Changes between Initial Version and Version 1 of Ticket #16542


Ignore:
Timestamp:
Jan 2, 2025, 11:29:50 AM (11 months ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #16542

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

  • Ticket #16542 – Description

    initial v1  
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    1991     "name" : "libgfortran.5.dylib"
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    2000     "name" : "libquadmath.0.dylib"
    2001   },
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    2009     "name" : "libgcc_s.1.1.dylib"
    2010   },
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    2018     "name" : "_arrays.cpython-311-darwin.so"
    2019   },
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    2027     "name" : "libarrays.dylib"
    2028   },
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    2035     "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/select.cpython-311-darwin.so",
    2036     "name" : "select.cpython-311-darwin.so"
    2037   },
    2038   {
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    2047   {
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    2054     "name" : "fcntl.cpython-311-darwin.so"
    2055   },
    2056   {
    2057     "source" : "P",
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    2063     "name" : "_struct.cpython-311-darwin.so"
    2064   },
    2065   {
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    2072     "name" : "binascii.cpython-311-darwin.so"
    2073   },
    2074   {
    2075     "source" : "P",
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    2080     "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_sha512.cpython-311-darwin.so",
    2081     "name" : "_sha512.cpython-311-darwin.so"
    2082   },
    2083   {
    2084     "source" : "P",
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    2087     "size" : 16384,
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    2089     "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_random.cpython-311-darwin.so",
    2090     "name" : "_random.cpython-311-darwin.so"
    2091   },
    2092   {
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    2099     "name" : "_bisect.cpython-311-darwin.so"
    2100   },
    2101   {
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    2107     "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_lzma.cpython-311-darwin.so",
    2108     "name" : "_lzma.cpython-311-darwin.so"
    2109   },
    2110   {
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    2117     "name" : "_bz2.cpython-311-darwin.so"
    2118   },
    2119   {
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    2125     "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/zlib.cpython-311-darwin.so",
    2126     "name" : "zlib.cpython-311-darwin.so"
    2127   },
    2128   {
    2129     "source" : "P",
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    2132     "size" : 16384,
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    2134     "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_typing.cpython-311-darwin.so",
    2135     "name" : "_typing.cpython-311-darwin.so"
    2136   },
    2137   {
    2138     "source" : "P",
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    2141     "size" : 81920,
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    2144     "name" : "_datetime.cpython-311-darwin.so"
    2145   },
    2146   {
    2147     "source" : "P",
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    2150     "size" : 49152,
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    2152     "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/math.cpython-311-darwin.so",
    2153     "name" : "math.cpython-311-darwin.so"
    2154   },
    2155   {
    2156     "source" : "P",
    2157     "arch" : "arm64",
    2158     "base" : 4393861120,
    2159     "CFBundleShortVersionString" : "3.11.4, (c) 2001-2023 Python Software Foundation.",
    2160     "CFBundleIdentifier" : "org.python.python",
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    2166   },
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    2176     "name" : "ChimeraX",
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    2178   },
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    2186     "name" : "libsystem_kernel.dylib"
    2187   },
    2188   {
    2189     "source" : "P",
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    2194     "path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
    2195     "name" : "libsystem_pthread.dylib"
    2196   },
    2197   {
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    2214   },
