Changes between Initial Version and Version 1 of Ticket #20246


Ignore:
Timestamp:
Apr 30, 2026, 10:10:45 AM (2 weeks ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #20246

    • Property Component Unassigned → Graphics
    • Property Owner set to Tom Goddard
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → glClear: invalid framebuffer operation on statusbar expose

  • Ticket #20246 – Description

    initial v1  
    33663366> close session
    33673367
    3368 > open
    3369 > /Users/tht13/Documents/JanusBind/binder_selections/complex_pdbs_for_BCHO/2_3_complex.pdb
    3370 
    3371 Chain information for 2_3_complex.pdb #1 
    3372 --- 
    3373 Chain | Description 
    3374 A | No description available 
    3375 B | No description available 
    3376  
    3377 Computing secondary structure 
    3378 
    3379 > open
    3380 > /Users/tht13/Documents/JanusBind/binder_selections/complex_pdbs_for_BCHO/4_0_complex.pdb
    3381 
    3382 Chain information for 4_0_complex.pdb #2 
    3383 --- 
    3384 Chain | Description 
    3385 A | No description available 
    3386 B | No description available 
    3387  
    3388 
    3389 > open
    3390 > /Users/tht13/Documents/JanusBind/binder_selections/complex_pdbs_for_BCHO/6_5_complex.pdb
    3391 
    3392 Chain information for 6_5_complex.pdb #3 
    3393 --- 
    3394 Chain | Description 
    3395 A | No description available 
    3396 B | No description available 
    3397  
    3398 
    3399 > open
    3400 > /Users/tht13/Documents/JanusBind/binder_selections/complex_pdbs_for_BCHO/9_1_complex.pdb
    3401 
    3402 Chain information for 9_1_complex.pdb #4 
    3403 --- 
    3404 Chain | Description 
    3405 A | No description available 
    3406 B | No description available 
    3407  
    3408 
    3409 > open
    3410 > /Users/tht13/Documents/JanusBind/binder_selections/complex_pdbs_for_BCHO/9_5_complex.pdb
    3411 
    3412 Chain information for 9_5_complex.pdb #5 
    3413 --- 
    3414 Chain | Description 
    3415 A | No description available 
    3416 B | No description available 
    3417  
    3418 
    3419 > open
    3420 > /Users/tht13/Documents/JanusBind/binder_selections/complex_pdbs_for_BCHO/12_0_complex.pdb
    3421 
    3422 Chain information for 12_0_complex.pdb #6 
    3423 --- 
    3424 Chain | Description 
    3425 A | No description available 
    3426 B | No description available 
    3427  
    3428 
    3429 > open
    3430 > /Users/tht13/Documents/JanusBind/binder_selections/complex_pdbs_for_BCHO/12_1_complex.pdb
    3431 
    3432 Chain information for 12_1_complex.pdb #7 
    3433 --- 
    3434 Chain | Description 
    3435 A | No description available 
    3436 B | No description available 
    3437  
    3438 
    3439 > open
    3440 > /Users/tht13/Documents/JanusBind/binder_selections/complex_pdbs_for_BCHO/16_6_complex.pdb
    3441 
    3442 Chain information for 16_6_complex.pdb #8 
    3443 --- 
    3444 Chain | Description 
    3445 A | No description available 
    3446 B | No description available 
    3447  
    3448 Computing secondary structure 
    3449 [Repeated 6 time(s)]
    3450 
    3451 > hide #!2-8 target m
    3452 
    3453 > color /B red
    3454 
    3455 > color /A blue
    3456 
    3457 > show #!2 target m
    3458 
    3459 > hide #!1 target m
    3460 
    3461 > show #!3 target m
    3462 
    3463 > hide #!2 target m
    3464 
    3465 > show #!4 target m
    3466 
    3467 > hide #!3 target m
    3468 
    3469 > show #!5 target m
    3470 
    3471 > hide #!4 target m
    3472 
    3473 > show #!6 target m
    3474 
    3475 > hide #!5 target m
    3476 
    3477 > show #!7 target m
    3478 
    3479 > hide #!6 target m
    3480 
    3481 > show #!8 target m
    3482 
    3483 > hide #!7 target m
    3484 
    3485 > show #!1 target m
    3486 
    3487 > hide #!8 target m
    3488 
    3489 > show #!2 target m
    3490 
    3491 > hide #!1 target m
    3492 
    3493 > show #!3 target m
    3494 
    3495 > hide #!2 target m
    3496 
    3497 > show #!4 target m
    3498 
    3499 > hide #!3 target m
    3500 
    3501 > open
    3502 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/BC1F25AE-54DA-4907-9544-6C5506739F2F/MATNNQRGNLAEHGVRTARAPATGTYNL__1.pdb
    3503 
    3504 Summary of feedback from opening
    3505 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/BC1F25AE-54DA-4907-9544-6C5506739F2F/MATNNQRGNLAEHGVRTARAPATGTYNL__1.pdb 
    3506 --- 
    3507 warnings | Ignored bad PDB record found on line 24589 
    3508 # All scores below are weighted scores, not raw scores. 
    3509  
    3510 Ignored bad PDB record found on line 24590 
    3511 #BEGIN_POSE_ENERGIES_TABLE 
    3512  
    3513 Ignored bad PDB record found on line 24591 
    3514 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    3515 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    3516 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    3517  
    3518 Ignored bad PDB record found on line 24592 
    3519 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    3520  
    3521 Ignored bad PDB record found on line 24593 
    3522 pose -8082.38 64254.4 5586.92 39.7419 385.653 -194.911 -801.513 1866.45
    3523 -96.141 -187.551 -113.632 -23.7858 0 45.6005 7954.01 -101.174 0 294.097
    3524 1108.52 71934.3 
    3525  
    3526 3318 messages similar to the above omitted 
    3527  
    3528 Chain information for MATNNQRGNLAEHGVRTARAPATGTYNL__1.pdb #9 
    3529 --- 
    3530 Chain | Description 
    3531 A B C | No description available 
    3532  
    3533 Computing secondary structure 
    3534 
    3535 > close #1-8
    3536 
    3537 > show target m
    3538 
    3539 [Repeated 1 time(s)]
    3540 
    3541 > view clip false
    3542 
    3543 > close session
    3544 
    3545 > open
    3546 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/2CFF68D2-ACB0-450A-9086-79C18D7DC9DE/MATNNQRGNLAEHGVRTARAPATGTY__1.pdb
    3547 
    3548 Summary of feedback from opening
    3549 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/2CFF68D2-ACB0-450A-9086-79C18D7DC9DE/MATNNQRGNLAEHGVRTARAPATGTY__1.pdb 
    3550 --- 
    3551 warnings | Ignored bad PDB record found on line 24574 
    3552 # All scores below are weighted scores, not raw scores. 
    3553  
    3554 Ignored bad PDB record found on line 24575 
    3555 #BEGIN_POSE_ENERGIES_TABLE 
    3556  
    3557 Ignored bad PDB record found on line 24576 
    3558 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    3559 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    3560 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    3561  
    3562 Ignored bad PDB record found on line 24577 
    3563 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    3564  
    3565 Ignored bad PDB record found on line 24578 
    3566 pose -8018.13 52021.8 5488.06 39.6483 384.485 -187.824 -800.964 1980.78
    3567 -94.9382 -187.551 -117.742 -23.7858 0 65.2895 7953.75 -108.491 0 292.567
    3568 1054.61 59741.5 
    3569  
    3570 3318 messages similar to the above omitted 
    3571  
    3572 Chain information for MATNNQRGNLAEHGVRTARAPATGTY__1.pdb #1 
    3573 --- 
    3574 Chain | Description 
    3575 A B C | No description available 
    3576  
    3577 Computing secondary structure 
    3578 
    3579 > open
    3580 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/BC1F25AE-54DA-4907-9544-6C5506739F2F/MATNNQRGNLAEHGVRTARAPATGTYNL__1.pdb
    3581 
    3582 Summary of feedback from opening
    3583 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/BC1F25AE-54DA-4907-9544-6C5506739F2F/MATNNQRGNLAEHGVRTARAPATGTYNL__1.pdb 
    3584 --- 
    3585 warnings | Ignored bad PDB record found on line 24589 
    3586 # All scores below are weighted scores, not raw scores. 
    3587  
    3588 Ignored bad PDB record found on line 24590 
    3589 #BEGIN_POSE_ENERGIES_TABLE 
    3590  
    3591 Ignored bad PDB record found on line 24591 
    3592 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    3593 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    3594 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    3595  
    3596 Ignored bad PDB record found on line 24592 
    3597 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    3598  
    3599 Ignored bad PDB record found on line 24593 
    3600 pose -8082.38 64254.4 5586.92 39.7419 385.653 -194.911 -801.513 1866.45
    3601 -96.141 -187.551 -113.632 -23.7858 0 45.6005 7954.01 -101.174 0 294.097
    3602 1108.52 71934.3 
    3603  
    3604 3318 messages similar to the above omitted 
    3605  
    3606 Chain information for MATNNQRGNLAEHGVRTARAPATGTYNL__1.pdb #2 
    3607 --- 
    3608 Chain | Description 
    3609 A B C | No description available 
    3610  
    3611 Computing secondary structure 
    3612 
    3613 > hide #1 models
    3614 
    3615 > hide #2 models
    3616 
    3617 > show #1 models
    3618 
    3619 > show #2 models
    3620 
    3621 > hide #1 models
    3622 
    3623 > hide #2 models
    3624 
    3625 > show #1 models
    3626 
    3627 > show #2 models
    3628 
    3629 > hide #2 models
    3630 
    3631 > hide #1 models
    3632 
    3633 > open
    3634 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/B81A095D-5C45-4A0C-B184-AAEA5E66FDCC/MSTNLQRGNLAEHGVRTARQAATADY__1.pdb
    3635 
    3636 Summary of feedback from opening
    3637 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/B81A095D-5C45-4A0C-B184-AAEA5E66FDCC/MSTNLQRGNLAEHGVRTARQAATADY__1.pdb 
    3638 --- 
    3639 warnings | Ignored bad PDB record found on line 24604 
    3640 # All scores below are weighted scores, not raw scores. 
    3641  
    3642 Ignored bad PDB record found on line 24605 
    3643 #BEGIN_POSE_ENERGIES_TABLE 
    3644  
    3645 Ignored bad PDB record found on line 24606 
    3646 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    3647 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    3648 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    3649  
    3650 Ignored bad PDB record found on line 24607 
    3651 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    3652  
    3653 Ignored bad PDB record found on line 24608 
    3654 pose -9722.86 18158.7 6291.36 39.8525 387.324 -151.629 -1294.59 1594.07
    3655 -90.2176 -326.14 -177.866 -39.4595 0 37.774 7994.25 -123.308 0 288.993 1028.64
    3656 23894.9 
    3657  
    3658 3318 messages similar to the above omitted 
    3659  
    3660 Chain information for MSTNLQRGNLAEHGVRTARQAATADY__1.pdb #3 
    3661 --- 
    3662 Chain | Description 
    3663 A B C | No description available 
    3664  
    3665 Computing secondary structure 
    3666 
    3667 > open
    3668 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/FB507953-9E60-4E3C-9BF4-7DEC42B128DC/MATNLQRGNRQAATGTY_aav2_trimer_INPUT_fixbb_0001.pdb
    3669 
    3670 Summary of feedback from opening
    3671 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/FB507953-9E60-4E3C-9BF4-7DEC42B128DC/MATNLQRGNRQAATGTY_aav2_trimer_INPUT_fixbb_0001.pdb 
    3672 --- 
    3673 warnings | Ignored bad PDB record found on line 24202 
    3674 # All scores below are weighted scores, not raw scores. 
    3675  
    3676 Ignored bad PDB record found on line 24203 
    3677 #BEGIN_POSE_ENERGIES_TABLE MATNLQRGNRQAATGTY_aav2_trimer_INPUT_fixbb_0001.pdb 
    3678  
    3679 Ignored bad PDB record found on line 24204 
    3680 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    3681 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    3682 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    3683  
    3684 Ignored bad PDB record found on line 24205 
    3685 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    3686  
    3687 Ignored bad PDB record found on line 24206 
    3688 pose -9101 6065.81 5590.78 21.0089 350.14 -185.857 -1709.35 885.409 -97.6146
    3689 -320.122 -213.557 -147.733 0 35.8657 3138.43 -125.807 1.69807 284.799 1024.78
    3690 5497.68 
    3691  
    3692 1566 messages similar to the above omitted 
    3693  
    3694 Chain information for MATNLQRGNRQAATGTY_aav2_trimer_INPUT_fixbb_0001.pdb #4 
    3695 --- 
    3696 Chain | Description 
    3697 A B C | No description available 
    3698  
    3699 Computing secondary structure 
    3700 
    3701 > close #1-3
    3702 
    3703 > sequence chain #4/A,B,C
    3704 
    3705 Alignment identifier is 1 
    3706 
    3707 > select /A-C:442
    3708 
    3709 51 atoms, 48 bonds, 3 residues, 1 model selected 
    3710 
    3711 > select /A-C:442-458
    3712 
    3713 759 atoms, 759 bonds, 51 residues, 1 model selected 
    3714 
    3715 > show sel atoms
    3716 
    3717 > select clear
    3718 
    3719 > show atoms
    3720 
    3721 > close session
    3722 
    3723 > open
    3724 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/9AAD0819-1F77-4105-8C90-484614A2DB67/MATNLQRGNLAEHGVRTARQAATGTY__1.pdb
    3725 
    3726 Summary of feedback from opening
    3727 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/9AAD0819-1F77-4105-8C90-484614A2DB67/MATNLQRGNLAEHGVRTARQAATGTY__1.pdb 
    3728 --- 
    3729 warnings | Ignored bad PDB record found on line 24598 
    3730 # All scores below are weighted scores, not raw scores. 
    3731  
    3732 Ignored bad PDB record found on line 24599 
    3733 #BEGIN_POSE_ENERGIES_TABLE 
    3734  
    3735 Ignored bad PDB record found on line 24600 
    3736 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    3737 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    3738 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    3739  
    3740 Ignored bad PDB record found on line 24601 
    3741 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    3742  
    3743 Ignored bad PDB record found on line 24602 
    3744 pose -9739.49 18122.9 6294.95 39.8143 388.026 -150.502 -1311.9 1594.07
    3745 -94.7271 -329.737 -177.791 -39.4595 0 35.9341 7971.42 -112.931 0 302.149
    3746 1038.34 23831.1 
    3747  
    3748 3318 messages similar to the above omitted 
    3749  
    3750 Chain information for MATNLQRGNLAEHGVRTARQAATGTY__1.pdb #1 
    3751 --- 
    3752 Chain | Description 
    3753 A B C | No description available 
    3754  
    3755 Computing secondary structure 
    3756 
    3757 > open
    3758 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/50E186F9-8AD0-4530-A21D-B35F1A286484/MATNLQRGNLAHDQVRPARQAATGTY__1.pdb
    3759 
    3760 Summary of feedback from opening
    3761 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/50E186F9-8AD0-4530-A21D-B35F1A286484/MATNLQRGNLAHDQVRPARQAATGTY__1.pdb 
    3762 --- 
    3763 warnings | Ignored bad PDB record found on line 24619 
    3764 # All scores below are weighted scores, not raw scores. 
    3765  
    3766 Ignored bad PDB record found on line 24620 
    3767 #BEGIN_POSE_ENERGIES_TABLE 
    3768  
    3769 Ignored bad PDB record found on line 24621 
    3770 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    3771 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    3772 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    3773  
    3774 Ignored bad PDB record found on line 24622 
    3775 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    3776  
    3777 Ignored bad PDB record found on line 24623 
    3778 pose -9693.27 16881.5 6247.75 40.142 388.052 -156.098 -1317.6 1804.74 -92.1992
    3779 -326.198 -177.402 -39.4595 0 36.2885 7991.58 -112.262 0 288.754 1066 22830.4 
    3780  
    3781 3318 messages similar to the above omitted 
    3782  
    3783 Chain information for MATNLQRGNLAHDQVRPARQAATGTY__1.pdb #2 
    3784 --- 
    3785 Chain | Description 
    3786 A B C | No description available 
    3787  
    3788 
    3789 > open
    3790 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/2CFF68D2-ACB0-450A-9086-79C18D7DC9DE/MATNNQRGNLAEHGVRTARAPATGTY__1.pdb
    3791 
    3792 Summary of feedback from opening
    3793 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/2CFF68D2-ACB0-450A-9086-79C18D7DC9DE/MATNNQRGNLAEHGVRTARAPATGTY__1.pdb 
    3794 --- 
    3795 warnings | Ignored bad PDB record found on line 24574 
    3796 # All scores below are weighted scores, not raw scores. 
    3797  
    3798 Ignored bad PDB record found on line 24575 
    3799 #BEGIN_POSE_ENERGIES_TABLE 
    3800  
    3801 Ignored bad PDB record found on line 24576 
    3802 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    3803 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    3804 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    3805  
    3806 Ignored bad PDB record found on line 24577 
    3807 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    3808  
    3809 Ignored bad PDB record found on line 24578 
    3810 pose -8018.13 52021.8 5488.06 39.6483 384.485 -187.824 -800.964 1980.78
    3811 -94.9382 -187.551 -117.742 -23.7858 0 65.2895 7953.75 -108.491 0 292.567
    3812 1054.61 59741.5 
    3813  
    3814 3318 messages similar to the above omitted 
    3815  
    3816 Chain information for MATNNQRGNLAEHGVRTARAPATGTY__1.pdb #3 
    3817 --- 
    3818 Chain | Description 
    3819 A B C | No description available 
    3820  
    3821 
    3822 > open
    3823 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/BC1F25AE-54DA-4907-9544-6C5506739F2F/MATNNQRGNLAEHGVRTARAPATGTYNL__1.pdb
    3824 
    3825 Summary of feedback from opening
    3826 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/BC1F25AE-54DA-4907-9544-6C5506739F2F/MATNNQRGNLAEHGVRTARAPATGTYNL__1.pdb 
    3827 --- 
    3828 warnings | Ignored bad PDB record found on line 24589 
    3829 # All scores below are weighted scores, not raw scores. 
    3830  
    3831 Ignored bad PDB record found on line 24590 
    3832 #BEGIN_POSE_ENERGIES_TABLE 
    3833  
    3834 Ignored bad PDB record found on line 24591 
    3835 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    3836 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    3837 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    3838  
    3839 Ignored bad PDB record found on line 24592 
    3840 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    3841  
    3842 Ignored bad PDB record found on line 24593 
    3843 pose -8082.38 64254.4 5586.92 39.7419 385.653 -194.911 -801.513 1866.45
    3844 -96.141 -187.551 -113.632 -23.7858 0 45.6005 7954.01 -101.174 0 294.097
    3845 1108.52 71934.3 
    3846  
    3847 3318 messages similar to the above omitted 
    3848  
    3849 Chain information for MATNNQRGNLAEHGVRTARAPATGTYNL__1.pdb #4 
    3850 --- 
    3851 Chain | Description 
    3852 A B C | No description available 
    3853  
    3854 Computing secondary structure 
    3855 [Repeated 2 time(s)]
    3856 
    3857 > hide #2-4 target m
    3858 
    3859 > show #2 target m
    3860 
    3861 > hide #1 target m
    3862 
    3863 > show #3 target m
    3864 
    3865 > hide #2 target m
    3866 
    3867 > show #4 target m
    3868 
    3869 > hide #3 target m
    3870 
    3871 > show #3 target m
    3872 
    3873 > hide #4 target m
    3874 
    3875 > show #2 target m
    3876 
    3877 > hide #3 target m
    3878 
    3879 > show #3 target m
    3880 
    3881 > hide #2 target m
    3882 
    3883 > show #4 target m
    3884 
    3885 > hide #3 target m
    3886 
    3887 > show #3 target m
    3888 
    3889 > hide #4 target m
    3890 
    3891 > show #2 target m
    3892 
    3893 > hide #3 target m
    3894 
    3895 > show #3 target m
    3896 
    3897 > hide #2 target m
    3898 
    3899 > show #4 target m
    3900 
    3901 > hide #3 target m
    3902 
    3903 > show #3 target m
    3904 
    3905 > hide #4 target m
    3906 
    3907 > show #2 target m
    3908 
    3909 > hide #3 target m
    3910 
    3911 > show #3 target m
    3912 
    3913 > hide #2 target m
    3914 
    3915 > show #2 target m
    3916 
    3917 > hide #3 target m
    3918 
    3919 > show #3 target m
    3920 
    3921 > hide #2 target m
    3922 
    3923 > show #4 target m
    3924 
    3925 > hide #3 target m
    3926 
    3927 > show #1 target m
    3928 
    3929 > hide #4 target m
    3930 
    3931 > show #2 target m
    3932 
    3933 > hide #1 target m
    3934 
    3935 > show #3 target m
    3936 
    3937 > hide #2 target m
    3938 
    3939 > show #4 target m
    3940 
    3941 > hide #3 target m
    3942 
    3943 > show #1 target m
    3944 
    3945 > hide #4 target m
    3946 
    3947 > show #2 target m
    3948 
    3949 > hide #1 target m
    3950 
    3951 > show #3 target m
    3952 
    3953 > hide #2 target m
    3954 
    3955 > show #4 target m
    3956 
    3957 > hide #3 target m
    3958 
    3959 > show #1 target m
    3960 
    3961 > hide #4 target m
    3962 
    3963 > show #2 target m
    3964 
    3965 > hide #1 target m
    3966 
    3967 > show #3 target m
    3968 
    3969 > hide #2 target m
    3970 
    3971 > show #4 target m
    3972 
    3973 > hide #3 target m
    3974 
    3975 > show #1 target m
    3976 
    3977 > hide #4 target m
    3978 
    3979 > close session
    3980 
    3981 > open
    3982 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/B81A095D-5C45-4A0C-B184-AAEA5E66FDCC/MSTNLQRGNLAEHGVRTARQAATADY__1.pdb
    3983 
    3984 Summary of feedback from opening
    3985 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/B81A095D-5C45-4A0C-B184-AAEA5E66FDCC/MSTNLQRGNLAEHGVRTARQAATADY__1.pdb 
    3986 --- 
    3987 warnings | Ignored bad PDB record found on line 24604 
    3988 # All scores below are weighted scores, not raw scores. 
