values float32 
    11179 Opened J407_component_000_frame_014.mrc as #1.11, grid size 440,440,440, pixel
    11180 0.827, shown at level 0.0267, step 2, values float32 
    11181 Opened J407_component_000_frame_013.mrc as #1.12, grid size 440,440,440, pixel
    11182 0.827, shown at level 0.0268, step 2, values float32 
    11183 Opened J407_component_000_frame_012.mrc as #1.13, grid size 440,440,440, pixel
    11184 0.827, shown at level 0.0269, step 2, values float32 
    11185 Opened J407_component_000_frame_011.mrc as #1.14, grid size 440,440,440, pixel
    11186 0.827, shown at level 0.0269, step 2, values float32 
    11187 Opened J407_component_000_frame_010.mrc as #1.15, grid size 440,440,440, pixel
    11188 0.827, shown at level 0.0268, step 2, values float32 
    11189 Opened J407_component_000_frame_009.mrc as #1.16, grid size 440,440,440, pixel
    11190 0.827, shown at level 0.0266, step 2, values float32 
    11191 Opened J407_component_000_frame_008.mrc as #1.17, grid size 440,440,440, pixel
    11192 0.827, shown at level 0.0265, step 2, values float32 
    11193 Opened J407_component_000_frame_007.mrc as #1.18, grid size 440,440,440, pixel
    11194 0.827, shown at level 0.0263, step 2, values float32 
    11195 Opened J407_component_000_frame_006.mrc as #1.19, grid size 440,440,440, pixel
    11196 0.827, shown at level 0.0261, step 2, values float32 
    11197 Opened J407_component_000_frame_005.mrc as #1.20, grid size 440,440,440, pixel
    11198 0.827, shown at level 0.026, step 2, values float32 
    11199 Opened J407_component_000_frame_004.mrc as #1.21, grid size 440,440,440, pixel
    11200 0.827, shown at level 0.0258, step 2, values float32 
    11201 Opened J407_component_000_frame_003.mrc as #1.22, grid size 440,440,440, pixel
    11202 0.827, shown at level 0.0257, step 2, values float32 
    11203 Opened J407_component_000_frame_002.mrc as #1.23, grid size 440,440,440, pixel
    11204 0.827, shown at level 0.0257, step 2, values float32 
    11205 Opened J407_component_000_frame_001.mrc as #1.24, grid size 440,440,440, pixel
    11206 0.827, shown at level 0.0257, step 2, values float32 
    11207 Opened J407_component_000_frame_000.mrc as #1.25, grid size 440,440,440, pixel
    11208 0.827, shown at level 0.0258, step 2, values float32 
    11209 
    11210 > volume step 1
    11211 
    11212 > volume level 0.1
    11213 
    11214 > morph #1
    11215 
    11216 Require at least 2 structures for morph 
    11217 
    11218 > morph #1.1-1.25
    11219 
    11220 Require at least 2 structures for morph 
    11221 
    11222 > volume morph #1
    11223 
    11224 Opened morph as #2, grid size 440,440,440, pixel 0.827, shown at step 1,
    11225 values float32 
    11226 
    11227 > close #2
    11228 
    11229 > vop flip #1
    11230 
    11231 Opened J407_component_000_frame_024.mrc z flip as #2, grid size 440,440,440,
    11232 pixel 0.827, shown at step 1, values float32 
    11233 Opened J407_component_000_frame_023.mrc z flip as #3, grid size 440,440,440,
    11234 pixel 0.827, shown at step 1, values float32 
    11235 Opened J407_component_000_frame_022.mrc z flip as #4, grid size 440,440,440,
    11236 pixel 0.827, shown at step 1, values float32 
    11237 Opened J407_component_000_frame_021.mrc z flip as #5, grid size 440,440,440,
    11238 pixel 0.827, shown at step 1, values float32 
    11239 Opened J407_component_000_frame_020.mrc z flip as #6, grid size 440,440,440,
    11240 pixel 0.827, shown at step 1, values float32 
    11241 Opened J407_component_000_frame_019.mrc z flip as #7, grid size 440,440,440,
    11242 pixel 0.827, shown at step 1, values float32 
    11243 Opened J407_component_000_frame_018.mrc z flip as #8, grid size 440,440,440,
    11244 pixel 0.827, shown at step 1, values float32 
    11245 Opened J407_component_000_frame_017.mrc z flip as #9, grid size 440,440,440,
    11246 pixel 0.827, shown at step 1, values float32 
    11247 Opened J407_component_000_frame_016.mrc z flip as #10, grid size 440,440,440,
    11248 pixel 0.827, shown at step 1, values float32 
    11249 Opened J407_component_000_frame_015.mrc z flip as #11, grid size 440,440,440,
    11250 pixel 0.827, shown at step 1, values float32 
    11251 Opened J407_component_000_frame_014.mrc z flip as #12, grid size 440,440,440,
    11252 pixel 0.827, shown at step 1, values float32 
    11253 Opened J407_component_000_frame_013.mrc z flip as #13, grid size 440,440,440,
    11254 pixel 0.827, shown at step 1, values float32 
    11255 Opened J407_component_000_frame_012.mrc z flip as #14, grid size 440,440,440,
    11256 pixel 0.827, shown at step 1, values float32 
    11257 Opened J407_component_000_frame_011.mrc z flip as #15, grid size 440,440,440,
    11258 pixel 0.827, shown at step 1, values float32 
    11259 Opened J407_component_000_frame_010.mrc z flip as #16, grid size 440,440,440,
    11260 pixel 0.827, shown at step 1, values float32 
    11261 Opened J407_component_000_frame_009.mrc z flip as #17, grid size 440,440,440,
    11262 pixel 0.827, shown at step 1, values float32 
    11263 Opened J407_component_000_frame_008.mrc z flip as #18, grid size 440,440,440,
    11264 pixel 0.827, shown at step 1, values float32 
    11265 Opened J407_component_000_frame_007.mrc z flip as #19, grid size 440,440,440,
    11266 pixel 0.827, shown at step 1, values float32 
    11267 Opened J407_component_000_frame_006.mrc z flip as #20, grid size 440,440,440,
    11268 pixel 0.827, shown at step 1, values float32 
    11269 Opened J407_component_000_frame_005.mrc z flip as #21, grid size 440,440,440,
    11270 pixel 0.827, shown at step 1, values float32 
    11271 Opened J407_component_000_frame_004.mrc z flip as #22, grid size 440,440,440,