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    2237   },
    2238   {
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    2269   },
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     70[deleted to fit within ticket limits]
    229471],
    229572  "sharedCache" : {
    … …  
    33771154level 0.0002, step 2, values float32 
    33781155
    3379 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    3380 > Model/INO-40Xenuc-ADPBe/onlyies2-lowres.mrc"
    3381 
    3382 Opened onlyies2-lowres.mrc as #7, grid size 448,448,448, pixel 0.831, shown at
    3383 level 2.07e-05, step 2, values float32 
    3384 
    3385 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    3386 > Model/INO-40Xenuc-ADPBe/onlynuc.mrc"
    3387 
    3388 Opened onlynuc.mrc as #8, grid size 448,448,448, pixel 0.831, shown at level
    3389 9.79e-05, step 2, values float32 
    3390 
    3391 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    3392 > Model/INO-40Xenuc-ADPBe/inocore.mrc"
    3393 
    3394 Opened inocore.mrc as #9, grid size 448,448,448, pixel 0.831, shown at level
    3395 3.68e-05, step 2, values float32 
    3396 
    3397 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    3398 > Model/INO-40Xenuc-ADPBe/nuc-resample.mrc"
    3399 
    3400 Opened nuc-resample.mrc as #10, grid size 448,448,448, pixel 0.831, shown at
    3401 level 0.326, step 2, values float32 
    3402 
    3403 > surface dust #1 size 8.35
    3404 
    3405 > surface dust #3 size 8.35
    3406 
    3407 > surface dust #5.1 size 8.35
    3408 
    3409 > surface dust #5.2 size 8.35
    3410 
    3411 > surface dust #5.4 size 8.35
    3412 
    3413 > surface dust #5.5 size 8.35
    3414 
    3415 > surface dust #5.6 size 8.35
    3416 
    3417 > surface dust #5.7 size 8.35
    3418 
    3419 > surface dust #5.8 size 8.35
    3420 
    3421 > surface dust #5.9 size 8.35
    3422 
    3423 > surface dust #5.10 size 8.35
    3424 
    3425 > surface dust #6 size 8.35
    3426 
    3427 > surface dust #4 size 8.31
    3428 
    3429 > surface dust #7 size 8.31
    3430 
    3431 > surface dust #8 size 8.31
    3432 
    3433 > surface dust #9 size 8.31
    3434 
    3435 > surface dust #10 size 8.31
    3436 
    3437 > hide #!7 models
    3438 
    3439 > hide #!8 models
    3440 
    3441 > hide #!9 models
    3442 
    3443 > hide #!10 models
    3444 
    3445 > rename #7 onlyies2-lowres-Xl040.mrc
    3446 
    3447 > rename #8 onlynuc_Xl040.mrc
    3448 
    3449 > rename #9 inocore_Xl040.mrc
    3450 
    3451 > rename #10 nuc-resample_Xl040.mrc
    3452 
    3453 > surface dust #1 size 8.35
    3454 
    3455 > surface dust #3 size 8.35
    3456 
    3457 > surface dust #5.1 size 8.35
    3458 
    3459 > surface dust #5.2 size 8.35
    3460 
    3461 > surface dust #5.4 size 8.35
    3462 
    3463 > surface dust #5.5 size 8.35
    3464 
    3465 > surface dust #5.6 size 8.35
    3466 
    3467 > surface dust #5.7 size 8.35
    3468 
    3469 > surface dust #5.8 size 8.35
    3470 
    3471 > surface dust #5.9 size 8.35
    3472 
    3473 > surface dust #5.10 size 8.35
    3474 
    3475 > surface dust #6 size 8.35
    3476 
    3477 > surface dust #4 size 8.31
    3478 
    3479 > surface dust #10 size 8.31
    3480 
    3481 > volume #7 step 1
    3482 
    3483 > volume #8 step 1
    3484 
    3485 > volume #9 step 1
    3486 
    3487 > volume #10 step 1
    3488 
    3489 > volume #7 level 0.00766
    3490 
    3491 > volume #7 level 0.04253
    3492 
    3493 > volume #8 level 0.1849
    3494 
    3495 > volume #9 level 0.1834
    3496 
    3497 > hide #!1 models
    3498 
    3499 > hide #!3 models
    3500 
    3501 > hide #!4 models
    3502 
    3503 > hide #!5 models
    3504 
    3505 > hide #!6 models
    3506 
    3507 > show #!4 models
    3508 
    3509 > hide #!4 models
    3510 
    3511 > volume #10 level 0.6999
    3512 
    3513 > volume #8 level 0.4115
    3514 
    3515 > volume #7 level 0.05194
    3516 
    3517 > volume #9 level 0.2181
    3518 
    3519 > surface dust #7 size 8.31
    3520 
    3521 > surface dust #8 size 8.31
    3522 
    3523 > surface dust #9 size 8.31
    3524 
    3525 > show #!4 models
    3526 
    3527 > volume #4 step 1
    3528 
    3529 > volume #4 level 0.002465
    3530 
    3531 > lighting simple
    3532 
    3533 > lighting soft
    3534 
    3535 > volume #4 level 0.0026
    3536 
    3537 > close #10
    3538 
    3539 > rename #4 121124-a8-split_Xl040.mrc
    3540 
    3541 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    3542 > Model/Final-withADPBeF/042624-x40-wt-adpbef-withadpbef-final.pdb"
    3543 
    3544 Chain information for 042624-x40-wt-adpbef-withadpbef-final.pdb #10 
    3545 --- 
    3546 Chain | Description 