    3989  
    3990 Ignored bad PDB record found on line 24605 
    3991 #BEGIN_POSE_ENERGIES_TABLE 
    3992  
    3993 Ignored bad PDB record found on line 24606 
    3994 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    3995 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    3996 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    3997  
    3998 Ignored bad PDB record found on line 24607 
    3999 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    4000  
    4001 Ignored bad PDB record found on line 24608 
    4002 pose -9722.86 18158.7 6291.36 39.8525 387.324 -151.629 -1294.59 1594.07
    4003 -90.2176 -326.14 -177.866 -39.4595 0 37.774 7994.25 -123.308 0 288.993 1028.64
    4004 23894.9 
    4005  
    4006 3318 messages similar to the above omitted 
    4007  
    4008 Chain information for MSTNLQRGNLAEHGVRTARQAATADY__1.pdb #1 
    4009 --- 
    4010 Chain | Description 
    4011 A B C | No description available 
    4012  
    4013 Computing secondary structure 
    4014 
    4015 > open
    4016 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/BF1C6DEA-0B27-4F2B-883A-88680521DB1A/MSTNLQRGNLAHDQVRPARQAATADY__1.pdb
    4017 
    4018 Summary of feedback from opening
    4019 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/BF1C6DEA-0B27-4F2B-883A-88680521DB1A/MSTNLQRGNLAHDQVRPARQAATADY__1.pdb 
    4020 --- 
    4021 warnings | Ignored bad PDB record found on line 24625 
    4022 # All scores below are weighted scores, not raw scores. 
    4023  
    4024 Ignored bad PDB record found on line 24626 
    4025 #BEGIN_POSE_ENERGIES_TABLE 
    4026  
    4027 Ignored bad PDB record found on line 24627 
    4028 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    4029 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    4030 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    4031  
    4032 Ignored bad PDB record found on line 24628 
    4033 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    4034  
    4035 Ignored bad PDB record found on line 24629 
    4036 pose -9713.98 18345.8 6273.78 39.8107 387.73 -158.494 -1303.73 1608.99
    4037 -97.0381 -326.063 -175.499 -39.4595 0 36.1793 8035.01 -124.935 0 275.597
    4038 1044.91 24108.6 
    4039  
    4040 3318 messages similar to the above omitted 
    4041  
    4042 Chain information for MSTNLQRGNLAHDQVRPARQAATADY__1.pdb #2 
    4043 --- 
    4044 Chain | Description 
    4045 A B C | No description available 
    4046  
    4047 
    4048 > open
    4049 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/EAA52BEB-5FC2-4EAD-A81D-ED20B1DB8856/VSTNAQRGNNIKQGSTIDHRQAATADV__1.pdb
    4050 
    4051 Summary of feedback from opening
    4052 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/EAA52BEB-5FC2-4EAD-A81D-ED20B1DB8856/VSTNAQRGNNIKQGSTIDHRQAATADV__1.pdb 
    4053 --- 
    4054 warnings | Ignored bad PDB record found on line 24619 
    4055 # All scores below are weighted scores, not raw scores. 
    4056  
    4057 Ignored bad PDB record found on line 24620 
    4058 #BEGIN_POSE_ENERGIES_TABLE 
    4059  
    4060 Ignored bad PDB record found on line 24621 
    4061 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    4062 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    4063 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    4064  
    4065 Ignored bad PDB record found on line 24622 
    4066 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    4067  
    4068 Ignored bad PDB record found on line 24623 
    4069 pose -9693.8 11144.7 6293.77 39.912 392.89 -162.123 -1289.39 1594.07 -90.1243
    4070 -325.946 -178.331 -39.4595 0 43.497 8030.65 -124.509 0 280.716 1031.64 16948.1 
    4071  
    4072 3324 messages similar to the above omitted 
    4073  
    4074 Chain information for VSTNAQRGNNIKQGSTIDHRQAATADV__1.pdb #3 
    4075 --- 
    4076 Chain | Description 
    4077 A B C | No description available 
    4078  
    4079 
    4080 > open
    4081 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/374A012C-7437-44A0-B9C7-7E7BC9327C02/VSTNFQTHPVLSESSSGNRQAAAADV__1.pdb
    4082 
    4083 Summary of feedback from opening
    4084 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/374A012C-7437-44A0-B9C7-7E7BC9327C02/VSTNFQTHPVLSESSSGNRQAAAADV__1.pdb 
    4085 --- 
    4086 warnings | Ignored bad PDB record found on line 24526 
    4087 # All scores below are weighted scores, not raw scores. 
    4088  
    4089 Ignored bad PDB record found on line 24527 
    4090 #BEGIN_POSE_ENERGIES_TABLE 
    4091  
    4092 Ignored bad PDB record found on line 24528 
    4093 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    4094 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    4095 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    4096  
    4097 Ignored bad PDB record found on line 24529 
    4098 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    4099  
    4100 Ignored bad PDB record found on line 24530 
    4101 pose -9745.76 13319.8 6328.9 39.6563 383.541 -152.569 -1327.02 1597.96
    4102 -94.3902 -320.122 -169.093 -41.1023 0 38.9892 8020.67 -123.044 0 279.14
    4103 1067.56 19103.1 
    4104  
    4105 3318 messages similar to the above omitted 
    4106  
    4107 Chain information for VSTNFQTHPVLSESSSGNRQAAAADV__1.pdb #4 
    4108 --- 
    4109 Chain | Description 
    4110 A B C | No description available 
    4111  
    4112 
    4113 > open
    4114 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/A47619E7-4B82-4E65-94F8-1ABB70D621CB/VSTNLEGLRDSDAGIQRSNRQAATADV__1.pdb
    4115 
    4116 Summary of feedback from opening
    4117 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/A47619E7-4B82-4E65-94F8-1ABB70D621CB/VSTNLEGLRDSDAGIQRSNRQAATADV__1.pdb 
    4118 --- 
    4119 warnings | Ignored bad PDB record found on line 24610 
    4120 # All scores below are weighted scores, not raw scores. 
    4121  
    4122 Ignored bad PDB record found on line 24611 
    4123 #BEGIN_POSE_ENERGIES_TABLE 
    4124  
    4125 Ignored bad PDB record found on line 24612 
    4126 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    4127 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    4128 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    4129  
    4130 Ignored bad PDB record found on line 24613 
    4131 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    4132  
    4133 Ignored bad PDB record found on line 24614 
    4134 pose -9769.03 13845.9 6346 39.8644 386.638 -163.74 -1351.76 1594.07 -97.6146
    4135 -323.413 -172.164 -40.3679 0 36.6254 8072.01 -114.713 0 275.974 1047.1 19611.4 
    4136  
    4137 3324 messages similar to the above omitted 
    4138  
    4139 Chain information for VSTNLEGLRDSDAGIQRSNRQAATADV__1.pdb #5 
    4140 --- 
    4141 Chain | Description 
    4142 A B C | No description available 
    4143  
    4144 
    4145 > open
    4146 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/3CE322E6-A611-4674-98CF-
    4147 > EB323964A8EE/VSTNLGGKFVERTDGQRGNLQAATADV__1.pdb
    4148 
    4149 Summary of feedback from opening
    4150 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/3CE322E6-A611-4674-98CF-
    4151 EB323964A8EE/VSTNLGGKFVERTDGQRGNLQAATADV__1.pdb 
    4152 --- 
    4153 warnings | Ignored bad PDB record found on line 24607 
    4154 # All scores below are weighted scores, not raw scores. 
    4155  
    4156 Ignored bad PDB record found on line 24608 
    4157 #BEGIN_POSE_ENERGIES_TABLE 
    4158  
    4159 Ignored bad PDB record found on line 24609 
    4160 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    4161 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    4162 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    4163  
    4164 Ignored bad PDB record found on line 24610 
    4165 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    4166  
    4167 Ignored bad PDB record found on line 24611 
    4168 pose -9732.07 15274.9 6277.36 39.9495 385.663 -156.339 -1316.14 1594.07
    4169 -99.2386 -322.402 -169.093 -39.4595 0 42.0265 8026.96 -114.748 0 291.232
    4170 1040.62 21023.3 
    4171  
    4172 3324 messages similar to the above omitted 
    4173  
    4174 Chain information for VSTNLGGKFVERTDGQRGNLQAATADV__1.pdb #6 
    4175 --- 
    4176 Chain | Description 
    4177 A B C | No description available 
    4178  
    4179 
    4180 > open
    4181 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/D449F17C-EE37-490B-9FED-2EF14F253FFE/VSTNLHRGNLMMEKGSEAQRQAATADV__1.pdb
    4182 
    4183 Summary of feedback from opening
    4184 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/D449F17C-EE37-490B-9FED-2EF14F253FFE/VSTNLHRGNLMMEKGSEAQRQAATADV__1.pdb 
    4185 --- 
    4186 warnings | Ignored bad PDB record found on line 24640 
    4187 # All scores below are weighted scores, not raw scores. 
    4188  
    4189 Ignored bad PDB record found on line 24641 
    4190 #BEGIN_POSE_ENERGIES_TABLE 
    4191  
    4192 Ignored bad PDB record found on line 24642 
    4193 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    4194 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    4195 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    4196  
    4197 Ignored bad PDB record found on line 24643 
    4198 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    4199  
    4200 Ignored bad PDB record found on line 24644 
    4201 pose -9687.15 8656.93 6255.74 39.723 384.605 -156.705 -1311.42 1594.07
    4202 -90.1243 -326.141 -170.605 -41.9298 0 37.7339 8016.17 -123.287 0 281.815
    4203 1027.92 14387.3 
    4204  
    4205 3324 messages similar to the above omitted 
    4206  
    4207 Chain information for VSTNLHRGNLMMEKGSEAQRQAATADV__1.pdb #7 
    4208 --- 
    4209 Chain | Description 
    4210 A B C | No description available 
    4211  
    4212 
    4213 > open
    4214 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/9934C4F7-D5D5-4DAE-88D2-B050A0AA6B15/VSTNLKQPQIQSGVDQRGNRQAATADV__1.pdb
    4215 
    4216 Summary of feedback from opening
    4217 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/9934C4F7-D5D5-4DAE-88D2-B050A0AA6B15/VSTNLKQPQIQSGVDQRGNRQAATADV__1.pdb 
    4218 --- 
    4219 warnings | Ignored bad PDB record found on line 24646 
    4220 # All scores below are weighted scores, not raw scores. 
    4221  
    4222 Ignored bad PDB record found on line 24647 
    4223 #BEGIN_POSE_ENERGIES_TABLE 
    4224  
    4225 Ignored bad PDB record found on line 24648 
    4226 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    4227 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    4228 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    4229  
    4230 Ignored bad PDB record found on line 24649 
    4231 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    4232  
    4233 Ignored bad PDB record found on line 24650 
    4234 pose -9848.86 18193.5 6457.65 40.0394 387.952 -156.818 -1362.86 1596.4
    4235 -99.9531 -325.181 -172.57 -43.9966 0 37.2542 8068.15 -116.909 0 270.576
    4236 1047.09 23971.4 
    4237  
    4238 3324 messages similar to the above omitted 
    4239  
    4240 Chain information for VSTNLKQPQIQSGVDQRGNRQAATADV__1.pdb #8 
    4241 --- 
    4242 Chain | Description 
    4243 A B C | No description available 
    4244  
    4245 
    4246 > open
    4247 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/6A610587-B5DD-40EF-8064-9FA38260F849/VSTNLQRGNAAAAGNHAKYAAAARQAATADV__1.pdb
    4248 
    4249 Summary of feedback from opening
    4250 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/6A610587-B5DD-40EF-8064-9FA38260F849/VSTNLQRGNAAAAGNHAKYAAAARQAATADV__1.pdb 
    4251 --- 
    4252 warnings | Ignored bad PDB record found on line 24703 
    4253 # All scores below are weighted scores, not raw scores. 
    4254  
    4255 Ignored bad PDB record found on line 24704 
    4256 #BEGIN_POSE_ENERGIES_TABLE 
    4257  
    4258 Ignored bad PDB record found on line 24705 
    4259 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    4260 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    4261 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    4262  
    4263 Ignored bad PDB record found on line 24706 
    4264 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    4265  
    4266 Ignored bad PDB record found on line 24707 
    4267 pose -9688.41 10080.4 6253.58 39.8007 386.37 -167.149 -1296.58 1594.07
    4268 -96.7887 -326.024 -175.499 -39.4595 0 36.5655 8006.38 -120.27 0 313.621
    4269 1024.55 15825.1 
    4270  
    4271 3348 messages similar to the above omitted 
    4272  
    4273 Chain information for VSTNLQRGNAAAAGNHAKYAAAARQAATADV__1.pdb #9 
    4274 --- 
    4275 Chain | Description 
    4276 A B C | No description available 
    4277  
    4278 Computing secondary structure 
    4279 [Repeated 7 time(s)]
    4280 
    4281 > hide #2-9 target m
    4282 
    4283 > show #2 target m
    4284 
    4285 > hide #1 target m
    4286 
    4287 > show #3 target m
    4288 
    4289 > hide #2 target m
    4290 
    4291 > show #4 target m
    4292 
    4293 > hide #3 target m
    4294 
    4295 > show #5 target m
    4296 
    4297 > hide #4 target m
    4298 
    4299 > show #6 target m
    4300 
    4301 > hide #5 target m
    4302 
    4303 > show #7 target m
    4304 
    4305 > hide #6 target m
    4306 
    4307 > show #8 target m
    4308 
    4309 > hide #7 target m
    4310 
    4311 > show #9 target m
    4312 
    4313 > hide #8 target m
    4314 
    4315 > show #9 atoms
    4316 
    4317 > open
    4318 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/B4C2AF32-2167-4541-AAEA-261EA7DDE048/MATNNQRGNLAHDQVRPARAPATGTYNL__1.pdb
    4319 
    4320 Summary of feedback from opening
    4321 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/B4C2AF32-2167-4541-AAEA-261EA7DDE048/MATNNQRGNLAHDQVRPARAPATGTYNL__1.pdb 
    4322 --- 
    4323 warnings | Ignored bad PDB record found on line 24610 
    4324 # All scores below are weighted scores, not raw scores. 
    4325  
    4326 Ignored bad PDB record found on line 24611 
    4327 #BEGIN_POSE_ENERGIES_TABLE 
    4328  
    4329 Ignored bad PDB record found on line 24612 
    4330 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    4331 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    4332 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    4333  
    4334 Ignored bad PDB record found on line 24613 
    4335 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    4336  
    4337 Ignored bad PDB record found on line 24614 
    4338 pose -7994.24 52100.6 5474.71 39.5868 385.322 -191.564 -791.336 1746.9
    4339 -94.9526 -187.551 -116.656 -23.7835 0 41.2829 7941.1 -101.434 0 280.701
    4340 1143.79 59652.5 
    4341  
    4342 3318 messages similar to the above omitted 
    4343  
    4344 Chain information for MATNNQRGNLAHDQVRPARAPATGTYNL__1.pdb #10 
    4345 --- 
    4346 Chain | Description 
    4347 A B C | No description available 
    4348  
    4349 Computing secondary structure 
    4350 
    4351 > hide #9 models
    4352 
    4353 > view clip false
    4354 
    4355 > show target m
    4356 
    4357 > hide target m
    4358 
    4359 > show #10 models
    4360 
    4361 > show #9 models
    4362 
    4363 > hide #9 models
    4364 
    4365 > close session
    4366 
    4367 > open
    4368 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/2CFF68D2-ACB0-450A-9086-79C18D7DC9DE/MATNNQRGNLAEHGVRTARAPATGTY__1.pdb
    4369 
    4370 Summary of feedback from opening
    4371 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/2CFF68D2-ACB0-450A-9086-79C18D7DC9DE/MATNNQRGNLAEHGVRTARAPATGTY__1.pdb 
    4372 --- 
    4373 warnings | Ignored bad PDB record found on line 24574 
    4374 # All scores below are weighted scores, not raw scores. 
    4375  
    4376 Ignored bad PDB record found on line 24575 
    4377 #BEGIN_POSE_ENERGIES_TABLE 
    4378  
    4379 Ignored bad PDB record found on line 24576 
    4380 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    4381 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    4382 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    4383  
    4384 Ignored bad PDB record found on line 24577 
    4385 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    4386  
    4387 Ignored bad PDB record found on line 24578 
    4388 pose -8018.13 52021.8 5488.06 39.6483 384.485 -187.824 -800.964 1980.78
    4389 -94.9382 -187.551 -117.742 -23.7858 0 65.2895 7953.75 -108.491 0 292.567
    4390 1054.61 59741.5 
    4391  
    4392 3318 messages similar to the above omitted 
    4393  
    4394 Chain information for MATNNQRGNLAEHGVRTARAPATGTY__1.pdb #1 
    4395 --- 
    4396 Chain | Description 
    4397 A B C | No description available 
    4398  
    4399 Computing secondary structure 
    4400 
    4401 > open
    4402 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/BC1F25AE-54DA-4907-9544-6C5506739F2F/MATNNQRGNLAEHGVRTARAPATGTYNL__1.pdb
    4403 
    4404 Summary of feedback from opening
    4405 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/BC1F25AE-54DA-4907-9544-6C5506739F2F/MATNNQRGNLAEHGVRTARAPATGTYNL__1.pdb 
    4406 --- 
    4407 warnings | Ignored bad PDB record found on line 24589 
    4408 # All scores below are weighted scores, not raw scores. 
    4409  
    4410 Ignored bad PDB record found on line 24590 
    4411 #BEGIN_POSE_ENERGIES_TABLE 
    4412  
    4413 Ignored bad PDB record found on line 24591 
    4414 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    4415 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    4416 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    4417  
    4418 Ignored bad PDB record found on line 24592 
    4419 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    4420  
    4421 Ignored bad PDB record found on line 24593 
    4422 pose -8082.38 64254.4 5586.92 39.7419 385.653 -194.911 -801.513 1866.45
    4423 -96.141 -187.551 -113.632 -23.7858 0 45.6005 7954.01 -101.174 0 294.097
    4424 1108.52 71934.3 
    4425  
    4426 3318 messages similar to the above omitted 
    4427  
    4428 Chain information for MATNNQRGNLAEHGVRTARAPATGTYNL__1.pdb #2 
    4429 --- 
    4430 Chain | Description 
    4431 A B C | No description available 
    4432  
    4433 
    4434 > open
    4435 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/B4C2AF32-2167-4541-AAEA-261EA7DDE048/MATNNQRGNLAHDQVRPARAPATGTYNL__1.pdb
    4436 
    4437 Summary of feedback from opening
    4438 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/B4C2AF32-2167-4541-AAEA-261EA7DDE048/MATNNQRGNLAHDQVRPARAPATGTYNL__1.pdb 
    4439 --- 
    4440 warnings | Ignored bad PDB record found on line 24610 
    4441 # All scores below are weighted scores, not raw scores. 
    4442  
    4443 Ignored bad PDB record found on line 24611 
    4444 #BEGIN_POSE_ENERGIES_TABLE 
    4445  
    4446 Ignored bad PDB record found on line 24612 
    4447 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    4448 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    4449 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    4450  
    4451 Ignored bad PDB record found on line 24613 
    4452 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    4453  
    4454 Ignored bad PDB record found on line 24614 
    4455 pose -7994.24 52100.6 5474.71 39.5868 385.322 -191.564 -791.336 1746.9
    4456 -94.9526 -187.551 -116.656 -23.7835 0 41.2829 7941.1 -101.434 0 280.701
    4457 1143.79 59652.5 
    4458  
    4459 3318 messages similar to the above omitted 
    4460  
    4461 Chain information for MATNNQRGNLAHDQVRPARAPATGTYNL__1.pdb #3 
    4462 --- 
    4463 Chain | Description 
    4464 A B C | No description available 
    4465  
    4466 
    4467 > open
    4468 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/B81A095D-5C45-4A0C-B184-AAEA5E66FDCC/MSTNLQRGNLAEHGVRTARQAATADY__1.pdb
    4469 
    4470 Summary of feedback from opening
    4471 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/B81A095D-5C45-4A0C-B184-AAEA5E66FDCC/MSTNLQRGNLAEHGVRTARQAATADY__1.pdb 
    4472 --- 
    4473 warnings | Ignored bad PDB record found on line 24604 
    4474 # All scores below are weighted scores, not raw scores. 
    4475  
    4476 Ignored bad PDB record found on line 24605 
    4477 #BEGIN_POSE_ENERGIES_TABLE 
    4478  
    4479 Ignored bad PDB record found on line 24606 
    4480 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    4481 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    4482 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    4483  
    4484 Ignored bad PDB record found on line 24607 
    4485 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    4486  
    4487 Ignored bad PDB record found on line 24608 
    4488 pose -9722.86 18158.7 6291.36 39.8525 387.324 -151.629 -1294.59 1594.07
    4489 -90.2176 -326.14 -177.866 -39.4595 0 37.774 7994.25 -123.308 0 288.993 1028.64
    4490 23894.9 
    4491  
    4492 3318 messages similar to the above omitted 
    4493  
    4494 Chain information for MSTNLQRGNLAEHGVRTARQAATADY__1.pdb #4 
    4495 --- 
    4496 Chain | Description 
    4497 A B C | No description available 
    4498  
    4499 Computing secondary structure 
    4500 [Repeated 2 time(s)]
    4501 
    4502 > hide target m
    4503 
    4504 > show #1 target m
    4505 
    4506 > show #2 target m
    4507 
    4508 > hide #1 target m
    4509 
    4510 > show #3 target m
    4511 
    4512 > hide #2 target m
    4513 
    4514 > show #4 target m
    4515 
    4516 > hide #3 target m
    4517 
    4518 > show #1 target m
    4519 
    4520 > hide #4 target m
    4521 
    4522 > show #2 target m
    4523 
    4524 > hide #1 target m
    4525 
    4526 > show #3 target m
    4527 
    4528 > hide #2 target m
    4529 
    4530 > show #2 target m
    4531 
    4532 > hide #3 target m
    4533 
    4534 > show #3 target m
    4535 
    4536 > hide #2 target m
    4537 
    4538 > show #4 target m
    4539 
    4540 > hide #3 target m
    4541 
    4542 > close session
    4543 
    4544 > open
    4545 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/ADA12392-5DF2-4277-A205-6AA7C14347B3/VSTNFQTHPVLSESSSGNRQAAAADV__2.pdb
    4546 
    4547 Summary of feedback from opening
    4548 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/ADA12392-5DF2-4277-A205-6AA7C14347B3/VSTNFQTHPVLSESSSGNRQAAAADV__2.pdb 
    4549 --- 
    4550 warnings | Ignored bad PDB record found on line 24526 
    4551 # All scores below are weighted scores, not raw scores. 