    11272 pixel 0.827, shown at step 1, values float32 
    11273 Opened J407_component_000_frame_003.mrc z flip as #23, grid size 440,440,440,
    11274 pixel 0.827, shown at step 1, values float32 
    11275 Opened J407_component_000_frame_002.mrc z flip as #24, grid size 440,440,440,
    11276 pixel 0.827, shown at step 1, values float32 
    11277 Opened J407_component_000_frame_001.mrc z flip as #25, grid size 440,440,440,
    11278 pixel 0.827, shown at step 1, values float32 
    11279 Opened J407_component_000_frame_000.mrc z flip as #26, grid size 440,440,440,
    11280 pixel 0.827, shown at step 1, values float32 
    11281 
    11282 > close #1
    11283 
    11284 > color #808080
    11285 
    11286 > color grey
    11287 
    11288 > color lightgrey
    11289 
    11290 > color darkgrey
    11291 
    11292 > volume morph #2-26
    11293 
    11294 Opened morph as #1, grid size 440,440,440, pixel 0.827, shown at step 1,
    11295 values float32 
    11296 
    11297 > close #1
    11298 
    11299 > open "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11300 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11301 > structures/intermediate
    11302 > results/cryosparc_P370_J408_component_000/J408_component_000_frame_024.mrc"
    11303 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11304 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11305 > structures/intermediate
    11306 > results/cryosparc_P370_J408_component_000/J408_component_000_frame_023.mrc"
    11307 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11308 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11309 > structures/intermediate
    11310 > results/cryosparc_P370_J408_component_000/J408_component_000_frame_022.mrc"
    11311 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11312 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11313 > structures/intermediate
    11314 > results/cryosparc_P370_J408_component_000/J408_component_000_frame_021.mrc"
    11315 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11316 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11317 > structures/intermediate
    11318 > results/cryosparc_P370_J408_component_000/J408_component_000_frame_020.mrc"
    11319 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11320 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11321 > structures/intermediate
    11322 > results/cryosparc_P370_J408_component_000/J408_component_000_frame_019.mrc"
    11323 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11324 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11325 > structures/intermediate
    11326 > results/cryosparc_P370_J408_component_000/J408_component_000_frame_018.mrc"
    11327 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11328 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11329 > structures/intermediate
    11330 > results/cryosparc_P370_J408_component_000/J408_component_000_frame_017.mrc"
    11331 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11332 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11333 > structures/intermediate
    11334 > results/cryosparc_P370_J408_component_000/J408_component_000_frame_016.mrc"
    11335 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11336 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11337 > structures/intermediate
    11338 > results/cryosparc_P370_J408_component_000/J408_component_000_frame_015.mrc"
    11339 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11340 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11341 > structures/intermediate
    11342 > results/cryosparc_P370_J408_component_000/J408_component_000_frame_014.mrc"
    11343 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11344 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11345 > structures/intermediate
    11346 > results/cryosparc_P370_J408_component_000/J408_component_000_frame_013.mrc"
    11347 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11348 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11349 > structures/intermediate
    11350 > results/cryosparc_P370_J408_component_000/J408_component_000_frame_012.mrc"
    11351 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11352 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11353 > structures/intermediate
    11354 > results/cryosparc_P370_J408_component_000/J408_component_000_frame_011.mrc"
    11355 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11356 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11357 > structures/intermediate
    11358 > results/cryosparc_P370_J408_component_000/J408_component_000_frame_010.mrc"
    11359 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11360 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11361 > structures/intermediate
    11362 > results/cryosparc_P370_J408_component_000/J408_component_000_frame_009.mrc"
    11363 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11364 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11365 > structures/intermediate
    11366 > results/cryosparc_P370_J408_component_000/J408_component_000_frame_008.mrc"
    11367 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11368 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11369 > structures/intermediate
    11370 > results/cryosparc_P370_J408_component_000/J408_component_000_frame_007.mrc"
    11371 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11372 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11373 > structures/intermediate
    11374 > results/cryosparc_P370_J408_component_000/J408_component_000_frame_006.mrc"
    11375 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11376 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11377 > structures/intermediate