    3547 A | No description available 
    3548 B | No description available 
    3549 C G | No description available 
    3550 D | No description available 
    3551 E | No description available 
    3552 F | No description available 
    3553 H | No description available 
    3554 I | No description available 
    3555 J | No description available 
    3556 L | No description available 
    3557 M | No description available 
    3558 N | No description available 
    3559 O | No description available 
    3560 Q | No description available 
    3561 R | No description available 
    3562 S | No description available 
    3563 T | No description available 
    3564 U | No description available 
    3565 V | No description available 
    3566 W | No description available 
    3567 X | No description available 
    3568 Y | No description available 
    3569 Z | No description available 
    3570  
    3571 
    3572 > hide #!10 cartoons
    3573 
    3574 > hide #!10 atoms
    3575 
    3576 > show #!10 cartoons
    3577 
    3578 > hide #!7 models
    3579 
    3580 > hide #!8 models
    3581 
    3582 > hide #!9 models
    3583 
    3584 > hide #!10 models
    3585 
    3586 > hide #!4 models
    3587 
    3588 > show #!10 models
    3589 
    3590 > color #10/Q firebrick
    3591 
    3592 Drag select of 808 residues 
    3593 
    3594 > color #10/R,S medium seagreen
    3595 
    3596 > color #10/T-Y,A-H medium seagreen
    3597 
    3598 > color #10/T-Y,A-H light gray
    3599 
    3600 > select clear
    3601 
    3602 > color #10/T-Y,I,J light slate gray
    3603 
    3604 > color #10/I,J light slate gray
    3605 
    3606 > nucleotides #!10 ladder
    3607 
    3608 > show #!10 atoms
    3609 
    3610 > undo
    3611 
    3612 > select #10/I,J
    3613 
    3614 6601 atoms, 7404 bonds, 322 residues, 1 model selected 
    3615 
    3616 > show sel atoms
    3617 
    3618 > select clear
    3619 
    3620 > select #10/K
    3621 
    3622 32 atoms, 32 bonds, 2 pseudobonds, 3 residues, 2 models selected 
    3623 
    3624 > color #10/N medium blue
    3625 
    3626 [Repeated 1 time(s)]
    3627 
    3628 > select #10/L
    3629 
    3630 2824 atoms, 2886 bonds, 1 pseudobond, 361 residues, 2 models selected 
    3631 
    3632 > ui tool show "Color Actions"
    3633 
    3634 > color sel sandy brown
    3635 
    3636 > color sel goldenrod
    3637 
    3638 [Repeated 1 time(s)]
    3639 
    3640 > show #!2 models
    3641 
    3642 > cartoon style (#!10 & sel) modeHelix tube sides 20
    3643 
    3644 > select up
    3645 
    3646 55996 atoms, 57633 bonds, 12 pseudobonds, 6600 residues, 2 models selected 
    3647 
    3648 > select up
    3649 
    3650 55996 atoms, 57633 bonds, 14 pseudobonds, 6600 residues, 3 models selected 
    3651 
    3652 > select up
    3653 
    3654 55996 atoms, 57633 bonds, 14 pseudobonds, 6600 residues, 3 models selected 
    3655 
    3656 > select up
    3657 
    3658 114335 atoms, 117752 bonds, 14 pseudobonds, 13459 residues, 19 models selected 
    3659 
    3660 > select down
    3661 
    3662 55996 atoms, 57633 bonds, 14 pseudobonds, 6600 residues, 3 models selected 
    3663 
    3664 > select down
    3665 
    3666 14 pseudobonds, 2 models selected 
    3667 
    3668 > cartoon style modeHelix tube radius 1.5
    3669 
    3670 > select #10/Z
    3671 
    3672 467 atoms, 472 bonds, 1 pseudobond, 72 residues, 2 models selected 
    3673 
    3674 > color sel salmon
    3675 
    3676 [Repeated 1 time(s)]
    3677 
    3678 > color sel dark salmon
    3679 
    3680 > color sel salmon
    3681 
    3682 > select #10/L
    3683 
    3684 2824 atoms, 2886 bonds, 1 pseudobond, 361 residues, 2 models selected 
    3685 
    3686 > color (#!10 & sel) #ffd479ff
    3687 
    3688 > color (#!10 & sel) #feff80ff
    3689 
    3690 [Repeated 1 time(s)]
    3691 
    3692 > select clear
    3693 
    3694 > select #10/M
    3695 
    3696 3422 atoms, 3498 bonds, 1 pseudobond, 431 residues, 2 models selected 
    3697 
    3698 > color sel deep sky blue
    3699 
    3700 > select #10/O\
    3701 
    3702 Nothing selected 
    3703 
    3704 > select #10/O
    3705 
    3706 287 atoms, 296 bonds, 34 residues, 1 model selected 
    3707 
    3708 > color sel royal blue
    3709 
    3710 > color sel #2163a6ff
    3711 
    3712 [Repeated 1 time(s)]
    3713 
    3714 > select clear
    3715 
    3716 > hide #!2 models
    3717 
    3718 > show #!9 models
    3719 
    3720 > show #!8 models
    3721 
    3722 > show #!4 models
    3723 
    3724 > show #!7 models
    3725 
    3726 > ui tool show "Color Zone"
    3727 
    3728 > color zone #4 near #10 distance 4.99
    3729 
    3730 > color zone #4 near #10 distance 1