    4552  
    4553 Ignored bad PDB record found on line 24527 
    4554 #BEGIN_POSE_ENERGIES_TABLE 
    4555  
    4556 Ignored bad PDB record found on line 24528 
    4557 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    4558 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    4559 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    4560  
    4561 Ignored bad PDB record found on line 24529 
    4562 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    4563  
    4564 Ignored bad PDB record found on line 24530 
    4565 pose -9719.16 17017.4 6310.46 39.815 380.016 -147.54 -1323.16 1652.98 -91.5231
    4566 -320.122 -178.393 -39.7047 0 37.2527 8019.37 -111.48 0 279.14 1076.91 22882.3 
    4567  
    4568 3318 messages similar to the above omitted 
    4569  
    4570 Chain information for VSTNFQTHPVLSESSSGNRQAAAADV__2.pdb #1 
    4571 --- 
    4572 Chain | Description 
    4573 A B C | No description available 
    4574  
    4575 Computing secondary structure 
    4576 
    4577 > sequence chain #1/A,B,C
    4578 
    4579 Alignment identifier is 1 
    4580 
    4581 > select /A:363-367/B:891-895/C:1419-1423
    4582 
    4583 225 atoms, 225 bonds, 15 residues, 1 model selected 
    4584 
    4585 > select /A:363-389/B:891-917/C:1419-1445
    4586 
    4587 1125 atoms, 1131 bonds, 81 residues, 1 model selected 
    4588 
    4589 > show sel atoms
    4590 
    4591 > open
    4592 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/9AAD0819-1F77-4105-8C90-484614A2DB67/MATNLQRGNLAEHGVRTARQAATGTY__1.pdb
    4593 
    4594 Summary of feedback from opening
    4595 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/9AAD0819-1F77-4105-8C90-484614A2DB67/MATNLQRGNLAEHGVRTARQAATGTY__1.pdb 
    4596 --- 
    4597 warnings | Ignored bad PDB record found on line 24598 
    4598 # All scores below are weighted scores, not raw scores. 
    4599  
    4600 Ignored bad PDB record found on line 24599 
    4601 #BEGIN_POSE_ENERGIES_TABLE 
    4602  
    4603 Ignored bad PDB record found on line 24600 
    4604 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    4605 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    4606 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    4607  
    4608 Ignored bad PDB record found on line 24601 
    4609 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    4610  
    4611 Ignored bad PDB record found on line 24602 
    4612 pose -9739.49 18122.9 6294.95 39.8143 388.026 -150.502 -1311.9 1594.07
    4613 -94.7271 -329.737 -177.791 -39.4595 0 35.9341 7971.42 -112.931 0 302.149
    4614 1038.34 23831.1 
    4615  
    4616 3318 messages similar to the above omitted 
    4617  
    4618 Chain information for MATNLQRGNLAEHGVRTARQAATGTY__1.pdb #2 
    4619 --- 
    4620 Chain | Description 
    4621 A B C | No description available 
    4622  
    4623 Computing secondary structure 
    4624 
    4625 > hide #2 target m
    4626 
    4627 > show #2 target m
    4628 
    4629 > hide #1 target m
    4630 
    4631 > show #1 target m
    4632 
    4633 > hide #2 target m
    4634 
    4635 > show #2 target m
    4636 
    4637 > hide #1 target m
    4638 
    4639 > show #1 target m
    4640 
    4641 > hide #2 target m
    4642 
    4643 > show #2 target m
    4644 
    4645 > hide #1 target m
    4646 
    4647 > show #1 target m
    4648 
    4649 > hide #2 target m
    4650 
    4651 > show #2 target m
    4652 
    4653 > hide #1 target m
    4654 
    4655 > show #1 target m
    4656 
    4657 > hide #2 target m
    4658 
    4659 > select clear
    4660 
    4661 > open
    4662 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/4C407BFD-D6AA-4F9F-9A41-FF2EE808115B/MATNNQRGNRAPATGTY_aav2_trimer_INPUT_fixbb_0001.pdb
    4663 
    4664 Summary of feedback from opening
    4665 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/4C407BFD-D6AA-4F9F-9A41-FF2EE808115B/MATNNQRGNRAPATGTY_aav2_trimer_INPUT_fixbb_0001.pdb 
    4666 --- 
    4667 warnings | Ignored bad PDB record found on line 24178 
    4668 # All scores below are weighted scores, not raw scores. 
    4669  
    4670 Ignored bad PDB record found on line 24179 
    4671 #BEGIN_POSE_ENERGIES_TABLE MATNNQRGNRAPATGTY_aav2_trimer_INPUT_fixbb_0001.pdb 
    4672  
    4673 Ignored bad PDB record found on line 24180 
    4674 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    4675 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    4676 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    4677  
    4678 Ignored bad PDB record found on line 24181 
    4679 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    4680  
    4681 Ignored bad PDB record found on line 24182 
    4682 pose -9105.1 6324.71 5631.69 22.4099 347.633 -178.89 -1670.87 924.218 -97.6146
    4683 -320.122 -221.365 -127.065 0 35.9598 3182.81 -126.404 0.23392 275.217 1025.61
    4684 5923.06 
    4685  
    4686 1566 messages similar to the above omitted 
    4687  
    4688 Chain information for MATNNQRGNRAPATGTY_aav2_trimer_INPUT_fixbb_0001.pdb #3 
    4689 --- 
    4690 Chain | Description 
    4691 A B C | No description available 
    4692  
    4693 
    4694 > open
    4695 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/18E8D34A-C544-4AC5-9DD3-1E96E5D5B1EE/MSTNLQRGNRQAATADY_aav2_trimer_INPUT_fixbb_0001.pdb
    4696 
    4697 Summary of feedback from opening
    4698 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/18E8D34A-C544-4AC5-9DD3-1E96E5D5B1EE/MSTNLQRGNRQAATADY_aav2_trimer_INPUT_fixbb_0001.pdb 
    4699 --- 
    4700 warnings | Ignored bad PDB record found on line 24208 
    4701 # All scores below are weighted scores, not raw scores. 
    4702  
    4703 Ignored bad PDB record found on line 24209 
    4704 #BEGIN_POSE_ENERGIES_TABLE MSTNLQRGNRQAATADY_aav2_trimer_INPUT_fixbb_0001.pdb 
    4705  
    4706 Ignored bad PDB record found on line 24210 
    4707 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    4708 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    4709 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    4710  
    4711 Ignored bad PDB record found on line 24211 
    4712 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    4713  
    4714 Ignored bad PDB record found on line 24212 
    4715 pose -9117.17 6368.28 5645.87 21.9804 347.705 -191.167 -1683.29 884.273
    4716 -97.6146 -320.122 -207.396 -131.546 0 36.1999 3238.34 -128.117 0.2709 271.643
    4717 1021.26 5959.4 
    4718  
    4719 1566 messages similar to the above omitted 
    4720  
    4721 Chain information for MSTNLQRGNRQAATADY_aav2_trimer_INPUT_fixbb_0001.pdb #4 
    4722 --- 
    4723 Chain | Description 
    4724 A B C | No description available 
    4725  
    4726 Computing secondary structure 
    4727 [Repeated 1 time(s)]
    4728 
    4729 > close #1-2
    4730 
    4731 > sequence chain #3/A,B,C
    4732 
    4733 Alignment identifier is 1 
    4734 
    4735 > sequence chain #4/A,B,C
    4736 
    4737 Alignment identifier is 2 
    4738 
    4739 > hide #4 models
    4740 
    4741 > select #3/A-C:442-443
    4742 
    4743 81 atoms, 78 bonds, 6 residues, 1 model selected 
    4744 
    4745 > select #3/A-C:442-444
    4746 
    4747 123 atoms, 120 bonds, 9 residues, 1 model selected 
    4748 
    4749 > select #3/A-C:442-443
    4750 
    4751 81 atoms, 78 bonds, 6 residues, 1 model selected 
    4752 
    4753 > select #3/A-C:442-458
    4754 
    4755 735 atoms, 738 bonds, 51 residues, 1 model selected 
    4756 
    4757 > show sel atoms
    4758 
    4759 > open
    4760 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/E2A92555-AD83-4873-ACFF-
    4761 > AD7EC5C532D9/MATNNQRGNRAPATGTYNL_aav2_trimer_INPUT_fixbb_0001.pdb
    4762 
    4763 Summary of feedback from opening
    4764 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/E2A92555-AD83-4873-ACFF-
    4765 AD7EC5C532D9/MATNNQRGNRAPATGTYNL_aav2_trimer_INPUT_fixbb_0001.pdb 
    4766 --- 
    4767 warnings | Ignored bad PDB record found on line 24193 
    4768 # All scores below are weighted scores, not raw scores. 
    4769  
    4770 Ignored bad PDB record found on line 24194 
    4771 #BEGIN_POSE_ENERGIES_TABLE
    4772 MATNNQRGNRAPATGTYNL_aav2_trimer_INPUT_fixbb_0001.pdb 
    4773  
    4774 Ignored bad PDB record found on line 24195 
    4775 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    4776 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    4777 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    4778  
    4779 Ignored bad PDB record found on line 24196 
    4780 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    4781  
    4782 Ignored bad PDB record found on line 24197 
    4783 pose -9175.05 9874.11 5619.12 23.1652 352.333 -177.277 -1665.22 918.684
    4784 -97.6146 -320.122 -224.116 -124.927 0 35.9598 3175.51 -128.62 0.42371 276.746
    4785 1023.29 9386.39 
    4786  
    4787 1566 messages similar to the above omitted 
    4788  
    4789 Chain information for MATNNQRGNRAPATGTYNL_aav2_trimer_INPUT_fixbb_0001.pdb #1 
    4790 --- 
    4791 Chain | Description 
    4792 A B C | No description available 
    4793  
    4794 Computing secondary structure 
    4795 
    4796 > hide #1 models
    4797 
    4798 > hide #3 models
    4799 
    4800 > select add #3
    4801 
    4802 24165 atoms, 24540 bonds, 1557 residues, 1 model selected 
    4803 
    4804 > sequence chain #3/A,B,C
    4805 
    4806 Alignment identifier is 3 
    4807 
    4808 > select subtract #3
    4809 
    4810 Nothing selected 
    4811 
    4812 > show #4 target m
    4813 
    4814 [Repeated 1 time(s)]
    4815 
    4816 > select clear
    4817 
    4818 > show target m
    4819 
    4820 > sequence chain #3/A,B,C
    4821 
    4822 Alignment identifier is 1 
    4823 
    4824 > sequence chain #4/A,B,C
    4825 
    4826 Alignment identifier is 2 
    4827 
    4828 > sequence chain #1/A,B,C
    4829 
    4830 Alignment identifier is 3 
    4831 
    4832 > hide #3 models
    4833 
    4834 > hide #4 models
    4835 
    4836 > select #1/A-C:442-443
    4837 
    4838 81 atoms, 78 bonds, 6 residues, 1 model selected 
    4839 
    4840 > select #1/A-C:442-460
    4841 
    4842 834 atoms, 837 bonds, 57 residues, 1 model selected 
    4843 
    4844 > show sel atoms
    4845 
    4846 > close session
    4847 
    4848 > open
    4849 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/18E8D34A-C544-4AC5-9DD3-1E96E5D5B1EE/MSTNLQRGNRQAATADY_aav2_trimer_INPUT_fixbb_0001.pdb
    4850 
    4851 Summary of feedback from opening
    4852 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/18E8D34A-C544-4AC5-9DD3-1E96E5D5B1EE/MSTNLQRGNRQAATADY_aav2_trimer_INPUT_fixbb_0001.pdb 
    4853 --- 
    4854 warnings | Ignored bad PDB record found on line 24208 
    4855 # All scores below are weighted scores, not raw scores. 
    4856  
    4857 Ignored bad PDB record found on line 24209 
    4858 #BEGIN_POSE_ENERGIES_TABLE MSTNLQRGNRQAATADY_aav2_trimer_INPUT_fixbb_0001.pdb 
    4859  
    4860 Ignored bad PDB record found on line 24210 
    4861 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    4862 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    4863 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    4864  
    4865 Ignored bad PDB record found on line 24211 
    4866 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    4867  
    4868 Ignored bad PDB record found on line 24212 
    4869 pose -9117.17 6368.28 5645.87 21.9804 347.705 -191.167 -1683.29 884.273
    4870 -97.6146 -320.122 -207.396 -131.546 0 36.1999 3238.34 -128.117 0.2709 271.643
    4871 1021.26 5959.4 
    4872  
    4873 1566 messages similar to the above omitted 
    4874  
    4875 Chain information for MSTNLQRGNRQAATADY_aav2_trimer_INPUT_fixbb_0001.pdb #1 
    4876 --- 
    4877 Chain | Description 
    4878 A B C | No description available 
    4879  
    4880 Computing secondary structure 
    4881 
    4882 > open
    4883 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/31D4F870-732C-40A7-B6AE-86BEE200440E/MSTNLQRGNRQAATADY_aav2_trimer_INPUT_fixbb_0002.pdb
    4884 
    4885 Summary of feedback from opening
    4886 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/31D4F870-732C-40A7-B6AE-86BEE200440E/MSTNLQRGNRQAATADY_aav2_trimer_INPUT_fixbb_0002.pdb 
    4887 --- 
    4888 warnings | Ignored bad PDB record found on line 24208 
    4889 # All scores below are weighted scores, not raw scores. 
    4890  
    4891 Ignored bad PDB record found on line 24209 
    4892 #BEGIN_POSE_ENERGIES_TABLE MSTNLQRGNRQAATADY_aav2_trimer_INPUT_fixbb_0002.pdb 
    4893  
    4894 Ignored bad PDB record found on line 24210 
    4895 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    4896 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    4897 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    4898  
    4899 Ignored bad PDB record found on line 24211 
    4900 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    4901  
    4902 Ignored bad PDB record found on line 24212 
    4903 pose -9082.08 6366.94 5615.11 22.2027 341.919 -187.334 -1669.15 882.365
    4904 -97.6146 -320.122 -198.936 -124.579 0 36.1999 3213.45 -128.117 0.22178 271.643
    4905 1021.26 5963.37 
    4906  
    4907 1566 messages similar to the above omitted 
    4908  
    4909 Chain information for MSTNLQRGNRQAATADY_aav2_trimer_INPUT_fixbb_0002.pdb #2 
    4910 --- 
    4911 Chain | Description 
    4912 A B C | No description available 
    4913  
    4914 
    4915 > open
    4916 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/27686B66-53BE-4439-8300-8FA62B1CB39F/MSTNLQRGNRQAATADY_aav2_trimer_INPUT_fixbb_0003.pdb
    4917 
    4918 Summary of feedback from opening
    4919 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/27686B66-53BE-4439-8300-8FA62B1CB39F/MSTNLQRGNRQAATADY_aav2_trimer_INPUT_fixbb_0003.pdb 
    4920 --- 
    4921 warnings | Ignored bad PDB record found on line 24208 
    4922 # All scores below are weighted scores, not raw scores. 
    4923  
    4924 Ignored bad PDB record found on line 24209 
    4925 #BEGIN_POSE_ENERGIES_TABLE MSTNLQRGNRQAATADY_aav2_trimer_INPUT_fixbb_0003.pdb 
    4926  
    4927 Ignored bad PDB record found on line 24210 
    4928 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    4929 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    4930 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    4931  
    4932 Ignored bad PDB record found on line 24211 
    4933 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    4934  
    4935 Ignored bad PDB record found on line 24212 
    4936 pose -9117.3 6388.05 5604.23 23.456 348.62 -182.042 -1673.92 886.171 -97.6146
    4937 -320.122 -198.766 -135.858 0 36.1999 3136.77 -128.117 0.45119 271.643 1021.26
    4938 5863.12 
    4939  
    4940 1566 messages similar to the above omitted 
    4941  
    4942 Chain information for MSTNLQRGNRQAATADY_aav2_trimer_INPUT_fixbb_0003.pdb #3 
    4943 --- 
    4944 Chain | Description 
    4945 A B C | No description available 
    4946  
    4947 
    4948 > open
    4949 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/336ECDD1-344C-4C93-894D-5F432B02058F/MSTNLQRGNRQAATADY_aav2_trimer_INPUT_fixbb_0004.pdb
    4950 
    4951 Summary of feedback from opening
    4952 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/336ECDD1-344C-4C93-894D-5F432B02058F/MSTNLQRGNRQAATADY_aav2_trimer_INPUT_fixbb_0004.pdb 
    4953 --- 
    4954 warnings | Ignored bad PDB record found on line 24208 
    4955 # All scores below are weighted scores, not raw scores. 
    4956  
    4957 Ignored bad PDB record found on line 24209 
    4958 #BEGIN_POSE_ENERGIES_TABLE MSTNLQRGNRQAATADY_aav2_trimer_INPUT_fixbb_0004.pdb 
    4959  
    4960 Ignored bad PDB record found on line 24210 
    4961 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    4962 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    4963 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    4964  
    4965 Ignored bad PDB record found on line 24211 
    4966 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    4967  
    4968 Ignored bad PDB record found on line 24212 
    4969 pose -9083.22 6321.53 5609.77 22.0529 345.219 -182.239 -1674.69 886.456
    4970 -97.6146 -320.122 -213.152 -123.696 0 36.1999 3191.32 -128.117 0.19069 271.643
    4971 1021.26 5882.79 
    4972  
    4973 1566 messages similar to the above omitted 
    4974  
    4975 Chain information for MSTNLQRGNRQAATADY_aav2_trimer_INPUT_fixbb_0004.pdb #4 
    4976 --- 
    4977 Chain | Description 
    4978 A B C | No description available 
    4979  
    4980 
    4981 > open
    4982 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/27EDDB98-83B5-4CB0-92BC-3BD3C1F4988C/MSTNLQRGNRQAATADY_aav2_trimer_INPUT_fixbb_0005.pdb
    4983 
    4984 Summary of feedback from opening
    4985 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/27EDDB98-83B5-4CB0-92BC-3BD3C1F4988C/MSTNLQRGNRQAATADY_aav2_trimer_INPUT_fixbb_0005.pdb 
    4986 --- 
    4987 warnings | Ignored bad PDB record found on line 24208 
    4988 # All scores below are weighted scores, not raw scores. 
    4989  
    4990 Ignored bad PDB record found on line 24209 
    4991 #BEGIN_POSE_ENERGIES_TABLE MSTNLQRGNRQAATADY_aav2_trimer_INPUT_fixbb_0005.pdb 
    4992  
    4993 Ignored bad PDB record found on line 24210 
    4994 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    4995 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    4996 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    4997  
    4998 Ignored bad PDB record found on line 24211 
    4999 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    5000  
    5001 Ignored bad PDB record found on line 24212 
    5002 pose -9080.23 6306.18 5618.51 22.8739 349.274 -185.984 -1665.13 889.003
    5003 -97.6146 -320.122 -200.495 -127.01 0 36.1999 3205.75 -128.117 0.31226 271.643
    5004 1021.26 5916.31 
    5005  
    5006 1566 messages similar to the above omitted 
    5007  
    5008 Chain information for MSTNLQRGNRQAATADY_aav2_trimer_INPUT_fixbb_0005.pdb #5 
    5009 --- 
    5010 Chain | Description 
    5011 A B C | No description available 
    5012  
    5013 Computing secondary structure 
    5014 [Repeated 3 time(s)]
    5015 
    5016 > show atoms
    5017 
    5018 > hide #2-5 target m
    5019 
    5020 > show #2 target m
    5021 
    5022 > hide #1 target m
    5023 
    5024 > show #3 target m
    5025 
    5026 > hide #2 target m
    5027 
    5028 > show #2 models
    5029 
    5030 > show #1 models
    5031 
    5032 > hide #2 models
    5033 
    5034 > show #2 models
    5035 
    5036 > show #4 models
    5037 
    5038 > hide #4 models
    5039 
    5040 > show #5 models
    5041 
    5042 > show #4 models
    5043 
    5044 > hide #1 models
    5045 
    5046 > hide #2 models
    5047 
    5048 > hide #4 models
    5049 
    5050 > hide #5 models
    5051 
    5052 > close session
    5053 
    5054 > open
    5055 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/2CFF68D2-ACB0-450A-9086-79C18D7DC9DE/MATNNQRGNLAEHGVRTARAPATGTY__1.pdb
    5056 
    5057 Summary of feedback from opening
    5058 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/2CFF68D2-ACB0-450A-9086-79C18D7DC9DE/MATNNQRGNLAEHGVRTARAPATGTY__1.pdb 
    5059 --- 
    5060 warnings | Ignored bad PDB record found on line 24574 
    5061 # All scores below are weighted scores, not raw scores. 
    5062  
    5063 Ignored bad PDB record found on line 24575 
    5064 #BEGIN_POSE_ENERGIES_TABLE 
    5065  
    5066 Ignored bad PDB record found on line 24576 
    5067 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    5068 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    5069 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    5070  
    5071 Ignored bad PDB record found on line 24577 
    5072 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    5073  
    5074 Ignored bad PDB record found on line 24578 
    5075 pose -8018.13 52021.8 5488.06 39.6483 384.485 -187.824 -800.964 1980.78
    5076 -94.9382 -187.551 -117.742 -23.7858 0 65.2895 7953.75 -108.491 0 292.567
    5077 1054.61 59741.5 
    5078  
    5079 3318 messages similar to the above omitted 
    5080  
    5081 Chain information for MATNNQRGNLAEHGVRTARAPATGTY__1.pdb #1 
    5082 --- 
    5083 Chain | Description 
    5084 A B C | No description available 
    5085  
    5086 Computing secondary structure 
    5087 
    5088 > close
    5089 
    5090 > open
    5091 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/D664E51E-4C75-4ABE-8AEE-5700FC630E22/MATNNQRGNLAEHGVRTARAPATGTY__1.pdb
    5092 
    5093 Summary of feedback from opening
    5094 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/D664E51E-4C75-4ABE-8AEE-5700FC630E22/MATNNQRGNLAEHGVRTARAPATGTY__1.pdb 
    5095 --- 
    5096 warnings | Ignored bad PDB record found on line 24574 
    5097 # All scores below are weighted scores, not raw scores. 