    11378 > results/cryosparc_P370_J408_component_000/J408_component_000_frame_005.mrc"
    11379 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11380 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11381 > structures/intermediate
    11382 > results/cryosparc_P370_J408_component_000/J408_component_000_frame_004.mrc"
    11383 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11384 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11385 > structures/intermediate
    11386 > results/cryosparc_P370_J408_component_000/J408_component_000_frame_003.mrc"
    11387 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11388 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11389 > structures/intermediate
    11390 > results/cryosparc_P370_J408_component_000/J408_component_000_frame_002.mrc"
    11391 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11392 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11393 > structures/intermediate
    11394 > results/cryosparc_P370_J408_component_000/J408_component_000_frame_001.mrc"
    11395 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11396 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11397 > structures/intermediate
    11398 > results/cryosparc_P370_J408_component_000/J408_component_000_frame_000.mrc"
    11399 
    11400 Opened J408_component_000_frame_024.mrc as #1.1, grid size 440,440,440, pixel
    11401 0.827, shown at level 0.135, step 2, values float32 
    11402 Opened J408_component_000_frame_023.mrc as #1.2, grid size 440,440,440, pixel
    11403 0.827, shown at level 0.112, step 2, values float32 
    11404 Opened J408_component_000_frame_022.mrc as #1.3, grid size 440,440,440, pixel
    11405 0.827, shown at level 0.103, step 2, values float32 
    11406 Opened J408_component_000_frame_021.mrc as #1.4, grid size 440,440,440, pixel
    11407 0.827, shown at level 0.0998, step 2, values float32 
    11408 Opened J408_component_000_frame_020.mrc as #1.5, grid size 440,440,440, pixel
    11409 0.827, shown at level 0.0974, step 2, values float32 
    11410 Opened J408_component_000_frame_019.mrc as #1.6, grid size 440,440,440, pixel
    11411 0.827, shown at level 0.0929, step 2, values float32 
    11412 Opened J408_component_000_frame_018.mrc as #1.7, grid size 440,440,440, pixel
    11413 0.827, shown at level 0.0878, step 2, values float32 
    11414 Opened J408_component_000_frame_017.mrc as #1.8, grid size 440,440,440, pixel
    11415 0.827, shown at level 0.0867, step 2, values float32 
    11416 Opened J408_component_000_frame_016.mrc as #1.9, grid size 440,440,440, pixel
    11417 0.827, shown at level 0.092, step 2, values float32 
    11418 Opened J408_component_000_frame_015.mrc as #1.10, grid size 440,440,440, pixel
    11419 0.827, shown at level 0.105, step 2, values float32 
    11420 Opened J408_component_000_frame_014.mrc as #1.11, grid size 440,440,440, pixel
    11421 0.827, shown at level 0.128, step 2, values float32 
    11422 Opened J408_component_000_frame_013.mrc as #1.12, grid size 440,440,440, pixel
    11423 0.827, shown at level 0.167, step 2, values float32 
    11424 Opened J408_component_000_frame_012.mrc as #1.13, grid size 440,440,440, pixel
    11425 0.827, shown at level 0.216, step 2, values float32 
    11426 Opened J408_component_000_frame_011.mrc as #1.14, grid size 440,440,440, pixel
    11427 0.827, shown at level 0.235, step 2, values float32 
    11428 Opened J408_component_000_frame_010.mrc as #1.15, grid size 440,440,440, pixel
    11429 0.827, shown at level 0.205, step 2, values float32 
    11430 Opened J408_component_000_frame_009.mrc as #1.16, grid size 440,440,440, pixel
    11431 0.827, shown at level 0.166, step 2, values float32 
    11432 Opened J408_component_000_frame_008.mrc as #1.17, grid size 440,440,440, pixel
    11433 0.827, shown at level 0.143, step 2, values float32 
    11434 Opened J408_component_000_frame_007.mrc as #1.18, grid size 440,440,440, pixel
    11435 0.827, shown at level 0.133, step 2, values float32 
    11436 Opened J408_component_000_frame_006.mrc as #1.19, grid size 440,440,440, pixel
    11437 0.827, shown at level 0.128, step 2, values float32 
    11438 Opened J408_component_000_frame_005.mrc as #1.20, grid size 440,440,440, pixel
    11439 0.827, shown at level 0.127, step 2, values float32 
    11440 Opened J408_component_000_frame_004.mrc as #1.21, grid size 440,440,440, pixel
    11441 0.827, shown at level 0.124, step 2, values float32 
    11442 Opened J408_component_000_frame_003.mrc as #1.22, grid size 440,440,440, pixel
    11443 0.827, shown at level 0.123, step 2, values float32 
    11444 Opened J408_component_000_frame_002.mrc as #1.23, grid size 440,440,440, pixel
    11445 0.827, shown at level 0.125, step 2, values float32 
    11446 Opened J408_component_000_frame_001.mrc as #1.24, grid size 440,440,440, pixel
    11447 0.827, shown at level 0.135, step 2, values float32 
    11448 Opened J408_component_000_frame_000.mrc as #1.25, grid size 440,440,440, pixel
    11449 0.827, shown at level 0.154, step 2, values float32 
    11450 
    11451 > volume step 1
    11452 
    11453 > volume level 0.1 #1
    11454 
    11455 Expected a keyword 
    11456 
    11457 > vop level 0.2 #1
    11458 
    11459 > volume level 0.2 #1
    11460 
    11461 Expected a keyword 
    11462 
    11463 > vop level #1 0.2
    11464 
    11465 > volume level #1 0.2
    11466 
    11467 Invalid "level" argument: Expected a number 
    11468 
    11469 > vop level
    11470 
    11471 > volume level
    11472 
    11473 Missing "level" keyword's argument 
    11474 
    11475 > volume #1.10 level 0.12
    11476 
    11477 > vop #1 level 0.2
    11478 
    11479 > vop #1 level 0.3
    11480 
    11481 > vop #1 level 0.2
    11482 
    11483 > surface dust #1.1 size 8.27
    11484 
    11485 > surface dust #1.2 size 8.27
    11486 
    11487 > surface dust #1.3 size 8.27
    11488 
    11489 > surface dust #1.4 size 8.27
    11490 
    11491 > surface dust #1.5 size 8.27
    11492 
    11493 > surface dust #1.6 size 8.27
    11494 
    11495 > surface dust #1.7 size 8.27
    11496 
    11497 > surface dust #1.8 size 8.27
    11498 
    11499 > surface dust #1.9 size 8.27
    11500 
    11501 > surface dust #1.10 size 8.27
    11502 
    11503 > surface dust #1.11 size 8.27
    11504 
    11505 > surface dust #1.12 size 8.27
    11506 
    11507 > surface dust #1.13 size 8.27
    11508 
    11509 > surface dust #1.14 size 8.27
    11510 
    11511 > surface dust #1.15 size 8.27
    11512 
    11513 > surface dust #1.16 size 8.27
    11514 
    11515 > surface dust #1.17 size 8.27
    11516 
    11517 > surface dust #1.18 size 8.27
    11518 
    11519 > surface dust #1.19 size 8.27
    11520 
    11521 > surface dust #1.20 size 8.27
    11522 
    11523 > surface dust #1.21 size 8.27
    11524 
    11525 > surface dust #1.22 size 8.27
    11526 
    11527 > surface dust #1.23 size 8.27
    11528 
    11529 > surface dust #1.24 size 8.27
    11530 
    11531 > surface dust #1.25 size 8.27
    11532 
    11533 > volume morph #1
    11534 
    11535 Opened morph as #27, grid size 440,440,440, pixel 0.827, shown at step 1,
    11536 values float32 
    11537 
    11538 > surface dust #27 size 8.27
    11539 
    11540 > close #1
    11541 
    11542 > close #27
    11543 
    11544 > volume show
    11545 
    11546 > volume hide
    11547 
    11548 > volume morph #2-26
    11549 
    11550 Opened morph as #1, grid size 440,440,440, pixel 0.827, shown at step 1,
    11551 values float32 
    11552 
    11553 > hide #!1 models
    11554 
    11555 > show #!26 models
    11556 
    11557 > open "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11558 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11559 > structures/PDBs/ylODC_54bp-
    11560 > oriC061_complete/ylODC_54bpOriC061_rev31_PostPhenix.pdb"
    11561 
    11562 Chain information for ylODC_54bpOriC061_rev31_PostPhenix.pdb #27 
    11563 --- 
    11564 Chain | Description 
    11565 A | No description available 
    11566 B | No description available 
    11567 C | No description available 
    11568 D | No description available 
    11569 E | No description available 
    11570 F | No description available 
    11571 G | No description available 
    11572 H | No description available 
    11573 I | No description available 
    11574  
    11575 
    11576 > modelfix
    11577 
    11578 Changed 25299 atom styles 
    11579 23699 atoms, 24145 bonds, 9 pseudobonds, 2970 residues, 2 models selected 
    11580 
    11581 > select /C:220
    11582 
    11583 11 atoms, 10 bonds, 1 residue, 1 model selected 
    11584 
    11585 > show #!1 models
    11586 
    11587 > open "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11588 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11589 > structures/intermediate results/cryosparc_P370_J380_005_volume_map.mrc"
    11590 
    11591 Opened cryosparc_P370_J380_005_volume_map.mrc as #28, grid size 440,440,440,
    11592 pixel 0.827, shown at level 0.0231, step 2, values float32 
    11593 
    11594 > vop flip #28
    11595 
    11596 Opened cryosparc_P370_J380_005_volume_map.mrc z flip as #29, grid size
    11597 440,440,440, pixel 0.827, shown at step 1, values float32 
    11598 
    11599 > close #28
    11600 
    11601 > volume #29 level 0.09557
    11602 
    11603 > hide #!27 models
    11604 
    11605 > select add #27
    11606 
    11607 25299 atoms, 25927 bonds, 11 pseudobonds, 3050 residues, 3 models selected 
    11608 
    11609 > select subtract #27
    11610 
    11611 Nothing selected 
    11612 
    11613 > close #29
    11614 
    11615 > close #27
    11616 
    11617 > show #!1 models
    11618 
    11619 > save "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11620 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11621 > structures/intermediate results/J407_component0_ORC_OPEN-CLOSE.cxs"
    11622 
    11623 > close #1
    11624 
    11625 > close
    11626 
    11627 > open "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11628 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11629 > structures/intermediate
    11630 > results/cryosparc_P370_J407_component_001/J407_component_001_frame_000.mrc"
    11631 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11632 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11633 > structures/intermediate
    11634 > results/cryosparc_P370_J407_component_001/J407_component_001_frame_001.mrc"
    11635 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11636 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11637 > structures/intermediate
    11638 > results/cryosparc_P370_J407_component_001/J407_component_001_frame_002.mrc"
    11639 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11640 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11641 > structures/intermediate
    11642 > results/cryosparc_P370_J407_component_001/J407_component_001_frame_003.mrc"
    11643 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11644 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11645 > structures/intermediate
    11646 > results/cryosparc_P370_J407_component_001/J407_component_001_frame_004.mrc"
    11647 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11648 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11649 > structures/intermediate
    11650 > results/cryosparc_P370_J407_component_001/J407_component_001_frame_005.mrc"
    11651 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11652 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11653 > structures/intermediate