    5098  
    5099 Ignored bad PDB record found on line 24575 
    5100 #BEGIN_POSE_ENERGIES_TABLE 
    5101  
    5102 Ignored bad PDB record found on line 24576 
    5103 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    5104 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    5105 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    5106  
    5107 Ignored bad PDB record found on line 24577 
    5108 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    5109  
    5110 Ignored bad PDB record found on line 24578 
    5111 pose -9714.01 18595.6 6285.73 39.8103 386.278 -153.587 -1321.63 1601.21
    5112 -95.6222 -330.922 -180.403 -39.4595 0 38.9146 7951.26 -114.391 0 292.567
    5113 1050.48 24291.9 
    5114  
    5115 3318 messages similar to the above omitted 
    5116  
    5117 Chain information for MATNNQRGNLAEHGVRTARAPATGTY__1.pdb #1 
    5118 --- 
    5119 Chain | Description 
    5120 A B C | No description available 
    5121  
    5122 Computing secondary structure 
    5123 
    5124 > open
    5125 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/2CFF68D2-ACB0-450A-9086-79C18D7DC9DE/MATNNQRGNLAEHGVRTARAPATGTY__1.pdb
    5126 
    5127 Summary of feedback from opening
    5128 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/2CFF68D2-ACB0-450A-9086-79C18D7DC9DE/MATNNQRGNLAEHGVRTARAPATGTY__1.pdb 
    5129 --- 
    5130 warnings | Ignored bad PDB record found on line 24574 
    5131 # All scores below are weighted scores, not raw scores. 
    5132  
    5133 Ignored bad PDB record found on line 24575 
    5134 #BEGIN_POSE_ENERGIES_TABLE 
    5135  
    5136 Ignored bad PDB record found on line 24576 
    5137 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    5138 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    5139 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    5140  
    5141 Ignored bad PDB record found on line 24577 
    5142 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    5143  
    5144 Ignored bad PDB record found on line 24578 
    5145 pose -8018.13 52021.8 5488.06 39.6483 384.485 -187.824 -800.964 1980.78
    5146 -94.9382 -187.551 -117.742 -23.7858 0 65.2895 7953.75 -108.491 0 292.567
    5147 1054.61 59741.5 
    5148  
    5149 3318 messages similar to the above omitted 
    5150  
    5151 Chain information for MATNNQRGNLAEHGVRTARAPATGTY__1.pdb #2 
    5152 --- 
    5153 Chain | Description 
    5154 A B C | No description available 
    5155  
    5156 Computing secondary structure 
    5157 
    5158 > close #2
    5159 
    5160 > show atoms
    5161 
    5162 > open
    5163 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/30DC2AF1-30F5-40A3-9497-F7EC478B63C8/MATNNQRGNLAEHGVRTARAPATGTY__2.pdb
    5164 
    5165 Summary of feedback from opening
    5166 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/30DC2AF1-30F5-40A3-9497-F7EC478B63C8/MATNNQRGNLAEHGVRTARAPATGTY__2.pdb 
    5167 --- 
    5168 warnings | Ignored bad PDB record found on line 24574 
    5169 # All scores below are weighted scores, not raw scores. 
    5170  
    5171 Ignored bad PDB record found on line 24575 
    5172 #BEGIN_POSE_ENERGIES_TABLE 
    5173  
    5174 Ignored bad PDB record found on line 24576 
    5175 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    5176 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    5177 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    5178  
    5179 Ignored bad PDB record found on line 24577 
    5180 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    5181  
    5182 Ignored bad PDB record found on line 24578 
    5183 pose -9739.53 21588.5 6300.16 40.0093 386.659 -151.136 -1328.65 1601.21
    5184 -94.8707 -325.933 -177.987 -39.4598 0 38.0782 7967.02 -120.728 0 292.567
    5185 1050.45 27286.4 
    5186  
    5187 3318 messages similar to the above omitted 
    5188  
    5189 Chain information for MATNNQRGNLAEHGVRTARAPATGTY__2.pdb #2 
    5190 --- 
    5191 Chain | Description 
    5192 A B C | No description available 
    5193  
    5194 
    5195 > open
    5196 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/4B9634D3-C67A-423B-8A6B-35E751738FB7/MATNNQRGNLAEHGVRTARAPATGTY__3.pdb
    5197 
    5198 Summary of feedback from opening
    5199 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/4B9634D3-C67A-423B-8A6B-35E751738FB7/MATNNQRGNLAEHGVRTARAPATGTY__3.pdb 
    5200 --- 
    5201 warnings | Ignored bad PDB record found on line 24574 
    5202 # All scores below are weighted scores, not raw scores. 
    5203  
    5204 Ignored bad PDB record found on line 24575 
    5205 #BEGIN_POSE_ENERGIES_TABLE 
    5206  
    5207 Ignored bad PDB record found on line 24576 
    5208 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    5209 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    5210 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    5211  
    5212 Ignored bad PDB record found on line 24577 
    5213 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    5214  
    5215 Ignored bad PDB record found on line 24578 
    5216 pose -9690.17 21936.6 6267.08 39.8845 386.943 -153.019 -1307.5 1601.21
    5217 -90.1243 -326.192 -177.987 -39.4595 0 35.594 7964.57 -122.256 0 292.567
    5218 1018.57 27636.3 
    5219  
    5220 3318 messages similar to the above omitted 
    5221  
    5222 Chain information for MATNNQRGNLAEHGVRTARAPATGTY__3.pdb #3 
    5223 --- 
    5224 Chain | Description 
    5225 A B C | No description available 
    5226  
    5227 Computing secondary structure 
    5228 [Repeated 1 time(s)]
    5229 
    5230 > show atoms
    5231 
    5232 > hide #2 models
    5233 
    5234 > close
    5235 
    5236 > open
    5237 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/ECAD92AA-
    5238 > ED4F-4A8D-A51C-CD5EADF96729/MATNLQRGNLAEHGVRTARQAATGTY__1.pdb
    5239 
    5240 Summary of feedback from opening
    5241 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/ECAD92AA-
    5242 ED4F-4A8D-A51C-CD5EADF96729/MATNLQRGNLAEHGVRTARQAATGTY__1.pdb 
    5243 --- 
    5244 warnings | Ignored bad PDB record found on line 24598 
    5245 # All scores below are weighted scores, not raw scores. 
    5246  
    5247 Ignored bad PDB record found on line 24599 
    5248 #BEGIN_POSE_ENERGIES_TABLE 
    5249  
    5250 Ignored bad PDB record found on line 24600 
    5251 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    5252 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    5253 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    5254  
    5255 Ignored bad PDB record found on line 24601 
    5256 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    5257  
    5258 Ignored bad PDB record found on line 24602 
    5259 pose -9742.69 24391.9 6286.89 39.8656 388.746 -155.762 -1313.27 1594.07
    5260 -96.9789 -326.022 -176.234 -39.4595 0 39.6845 7973.36 -116.36 0 302.149 1033.3
    5261 30083.2 
    5262  
    5263 3318 messages similar to the above omitted 
    5264  
    5265 Chain information for MATNLQRGNLAEHGVRTARQAATGTY__1.pdb #1 
    5266 --- 
    5267 Chain | Description 
    5268 A B C | No description available 
    5269  
    5270 Computing secondary structure 
    5271 
    5272 > open
    5273 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/4BD4994A-72AD-4ACA-9BAA-D35666018028/MATNLQRGNLAHDQVRPARQAATGTY__1.pdb
    5274 
    5275 Summary of feedback from opening
    5276 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/4BD4994A-72AD-4ACA-9BAA-D35666018028/MATNLQRGNLAHDQVRPARQAATGTY__1.pdb 
    5277 --- 
    5278 warnings | Ignored bad PDB record found on line 24619 
    5279 # All scores below are weighted scores, not raw scores. 
    5280  
    5281 Ignored bad PDB record found on line 24620 
    5282 #BEGIN_POSE_ENERGIES_TABLE 
    5283  
    5284 Ignored bad PDB record found on line 24621 
    5285 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    5286 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    5287 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    5288  
    5289 Ignored bad PDB record found on line 24622 
    5290 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    5291  
    5292 Ignored bad PDB record found on line 24623 
    5293 pose -9714.19 17557.2 6259.26 39.854 388.713 -150.451 -1312.08 1597.34
    5294 -90.1243 -326.156 -179.167 -39.4595 0 38.9651 7991.66 -119.058 0 288.754
    5295 1019.71 23250.8 
    5296  
    5297 3318 messages similar to the above omitted 
    5298  
    5299 Chain information for MATNLQRGNLAHDQVRPARQAATGTY__1.pdb #2 
    5300 --- 
    5301 Chain | Description 
    5302 A B C | No description available 
    5303  
    5304 
    5305 > open
    5306 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/8741FC92-5346-496F-8E8C-C655AD9B22E0/MATNLQRGNRQAATGTY_aav2_trimer_INPUT_fixbb_0001.pdb
    5307 
    5308 Summary of feedback from opening
    5309 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/8741FC92-5346-496F-8E8C-C655AD9B22E0/MATNLQRGNRQAATGTY_aav2_trimer_INPUT_fixbb_0001.pdb 
    5310 --- 
    5311 warnings | Ignored bad PDB record found on line 24202 
    5312 # All scores below are weighted scores, not raw scores. 
    5313  
    5314 Ignored bad PDB record found on line 24203 
    5315 #BEGIN_POSE_ENERGIES_TABLE MATNLQRGNRQAATGTY_aav2_trimer_INPUT_fixbb_0001.pdb 
    5316  
    5317 Ignored bad PDB record found on line 24204 
    5318 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    5319 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    5320 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    5321  
    5322 Ignored bad PDB record found on line 24205 
    5323 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    5324  
    5325 Ignored bad PDB record found on line 24206 
    5326 pose -9116.73 6245.17 5564.26 26.2134 349.637 -176.379 -1699.87 886.415
    5327 -97.6146 -320.122 -208.978 -141.029 0 35.8657 3159.11 -125.807 1.07721 284.799
    5328 1024.78 5690.79 
    5329  
    5330 1566 messages similar to the above omitted 
    5331  
    5332 Chain information for MATNLQRGNRQAATGTY_aav2_trimer_INPUT_fixbb_0001.pdb #3 
    5333 --- 
    5334 Chain | Description 
    5335 A B C | No description available 
    5336  
    5337 
    5338 > open
    5339 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/D664E51E-4C75-4ABE-8AEE-5700FC630E22/MATNNQRGNLAEHGVRTARAPATGTY__1.pdb
    5340 
    5341 Summary of feedback from opening
    5342 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/D664E51E-4C75-4ABE-8AEE-5700FC630E22/MATNNQRGNLAEHGVRTARAPATGTY__1.pdb 
    5343 --- 
    5344 warnings | Ignored bad PDB record found on line 24574 
    5345 # All scores below are weighted scores, not raw scores. 
    5346  
    5347 Ignored bad PDB record found on line 24575 
    5348 #BEGIN_POSE_ENERGIES_TABLE 
    5349  
    5350 Ignored bad PDB record found on line 24576 
    5351 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    5352 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    5353 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    5354  
    5355 Ignored bad PDB record found on line 24577 
    5356 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    5357  
    5358 Ignored bad PDB record found on line 24578 
    5359 pose -9714.01 18595.6 6285.73 39.8103 386.278 -153.587 -1321.63 1601.21
    5360 -95.6222 -330.922 -180.403 -39.4595 0 38.9146 7951.26 -114.391 0 292.567
    5361 1050.48 24291.9 
    5362  
    5363 3318 messages similar to the above omitted 
    5364  
    5365 Chain information for MATNNQRGNLAEHGVRTARAPATGTY__1.pdb #4 
    5366 --- 
    5367 Chain | Description 
    5368 A B C | No description available 
    5369  
    5370 
    5371 > open
    5372 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/8AC1A12D-C5E4-4251-8F40-428B2AF47603/MATNNQRGNLAHDQVRPARAPATGTY__1.pdb
    5373 
    5374 Summary of feedback from opening
    5375 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/8AC1A12D-C5E4-4251-8F40-428B2AF47603/MATNNQRGNLAHDQVRPARAPATGTY__1.pdb 
    5376 --- 
    5377 warnings | Ignored bad PDB record found on line 24595 
    5378 # All scores below are weighted scores, not raw scores. 
    5379  
    5380 Ignored bad PDB record found on line 24596 
    5381 #BEGIN_POSE_ENERGIES_TABLE 
    5382  
    5383 Ignored bad PDB record found on line 24597 
    5384 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    5385 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    5386 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    5387  
    5388 Ignored bad PDB record found on line 24598 
    5389 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    5390  
    5391 Ignored bad PDB record found on line 24599 
    5392 pose -9696.02 16881.1 6254.91 39.6775 386.663 -155.123 -1316.82 1625.93
    5393 -94.2128 -326.259 -188.056 -39.4595 0 35.6094 7954.82 -119.478 0 279.172
    5394 1069.29 22591.7 
    5395  
    5396 3318 messages similar to the above omitted 
    5397  
    5398 Chain information for MATNNQRGNLAHDQVRPARAPATGTY__1.pdb #5 
    5399 --- 
    5400 Chain | Description 
    5401 A B C | No description available 
    5402  
    5403 
    5404 > open
    5405 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/FBD1A9E2-6191-47E1-93FA-5F3DB0A43C5A/MATNNQRGNLAHDQVRPARAPATGTYNL__1.pdb
    5406 
    5407 Summary of feedback from opening
    5408 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/FBD1A9E2-6191-47E1-93FA-5F3DB0A43C5A/MATNNQRGNLAHDQVRPARAPATGTYNL__1.pdb 
    5409 --- 
    5410 warnings | Ignored bad PDB record found on line 24610 
    5411 # All scores below are weighted scores, not raw scores. 
    5412  
    5413 Ignored bad PDB record found on line 24611 
    5414 #BEGIN_POSE_ENERGIES_TABLE 
    5415  
    5416 Ignored bad PDB record found on line 24612 
    5417 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    5418 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    5419 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    5420  
    5421 Ignored bad PDB record found on line 24613 
    5422 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    5423  
    5424 Ignored bad PDB record found on line 24614 
    5425 pose -9747.87 21017.5 6253.56 39.6902 387.205 -156.524 -1328.7 1614.24
    5426 -94.6382 -328.006 -180.568 -40.6925 0 35.3967 7956.9 -128.673 0 280.701
    5427 1045.16 26624.6 
    5428  
    5429 3318 messages similar to the above omitted 
    5430  
    5431 Chain information for MATNNQRGNLAHDQVRPARAPATGTYNL__1.pdb #6 
    5432 --- 
    5433 Chain | Description 
    5434 A B C | No description available 
    5435  
    5436 
    5437 > open
    5438 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/4C407BFD-D6AA-4F9F-9A41-FF2EE808115B/MATNNQRGNRAPATGTY_aav2_trimer_INPUT_fixbb_0001.pdb
    5439 
    5440 Summary of feedback from opening
    5441 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/4C407BFD-D6AA-4F9F-9A41-FF2EE808115B/MATNNQRGNRAPATGTY_aav2_trimer_INPUT_fixbb_0001.pdb 
    5442 --- 
    5443 warnings | Ignored bad PDB record found on line 24178 
    5444 # All scores below are weighted scores, not raw scores. 
    5445  
    5446 Ignored bad PDB record found on line 24179 
    5447 #BEGIN_POSE_ENERGIES_TABLE MATNNQRGNRAPATGTY_aav2_trimer_INPUT_fixbb_0001.pdb 
    5448  
    5449 Ignored bad PDB record found on line 24180 
    5450 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    5451 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    5452 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    5453  
    5454 Ignored bad PDB record found on line 24181 
    5455 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    5456  
    5457 Ignored bad PDB record found on line 24182 
    5458 pose -9105.1 6324.71 5631.69 22.4099 347.633 -178.89 -1670.87 924.218 -97.6146
    5459 -320.122 -221.365 -127.065 0 35.9598 3182.81 -126.404 0.23392 275.217 1025.61
    5460 5923.06 
    5461  
    5462 1566 messages similar to the above omitted 
    5463  
    5464 Chain information for MATNNQRGNRAPATGTY_aav2_trimer_INPUT_fixbb_0001.pdb #7 
    5465 --- 
    5466 Chain | Description 
    5467 A B C | No description available 
    5468  
    5469 
    5470 > open
    5471 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/E2A92555-AD83-4873-ACFF-
    5472 > AD7EC5C532D9/MATNNQRGNRAPATGTYNL_aav2_trimer_INPUT_fixbb_0001.pdb
    5473 
    5474 Summary of feedback from opening
    5475 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/E2A92555-AD83-4873-ACFF-
    5476 AD7EC5C532D9/MATNNQRGNRAPATGTYNL_aav2_trimer_INPUT_fixbb_0001.pdb 
    5477 --- 
    5478 warnings | Ignored bad PDB record found on line 24193 
    5479 # All scores below are weighted scores, not raw scores. 
    5480  
    5481 Ignored bad PDB record found on line 24194 
    5482 #BEGIN_POSE_ENERGIES_TABLE
    5483 MATNNQRGNRAPATGTYNL_aav2_trimer_INPUT_fixbb_0001.pdb 
    5484  
    5485 Ignored bad PDB record found on line 24195 
    5486 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    5487 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    5488 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    5489  
    5490 Ignored bad PDB record found on line 24196 
    5491 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    5492  
    5493 Ignored bad PDB record found on line 24197 
    5494 pose -9175.05 9874.11 5619.12 23.1652 352.333 -177.277 -1665.22 918.684
    5495 -97.6146 -320.122 -224.116 -124.927 0 35.9598 3175.51 -128.62 0.42371 276.746
    5496 1023.29 9386.39 
    5497  
    5498 1566 messages similar to the above omitted 
    5499  
    5500 Chain information for MATNNQRGNRAPATGTYNL_aav2_trimer_INPUT_fixbb_0001.pdb #8 
    5501 --- 
    5502 Chain | Description 
    5503 A B C | No description available 
    5504  
    5505 
    5506 > open
    5507 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/2C6C2B3B-111F-4B6A-A0A6-95E04626C9E0/MSTNLQRGNLAEHGVRTARQAATADY__1.pdb
    5508 
    5509 Summary of feedback from opening
    5510 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/2C6C2B3B-111F-4B6A-A0A6-95E04626C9E0/MSTNLQRGNLAEHGVRTARQAATADY__1.pdb 
    5511 --- 
    5512 warnings | Ignored bad PDB record found on line 24604 
    5513 # All scores below are weighted scores, not raw scores. 
    5514  
    5515 Ignored bad PDB record found on line 24605 
    5516 #BEGIN_POSE_ENERGIES_TABLE 
    5517  
    5518 Ignored bad PDB record found on line 24606 
    5519 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    5520 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    5521 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    5522  
    5523 Ignored bad PDB record found on line 24607 
    5524 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    5525  
    5526 Ignored bad PDB record found on line 24608 
    5527 pose -9665.81 17873.2 6259.61 39.8679 388.872 -163.798 -1302.76 1594.07
    5528 -91.3315 -328.004 -175.499 -39.4595 0 37.408 7993.91 -114.35 0 288.993 1045.31
    5529 23640.3 
    5530  
    5531 3318 messages similar to the above omitted 
    5532  
    5533 Chain information for MSTNLQRGNLAEHGVRTARQAATADY__1.pdb #9 
    5534 --- 
    5535 Chain | Description 
    5536 A B C | No description available 
    5537  
    5538 
    5539 > open
    5540 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/604BA23C-45EA-4003-A237-936F023B8C8A/MSTNLQRGNLAHDQVRPARQAATADY__1.pdb
    5541 
    5542 Summary of feedback from opening
    5543 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/604BA23C-45EA-4003-A237-936F023B8C8A/MSTNLQRGNLAHDQVRPARQAATADY__1.pdb 
    5544 --- 
    5545 warnings | Ignored bad PDB record found on line 24625 
    5546 # All scores below are weighted scores, not raw scores. 
    5547  
    5548 Ignored bad PDB record found on line 24626 
    5549 #BEGIN_POSE_ENERGIES_TABLE 
    5550  
    5551 Ignored bad PDB record found on line 24627 
    5552 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    5553 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    5554 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    5555  
    5556 Ignored bad PDB record found on line 24628 
    5557 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    5558  
    5559 Ignored bad PDB record found on line 24629 
    5560 pose -9772.36 20064.3 6315.06 40.1416 389.613 -153.773 -1330.94 1601.98
    5561 -95.4482 -329.013 -184.05 -39.4595 0 40.1689 8003.52 -122.509 0 275.597
    5562 1054.39 25757.2 
    5563  
    5564 3318 messages similar to the above omitted 
    5565  
    5566 Chain information for MSTNLQRGNLAHDQVRPARQAATADY__1.pdb #10 
    5567 --- 
    5568 Chain | Description 
    5569 A B C | No description available 
    5570  
    5571 
    5572 > open
    5573 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/18E8D34A-C544-4AC5-9DD3-1E96E5D5B1EE/MSTNLQRGNRQAATADY_aav2_trimer_INPUT_fixbb_0001.pdb
    5574 
    5575 Summary of feedback from opening
    5576 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/18E8D34A-C544-4AC5-9DD3-1E96E5D5B1EE/MSTNLQRGNRQAATADY_aav2_trimer_INPUT_fixbb_0001.pdb 
    5577 --- 
    5578 warnings | Ignored bad PDB record found on line 24208 
    5579 # All scores below are weighted scores, not raw scores. 
    5580  
    5581 Ignored bad PDB record found on line 24209 
    5582 #BEGIN_POSE_ENERGIES_TABLE MSTNLQRGNRQAATADY_aav2_trimer_INPUT_fixbb_0001.pdb 
    5583  
    5584 Ignored bad PDB record found on line 24210 
    5585 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    5586 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    5587 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    5588  
    5589 Ignored bad PDB record found on line 24211 
    5590 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    5591  
    5592 Ignored bad PDB record found on line 24212 
    5593 pose -9117.17 6368.28 5645.87 21.9804 347.705 -191.167 -1683.29 884.273
    5594 -97.6146 -320.122 -207.396 -131.546 0 36.1999 3238.34 -128.117 0.2709 271.643
    5595 1021.26 5959.4 
    5596  
    5597 1566 messages similar to the above omitted 
    5598  
    5599 Chain information for MSTNLQRGNRQAATADY_aav2_trimer_INPUT_fixbb_0001.pdb #11 
    5600 --- 
    5601 Chain | Description 
    5602 A B C | No description available 
    5603  
    5604 
    5605 > open
    5606 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/7EF69882-C241-42EA-9C99-6FDE6F918FC1/VSTNLEGLRDSDAGIQRSNRQAATADV__1.pdb
    5607 
    5608 Summary of feedback from opening
    5609 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/7EF69882-C241-42EA-9C99-6FDE6F918FC1/VSTNLEGLRDSDAGIQRSNRQAATADV__1.pdb 
    5610 --- 
    5611 warnings | Ignored bad PDB record found on line 24610 
    5612 # All scores below are weighted scores, not raw scores. 