    11654 > results/cryosparc_P370_J407_component_001/J407_component_001_frame_006.mrc"
    11655 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11656 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11657 > structures/intermediate
    11658 > results/cryosparc_P370_J407_component_001/J407_component_001_frame_007.mrc"
    11659 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11660 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11661 > structures/intermediate
    11662 > results/cryosparc_P370_J407_component_001/J407_component_001_frame_008.mrc"
    11663 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11664 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11665 > structures/intermediate
    11666 > results/cryosparc_P370_J407_component_001/J407_component_001_frame_009.mrc"
    11667 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11668 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11669 > structures/intermediate
    11670 > results/cryosparc_P370_J407_component_001/J407_component_001_frame_010.mrc"
    11671 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11672 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11673 > structures/intermediate
    11674 > results/cryosparc_P370_J407_component_001/J407_component_001_frame_011.mrc"
    11675 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11676 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11677 > structures/intermediate
    11678 > results/cryosparc_P370_J407_component_001/J407_component_001_frame_012.mrc"
    11679 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11680 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11681 > structures/intermediate
    11682 > results/cryosparc_P370_J407_component_001/J407_component_001_frame_013.mrc"
    11683 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11684 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11685 > structures/intermediate
    11686 > results/cryosparc_P370_J407_component_001/J407_component_001_frame_014.mrc"
    11687 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11688 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11689 > structures/intermediate
    11690 > results/cryosparc_P370_J407_component_001/J407_component_001_frame_015.mrc"
    11691 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11692 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11693 > structures/intermediate
    11694 > results/cryosparc_P370_J407_component_001/J407_component_001_frame_016.mrc"
    11695 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11696 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11697 > structures/intermediate
    11698 > results/cryosparc_P370_J407_component_001/J407_component_001_frame_017.mrc"
    11699 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11700 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11701 > structures/intermediate
    11702 > results/cryosparc_P370_J407_component_001/J407_component_001_frame_018.mrc"
    11703 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11704 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11705 > structures/intermediate
    11706 > results/cryosparc_P370_J407_component_001/J407_component_001_frame_019.mrc"
    11707 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11708 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11709 > structures/intermediate
    11710 > results/cryosparc_P370_J407_component_001/J407_component_001_frame_020.mrc"
    11711 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11712 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11713 > structures/intermediate
    11714 > results/cryosparc_P370_J407_component_001/J407_component_001_frame_021.mrc"
    11715 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11716 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11717 > structures/intermediate
    11718 > results/cryosparc_P370_J407_component_001/J407_component_001_frame_022.mrc"
    11719 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11720 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11721 > structures/intermediate
    11722 > results/cryosparc_P370_J407_component_001/J407_component_001_frame_023.mrc"
    11723 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11724 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11725 > structures/intermediate
    11726 > results/cryosparc_P370_J407_component_001/J407_component_001_frame_024.mrc"
    11727 
    11728 Opened J407_component_001_frame_000.mrc as #1.1, grid size 440,440,440, pixel
    11729 0.827, shown at level 0.0267, step 2, values float32 
    11730 Opened J407_component_001_frame_001.mrc as #1.2, grid size 440,440,440, pixel
    11731 0.827, shown at level 0.0266, step 2, values float32 
    11732 Opened J407_component_001_frame_002.mrc as #1.3, grid size 440,440,440, pixel
    11733 0.827, shown at level 0.0265, step 2, values float32 
    11734 Opened J407_component_001_frame_003.mrc as #1.4, grid size 440,440,440, pixel
    11735 0.827, shown at level 0.0264, step 2, values float32 
    11736 Opened J407_component_001_frame_004.mrc as #1.5, grid size 440,440,440, pixel
    11737 0.827, shown at level 0.0264, step 2, values float32 
    11738 Opened J407_component_001_frame_005.mrc as #1.6, grid size 440,440,440, pixel
    11739 0.827, shown at level 0.0263, step 2, values float32 
    11740 Opened J407_component_001_frame_006.mrc as #1.7, grid size 440,440,440, pixel
    11741 0.827, shown at level 0.0264, step 2, values float32 
    11742 Opened J407_component_001_frame_007.mrc as #1.8, grid size 440,440,440, pixel
    11743 0.827, shown at level 0.0264, step 2, values float32 
    11744 Opened J407_component_001_frame_008.mrc as #1.9, grid size 440,440,440, pixel
    11745 0.827, shown at level 0.0264, step 2, values float32 
    11746 Opened J407_component_001_frame_009.mrc as #1.10, grid size 440,440,440, pixel
    11747 0.827, shown at level 0.0265, step 2, values float32 
    11748 Opened J407_component_001_frame_010.mrc as #1.11, grid size 440,440,440, pixel
    11749 0.827, shown at level 0.0266, step 2, values float32 
    11750 Opened J407_component_001_frame_011.mrc as #1.12, grid size 440,440,440, pixel
    11751 0.827, shown at level 0.0266, step 2, values float32 
    11752 Opened J407_component_001_frame_012.mrc as #1.13, grid size 440,440,440, pixel
    11753 0.827, shown at level 0.0267, step 2, values float32 
    11754 Opened J407_component_001_frame_013.mrc as #1.14, grid size 440,440,440, pixel
    11755 0.827, shown at level 0.0268, step 2, values float32 
    11756 Opened J407_component_001_frame_014.mrc as #1.15, grid size 440,440,440, pixel
    11757 0.827, shown at level 0.0269, step 2, values float32 
    11758 Opened J407_component_001_frame_015.mrc as #1.16, grid size 440,440,440, pixel
    11759 0.827, shown at level 0.0269, step 2, values float32 
    11760 Opened J407_component_001_frame_016.mrc as #1.17, grid size 440,440,440, pixel
    11761 0.827, shown at level 0.0269, step 2, values float32 
    11762 Opened J407_component_001_frame_017.mrc as #1.18, grid size 440,440,440, pixel
    11763 0.827, shown at level 0.027, step 2, values float32 
    11764 Opened J407_component_001_frame_018.mrc as #1.19, grid size 440,440,440, pixel
    11765 0.827, shown at level 0.0271, step 2, values float32 
    11766 Opened J407_component_001_frame_019.mrc as #1.20, grid size 440,440,440, pixel
    11767 0.827, shown at level 0.0271, step 2, values float32 
    11768 Opened J407_component_001_frame_020.mrc as #1.21, grid size 440,440,440, pixel
    11769 0.827, shown at level 0.0272, step 2, values float32 
    11770 Opened J407_component_001_frame_021.mrc as #1.22, grid size 440,440,440, pixel
    11771 0.827, shown at level 0.0273, step 2, values float32 
    11772 Opened J407_component_001_frame_022.mrc as #1.23, grid size 440,440,440, pixel
    11773 0.827, shown at level 0.0273, step 2, values float32 
    11774 Opened J407_component_001_frame_023.mrc as #1.24, grid size 440,440,440, pixel
    11775 0.827, shown at level 0.0275, step 2, values float32 
    11776 Opened J407_component_001_frame_024.mrc as #1.25, grid size 440,440,440, pixel
    11777 0.827, shown at level 0.0276, step 2, values float32 
    11778 
    11779 > vop flip #1
    11780 
    11781 Opened J407_component_001_frame_000.mrc z flip as #2, grid size 440,440,440,
    11782 pixel 0.827, shown at step 1, values float32 
    11783 Opened J407_component_001_frame_001.mrc z flip as #3, grid size 440,440,440,
    11784 pixel 0.827, shown at step 1, values float32 
    11785 Opened J407_component_001_frame_002.mrc z flip as #4, grid size 440,440,440,
    11786 pixel 0.827, shown at step 1, values float32 
    11787 Opened J407_component_001_frame_003.mrc z flip as #5, grid size 440,440,440,
    11788 pixel 0.827, shown at step 1, values float32 
    11789 Opened J407_component_001_frame_004.mrc z flip as #6, grid size 440,440,440,
    11790 pixel 0.827, shown at step 1, values float32 
    11791 Opened J407_component_001_frame_005.mrc z flip as #7, grid size 440,440,440,
    11792 pixel 0.827, shown at step 1, values float32 
    11793 Opened J407_component_001_frame_006.mrc z flip as #8, grid size 440,440,440,
    11794 pixel 0.827, shown at step 1, values float32 
    11795 Opened J407_component_001_frame_007.mrc z flip as #9, grid size 440,440,440,
    11796 pixel 0.827, shown at step 1, values float32 
    11797 Opened J407_component_001_frame_008.mrc z flip as #10, grid size 440,440,440,
    11798 pixel 0.827, shown at step 1, values float32 
    11799 Opened J407_component_001_frame_009.mrc z flip as #11, grid size 440,440,440,
    11800 pixel 0.827, shown at step 1, values float32 
    11801 Opened J407_component_001_frame_010.mrc z flip as #12, grid size 440,440,440,
    11802 pixel 0.827, shown at step 1, values float32 
    11803 Opened J407_component_001_frame_011.mrc z flip as #13, grid size 440,440,440,
    11804 pixel 0.827, shown at step 1, values float32 
    11805 Opened J407_component_001_frame_012.mrc z flip as #14, grid size 440,440,440,
    11806 pixel 0.827, shown at step 1, values float32 
    11807 Opened J407_component_001_frame_013.mrc z flip as #15, grid size 440,440,440,
    11808 pixel 0.827, shown at step 1, values float32 
    11809 Opened J407_component_001_frame_014.mrc z flip as #16, grid size 440,440,440,
    11810 pixel 0.827, shown at step 1, values float32 
    11811 Opened J407_component_001_frame_015.mrc z flip as #17, grid size 440,440,440,
    11812 pixel 0.827, shown at step 1, values float32 
    11813 Opened J407_component_001_frame_016.mrc z flip as #18, grid size 440,440,440,
    11814 pixel 0.827, shown at step 1, values float32 
    11815 Opened J407_component_001_frame_017.mrc z flip as #19, grid size 440,440,440,
    11816 pixel 0.827, shown at step 1, values float32 
    11817 Opened J407_component_001_frame_018.mrc z flip as #20, grid size 440,440,440,
    11818 pixel 0.827, shown at step 1, values float32 
    11819 Opened J407_component_001_frame_019.mrc z flip as #21, grid size 440,440,440,
    11820 pixel 0.827, shown at step 1, values float32 
    11821 Opened J407_component_001_frame_020.mrc z flip as #22, grid size 440,440,440,
    11822 pixel 0.827, shown at step 1, values float32 
    11823 Opened J407_component_001_frame_021.mrc z flip as #23, grid size 440,440,440,
    11824 pixel 0.827, shown at step 1, values float32 
    11825 Opened J407_component_001_frame_022.mrc z flip as #24, grid size 440,440,440,