    5613  
    5614 Ignored bad PDB record found on line 24611 
    5615 #BEGIN_POSE_ENERGIES_TABLE 
    5616  
    5617 Ignored bad PDB record found on line 24612 
    5618 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    5619 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    5620 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    5621  
    5622 Ignored bad PDB record found on line 24613 
    5623 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    5624  
    5625 Ignored bad PDB record found on line 24614 
    5626 pose -9809.02 15560 6395.53 39.9501 385.686 -160.451 -1317.22 1594.07 -97.6146
    5627 -320.122 -175.277 -40.3679 0 40.5587 8059.55 -111.637 0 275.974 1065.42
    5628 21385.1 
    5629  
    5630 3324 messages similar to the above omitted 
    5631  
    5632 Chain information for VSTNLEGLRDSDAGIQRSNRQAATADV__1.pdb #12 
    5633 --- 
    5634 Chain | Description 
    5635 A B C | No description available 
    5636  
    5637 
    5638 > open
    5639 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/1EFDAAC7-A02B-4024-A050-90E4A72B1B52/VSTNLGGKFVERTDGQRGNLQAATADV__1.pdb
    5640 
    5641 Summary of feedback from opening
    5642 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/1EFDAAC7-A02B-4024-A050-90E4A72B1B52/VSTNLGGKFVERTDGQRGNLQAATADV__1.pdb 
    5643 --- 
    5644 warnings | Ignored bad PDB record found on line 24607 
    5645 # All scores below are weighted scores, not raw scores. 
    5646  
    5647 Ignored bad PDB record found on line 24608 
    5648 #BEGIN_POSE_ENERGIES_TABLE 
    5649  
    5650 Ignored bad PDB record found on line 24609 
    5651 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    5652 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    5653 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    5654  
    5655 Ignored bad PDB record found on line 24610 
    5656 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    5657  
    5658 Ignored bad PDB record found on line 24611 
    5659 pose -9777.62 15874 6334.04 40.0188 386.101 -156.855 -1342.39 1594.07 -101.843
    5660 -323.43 -169.093 -39.4595 0 36.9433 8027.07 -123.185 0 291.232 1033.13 21582.7 
    5661  
    5662 3324 messages similar to the above omitted 
    5663  
    5664 Chain information for VSTNLGGKFVERTDGQRGNLQAATADV__1.pdb #13 
    5665 --- 
    5666 Chain | Description 
    5667 A B C | No description available 
    5668  
    5669 
    5670 > open
    5671 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/FEAED0D6-DCF6-450C-8D7C-E04B2E38435B/VSTNLHRGNLMMEKGSEAQRQAATADV__1.pdb
    5672 
    5673 Summary of feedback from opening
    5674 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/FEAED0D6-DCF6-450C-8D7C-E04B2E38435B/VSTNLHRGNLMMEKGSEAQRQAATADV__1.pdb 
    5675 --- 
    5676 warnings | Ignored bad PDB record found on line 24640 
    5677 # All scores below are weighted scores, not raw scores. 
    5678  
    5679 Ignored bad PDB record found on line 24641 
    5680 #BEGIN_POSE_ENERGIES_TABLE 
    5681  
    5682 Ignored bad PDB record found on line 24642 
    5683 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    5684 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    5685 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    5686  
    5687 Ignored bad PDB record found on line 24643 
    5688 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    5689  
    5690 Ignored bad PDB record found on line 24644 
    5691 pose -9720.54 10140.9 6286.97 39.8096 384.442 -154.809 -1308.26 1594.07
    5692 -94.0565 -326.138 -170.489 -39.4595 0 35.8396 8004.8 -117.082 0 281.815
    5693 1028.83 15866.6 
    5694  
    5695 3324 messages similar to the above omitted 
    5696  
    5697 Chain information for VSTNLHRGNLMMEKGSEAQRQAATADV__1.pdb #14 
    5698 --- 
    5699 Chain | Description 
    5700 A B C | No description available 
    5701  
    5702 
    5703 > open
    5704 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/7BD89B01-74CA-4EDA-A2BD-10344C30C221/VSTNLPRNYVDTISMQRGNQAAATADV__1.pdb
    5705 
    5706 Summary of feedback from opening
    5707 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/7BD89B01-74CA-4EDA-A2BD-10344C30C221/VSTNLPRNYVDTISMQRGNQAAATADV__1.pdb 
    5708 --- 
    5709 warnings | Ignored bad PDB record found on line 24634 
    5710 # All scores below are weighted scores, not raw scores. 
    5711  
    5712 Ignored bad PDB record found on line 24635 
    5713 #BEGIN_POSE_ENERGIES_TABLE 
    5714  
    5715 Ignored bad PDB record found on line 24636 
    5716 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    5717 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    5718 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    5719  
    5720 Ignored bad PDB record found on line 24637 
    5721 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    5722  
    5723 Ignored bad PDB record found on line 24638 
    5724 pose -9825.4 12766 6354.04 39.9549 384.286 -146.891 -1324.49 1595.59 -99.3655
    5725 -320.122 -169.576 -39.4595 0 37.7428 8004.78 -130.307 0 293.511 1034.2 18454.5 
    5726  
    5727 3324 messages similar to the above omitted 
    5728  
    5729 Chain information for VSTNLPRNYVDTISMQRGNQAAATADV__1.pdb #15 
    5730 --- 
    5731 Chain | Description 
    5732 A B C | No description available 
    5733  
    5734 Computing secondary structure 
    5735 [Repeated 13 time(s)]
    5736 
    5737 > show atoms
    5738 
    5739 > hide #2-15 target m
    5740 
    5741 > show #2 target m
    5742 
    5743 > hide #1 target m
    5744 
    5745 > show #3 target m
    5746 
    5747 > hide #2 target m
    5748 
    5749 > show #4 target m
    5750 
    5751 > hide #3 target m
    5752 
    5753 > show #5 target m
    5754 
    5755 > hide #4 target m
    5756 
    5757 > show #6 target m
    5758 
    5759 > hide #5 target m
    5760 
    5761 > show #7 target m
    5762 
    5763 > hide #6 target m
    5764 
    5765 > show #8 target m
    5766 
    5767 > hide #7 target m
    5768 
    5769 > show #7 target m
    5770 
    5771 > hide #8 target m
    5772 
    5773 > show #6 target m
    5774 
    5775 > hide #7 target m
    5776 
    5777 > show #7 target m
    5778 
    5779 > hide #6 target m
    5780 
    5781 > show #8 target m
    5782 
    5783 > hide #7 target m
    5784 
    5785 > show #9 target m
    5786 
    5787 > hide #8 target m
    5788 
    5789 > show #10 target m
    5790 
    5791 > hide #9 target m
    5792 
    5793 > show #11 target m
    5794 
    5795 > hide #10 target m
    5796 
    5797 > show #12 target m
    5798 
    5799 > hide #11 target m
    5800 
    5801 > show #11 target m
    5802 
    5803 > hide #12 target m
    5804 
    5805 > show #12 target m
    5806 
    5807 > hide #11 target m
    5808 
    5809 > show #13 target m
    5810 
    5811 > hide #12 target m
    5812 
    5813 > close session
    5814 
    5815 > open
    5816 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/75AAC0DD-6AE8-4B65-BC87-337893A8A8F5/VSTNLQRGNAAASARAGAPAARQAATADV__1.pdb
    5817 
    5818 Summary of feedback from opening
    5819 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/75AAC0DD-6AE8-4B65-BC87-337893A8A8F5/VSTNLQRGNAAASARAGAPAARQAATADV__1.pdb 
    5820 --- 
    5821 warnings | Ignored bad PDB record found on line 24598 
    5822 # All scores below are weighted scores, not raw scores. 
    5823  
    5824 Ignored bad PDB record found on line 24599 
    5825 #BEGIN_POSE_ENERGIES_TABLE 
    5826  
    5827 Ignored bad PDB record found on line 24600 
    5828 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    5829 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    5830 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    5831  
    5832 Ignored bad PDB record found on line 24601 
    5833 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    5834  
    5835 Ignored bad PDB record found on line 24602 
    5836 pose -9673.17 8897.3 6247.33 39.7231 383.313 -154.833 -1331.25 1730.48
    5837 -98.7505 -329.548 -177.323 -39.4595 0 35.0922 7992.4 -111.141 0 308.884
    5838 1029.25 14748.3 
    5839  
    5840 3336 messages similar to the above omitted 
    5841  
    5842 Chain information for VSTNLQRGNAAASARAGAPAARQAATADV__1.pdb #1 
    5843 --- 
    5844 Chain | Description 
    5845 A B C | No description available 
    5846  
    5847 Computing secondary structure 
    5848 
    5849 > show atoms
    5850 
    5851 > close session
    5852 
    5853 > open
    5854 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/D664E51E-4C75-4ABE-8AEE-5700FC630E22/MATNNQRGNLAEHGVRTARAPATGTY__1.pdb
    5855 
    5856 Summary of feedback from opening
    5857 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/D664E51E-4C75-4ABE-8AEE-5700FC630E22/MATNNQRGNLAEHGVRTARAPATGTY__1.pdb 
    5858 --- 
    5859 warnings | Ignored bad PDB record found on line 24574 
    5860 # All scores below are weighted scores, not raw scores. 
    5861  
    5862 Ignored bad PDB record found on line 24575 
    5863 #BEGIN_POSE_ENERGIES_TABLE 
    5864  
    5865 Ignored bad PDB record found on line 24576 
    5866 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    5867 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    5868 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    5869  
    5870 Ignored bad PDB record found on line 24577 
    5871 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    5872  
    5873 Ignored bad PDB record found on line 24578 
    5874 pose -9714.01 18595.6 6285.73 39.8103 386.278 -153.587 -1321.63 1601.21
    5875 -95.6222 -330.922 -180.403 -39.4595 0 38.9146 7951.26 -114.391 0 292.567
    5876 1050.48 24291.9 
    5877  
    5878 3318 messages similar to the above omitted 
    5879  
    5880 Chain information for MATNNQRGNLAEHGVRTARAPATGTY__1.pdb #1 
    5881 --- 
    5882 Chain | Description 
    5883 A B C | No description available 
    5884  
    5885 Computing secondary structure 
    5886 
    5887 > sequence chain #1/A,B,C
    5888 
    5889 Alignment identifier is 1 
    5890 
    5891 > select /A:363-364/B:891-892/C:1419-1420
    5892 
    5893 81 atoms, 78 bonds, 6 residues, 1 model selected 
    5894 
    5895 > select /A:363-388/B:891-916/C:1419-1444
    5896 
    5897 1131 atoms, 1137 bonds, 78 residues, 1 model selected 
    5898 
    5899 > open
    5900 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/55DDBF5B-E4FF-406D-BC53-59586D37B05E/MATNNQRGNLAEHGVRTARAPATGTY_aav2_trimer_INPUT_remodeled_0001.pdb
    5901 
    5902 Summary of feedback from opening
    5903 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/55DDBF5B-E4FF-406D-BC53-59586D37B05E/MATNNQRGNLAEHGVRTARAPATGTY_aav2_trimer_INPUT_remodeled_0001.pdb 
    5904 --- 
    5905 warnings | Ignored bad PDB record found on line 24574 
    5906 # All scores below are weighted scores, not raw scores. 
    5907  
    5908 Ignored bad PDB record found on line 24575 
    5909 #BEGIN_POSE_ENERGIES_TABLE
    5910 MATNNQRGNLAEHGVRTARAPATGTY_aav2_trimer_INPUT_remodeled_0001.pdb 
    5911  
    5912 Ignored bad PDB record found on line 24576 
    5913 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    5914 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    5915 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    5916  
    5917 Ignored bad PDB record found on line 24577 
    5918 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    5919  
    5920 Ignored bad PDB record found on line 24578 
    5921 pose -9714.01 18595.6 6285.73 39.8103 386.278 -153.587 -1321.63 1601.21
    5922 -95.6222 -330.922 -180.403 -39.4595 0 38.9146 7951.26 -114.391 0 292.567
    5923 1050.48 24291.9 
    5924  
    5925 1593 messages similar to the above omitted 
    5926  
    5927 Chain information for
    5928 MATNNQRGNLAEHGVRTARAPATGTY_aav2_trimer_INPUT_remodeled_0001.pdb #2 
    5929 --- 
    5930 Chain | Description 
    5931 A B C | No description available 
    5932  
    5933 Computing secondary structure 
    5934 
    5935 > hide #2 models
    5936 
    5937 > show #2 models
    5938 
    5939 > hide #1 models
    5940 
    5941 > show #1 models
    5942 
    5943 > sequence chain #1/A,B,C
    5944 
    5945 Alignment identifier is 2 
    5946 
    5947 > close #1
    5948 
    5949 > sequence chain #2/A,B,C
    5950 
    5951 Alignment identifier is 1 
    5952 
    5953 > select /A:363-364/B:891-892/C:1419-1420
    5954 
    5955 81 atoms, 78 bonds, 6 residues, 1 model selected 
    5956 
    5957 > select /A:363-373/B:891-901/C:1419-1429
    5958 
    5959 480 atoms, 477 bonds, 33 residues, 1 model selected 
    5960 
    5961 > select clear
    5962 
    5963 > show atoms
    5964 
    5965 > open
    5966 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/B2A4069E-0E06-4B4E-AF89-AB8D59124817/VSTNAQRGNNIKQGSTIDHRQAATADV_aav2_trimer_INPUT_remodeled_0001.pdb
    5967 
    5968 Summary of feedback from opening
    5969 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/B2A4069E-0E06-4B4E-AF89-AB8D59124817/VSTNAQRGNNIKQGSTIDHRQAATADV_aav2_trimer_INPUT_remodeled_0001.pdb 
    5970 --- 
    5971 warnings | Ignored bad PDB record found on line 24619 
    5972 # All scores below are weighted scores, not raw scores. 
    5973  
    5974 Ignored bad PDB record found on line 24620 
    5975 #BEGIN_POSE_ENERGIES_TABLE
    5976 VSTNAQRGNNIKQGSTIDHRQAATADV_aav2_trimer_INPUT_remodeled_0001.pdb 
    5977  
    5978 Ignored bad PDB record found on line 24621 
    5979 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    5980 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    5981 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    5982  
    5983 Ignored bad PDB record found on line 24622 
    5984 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    5985  
    5986 Ignored bad PDB record found on line 24623 
    5987 pose -9719.96 9723.05 6321.33 40.0247 387.934 -152.519 -1345.58 1594.07 -97.72
    5988 -331.403 -177.759 -39.4595 0 38.0061 8029.02 -114.574 0 280.716 1057.96
    5989 15493.1 
    5990  
    5991 1596 messages similar to the above omitted 
    5992  
    5993 Chain information for
    5994 VSTNAQRGNNIKQGSTIDHRQAATADV_aav2_trimer_INPUT_remodeled_0001.pdb #1 
    5995 --- 
    5996 Chain | Description 
    5997 A B C | No description available 
    5998  
    5999 Computing secondary structure 
    6000 
    6001 > close
    6002 
    6003 > open
    6004 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/C8711C7F-45EC-464C-B078-0DE7419FB070/MSTNLQRGNRQAATADY_cg.pdb
    6005 
    6006 > style sphere
    6007 
    6008 Changed 1255 atom styles 
    6009 
    6010 > open
    6011 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/0D4BAA1E-3D5F-4E1F-8D1B-5F56AD3CD7BE/MATNLQRGNLAEHGVRTARQAATGTY_cleaned_chainA_noH.pdb
    6012 
    6013 Chain information for MATNLQRGNLAEHGVRTARQAATGTY_cleaned_chainA_noH.pdb #2 
    6014 --- 
    6015 Chain | Description 
    6016 A | No description available 
    6017  
    6018 Computing secondary structure 
    6019 
    6020 > open
    6021 > /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/ECAD92AA-
    6022 > ED4F-4A8D-A51C-CD5EADF96729/MATNLQRGNLAEHGVRTARQAATGTY__1.pdb
    6023 
    6024 Summary of feedback from opening
    6025 /Users/tht13/Library/Caches/com.binarynights.ForkLift/FileCache/ECAD92AA-
    6026 ED4F-4A8D-A51C-CD5EADF96729/MATNLQRGNLAEHGVRTARQAATGTY__1.pdb 
    6027 --- 
    6028 warnings | Ignored bad PDB record found on line 24598 
    6029 # All scores below are weighted scores, not raw scores. 
    6030  
    6031 Ignored bad PDB record found on line 24599 
    6032 #BEGIN_POSE_ENERGIES_TABLE 
    6033  
    6034 Ignored bad PDB record found on line 24600 
    6035 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
    6036 fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
    6037 fa_dun p_aa_pp yhh_planarity ref rama_prepro total 
    6038  
    6039 Ignored bad PDB record found on line 24601 
    6040 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA 
    6041  
    6042 Ignored bad PDB record found on line 24602 
    6043 pose -9742.69 24391.9 6286.89 39.8656 388.746 -155.762 -1313.27 1594.07
    6044 -96.9789 -326.022 -176.234 -39.4595 0 39.6845 7973.36 -116.36 0 302.149 1033.3
    6045 30083.2 
    6046  
    6047 3318 messages similar to the above omitted 
    6048  
    6049 Chain information for MATNLQRGNLAEHGVRTARQAATGTY__1.pdb #3 
    6050 --- 
    6051 Chain | Description 
    6052 A B C | No description available 
    6053  
    6054 Computing secondary structure 
    6055 
    6056 > hide #!1 models
    6057 
    6058 > close session
    6059 
    6060 > open 8fz0
    6061 
    6062 Summary of feedback from opening 8fz0 fetched from pdb 
    6063 --- 
    6064 note | Fetching compressed mmCIF 8fz0 from http://files.rcsb.org/download/8fz0.cif 
    6065  
    6066 8fz0 title: 
    6067 Cryo-EM Structure of empty AAV2 capsid [more info...] 
    6068  
    6069 Chain information for 8fz0 #1 
    6070 --- 
    6071 Chain | Description | UniProt 
    6072 1 2 3 4 5 6 7 8 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d e f g h i j k l m n o p q r s t u v w x y z | Capsid protein VP1 | CAPSD_AAV2S 1-735 
    6073  
    6074 960 atoms have alternate locations. Control/examine alternate locations with
    6075 Altloc Explorer [start tool...] or the altlocs command. 
    6076 
    6077 > show cartoons
    6078 
    6079 > hide atoms
    6080 
    6081 > color #1 #deefdfff
    6082 
    6083 > sequence chain
    6084 > #1/A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,v,w,x,y,z,1,2,3,4,5,6,7,8
    6085 
    6086 Alignment identifier is 1 
    6087 
    6088 > color #1:381-386 red
    6089 
    6090 > color #1:529-538 red
    6091 
    6092 > color #1:529-538 blue
    6093 
    6094 > color #1:553-563 green
    6095 
    6096 > color #1 #eef2f1ff
    6097 
    6098 > color #1 white
    6099 
    6100 > color #1:553-563 redd
    6101 
    6102 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    6103 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    6104 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    6105 
    6106 > color #1:553-563 red
    6107 
    6108 > select add /L:593
    6109 
    6110 5 atoms, 4 bonds, 1 residue, 1 model selected 
    6111 
    6112 > select add /O:446
    6113 
    6114 11 atoms, 9 bonds, 2 residues, 1 model selected 
    6115 
    6116 > select add /L:509
    6117 
    6118 21 atoms, 19 bonds, 3 residues, 1 model selected 
    6119 
    6120 > select add /r:459
    6121 
    6122 32 atoms, 29 bonds, 4 residues, 1 model selected 
    6123 
    6124 > select up
    6125 
    6126 206 atoms, 207 bonds, 24 residues, 1 model selected 
    6127 
    6128 > select up
    6129 
    6130 12456 atoms, 12825 bonds, 1557 residues, 1 model selected 
    6131 
    6132 > select up
    6133 
    6134 249120 atoms, 256500 bonds, 31140 residues, 1 model selected 
    6135 
    6136 > select down
    6137 
    6138 12456 atoms, 12825 bonds, 1557 residues, 1 model selected 
    6139 
    6140 > select ~sel & ##selected
    6141 
    6142 236664 atoms, 243675 bonds, 29583 residues, 1 model selected 
    6143 
    6144 > hide sel atoms
    6145 
    6146 > hide sel cartoons
    6147 
    6148 > undo
    6149 
    6150 > select clear
    6151 
    6152 > color #1:489-496 blue
    6153 
    6154 > namesel
    6155 
    6156 Unknown command: namesel 
    6157 
    6158 > name
    6159 
    6160 Missing or invalid "name" argument: Expected a text string 
    6161 
    6162 > name VR-I #1:262-269
    6163 
    6164 > select VR-I
    6165 
    6166 3120 atoms, 3060 bonds, 480 residues, 1 model selected 
    6167 
    6168 > select up
    6169 
    6170 4920 atoms, 4980 bonds, 660 residues, 1 model selected 
    6171 
    6172 > select down
    6173 
    6174 3120 atoms, 3060 bonds, 480 residues, 1 model selected 
    6175 
    6176 > select VR-II
    6177 
    6178 Expected an objects specifier or a keyword 
    6179 
    6180 > select clear
    6181 
    6182 > select all
    6183 
    6184 249120 atoms, 256500 bonds, 31140 residues, 1 model selected 
    6185 
    6186 > color sel white
    6187 
    6188 > select clear
    6189 
    6190 > name VR-IX #1:707-723
    6191 
    6192 > color VR-IX red
    6193 
    6194 > name VR-II #1:327-339
    6195 
    6196 > name VR-III #1:381-386
    6197 
    6198 > name VR-IV #1:447-457
    6199 
    6200 > name VR-V #1:489-496
    6201 
    6202 > name VR-VI #1:529-538
    6203 
    6204 > name VR-VII #1:553-563
    6205 
    6206 > name VR-VIII #1:585-593
    6207 
    6208 > name VR-IX #1:707-723
    6209 
    6210 > color all white
    6211 
    6212 Cell requested for row 37 is out of bounds for table with 37 rows! Resizing
    6213 table model. 
    6214 
    6215 > save /Users/tht13/Documents/VRs/8FZ0_VRs.cxs
    6216 
    6217 ——— End of log from Thu Apr 23 13:23:45 2026 ———
    6218 
    6219 > view name session-start
    6220 
    6221 opened ChimeraX session 
    6222 
    6223 > select VR-III
    6224 
    6225 2400 atoms, 2340 bonds, 360 residues, 1 model selected 
    6226 
    6227 > color sel red
    6228 
    6229 > select clear
    6230 
    6231 > color VR-VII green
    6232 
    6233 > color VR-I yellow
    6234 
    6235 > name
    6236 
    6237 Missing or invalid "name" argument: Expected a text string 
    6238 
    6239 > name VR-I :262-268
    6240 
    6241 > name VR-II :326-330
    6242 
    6243 > name VR-III :380-388
    6244 
    6245 > name VR-IV :449-468
    6246 
    6247 > name VR-V :487-504
    6248 
    6249 > name VR-VI :525-541
    6250 
    6251 > name VR-VII :544-556
    6252 
    6253 > name VR-VIII :579-594
    6254 
    6255 > name VR-IX :704-711
    6256 
    6257 > color all white
    6258 
    6259 > save /Users/tht13/Documents/VRs/8FZ0_VRs.cxs
    6260 
    6261 > color VR-VII red
    6262 
    6263 > color VR-IX blue
    6264 
    6265 > open 6nz0
    6266 
    6267 6nz0 title: 
    6268 Cryo-EM structure of AAV-2 in complex with AAVR PKD domains 1 and 2 [more
    6269 info...] 