    11826 pixel 0.827, shown at step 1, values float32 
    11827 Opened J407_component_001_frame_023.mrc z flip as #25, grid size 440,440,440,
    11828 pixel 0.827, shown at step 1, values float32 
    11829 Opened J407_component_001_frame_024.mrc z flip as #26, grid size 440,440,440,
    11830 pixel 0.827, shown at step 1, values float32 
    11831 
    11832 > vop level 0.1
    11833 
    11834 > hide #!1 models
    11835 
    11836 > vop morph #2-26
    11837 
    11838 Opened morph as #27, grid size 440,440,440, pixel 0.827, shown at step 1,
    11839 values float32 
    11840 
    11841 > close
    11842 
    11843 > open "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11844 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11845 > structures/intermediate results/cryosparc_P370_J339_component_002.zip"
    11846 
    11847 Unrecognized file suffix '.zip' 
    11848 
    11849 > open "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11850 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11851 > structures/intermediate
    11852 > results/cryosparc_P370_J339_component_002/J339_component_002_frame_000.mrc"
    11853 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11854 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11855 > structures/intermediate
    11856 > results/cryosparc_P370_J339_component_002/J339_component_002_frame_001.mrc"
    11857 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11858 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11859 > structures/intermediate
    11860 > results/cryosparc_P370_J339_component_002/J339_component_002_frame_002.mrc"
    11861 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11862 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11863 > structures/intermediate
    11864 > results/cryosparc_P370_J339_component_002/J339_component_002_frame_003.mrc"
    11865 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11866 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11867 > structures/intermediate
    11868 > results/cryosparc_P370_J339_component_002/J339_component_002_frame_004.mrc"
    11869 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11870 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11871 > structures/intermediate
    11872 > results/cryosparc_P370_J339_component_002/J339_component_002_frame_005.mrc"
    11873 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11874 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11875 > structures/intermediate
    11876 > results/cryosparc_P370_J339_component_002/J339_component_002_frame_006.mrc"
    11877 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11878 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11879 > structures/intermediate
    11880 > results/cryosparc_P370_J339_component_002/J339_component_002_frame_007.mrc"
    11881 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11882 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11883 > structures/intermediate
    11884 > results/cryosparc_P370_J339_component_002/J339_component_002_frame_008.mrc"
    11885 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11886 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11887 > structures/intermediate
    11888 > results/cryosparc_P370_J339_component_002/J339_component_002_frame_009.mrc"
    11889 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11890 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11891 > structures/intermediate
    11892 > results/cryosparc_P370_J339_component_002/J339_component_002_frame_010.mrc"
    11893 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11894 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11895 > structures/intermediate
    11896 > results/cryosparc_P370_J339_component_002/J339_component_002_frame_011.mrc"
    11897 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11898 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11899 > structures/intermediate
    11900 > results/cryosparc_P370_J339_component_002/J339_component_002_frame_012.mrc"
    11901 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11902 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11903 > structures/intermediate
    11904 > results/cryosparc_P370_J339_component_002/J339_component_002_frame_013.mrc"
    11905 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11906 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11907 > structures/intermediate
    11908 > results/cryosparc_P370_J339_component_002/J339_component_002_frame_014.mrc"
    11909 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11910 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11911 > structures/intermediate
    11912 > results/cryosparc_P370_J339_component_002/J339_component_002_frame_015.mrc"
    11913 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11914 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11915 > structures/intermediate
    11916 > results/cryosparc_P370_J339_component_002/J339_component_002_frame_016.mrc"
    11917 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11918 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11919 > structures/intermediate
    11920 > results/cryosparc_P370_J339_component_002/J339_component_002_frame_017.mrc"
    11921 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11922 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11923 > structures/intermediate
    11924 > results/cryosparc_P370_J339_component_002/J339_component_002_frame_018.mrc"
    11925 > "/Users/jtbauer/Library/CloudStorage/OneDrive-
    11926 > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
    11927 > structures/intermediate
    11928 > results/cryosparc_P370_J339_component_002/J339_component_002_frame_019.mrc"