    6270  
    6271 Chain information for 6nz0 #2 
    6272 --- 
    6273 Chain | Description | UniProt 
    6274 A | Capsid protein VP1 | CAPSD_AAV2S 1-735 
    6275 Z | Dyslexia-associated protein KIAA0319-like protein | K319L_HUMAN 311-597 
    6276  
    6277 Non-standard residues in 6nz0 #2 
    6278 --- 
    6279 MG — magnesium ion 
    6280  
    6281 6nz0 mmCIF Assemblies 
    6282 --- 
    6283 1| complete icosahedral assembly 
    6284 2| icosahedral asymmetric unit 
    6285 3| icosahedral pentamer 
    6286 4| icosahedral 23 hexamer 
    6287 5| icosahedral asymmetric unit, std point frame 
    6288  
    6289 
    6290 > view #2 clip false
    6291 
    6292 > ui tool show Matchmaker
    6293 
    6294 > matchmaker #!2 to #1
    6295 
    6296 Parameters 
    6297 --- 
    6298 Chain pairing | bb 
    6299 Alignment algorithm | Needleman-Wunsch 
    6300 Similarity matrix | BLOSUM-62 
    6301 SS fraction | 0.3 
    6302 Gap open (HH/SS/other) | 18/18/6 
    6303 Gap extend | 1 
    6304 SS matrix |  |  | H | S | O 
    6305 ---|---|---|--- 
    6306 H | 6 | -9 | -6 
    6307 S |  | 6 | -6 
    6308 O |  |  | 4 
    6309 Iteration cutoff | 2 
    6310  
    6311 Matchmaker 8fz0, chain A (#1) with 6nz0, chain A (#2), sequence alignment
    6312 score = 3322.3 
    6313 RMSD between 495 pruned atom pairs is 0.699 angstroms; (across all 499 pairs:
    6314 0.741) 
    6315  
    6316 
    6317 > align
    6318 
    6319 Missing or invalid "atoms" argument: empty atom specifier 
    6320 
    6321 > open 6nz0
    6322 
    6323 6nz0 title: 
    6324 Cryo-EM structure of AAV-2 in complex with AAVR PKD domains 1 and 2 [more
    6325 info...] 
    6326  
    6327 Chain information for 6nz0 #3 
    6328 --- 
    6329 Chain | Description | UniProt 
    6330 A | Capsid protein VP1 | CAPSD_AAV2S 1-735 
    6331 Z | Dyslexia-associated protein KIAA0319-like protein | K319L_HUMAN 311-597 
    6332  
    6333 Non-standard residues in 6nz0 #3 
    6334 --- 
    6335 MG — magnesium ion 
    6336  
    6337 6nz0 mmCIF Assemblies 
    6338 --- 
    6339 1| complete icosahedral assembly 
    6340 2| icosahedral asymmetric unit 
    6341 3| icosahedral pentamer 
    6342 4| icosahedral 23 hexamer 
    6343 5| icosahedral asymmetric unit, std point frame 
    6344  
    6345 
    6346 > align #3/A toAtoms #1/n
    6347 
    6348 Unequal number of atoms to pair, 4155 and 4152 
    6349 
    6350 > select #2/Z:446
    6351 
    6352 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6353 
    6354 > select up
    6355 
    6356 80 atoms, 83 bonds, 8 residues, 1 model selected 
    6357 
    6358 > select up
    6359 
    6360 728 atoms, 740 bonds, 95 residues, 1 model selected 
    6361 
    6362 > delete sel
    6363 
    6364 > align #3/A toAtoms #1/n
    6365 
    6366 Unequal number of atoms to pair, 4155 and 4152 
    6367 
    6368 > close #3
    6369 
    6370 > select #2/Z:601@MG
    6371 
    6372 1 atom, 1 residue, 1 model selected 
    6373 
    6374 > delete sel
    6375 
    6376 > undo
    6377 
    6378 Undo failed, probably because structures have been modified. 
    6379 
    6380 > close #2
    6381 
    6382 > open 6nz0
    6383 
    6384 6nz0 title: 
    6385 Cryo-EM structure of AAV-2 in complex with AAVR PKD domains 1 and 2 [more
    6386 info...] 
    6387  
    6388 Chain information for 6nz0 #2 
    6389 --- 
    6390 Chain | Description | UniProt 
    6391 A | Capsid protein VP1 | CAPSD_AAV2S 1-735 
    6392 Z | Dyslexia-associated protein KIAA0319-like protein | K319L_HUMAN 311-597 
    6393  
    6394 Non-standard residues in 6nz0 #2 
    6395 --- 
    6396 MG — magnesium ion 
    6397  
    6398 6nz0 mmCIF Assemblies 
    6399 --- 
    6400 1| complete icosahedral assembly 
    6401 2| icosahedral asymmetric unit 
    6402 3| icosahedral pentamer 
    6403 4| icosahedral 23 hexamer 
    6404 5| icosahedral asymmetric unit, std point frame 
    6405  
    6406 
    6407 > ui tool show Matchmaker
    6408 
    6409 > matchmaker #!2 to #1
    6410 
    6411 Parameters 
    6412 --- 
    6413 Chain pairing | bb 
    6414 Alignment algorithm | Needleman-Wunsch 
    6415 Similarity matrix | BLOSUM-62 
    6416 SS fraction | 0.3 
    6417 Gap open (HH/SS/other) | 18/18/6 
    6418 Gap extend | 1 
    6419 SS matrix |  |  | H | S | O 
    6420 ---|---|---|--- 
    6421 H | 6 | -9 | -6 
    6422 S |  | 6 | -6 
    6423 O |  |  | 4 
    6424 Iteration cutoff | 2 
    6425  
    6426 Matchmaker 8fz0, chain A (#1) with 6nz0, chain A (#2), sequence alignment
    6427 score = 3322.3 
    6428 RMSD between 495 pruned atom pairs is 0.699 angstroms; (across all 499 pairs:
    6429 0.741) 
    6430  
    6431 
    6432 > open 6nz0
    6433 
    6434 6nz0 title: 
    6435 Cryo-EM structure of AAV-2 in complex with AAVR PKD domains 1 and 2 [more
    6436 info...] 
    6437  
    6438 Chain information for 6nz0 #3 
    6439 --- 
    6440 Chain | Description | UniProt 
    6441 A | Capsid protein VP1 | CAPSD_AAV2S 1-735 
    6442 Z | Dyslexia-associated protein KIAA0319-like protein | K319L_HUMAN 311-597 
    6443  
    6444 Non-standard residues in 6nz0 #3 
    6445 --- 
    6446 MG — magnesium ion 
    6447  
    6448 6nz0 mmCIF Assemblies 
    6449 --- 
    6450 1| complete icosahedral assembly 
    6451 2| icosahedral asymmetric unit 
    6452 3| icosahedral pentamer 
    6453 4| icosahedral 23 hexamer 
    6454 5| icosahedral asymmetric unit, std point frame 
    6455  
    6456 
    6457 > ui tool show Matchmaker
    6458 
    6459 > matchmaker #!3 to #1/n pairing bs
    6460 
    6461 Parameters 
    6462 --- 
    6463 Chain pairing | bs 
    6464 Alignment algorithm | Needleman-Wunsch 
    6465 Similarity matrix | BLOSUM-62 
    6466 SS fraction | 0.3 
    6467 Gap open (HH/SS/other) | 18/18/6 
    6468 Gap extend | 1 
    6469 SS matrix |  |  | H | S | O 
    6470 ---|---|---|--- 
    6471 H | 6 | -9 | -6 
    6472 S |  | 6 | -6 
    6473 O |  |  | 4 
    6474 Iteration cutoff | 2 
    6475  
    6476 Matchmaker 8fz0, chain n (#1) with 6nz0, chain A (#3), sequence alignment
    6477 score = 3322.3 
    6478 RMSD between 495 pruned atom pairs is 0.700 angstroms; (across all 499 pairs:
    6479 0.742) 
    6480  
    6481 
    6482 > open 6nz0
    6483 
    6484 6nz0 title: 
    6485 Cryo-EM structure of AAV-2 in complex with AAVR PKD domains 1 and 2 [more
    6486 info...] 
    6487  
    6488 Chain information for 6nz0 #4 
    6489 --- 
    6490 Chain | Description | UniProt 
    6491 A | Capsid protein VP1 | CAPSD_AAV2S 1-735 
    6492 Z | Dyslexia-associated protein KIAA0319-like protein | K319L_HUMAN 311-597 
    6493  
    6494 Non-standard residues in 6nz0 #4 
    6495 --- 
    6496 MG — magnesium ion 
    6497  
    6498 6nz0 mmCIF Assemblies 
    6499 --- 
    6500 1| complete icosahedral assembly 
    6501 2| icosahedral asymmetric unit 
    6502 3| icosahedral pentamer 
    6503 4| icosahedral 23 hexamer 
    6504 5| icosahedral asymmetric unit, std point frame 
    6505  
    6506 
    6507 > ui tool show Matchmaker
    6508 
    6509 > matchmaker #!4 to #1/f pairing bs
    6510 
    6511 Parameters 
    6512 --- 
    6513 Chain pairing | bs 
    6514 Alignment algorithm | Needleman-Wunsch 
    6515 Similarity matrix | BLOSUM-62 
    6516 SS fraction | 0.3 
    6517 Gap open (HH/SS/other) | 18/18/6 
    6518 Gap extend | 1 
    6519 SS matrix |  |  | H | S | O 
    6520 ---|---|---|--- 
    6521 H | 6 | -9 | -6 
    6522 S |  | 6 | -6 
    6523 O |  |  | 4 
    6524 Iteration cutoff | 2 
    6525  
    6526 Matchmaker 8fz0, chain f (#1) with 6nz0, chain A (#4), sequence alignment
    6527 score = 3316.3 
    6528 RMSD between 495 pruned atom pairs is 0.700 angstroms; (across all 499 pairs:
    6529 0.742) 
    6530  
    6531 
    6532 > hide #1 models
    6533 
    6534 > select #4/A:318
    6535 
    6536 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6537 
    6538 > select up
    6539 
    6540 211 atoms, 216 bonds, 24 residues, 1 model selected 
    6541 
    6542 > select up
    6543 
    6544 4012 atoms, 4131 bonds, 499 residues, 1 model selected 
    6545 
    6546 > delete sel
    6547 
    6548 > select #3/A:318
    6549 
    6550 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6551 
    6552 > select up
    6553 
    6554 211 atoms, 216 bonds, 24 residues, 1 model selected 
    6555 
    6556 > select up
    6557 
    6558 4012 atoms, 4131 bonds, 499 residues, 1 model selected 
    6559 
    6560 > select up
    6561 
    6562 4155 atoms, 4131 bonds, 642 residues, 1 model selected 
    6563 
    6564 > delete sel
    6565 
    6566 > select #2/A:317
    6567 
    6568 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6569 
    6570 > select up
    6571 
    6572 211 atoms, 216 bonds, 24 residues, 1 model selected 
    6573 
    6574 > select up
    6575 
    6576 4012 atoms, 4131 bonds, 499 residues, 1 model selected 
    6577 
    6578 > delete sel
    6579 
    6580 > show #1 models
    6581 
    6582 > color all white
    6583 
    6584 > color #2-4 blue
    6585 
    6586 > save /Users/tht13/Documents/VRs/8FZ0_VRs.cxs
    6587 
    6588 > select #1:652-669
    6589 
    6590 7800 atoms, 8100 bonds, 1080 residues, 1 model selected 
    6591 
    6592 > select clear
    6593 
    6594 > select VR-IV
    6595 
    6596 8988 atoms, 9048 bonds, 1260 residues, 4 models selected 
    6597 
    6598 > show sel atoms
    6599 
    6600 > style sel stick
    6601 
    6602 Changed 8988 atom styles 
    6603 
    6604 > color sel byhetero
    6605 
    6606 > sequence chain
    6607 > #1/A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,v,w,x,y,z,1,2,3,4,5,6,7,8
    6608 
    6609 Alignment identifier is 2 
    6610 
    6611 > sequence chain #2/Z#3/Z#4/Z
    6612 
    6613 Alignment identifier is 3 
    6614 
    6615 > select clear
    6616 
    6617 > color VR-V red
    6618 
    6619 > color VR-IV red
    6620 
    6621 > color all white
    6622 
    6623 > select #3/Z:410
    6624 
    6625 5 atoms, 4 bonds, 1 residue, 1 model selected 
    6626 
    6627 > select clear
    6628 
    6629 > select #3/Z:489
    6630 
    6631 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6632 
    6633 > select add #2/Z:489
    6634 
    6635 14 atoms, 12 bonds, 2 residues, 2 models selected 
    6636 
    6637 > select add #4/Z:490
    6638 
    6639 21 atoms, 18 bonds, 3 residues, 3 models selected 
    6640 
    6641 > select up
    6642 
    6643 234 atoms, 231 bonds, 33 residues, 3 models selected 
    6644 
    6645 > select up
    6646 
    6647 2184 atoms, 2220 bonds, 285 residues, 3 models selected 
    6648 
    6649 > color sel blue
    6650 
    6651 > select clear
    6652 
    6653 > name VR-I #1:262-268
    6654 
    6655 > name VR-II #2:326-330
    6656 
    6657 > name VR-II #1:326-330
    6658 
    6659 > name VR-III #1:380-388
    6660 
    6661 > name VR-IV #1:449-468
    6662 
    6663 > name VR-V #1:487-504
    6664 
    6665 > name VR-VI #1:525-541
    6666 
    6667 > name VR-VII #1:544-556
    6668 
    6669 > name VR-VIII #1:579-594
    6670 
    6671 > name VR-IX #1:704-711
    6672 
    6673 > save /Users/tht13/Documents/VRs/8FZ0_VRs.cxs
    6674 
    6675 ——— End of log from Mon Apr 27 10:11:34 2026 ———
    6676 
    6677 > view name session-start
    6678 
    6679 opened ChimeraX session 
    6680 
    6681 > show surfaces
    6682 
    6683 > lighting soft
    6684 
    6685 > select add #2
    6686 
    6687 872 atoms, 740 bonds, 5 pseudobonds, 239 residues, 2 models selected 
    6688 
    6689 > select add #3
    6690 
    6691 1601 atoms, 1480 bonds, 10 pseudobonds, 335 residues, 5 models selected 
    6692 
    6693 > select add #4
    6694 
    6695 2473 atoms, 2220 bonds, 15 pseudobonds, 574 residues, 8 models selected 
    6696 
    6697 > color sel orange
    6698 
    6699 > select subtract #2
    6700 
    6701 1601 atoms, 1480 bonds, 10 pseudobonds, 335 residues, 7 models selected 
    6702 
    6703 > select subtract #3
    6704 
    6705 872 atoms, 740 bonds, 5 pseudobonds, 239 residues, 4 models selected 
    6706 
    6707 > select subtract #4
    6708 
    6709 1 model selected 
    6710 
    6711 > select add #4
    6712 
    6713 872 atoms, 740 bonds, 5 pseudobonds, 239 residues, 2 models selected 
    6714 
    6715 > select add #3
    6716 
    6717 1601 atoms, 1480 bonds, 10 pseudobonds, 335 residues, 5 models selected 
    6718 
    6719 > select add #2
    6720 
    6721 2473 atoms, 2220 bonds, 15 pseudobonds, 574 residues, 8 models selected 
    6722 
    6723 > color sel cornflower blue
    6724 
    6725 > select add #1
    6726 
    6727 251593 atoms, 258720 bonds, 15 pseudobonds, 31714 residues, 10 models selected 
    6728 
    6729 > select subtract #2
    6730 
    6731 250721 atoms, 257980 bonds, 10 pseudobonds, 31475 residues, 68 models selected 
    6732 
    6733 > select subtract #3
    6734 
    6735 249992 atoms, 257240 bonds, 5 pseudobonds, 31379 residues, 65 models selected 
    6736 
    6737 > select subtract #4
    6738 
    6739 249120 atoms, 256500 bonds, 31140 residues, 62 models selected 
    6740 
    6741 > color sel orange
    6742 
    6743 > select clear
    6744 
    6745 > select #1/f:454@CG2
    6746 
    6747 1 atom, 1 residue, 1 model selected 
    6748 
    6749 > select add #1/n:455@CG2
    6750 
    6751 2 atoms, 2 residues, 2 models selected 
    6752 
    6753 > select add #1/A:454@CG2
    6754 
    6755 3 atoms, 3 residues, 3 models selected 
    6756 
    6757 > select up
    6758 
    6759 21 atoms, 18 bonds, 3 residues, 4 models selected 
    6760 
    6761 > select up
    6762 
    6763 114 atoms, 114 bonds, 18 residues, 4 models selected 
    6764 
    6765 > select up
    6766 
    6767 12456 atoms, 12825 bonds, 1557 residues, 4 models selected 
    6768 
    6769 > select up
    6770 
    6771 249120 atoms, 256500 bonds, 31140 residues, 4 models selected 
    6772 
    6773 > select up
    6774 
    6775 249120 atoms, 256500 bonds, 31140 residues, 61 models selected 
    6776 
    6777 > select down
    6778 
    6779 60 models selected 
    6780 
    6781 > select clear
    6782 
    6783 > select #1/n:455@CB
    6784 
    6785 1 atom, 1 residue, 1 model selected 
    6786 
    6787 > select #1/n:455@CG2
    6788 
    6789 1 atom, 1 residue, 1 model selected 
    6790 
    6791 > select add #1/A:454@OG1
    6792 
    6793 2 atoms, 2 residues, 2 models selected 
    6794 
    6795 > select add #1/f:454@OG1
    6796 
    6797 3 atoms, 3 residues, 3 models selected 
    6798 
    6799 > select up
    6800 
    6801 21 atoms, 18 bonds, 3 residues, 4 models selected 
    6802 
    6803 > select up
    6804 
    6805 114 atoms, 114 bonds, 18 residues, 4 models selected 
    6806 
    6807 > select up
    6808 
    6809 12456 atoms, 12825 bonds, 1557 residues, 4 models selected 
    6810 
    6811 > hide sel surfaces
    6812 
    6813 > select clear
    6814 
    6815 > color #1 light gray
    6816 
    6817 > select add #1/f:553
    6818 
    6819 8 atoms, 8 bonds, 1 residue, 1 model selected 
    6820 
    6821 > select add #1/n:543
    6822 
    6823 12 atoms, 11 bonds, 2 residues, 2 models selected 
    6824 
    6825 > select up
    6826 
    6827 14 atoms, 11 bonds, 3 residues, 3 models selected 
    6828 
    6829 > select up
    6830 
    6831 19 atoms, 17 bonds, 3 residues, 3 models selected 
    6832 
    6833 > select up
    6834 
    6835 163 atoms, 162 bonds, 22 residues, 3 models selected 
    6836 
    6837 > select up
    6838 
    6839 8304 atoms, 8550 bonds, 1038 residues, 3 models selected 
    6840 
    6841 > select up
    6842 
    6843 249120 atoms, 256500 bonds, 31140 residues, 3 models selected 
    6844 
    6845 > select down
    6846 
    6847 8304 atoms, 8550 bonds, 1038 residues, 61 models selected 
    6848 
    6849 > select clear
    6850 
    6851 > select #1/J:302@CG
    6852 
    6853 1 atom, 1 residue, 1 model selected 
    6854 
    6855 > select add #1/n:461
    6856 
    6857 10 atoms, 9 bonds, 2 residues, 2 models selected 
    6858 
    6859 > select up
    6860 
    6861 12 atoms, 9 bonds, 3 residues, 3 models selected 
    6862 
    6863 > select up
    6864 
    6865 26 atoms, 23 bonds, 3 residues, 4 models selected 
    6866 
    6867 > select up
    6868 
    6869 168 atoms, 169 bonds, 19 residues, 4 models selected 
    6870 
    6871 > select up
    6872 
    6873 12456 atoms, 12825 bonds, 1557 residues, 4 models selected 
    6874 
    6875 > select up
    6876 
    6877 249120 atoms, 256500 bonds, 31140 residues, 4 models selected 
    6878 
    6879 > select down
    6880 
    6881 12456 atoms, 12825 bonds, 1557 residues, 61 models selected 
    6882 
    6883 > color sel orange
    6884 
    6885 > select #1/f:543
    6886 
    6887 4 atoms, 3 bonds, 1 residue, 1 model selected 
    6888 
    6889 > select up
    6890 
    6891 23 atoms, 23 bonds, 3 residues, 2 models selected 
    6892 
    6893 > select up
    6894 
    6895 4152 atoms, 4275 bonds, 519 residues, 2 models selected 
    6896 
    6897 > color sel orange
    6898 
    6899 > select clear
    6900 
    6901 > select #1/y:454@CG2
    6902 
    6903 1 atom, 1 residue, 1 model selected 
    6904 
    6905 > select add #1/e:454@CG2
    6906 
    6907 2 atoms, 2 residues, 2 models selected 
    6908 
    6909 > select add #1/a:454@CG2
    6910 
    6911 3 atoms, 3 residues, 3 models selected 
    6912 
    6913 > select up
    6914 
    6915 21 atoms, 18 bonds, 3 residues, 4 models selected 
    6916 
    6917 > select up
    6918 
    6919 114 atoms, 114 bonds, 18 residues, 4 models selected 
    6920 
    6921 > select up
    6922 
    6923 12456 atoms, 12825 bonds, 1557 residues, 4 models selected 
    6924 
    6925 > color sel orange
    6926 
    6927 > hide sel surfaces
    6928 
    6929 > preset cartoons/nucleotides licorice/ovals
    6930 
    6931 Using preset: Cartoons/Nucleotides / Licorice/Ovals 
    6932 Changed 240600 atom styles 
    6933 Preset expands to these ChimeraX commands:
    6934 
    6935    
    6936    
    6937     show nucleic
    6938     hide protein|solvent|H
    6939     surf hide
    6940     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    6941     ~worm
    6942     cartoon
    6943     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    6944     cartoon style ~(nucleic|strand) x round
    6945     cartoon style (nucleic|strand) x rect
    6946     cartoon style protein modeh default arrows f x round width 1 thick 1
    6947     cartoon style nucleic x round width 1.6 thick 1.6
    6948     nucleotides tube/slab shape ellipsoid
    6949 
    6950  
    6951 
    6952 > undo
    6953 
    6954 > show sel surfaces
    6955 
    6956 > hide sel surfaces
    6957 
    6958 > select ~sel & ##selected
    6959 
    6960 236664 atoms, 243675 bonds, 29583 residues, 1 model selected 
    6961 
    6962 > select up
    6963 
    6964 249120 atoms, 256500 bonds, 31140 residues, 58 models selected 
    6965 
    6966 > select down
    6967 
    6968 236664 atoms, 243675 bonds, 29583 residues, 61 models selected 
    6969 
    6970 > show sel surfaces
    6971 
    6972 > select #1/f:454@OG1
    6973 
    6974 1 atom, 1 residue, 1 model selected 
    6975 
    6976 > select add #1/n:454@CG2
    6977 
    6978 2 atoms, 2 residues, 2 models selected 
    6979 
    6980 > select add #1/A:454@CG2
    6981 
    6982 3 atoms, 3 residues, 3 models selected 
    6983 
    6984 > select up
    6985 
    6986 21 atoms, 18 bonds, 3 residues, 4 models selected 
    6987 
    6988 > select up
    6989 
    6990 114 atoms, 114 bonds, 18 residues, 4 models selected 
    6991 
    6992 > select up
    6993 
    6994 12456 atoms, 12825 bonds, 1557 residues, 4 models selected 
    6995 
    6996 > hide sel surfaces
    6997 
    6998 > select clear
    6999 
    7000 > select #1/n:489
    7001 
    7002 6 atoms, 5 bonds, 1 residue, 1 model selected 
    7003 
    7004 > select add #1/n:462
    7005 
    7006 17 atoms, 16 bonds, 2 residues, 2 models selected 
    7007 
    7008 > select add #1/f:449
    7009 
    7010 25 atoms, 23 bonds, 3 residues, 2 models selected 
    7011 
    7012 > select add #2/Z:488
    7013 
    7014 31 atoms, 28 bonds, 4 residues, 4 models selected 
    7015 
    7016 > select add #3/Z:473
    7017 
    7018 43 atoms, 40 bonds, 5 residues, 6 models selected 
    7019 
    7020 > select add #4/Z:489
    7021 
    7022 50 atoms, 46 bonds, 6 residues, 8 models selected 
    7023 
    7024 > select up
    7025 
    7026 397 atoms, 396 bonds, 51 residues, 9 models selected 
    7027 
    7028 > select up
    7029 
    7030 10488 atoms, 10770 bonds, 1323 residues, 9 models selected 
    7031 
    7032 > select up
    7033 
    7034 10491 atoms, 10770 bonds, 1326 residues, 9 models selected 
    7035 
    7036 > select up
    7037 
    7038 251593 atoms, 258720 bonds, 31714 residues, 9 models selected 
    7039 
    7040 > select down
    7041 
    7042 10491 atoms, 10770 bonds, 1326 residues, 67 models selected 
    7043 
    7044 > select add #1/A:277
    7045 
    7046 10498 atoms, 10776 bonds, 1327 residues, 9 models selected 
    7047 
    7048 > select up
    7049 
    7050 10579 atoms, 10864 bonds, 1336 residues, 9 models selected 
    7051 
    7052 > select up
    7053 
    7054 14643 atoms, 15045 bonds, 1845 residues, 10 models selected 
    7055 
    7056 > save "/Users/miguel/Tresorit/Avista/Projects/AAVmers/Linked_AAVs/8FZ0_VRs
    7057 > 2.cxs"
    7058 
    7059 > preset cartoons/nucleotides licorice/ovals
    7060 
    7061 Using preset: Cartoons/Nucleotides / Licorice/Ovals 
    7062 Changed 240600 atom styles 
    7063 Preset expands to these ChimeraX commands:
    7064 
    7065    
    7066    
    7067     show nucleic
    7068     hide protein|solvent|H
    7069     surf hide
    7070     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    7071     ~worm
    7072     cartoon
    7073     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    7074     cartoon style ~(nucleic|strand) x round
    7075     cartoon style (nucleic|strand) x rect
    7076     cartoon style protein modeh default arrows f x round width 1 thick 1
    7077     cartoon style nucleic x round width 1.6 thick 1.6
    7078     nucleotides tube/slab shape ellipsoid
    7079 
    7080  
    7081 
    7082 > select clear
    7083 
    7084 > show surfaces
    7085 
    7086 > select add #3/Z:451@CD1
    7087 
    7088 1 atom, 1 residue, 1 model selected 
    7089 
    7090 > select #2/Z:451@CD1
    7091 
    7092 1 atom, 1 residue, 1 model selected 
    7093 
    7094 > select add #3/Z:451@CD1
    7095 
    7096 2 atoms, 2 residues, 3 models selected 
    7097 
    7098 > select add #4/Z:451@CD1
    7099 
    7100 3 atoms, 3 residues, 5 models selected 
    7101 
    7102 > select add #1/n:454@CG2
    7103 
    7104 4 atoms, 4 residues, 7 models selected 
    7105 
    7106 > select add #1/f:454@CG2
    7107 
    7108 5 atoms, 5 residues, 8 models selected 
    7109 
    7110 > select add #1/A:454@CG2
    7111 
    7112 6 atoms, 6 residues, 9 models selected 
    7113 
    7114 > select up
    7115 
    7116 45 atoms, 39 bonds, 6 residues, 10 models selected 
    7117 
    7118 > select up
    7119 
    7120 414 atoms, 414 bonds, 57 residues, 10 models selected 
    7121 
    7122 > select up
    7123 
    7124 14640 atoms, 15045 bonds, 1842 residues, 10 models selected 
    7125 
    7126 > hide sel surfaces
    7127 
    7128 > select clear
    7129 
    7130 > select #1/e:587@ND2
    7131 
    7132 1 atom, 1 residue, 1 model selected 
    7133 
    7134 > select add #1/a:587@O
    7135 
    7136 2 atoms, 2 residues, 2 models selected 
    7137 
    7138 > select add #1/y:454@CB
    7139 
    7140 3 atoms, 3 residues, 3 models selected 
    7141 
    7142 > select up
    7143 
    7144 23 atoms, 20 bonds, 3 residues, 4 models selected 
    7145 
    7146 > select up
    7147 
    7148 208 atoms, 206 bonds, 28 residues, 4 models selected 
    7149 
    7150 > select up
    7151 
    7152 12456 atoms, 12825 bonds, 1557 residues, 4 models selected 
    7153 
    7154 > hide sel surfaces
    7155 
    7156 > select clear
    7157 
    7158 > save "/Users/miguel/Tresorit/Avista/Projects/AAVmers/Linked_AAVs/8FZ0_VRs
    7159 > 2.cxs"
    7160 
    7161 > select #1/J:454@CG2
    7162 
    7163 1 atom, 1 residue, 1 model selected 
    7164 
    7165 > select up
    7166 
    7167 7 atoms, 6 bonds, 1 residue, 2 models selected 
    7168 
    7169 > select up
    7170 
    7171 38 atoms, 38 bonds, 6 residues, 2 models selected 
    7172 
    7173 > select up
    7174 
    7175 4152 atoms, 4275 bonds, 519 residues, 2 models selected 
    7176 
    7177 > color #1 light gray
    7178 
    7179 > select clear
    7180 
    7181 > select #1/y:593
    7182 
    7183 5 atoms, 4 bonds, 1 residue, 1 model selected 
    7184 
    7185 > select add #1/a:593
    7186 
    7187 10 atoms, 8 bonds, 2 residues, 2 models selected 
    7188 
    7189 > select add #1/e:591
    7190 
    7191 15 atoms, 12 bonds, 3 residues, 3 models selected 
    7192 
    7193 > select up
    7194 
    7195 139 atoms, 136 bonds, 19 residues, 4 models selected 
    7196 
    7197 > select up
    7198 
    7199 12456 atoms, 12825 bonds, 1557 residues, 4 models selected 
    7200 
    7201 > color sel orange
    7202 
    7203 > select #1/f:497
    7204 
    7205 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7206 
    7207 > select add #1/A:497
    7208 
    7209 16 atoms, 14 bonds, 2 residues, 2 models selected 
    7210 
    7211 > select add #1/n:496
    7212 
    7213 24 atoms, 21 bonds, 3 residues, 3 models selected 
    7214 
    7215 > select up
    7216 
    7217 387 atoms, 393 bonds, 51 residues, 4 models selected 
    7218 
    7219 > select up
    7220 
    7221 12456 atoms, 12825 bonds, 1557 residues, 4 models selected 
    7222 
    7223 > color sel orange
    7224 
    7225 > select clear
    7226 
    7227 > save "/Users/miguel/Tresorit/Avista/Projects/AAVmers/Linked_AAVs/8FZ0_VRs
    7228 > 2.cxs"
    7229 
    7230 > select #1/n
    7231 
    7232 4152 atoms, 4275 bonds, 519 residues, 1 model selected 
    7233 
    7234 > select #1/n:VR-IV
    7235 
    7236 Nothing selected 
    7237 
    7238 > select #1/n:VR-IV
    7239 
    7240 Nothing selected 
    7241 
    7242 > select VR-IV
    7243 
    7244 8520 atoms, 8580 bonds, 1200 residues, 1 model selected 
    7245 
    7246 > select #1/VR-IV
    7247 
    7248 Nothing selected 
    7249 
    7250 > select #1/n:"VR-IV"
    7251 
    7252 1855 atoms, 1735 bonds, 241 residues, 1 model selected 
    7253 
    7254 > select clear
    7255 
    7256 > select VR-IV #1/n
    7257 
    7258 Expected a keyword 
    7259 
    7260 > select VR-IV /n
    7261 
    7262 Expected a keyword 
    7263 
    7264 > select VR-IV /n,A,f
    7265 
    7266 Expected a keyword 
    7267 
    7268 > select VR-IV /n
    7269 
    7270 Expected a keyword 
    7271 
    7272 > select VR-IV
    7273 
    7274 8520 atoms, 8580 bonds, 1200 residues, 1 model selected 
    7275 
    7276 > select VR-IV /n
    7277 
    7278 Expected a keyword 
    7279 
    7280 > color VR-IV goldenrod
    7281 
    7282 > color VR-IV tomato
    7283 
    7284 > select clear
    7285 
    7286 > surface color light gray
    7287 
    7288 > color VR-VII tomato
    7289 
    7290 > surface color light gray
    7291 
    7292 > hide sel surfaces
    7293 
    7294 > select clear
    7295 
    7296 > show surfaces
    7297 
    7298 > select VR-IV
    7299 
    7300 8520 atoms, 8580 bonds, 1200 residues, 1 model selected 
    7301 
    7302 > select #1/a,N,f
    7303 
    7304 12456 atoms, 12825 bonds, 1557 residues, 1 model selected 
    7305 
    7306 > hide sel surfaces
    7307 
    7308 > show sel surfaces
    7309 
    7310 > select #1/A,n,f
    7311 
    7312 12456 atoms, 12825 bonds, 1557 residues, 1 model selected 
    7313 
    7314 > hide sel surfaces
    7315 
    7316 > select clear
    7317 
    7318 > select #2/Z:450@CG
    7319 
    7320 1 atom, 1 residue, 1 model selected 
    7321 
    7322 > select add #4/Z:472@CB
    7323 
    7324 2 atoms, 2 residues, 3 models selected 
    7325 
    7326 > select add #3/Z:449@CA
    7327 
    7328 3 atoms, 3 residues, 5 models selected 
    7329 
    7330 > select up
    7331 
    7332 19 atoms, 17 bonds, 3 residues, 6 models selected 
    7333 
    7334 > select up
    7335 
    7336 277 atoms, 278 bonds, 36 residues, 6 models selected 
    7337 
    7338 > select up
    7339 
    7340 2184 atoms, 2220 bonds, 285 residues, 6 models selected 
    7341 
    7342 > select up
    7343 
    7344 2187 atoms, 2220 bonds, 288 residues, 6 models selected 
    7345 
    7346 > select up
    7347 
    7348 2473 atoms, 2220 bonds, 574 residues, 6 models selected 
    7349 
    7350 > select up
    7351 
    7352 2473 atoms, 2220 bonds, 5 pseudobonds, 574 residues, 7 models selected 
    7353 
    7354 > select up
    7355 
    7356 2473 atoms, 2220 bonds, 10 pseudobonds, 574 residues, 8 models selected 
    7357 
    7358 > hide sel surfaces
    7359 
    7360 > select clear
    7361 
    7362 > open 6zcw
    7363 
    7364 Summary of feedback from opening 6zcw fetched from pdb 
    7365 --- 
    7366 notes | Fetching compressed mmCIF 6zcw from http://files.rcsb.org/download/6zcw.cif 
    7367 Fetching CCD PQQ from
    7368 https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Q/PQQ/PQQ.cif 
    7369 Fetching CCD PR from
    7370 https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/PR/PR.cif 
    7371  
    7372 6zcw title: 
    7373 Crystal structure of lanthanide-dependent alcohol dehydrogenase PedH from
    7374 Pseudomonas putida KT2440 [more info...] 
    7375  
    7376 Chain information for 6zcw #5 
    7377 --- 
    7378 Chain | Description | UniProt 
    7379 A | Quinoprotein ethanol dehydrogenase | Q88JH0_PSEPK 28-595 
    7380  
    7381 Non-standard residues in 6zcw #5 
    7382 --- 
    7383 PQQ — pyrroloquinoline quinone 
    7384 PR — praseodymium ion 
    7385  
    7386 81 atoms have alternate locations. Control/examine alternate locations with
    7387 Altloc Explorer [start tool...] or the altlocs command. 
    7388 4354 atoms have anisotropic B-factors. Depict anisotropic information with
    7389 Thermal Ellipsoids [start tool...] or the aniso command. 
    7390 
    7391 > close #5
    7392 
    7393 > open 9zcw
    7394 
    7395 9zcw title: 
    7396 Cryo-EM structure of the engineered vector AAV2.ATX002 [more info...] 
    7397  
    7398 Chain information for 9zcw #5 
    7399 --- 
    7400 Chain | Description | UniProt 
    7401 1 2 3 4 5 6 7 8 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d e f g h i j k l m n o p q r s t u v w x y z | Engineered AAV2 capsid protein VP3 | CAPSD_AAV2S 1-542 
    7402  
    7403 
    7404 > ui tool show Matchmaker
    7405 
    7406 > matchmaker #5 to #1
    7407 
    7408 Parameters 
    7409 --- 
    7410 Chain pairing | bb 
    7411 Alignment algorithm | Needleman-Wunsch 
    7412 Similarity matrix | BLOSUM-62 
    7413 SS fraction | 0.3 
    7414 Gap open (HH/SS/other) | 18/18/6 
    7415 Gap extend | 1 
    7416 SS matrix |  |  | H | S | O 
    7417 ---|---|---|--- 
    7418 H | 6 | -9 | -6 
    7419 S |  | 6 | -6 
    7420 O |  |  | 4 
    7421 Iteration cutoff | 2 
    7422  
    7423 Matchmaker 8fz0, chain A (#1) with 9zcw, chain O (#5), sequence alignment
    7424 score = 2624.5 
    7425 RMSD between 515 pruned atom pairs is 0.828 angstroms; (across all 517 pairs:
    7426 0.852) 
    7427  
    7428 
    7429 > select add #5
    7430 
    7431 252900 atoms, 260400 bonds, 31560 residues, 1 model selected 
    7432 
    7433 > color sel hot pink
    7434 
    7435 > preset cartoons/nucleotides licorice/ovals
    7436 
    7437 Using preset: Cartoons/Nucleotides / Licorice/Ovals 
    7438 Changed 252900 atom styles 
    7439 Preset expands to these ChimeraX commands:
    7440 
    7441    
    7442    
    7443     show nucleic
    7444     hide protein|solvent|H
    7445     surf hide
    7446     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    7447     ~worm
    7448     cartoon
    7449     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    7450     cartoon style ~(nucleic|strand) x round
    7451     cartoon style (nucleic|strand) x rect
    7452     cartoon style protein modeh default arrows f x round width 1 thick 1
    7453     cartoon style nucleic x round width 1.6 thick 1.6
    7454     nucleotides tube/slab shape ellipsoid
    7455 
    7456  
    7457 
    7458 > select clear
    7459 
    7460 > hide #!1 models
    7461 
    7462 > hide #!4 models
    7463 
    7464 > hide #!3 models
    7465 
    7466 > hide #!2 models
    7467 
    7468 > color #5 light gray
    7469 
    7470 > hide #5 models
    7471 
    7472 > show #!4 models
    7473 
    7474 > show #!3 models
    7475 
    7476 > show #!2 models
    7477 
    7478 > show #!1 models
    7479 
    7480 > hide #!1 models
    7481 
    7482 > select add #1.1
    7483 
    7484 4152 atoms, 519 residues, 1 model selected 
    7485 
    7486 > select add #1.2
    7487 
    7488 8304 atoms, 1038 residues, 2 models selected 
    7489 
    7490 > select add #1.3
    7491 
    7492 12456 atoms, 1557 residues, 3 models selected 
    7493 
    7494 > select add #1.4
    7495 
    7496 16608 atoms, 2076 residues, 4 models selected 
    7497 
    7498 > select add #1.5
    7499 
    7500 20760 atoms, 2595 residues, 5 models selected 
    7501 
    7502 > select add #1.6
    7503 
    7504 24912 atoms, 3114 residues, 6 models selected 
    7505 
    7506 > select add #1.7
    7507 
    7508 29064 atoms, 3633 residues, 7 models selected 
    7509 
    7510 > select add #1.8
    7511 
    7512 33216 atoms, 4152 residues, 8 models selected 
    7513 
    7514 > select add #1.9
    7515 
    7516 37368 atoms, 4671 residues, 9 models selected 
    7517 
    7518 > select add #1.10
    7519 
    7520 41520 atoms, 5190 residues, 10 models selected 
    7521 
    7522 > select add #1.11
    7523 
    7524 45672 atoms, 5709 residues, 11 models selected 
    7525 
    7526 > select add #1.12
    7527 
    7528 49824 atoms, 6228 residues, 12 models selected 
    7529 
    7530 > select add #1.13
    7531 
    7532 53976 atoms, 6747 residues, 13 models selected 
    7533 
    7534 > select add #1.14
    7535 
    7536 58128 atoms, 7266 residues, 14 models selected 
    7537 
    7538 > select add #1.15
    7539 
    7540 62280 atoms, 7785 residues, 15 models selected 
    7541 
    7542 > select add #1.16
    7543 
    7544 66432 atoms, 8304 residues, 16 models selected 
    7545 
    7546 > select add #1.17
    7547 
    7548 70584 atoms, 8823 residues, 17 models selected 
    7549 
    7550 > select add #1.18
    7551 
    7552 74736 atoms, 9342 residues, 18 models selected 
    7553 
    7554 > select add #1.19
    7555 
    7556 78888 atoms, 9861 residues, 19 models selected 
    7557 
    7558 > select add #1.20
    7559 
    7560 83040 atoms, 10380 residues, 20 models selected 
    7561 
    7562 > select add #1.21
    7563 
    7564 87192 atoms, 10899 residues, 21 models selected 
    7565 
    7566 > select #1
    7567 
    7568 249120 atoms, 256500 bonds, 31140 residues, 1 model selected 
    7569 
    7570 > show #!2-4 surfaces
    7571 
    7572 [Repeated 1 time(s)]
    7573 
    7574 > show #!1 models
    7575 
    7576 > show sel surfaces
    7577 
    7578 > select subtract #1
    7579 
    7580 60 models selected 
    7581 
    7582 > select add #2
    7583 
    7584 872 atoms, 740 bonds, 5 pseudobonds, 239 residues, 2 models selected 
    7585 
    7586 > select add #3
    7587 
    7588 1601 atoms, 1480 bonds, 10 pseudobonds, 335 residues, 5 models selected 
    7589 
    7590 > select add #4
    7591 
    7592 2473 atoms, 2220 bonds, 15 pseudobonds, 574 residues, 8 models selected 
    7593 
    7594 > hide sel surfaces
    7595 
    7596 > select #1/a,N,f
    7597 
    7598 12456 atoms, 12825 bonds, 1557 residues, 1 model selected 
    7599 
    7600 > select #1/A,n,f
    7601 
    7602 12456 atoms, 12825 bonds, 1557 residues, 1 model selected 
    7603 
    7604 > hide sel surfaces
    7605 
    7606 > select clear
    7607 
    7608 > show #5 models
    7609 
    7610 > hide #5 models
    7611 
    7612 > select #1/d:454@CG2
    7613 
    7614 1 atom, 1 residue, 1 model selected 
    7615 
    7616 > select #1/v,b,d
    7617 
    7618 12456 atoms, 12825 bonds, 1557 residues, 1 model selected 
    7619 
    7620 > hide sel surfaces
    7621 
    7622 > select clear
    7623 
    7624 > save "/Users/miguel/Tresorit/Avista/Projects/AAVmers/Linked_AAVs/8FZ0_VRs
    7625 > 2.cxs"
    7626 
    7627 > select #1/v,b,d
    7628 
    7629 12456 atoms, 12825 bonds, 1557 residues, 1 model selected 
    7630 
    7631 > select intersect VR-VIII
    7632 
    7633 351 bonds, 1 model selected 
    7634 
    7635 > color sel yellow
    7636 
    7637 > color sel orange
    7638 
    7639 > select #1/v,b,d intersect VR-VIII
    7640 
    7641 Expected a keyword 
    7642 
    7643 > select #1/v,b,d
    7644 
    7645 12456 atoms, 12825 bonds, 1557 residues, 1 model selected 
    7646 
    7647 > select intersect VR-IX
    7648 
    7649 195 atoms, 195 bonds, 24 residues, 1 model selected 
    7650 
    7651 > color (#!1 & sel) light sea green
    7652 
    7653 > select #1/v,b,d
    7654 
    7655 12456 atoms, 12825 bonds, 1557 residues, 1 model selected 
    7656 
    7657 > select intersect VR-V
    7658 
    7659 423 atoms, 429 bonds, 54 residues, 1 model selected 
    7660 
    7661 > color (#!1 & sel) hot pink
    7662 
    7663 > select #1/v,b,d
    7664 
    7665 12456 atoms, 12825 bonds, 1557 residues, 1 model selected 
    7666 
    7667 > select intersect VR-VI
    7668 
    7669 417 atoms, 426 bonds, 51 residues, 1 model selected 
    7670 
    7671 > color (#!1 & sel) cornflower blue
    7672 
    7673 > select #1/v,b,d
    7674 
    7675 12456 atoms, 12825 bonds, 1557 residues, 1 model selected 
    7676 
    7677 > select intersect VR-III
    7678 
    7679 177 atoms, 174 bonds, 27 residues, 1 model selected 
    7680 
    7681 > select #1/v,b,d
    7682 
    7683 12456 atoms, 12825 bonds, 1557 residues, 1 model selected 
    7684 
    7685 > select intersect VR-II
    7686 
    7687 102 atoms, 99 bonds, 15 residues, 1 model selected 
    7688 
    7689 > ui tool show "Color Actions"
    7690 
    7691 > color sel light green
    7692 
    7693 > select #1/v,b,d
    7694 
    7695 12456 atoms, 12825 bonds, 1557 residues, 1 model selected 
    7696 
    7697 > select intersect VR-III
    7698 
    7699 177 atoms, 174 bonds, 27 residues, 1 model selected 
    7700 
    7701 > ui tool show "Color Actions"
    7702 
    7703 > color sel pale green
    7704 
    7705 > color sel sky blue
    7706 
    7707 > color sel dark khaki
    7708 
    7709 > select #1/v,b,d
    7710 
    7711 12456 atoms, 12825 bonds, 1557 residues, 1 model selected 
    7712 
    7713 > select intersect VR-VII
    7714 
    7715 306 atoms, 303 bonds, 39 residues, 1 model selected 
    7716 
    7717 > select #1/v,b,d
    7718 
    7719 12456 atoms, 12825 bonds, 1557 residues, 1 model selected 
    7720 
    7721 > select intersect VR-VIII
    7722 
    7723 354 atoms, 351 bonds, 48 residues, 1 model selected 
    7724 
    7725 > select #1/v,b,d
    7726 
    7727 12456 atoms, 12825 bonds, 1557 residues, 1 model selected 
    7728 
    7729 > select intersect VR-IV
    7730 
    7731 426 atoms, 429 bonds, 60 residues, 1 model selected 
    7732 
    7733 > select #1/v,b,d
    7734 
    7735 12456 atoms, 12825 bonds, 1557 residues, 1 model selected 
    7736 
    7737 > select intersect VR-VII
    7738 
    7739 306 atoms, 303 bonds, 39 residues, 1 model selected 
    7740 
    7741 > ui tool show "Color Actions"
    7742 
    7743 > color sel tan
    7744 
    7745 > select clear
    7746 
    7747 > select #1/v,b,d
    7748 
    7749 12456 atoms, 12825 bonds, 1557 residues, 1 model selected 
    7750 
    7751 > select intersect VR-X
    7752 
    7753 Missing or invalid "objects" argument: invalid objects specifier 
    7754 
    7755 > select #1/v,b,d
    7756 
    7757 12456 atoms, 12825 bonds, 1557 residues, 1 model selected 
    7758 
    7759 > select intersect VR-IX
    7760 
    7761 195 atoms, 195 bonds, 24 residues, 1 model selected 
    7762 
    7763 > cartoon style protein modeHelix default arrows false xsection round width 2
    7764 > thickness 2
    7765 
    7766 > select clear
    7767 
    7768 > cartoon style protein modeHelix default arrows false xsection round width
    7769 > 1.5 thickness 1.5
    7770 
    7771 > graphics silhouettes true
    7772 
    7773 > select clear
    7774 
    7775 > set bgColor white
    7776 
    7777 > undo
    7778 
    7779 > set bgColor gray
    7780 
    7781 > set bgColor black
    7782 
    7783 > set bgColor white
    7784 
    7785 > save "/Users/miguel/Tresorit/Avista/Projects/AAVmers/Linked_AAVs/8FZ0_VRs
    7786 > MB.cxs"
    7787 
    7788 ——— End of log from Mon Apr 27 11:43:14 2026 ———