    11929 
    11930 Opened J339_component_002_frame_000.mrc as #1.1, grid size 440,440,440, pixel
    11931 0.827, shown at level 0.0255, step 2, values float32 
    11932 Opened J339_component_002_frame_001.mrc as #1.2, grid size 440,440,440, pixel
    11933 0.827, shown at level 0.0253, step 2, values float32 
    11934 Opened J339_component_002_frame_002.mrc as #1.3, grid size 440,440,440, pixel
    11935 0.827, shown at level 0.0252, step 2, values float32 
    11936 Opened J339_component_002_frame_003.mrc as #1.4, grid size 440,440,440, pixel
    11937 0.827, shown at level 0.025, step 2, values float32 
    11938 Opened J339_component_002_frame_004.mrc as #1.5, grid size 440,440,440, pixel
    11939 0.827, shown at level 0.0248, step 2, values float32 
    11940 Opened J339_component_002_frame_005.mrc as #1.6, grid size 440,440,440, pixel
    11941 0.827, shown at level 0.0248, step 2, values float32 
    11942 Opened J339_component_002_frame_006.mrc as #1.7, grid size 440,440,440, pixel
    11943 0.827, shown at level 0.0247, step 2, values float32 
    11944 Opened J339_component_002_frame_007.mrc as #1.8, grid size 440,440,440, pixel
    11945 0.827, shown at level 0.0246, step 2, values float32 
    11946 Opened J339_component_002_frame_008.mrc as #1.9, grid size 440,440,440, pixel
    11947 0.827, shown at level 0.0247, step 2, values float32 
    11948 Opened J339_component_002_frame_009.mrc as #1.10, grid size 440,440,440, pixel
    11949 0.827, shown at level 0.0247, step 2, values float32 
    11950 Opened J339_component_002_frame_010.mrc as #1.11, grid size 440,440,440, pixel
    11951 0.827, shown at level 0.0248, step 2, values float32 
    11952 Opened J339_component_002_frame_011.mrc as #1.12, grid size 440,440,440, pixel
    11953 0.827, shown at level 0.0249, step 2, values float32 
    11954 Opened J339_component_002_frame_012.mrc as #1.13, grid size 440,440,440, pixel
    11955 0.827, shown at level 0.025, step 2, values float32 
    11956 Opened J339_component_002_frame_013.mrc as #1.14, grid size 440,440,440, pixel
    11957 0.827, shown at level 0.0252, step 2, values float32 
    11958 Opened J339_component_002_frame_014.mrc as #1.15, grid size 440,440,440, pixel
    11959 0.827, shown at level 0.0253, step 2, values float32 
    11960 Opened J339_component_002_frame_015.mrc as #1.16, grid size 440,440,440, pixel
    11961 0.827, shown at level 0.0254, step 2, values float32 
    11962 Opened J339_component_002_frame_016.mrc as #1.17, grid size 440,440,440, pixel
    11963 0.827, shown at level 0.0256, step 2, values float32 
    11964 Opened J339_component_002_frame_017.mrc as #1.18, grid size 440,440,440, pixel
    11965 0.827, shown at level 0.0258, step 2, values float32 
    11966 Opened J339_component_002_frame_018.mrc as #1.19, grid size 440,440,440, pixel
    11967 0.827, shown at level 0.0259, step 2, values float32 
    11968 Opened J339_component_002_frame_019.mrc as #1.20, grid size 440,440,440, pixel
    11969 0.827, shown at level 0.0261, step 2, values float32 
    11970 
    11971 > vop flip #1
    11972 
    11973 Opened J339_component_002_frame_000.mrc z flip as #2, grid size 440,440,440,
    11974 pixel 0.827, shown at step 1, values float32 
    11975 Opened J339_component_002_frame_001.mrc z flip as #3, grid size 440,440,440,
    11976 pixel 0.827, shown at step 1, values float32 
    11977 Opened J339_component_002_frame_002.mrc z flip as #4, grid size 440,440,440,
    11978 pixel 0.827, shown at step 1, values float32 
    11979 Opened J339_component_002_frame_003.mrc z flip as #5, grid size 440,440,440,
    11980 pixel 0.827, shown at step 1, values float32 
    11981 Opened J339_component_002_frame_004.mrc z flip as #6, grid size 440,440,440,
    11982 pixel 0.827, shown at step 1, values float32 
    11983 Opened J339_component_002_frame_005.mrc z flip as #7, grid size 440,440,440,
    11984 pixel 0.827, shown at step 1, values float32 
    11985 Opened J339_component_002_frame_006.mrc z flip as #8, grid size 440,440,440,
    11986 pixel 0.827, shown at step 1, values float32 
    11987 Opened J339_component_002_frame_007.mrc z flip as #9, grid size 440,440,440,
    11988 pixel 0.827, shown at step 1, values float32 
    11989 Opened J339_component_002_frame_008.mrc z flip as #10, grid size 440,440,440,
    11990 pixel 0.827, shown at step 1, values float32 
    11991 Opened J339_component_002_frame_009.mrc z flip as #11, grid size 440,440,440,
    11992 pixel 0.827, shown at step 1, values float32 
    11993 Opened J339_component_002_frame_010.mrc z flip as #12, grid size 440,440,440,
    11994 pixel 0.827, shown at step 1, values float32 
    11995 Opened J339_component_002_frame_011.mrc z flip as #13, grid size 440,440,440,
    11996 pixel 0.827, shown at step 1, values float32 
    11997 Opened J339_component_002_frame_012.mrc z flip as #14, grid size 440,440,440,
    11998 pixel 0.827, shown at step 1, values float32 
    11999 Opened J339_component_002_frame_013.mrc z flip as #15, grid size 440,440,440,
    12000 pixel 0.827, shown at step 1, values float32 
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    12002 pixel 0.827, shown at step 1, values float32 
    12003 Opened J339_component_002_frame_015.mrc z flip as #17, grid size 440,440,440,
    12004 pixel 0.827, shown at step 1, values float32 
    12005 Opened J339_component_002_frame_016.mrc z flip as #18, grid size 440,440,440,
    12006 pixel 0.827, shown at step 1, values float32 
    12007 Opened J339_component_002_frame_017.mrc z flip as #19, grid size 440,440,440,
     3250J339_component_002_frame_017.mrc z flip as #19, grid size 440,440,440,
    120083251pixel 0.827, shown at step 1, values float32 
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