    7789 
    7790 > view name session-start
    7791 
    7792 opened ChimeraX session 
    7793 
    7794 > preset cartoons/nucleotides cylinders/stubs
    7795 
    7796 Using preset: Cartoons/Nucleotides / Cylinders/Stubs 
    7797 Changed 0 atom styles 
    7798 Preset expands to these ChimeraX commands:
    7799 
    7800    
    7801    
    7802     show nucleic
    7803     hide protein|solvent|H
    7804     surf hide
    7805     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    7806     ~worm
    7807     cartoon
    7808     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    7809     cartoon style ~(nucleic|strand) x round
    7810     cartoon style (nucleic|strand) x rect
    7811     cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    7812     cartoon style nucleic x round width 1.6 thick 1.6
    7813     nucleotides stubs
    7814 
    7815  
    7816 
    7817 > select #1/A,n,f
    7818 
    7819 12456 atoms, 12825 bonds, 1557 residues, 1 model selected 
    7820 
    7821 > select /v,b,d,A,n,f
    7822 
    7823 50488 atoms, 51690 bonds, 6556 residues, 4 models selected 
    7824 
    7825 > select ~sel & ##selected
    7826 
    7827 453276 atoms, 466690 bonds, 10 pseudobonds, 56622 residues, 6 models selected 
    7828 
    7829 > show sel & #!1-2,4 surfaces
    7830 
    7831 > select add #1
    7832 
    7833 478188 atoms, 492340 bonds, 10 pseudobonds, 59736 residues, 62 models selected 
    7834 
    7835 > select add #2
    7836 
    7837 478331 atoms, 492340 bonds, 10 pseudobonds, 59879 residues, 68 models selected 
    7838 
    7839 > select add #4
    7840 
    7841 478474 atoms, 492340 bonds, 10 pseudobonds, 60022 residues, 68 models selected 
    7842 
    7843 > select add #5
    7844 
    7845 503764 atoms, 518380 bonds, 10 pseudobonds, 63178 residues, 68 models selected 
    7846 
    7847 > select subtract #1
    7848 
    7849 254644 atoms, 261880 bonds, 10 pseudobonds, 32038 residues, 67 models selected 
    7850 
    7851 > select add #3
    7852 
    7853 255373 atoms, 262620 bonds, 15 pseudobonds, 32134 residues, 9 models selected 
    7854 
    7855 > select subtract #5
    7856 
    7857 2473 atoms, 2220 bonds, 15 pseudobonds, 574 residues, 9 models selected 
    7858 
    7859 > hide sel surfaces
    7860 
    7861 > select clear
    7862 
    7863 Traceback (most recent call last): 
    7864 File
    7865 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    7866 packages/chimerax/ui/statusbar.py", line 104, in _expose_event 
    7867 self.status(self._last_message, self._last_color) 
    7868 File
    7869 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    7870 packages/chimerax/ui/statusbar.py", line 170, in status 
    7871 r.draw_background() 
    7872 File
    7873 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    7874 packages/chimerax/graphics/opengl.py", line 1264, in draw_background 
    7875 GL.glClear(flags) 
    7876 File "src/errorchecker.pyx", line 59, in
    7877 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    7878 OpenGL.error.GLError: GLError( 
    7879 err = 1286, 
    7880 description = b'invalid framebuffer operation', 
    7881 baseOperation = glClear, 
    7882 cArguments = (16640,) 
    7883 ) 
    7884  
    7885 OpenGL.error.GLError: GLError( 
    7886 err = 1286, 
    7887 description = b'invalid framebuffer operation', 
    7888 baseOperation = glClear, 
    7889 cArguments = (16640,) 
    7890 ) 
    7891  
    7892 File "src/errorchecker.pyx", line 59, in
    7893 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    7894  
    7895 See log for complete Python traceback. 
    7896  
    7897 Traceback (most recent call last): 
    7898 File
    7899 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    7900 packages/chimerax/ui/statusbar.py", line 104, in _expose_event 
    7901 self.status(self._last_message, self._last_color) 
    7902 File
    7903 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    7904 packages/chimerax/ui/statusbar.py", line 170, in status 
    7905 r.draw_background() 
    7906 File
    7907 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    7908 packages/chimerax/graphics/opengl.py", line 1264, in draw_background 
    7909 GL.glClear(flags) 
    7910 File "src/errorchecker.pyx", line 59, in
    7911 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    7912 OpenGL.error.GLError: GLError( 
    7913 err = 1286, 
    7914 description = b'invalid framebuffer operation', 
    7915 baseOperation = glClear, 
    7916 cArguments = (16640,) 
    7917 ) 
    7918  
    7919 OpenGL.error.GLError: GLError( 
    7920 err = 1286, 
    7921 description = b'invalid framebuffer operation', 
    7922 baseOperation = glClear, 
    7923 cArguments = (16640,) 
    7924 ) 
    7925  
    7926 File "src/errorchecker.pyx", line 59, in
    7927 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    7928  
    7929 See log for complete Python traceback. 
    7930  
    7931 Traceback (most recent call last): 
    7932 File
    7933 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    7934 packages/chimerax/ui/statusbar.py", line 104, in _expose_event 
    7935 self.status(self._last_message, self._last_color) 
    7936 File
    7937 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    7938 packages/chimerax/ui/statusbar.py", line 170, in status 
    7939 r.draw_background() 
    7940 File
    7941 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    7942 packages/chimerax/graphics/opengl.py", line 1264, in draw_background 
    7943 GL.glClear(flags) 
    7944 File "src/errorchecker.pyx", line 59, in
    7945 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    7946 OpenGL.error.GLError: GLError( 
    7947 err = 1286, 
    7948 description = b'invalid framebuffer operation', 
    7949 baseOperation = glClear, 
    7950 cArguments = (16640,) 
    7951 ) 
    7952  
    7953 OpenGL.error.GLError: GLError( 
    7954 err = 1286, 
    7955 description = b'invalid framebuffer operation', 
    7956 baseOperation = glClear, 
    7957 cArguments = (16640,) 
    7958 ) 
    7959  
    7960 File "src/errorchecker.pyx", line 59, in
    7961 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    7962  
    7963 See log for complete Python traceback. 
    7964  
    7965 Traceback (most recent call last): 
    7966 File
    7967 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    7968 packages/chimerax/ui/statusbar.py", line 104, in _expose_event 
    7969 self.status(self._last_message, self._last_color) 
    7970 File
    7971 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    7972 packages/chimerax/ui/statusbar.py", line 170, in status 
    7973 r.draw_background() 
    7974 File
    7975 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    7976 packages/chimerax/graphics/opengl.py", line 1264, in draw_background 
    7977 GL.glClear(flags) 
    7978 File "src/errorchecker.pyx", line 59, in
    7979 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    7980 OpenGL.error.GLError: GLError( 
    7981 err = 1286, 
    7982 description = b'invalid framebuffer operation', 
    7983 baseOperation = glClear, 
    7984 cArguments = (16640,) 
    7985 ) 
    7986  
    7987 OpenGL.error.GLError: GLError( 
    7988 err = 1286, 
    7989 description = b'invalid framebuffer operation', 
    7990 baseOperation = glClear, 
    7991 cArguments = (16640,) 
    7992 ) 
    7993  
    7994 File "src/errorchecker.pyx", line 59, in
    7995 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    7996  
    7997 See log for complete Python traceback. 
    7998  
    7999 Traceback (most recent call last): 
    8000 File
    8001 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    8002 packages/chimerax/ui/statusbar.py", line 104, in _expose_event 
    8003 self.status(self._last_message, self._last_color) 
    8004 File
    8005 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    8006 packages/chimerax/ui/statusbar.py", line 170, in status 
    8007 r.draw_background() 
    8008 File
    8009 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    8010 packages/chimerax/graphics/opengl.py", line 1264, in draw_background 
    8011 GL.glClear(flags) 
    8012 File "src/errorchecker.pyx", line 59, in
    8013 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    8014 OpenGL.error.GLError: GLError( 
    8015 err = 1286, 
    8016 description = b'invalid framebuffer operation', 
    8017 baseOperation = glClear, 
    8018 cArguments = (16640,) 
    8019 ) 
    8020  
    8021 OpenGL.error.GLError: GLError( 
    8022 err = 1286, 
    8023 description = b'invalid framebuffer operation', 
    8024 baseOperation = glClear, 
    8025 cArguments = (16640,) 
    8026 ) 
    8027  
    8028 File "src/errorchecker.pyx", line 59, in
    8029 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    8030  
    8031 See log for complete Python traceback. 
    8032  
    8033 Traceback (most recent call last): 
    8034 File
    8035 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    8036 packages/chimerax/ui/statusbar.py", line 104, in _expose_event 
    8037 self.status(self._last_message, self._last_color) 
    8038 File
    8039 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    8040 packages/chimerax/ui/statusbar.py", line 170, in status 
    8041 r.draw_background() 
    8042 File
    8043 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    8044 packages/chimerax/graphics/opengl.py", line 1264, in draw_background 
    8045 GL.glClear(flags) 
    8046 File "src/errorchecker.pyx", line 59, in
    8047 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    8048 OpenGL.error.GLError: GLError( 
    8049 err = 1286, 
    8050 description = b'invalid framebuffer operation', 
    8051 baseOperation = glClear, 
    8052 cArguments = (16640,) 
    8053 ) 
    8054  
    8055 OpenGL.error.GLError: GLError( 
    8056 err = 1286, 
    8057 description = b'invalid framebuffer operation', 
    8058 baseOperation = glClear, 
    8059 cArguments = (16640,) 
    8060 ) 
    8061  
    8062 File "src/errorchecker.pyx", line 59, in
    8063 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    8064  
    8065 See log for complete Python traceback. 
    8066  
    8067 Traceback (most recent call last): 
    8068 File
    8069 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    8070 packages/chimerax/ui/statusbar.py", line 104, in _expose_event 
    8071 self.status(self._last_message, self._last_color) 
    8072 File
    8073 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    8074 packages/chimerax/ui/statusbar.py", line 170, in status 
    8075 r.draw_background() 
    8076 File
    8077 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    8078 packages/chimerax/graphics/opengl.py", line 1264, in draw_background 
    8079 GL.glClear(flags) 
    8080 File "src/errorchecker.pyx", line 59, in
    8081 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    8082 OpenGL.error.GLError: GLError( 
    8083 err = 1286, 
    8084 description = b'invalid framebuffer operation', 
    8085 baseOperation = glClear, 
    8086 cArguments = (16640,) 
    8087 ) 
    8088  
    8089 OpenGL.error.GLError: GLError( 
    8090 err = 1286, 
    8091 description = b'invalid framebuffer operation', 
    8092 baseOperation = glClear, 
    8093 cArguments = (16640,) 
    8094 ) 
    8095  
    8096 File "src/errorchecker.pyx", line 59, in
    8097 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    8098  
    8099 See log for complete Python traceback. 
    8100  
    8101 Traceback (most recent call last): 
    8102 File
    8103 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    8104 packages/chimerax/ui/statusbar.py", line 104, in _expose_event 
    8105 self.status(self._last_message, self._last_color) 
    8106 File
    8107 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    8108 packages/chimerax/ui/statusbar.py", line 170, in status 
    8109 r.draw_background() 
    8110 File
    8111 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    8112 packages/chimerax/graphics/opengl.py", line 1264, in draw_background 
    8113 GL.glClear(flags) 
    8114 File "src/errorchecker.pyx", line 59, in
    8115 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    8116 OpenGL.error.GLError: GLError( 
    8117 err = 1286, 
    8118 description = b'invalid framebuffer operation', 
    8119 baseOperation = glClear, 
    8120 cArguments = (16640,) 
    8121 ) 
    8122  
    8123 OpenGL.error.GLError: GLError( 
    8124 err = 1286, 
    8125 description = b'invalid framebuffer operation', 
    8126 baseOperation = glClear, 
    8127 cArguments = (16640,) 
    8128 ) 
    8129  
    8130 File "src/errorchecker.pyx", line 59, in
    8131 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    8132  
    8133 See log for complete Python traceback. 
    8134  
    8135 Traceback (most recent call last): 
    8136 File
    8137 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    8138 packages/chimerax/ui/statusbar.py", line 104, in _expose_event 
    8139 self.status(self._last_message, self._last_color) 
    8140 File
    8141 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    8142 packages/chimerax/ui/statusbar.py", line 170, in status 
    8143 r.draw_background() 
    8144 File
    8145 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    8146 packages/chimerax/graphics/opengl.py", line 1264, in draw_background 
    8147 GL.glClear(flags) 
    8148 File "src/errorchecker.pyx", line 59, in
    8149 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    8150 OpenGL.error.GLError: GLError( 
    8151 err = 1286, 
    8152 description = b'invalid framebuffer operation', 
    8153 baseOperation = glClear, 
    8154 cArguments = (16640,) 
    8155 ) 
    8156  
    8157 OpenGL.error.GLError: GLError( 
    8158 err = 1286, 
    8159 description = b'invalid framebuffer operation', 
    8160 baseOperation = glClear, 
    8161 cArguments = (16640,) 
    8162 ) 
    8163  
    8164 File "src/errorchecker.pyx", line 59, in
    8165 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    8166  
    8167 See log for complete Python traceback. 
    8168  
    8169 Traceback (most recent call last): 
    8170 File
    8171 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    8172 packages/chimerax/ui/statusbar.py", line 104, in _expose_event 
    8173 self.status(self._last_message, self._last_color) 
    8174 File
    8175 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    8176 packages/chimerax/ui/statusbar.py", line 170, in status 
    8177 r.draw_background() 
    8178 File
    8179 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    8180 packages/chimerax/graphics/opengl.py", line 1264, in draw_background 
    8181 GL.glClear(flags) 
    8182 File "src/errorchecker.pyx", line 59, in
    8183 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    8184 OpenGL.error.GLError: GLError( 
    8185 err = 1286, 
    8186 description = b'invalid framebuffer operation', 
    8187 baseOperation = glClear, 
    8188 cArguments = (16640,) 
    8189 ) 
    8190  
    8191 OpenGL.error.GLError: GLError( 
    8192 err = 1286, 
    8193 description = b'invalid framebuffer operation', 
    8194 baseOperation = glClear, 
    8195 cArguments = (16640,) 
    8196 ) 
    8197  
    8198 File "src/errorchecker.pyx", line 59, in
    8199 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    8200  
    8201 See log for complete Python traceback. 
    8202  
    8203 Traceback (most recent call last): 
    8204 File
    8205 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    8206 packages/chimerax/ui/statusbar.py", line 104, in _expose_event 
    8207 self.status(self._last_message, self._last_color) 
    8208 File
    8209 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    8210 packages/chimerax/ui/statusbar.py", line 170, in status 
    8211 r.draw_background() 
    8212 File
    8213 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    8214 packages/chimerax/graphics/opengl.py", line 1264, in draw_background 
    8215 GL.glClear(flags) 
    8216 File "src/errorchecker.pyx", line 59, in
    8217 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    8218 OpenGL.error.GLError: GLError( 
    8219 err = 1286, 
    8220 description = b'invalid framebuffer operation', 
    8221 baseOperation = glClear, 
    8222 cArguments = (16640,) 
    8223 ) 
    8224  
    8225 OpenGL.error.GLError: GLError( 
    8226 err = 1286, 
    8227 description = b'invalid framebuffer operation', 
    8228 baseOperation = glClear, 
    8229 cArguments = (16640,) 
    8230 ) 
    8231  
    8232 File "src/errorchecker.pyx", line 59, in
    8233 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    8234  
    8235 See log for complete Python traceback. 
    8236  
    8237 Traceback (most recent call last): 
    8238 File
    8239 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    8240 packages/chimerax/ui/statusbar.py", line 104, in _expose_event 
    8241 self.status(self._last_message, self._last_color) 
    8242 File
    8243 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    8244 packages/chimerax/ui/statusbar.py", line 170, in status 
    8245 r.draw_background() 
    8246 File
    8247 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    8248 packages/chimerax/graphics/opengl.py", line 1264, in draw_background 
    8249 GL.glClear(flags) 
    8250 File "src/errorchecker.pyx", line 59, in
    8251 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    8252 OpenGL.error.GLError: GLError( 
    8253 err = 1286, 
    8254 description = b'invalid framebuffer operation', 
    8255 baseOperation = glClear, 
    8256 cArguments = (16640,) 
    8257 ) 
    8258  
    8259 OpenGL.error.GLError: GLError( 
    8260 err = 1286, 
    8261 description = b'invalid framebuffer operation', 
    8262 baseOperation = glClear, 
    8263 cArguments = (16640,) 
    8264 ) 
    8265  
    8266 File "src/errorchecker.pyx", line 59, in
    8267 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    8268  
    8269 See log for complete Python traceback. 
    8270  
    8271 Traceback (most recent call last): 
    8272 File
    8273 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    8274 packages/chimerax/ui/statusbar.py", line 104, in _expose_event 
    8275 self.status(self._last_message, self._last_color) 
    8276 File
    8277 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    8278 packages/chimerax/ui/statusbar.py", line 170, in status 
    8279 r.draw_background() 
    8280 File
    8281 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    8282 packages/chimerax/graphics/opengl.py", line 1264, in draw_background 
    8283 GL.glClear(flags) 
    8284 File "src/errorchecker.pyx", line 59, in
    8285 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    8286 OpenGL.error.GLError: GLError( 
    8287 err = 1286, 
    8288 description = b'invalid framebuffer operation', 
    8289 baseOperation = glClear, 
    8290 cArguments = (16640,) 
    8291 ) 
    8292  
    8293 OpenGL.error.GLError: GLError( 
    8294 err = 1286, 
    8295 description = b'invalid framebuffer operation', 
    8296 baseOperation = glClear, 
    8297 cArguments = (16640,) 
    8298 ) 
    8299  
    8300 File "src/errorchecker.pyx", line 59, in
    8301 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    8302  
    8303 See log for complete Python traceback. 
    8304  
    8305 Traceback (most recent call last): 
    8306 File
    8307 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    8308 packages/chimerax/ui/statusbar.py", line 104, in _expose_event 
    8309 self.status(self._last_message, self._last_color) 
    8310 File
    8311 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    8312 packages/chimerax/ui/statusbar.py", line 170, in status 
    8313 r.draw_background() 
    8314 File
    8315 "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    8316 packages/chimerax/graphics/opengl.py", line 1264, in draw_background 
    8317 GL.glClear(flags) 
    8318 File "src/errorchecker.pyx", line 59, in
    8319 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    8320 OpenGL.error.GLError: GLError( 
    8321 err = 1286, 
    8322 description = b'invalid framebuffer operation', 
    8323 baseOperation = glClear, 
    8324 cArguments = (16640,) 
    8325 ) 
    8326  
     3368[deleted to fit within ticket limits]
     3369
    83273370OpenGL.error.GLError: GLError( 
    83283371err = 1286,