    3731 
    3732 > color zone #4 near #10 distance 10
    3733 
    3734 > color zone #7 near #10 distance 4.99
    3735 
    3736 > color zone #8 near #10 distance 4.99
    3737 
    3738 > color zone #9 near #10 distance 4.99
    3739 
    3740 > hide #!4 models
    3741 
    3742 > show #!4 models
    3743 
    3744 > hide #!10 models
    3745 
    3746 > ui tool show "Side View"
    3747 
    3748 > show #!2 models
    3749 
    3750 > hide #!2 models
    3751 
    3752 > show #!1 models
    3753 
    3754 > hide #!1 models
    3755 
    3756 > show #!6 models
    3757 
    3758 > hide #!6 models
    3759 
    3760 > show #!5 models
    3761 
    3762 > hide #!5 models
    3763 
    3764 > show #!1 models
    3765 
    3766 > hide #!7 models
    3767 
    3768 > hide #!8 models
    3769 
    3770 > hide #!9 models
    3771 
    3772 > hide #!4 models
    3773 
    3774 > show #!3 models
    3775 
    3776 > show #!4 models
    3777 
    3778 > hide #!4 models
    3779 
    3780 > show #!5 models
    3781 
    3782 > show #!6 models
    3783 
    3784 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    3785 > /Figure 1/Version 2/xl_080_map.png" width 3600 height 2934 supersample 3
    3786 > transparentBackground true
    3787 
    3788 > hide #!1 models
    3789 
    3790 > hide #!3 models
    3791 
    3792 > hide #!5 models
    3793 
    3794 > hide #!6 models
    3795 
    3796 > show #!8 models
    3797 
    3798 > show #!9 models
    3799 
    3800 > show #!7 models
    3801 
    3802 > show #!4 models
    3803 
    3804 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    3805 > /Figure 1/Version 2/xl_040_map.png" width 3600 height 2934 supersample 3
    3806 > transparentBackground true
    3807 
    3808 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    3809 > /Figure 1/Version 2-resubmission/Chimera Session/Figure1.cxs" includeMaps
    3810 > true
    3811 
    3812 > show #!10 models
    3813 
    3814 > select #10/L
    3815 
    3816 2824 atoms, 2886 bonds, 1 pseudobond, 361 residues, 2 models selected 
    3817 
    3818 > ui tool show "Color Actions"
    3819 
    3820 > color sel gold
    3821 
    3822 [Repeated 1 time(s)]
    3823 
    3824 > color zone #9 near #10 distance 4.99
    3825 
    3826 > color zone #4 near #10 distance 10
    3827 
    3828 > select clear
    3829 
    3830 > hide #!10 models
    3831 
    3832 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    3833 > /Figure 1/Version 2-resubmission/Chimera Session/Xl_0N40_map.png" width 3600
    3834 > height 2700 supersample 3 transparentBackground true
    3835 
    3836 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    3837 > /Figure 1/Version 2-resubmission/Chimera Session/Xl_0N40_map.png" width 3600
    3838 > height 2700 supersample 4 transparentBackground true
    3839 
    3840 > select clear
    3841 
    3842 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    3843 > /Figure 1/Version 2-resubmission/Chimera Session/Xl_0N40_map.png" width 3600
    3844 > height 2700 supersample 1 transparentBackground true
    3845 
    3846 > graphics silhouettes true
    3847 
    3848 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    3849 > /Figure 1/Version 2-resubmission/Chimera Session/Xl_0N40_map.png" width 3600
    3850 > height 2700 supersample 3 transparentBackground true
    3851 
    3852 > graphics silhouettes false
    3853 
    3854 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    3855 > /Figure 1/Version 2-resubmission/Chimera Session/Xl_0N40_map.png" width 3600
    3856 > height 2700 supersample 3 transparentBackground true
    3857 
    3858 > hide #!4 models
    3859 
    3860 > hide #!7 models
    3861 
    3862 > hide #!8 models
    3863 
    3864 > hide #!9 models
    3865 
    3866 > show #!1 models
    3867 
    3868 > show #!3 models
    3869 
    3870 > show #!5 models
    3871 
    3872 > show #!6 models
    3873 
    3874 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    3875 > /Figure 1/Version 2-resubmission/Chimera Session/Xl_0N80_map.png" width 3600
    3876 > height 2700 supersample 3 transparentBackground true
    3877 
    3878 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    3879 > /Figure 1/Version 2-resubmission/Chimera Session/Figure1.cxs" includeMaps
    3880 > true
    3881 
    3882 > undo
    3883 
    3884 > show #!6 models
    3885 
    3886 > hide #!6 models
    3887 
    3888 > hide #!5 models
    3889 
    3890 > hide #!3 models
    3891 
    3892 > hide #!1 models
    3893 
    3894 > show #!10 models
    3895 
    3896 > select #10/T-Y, Q:1022-1200
    3897 
    3898 1186 atoms, 1210 bonds, 1 pseudobond, 147 residues, 2 models selected 
    3899 
    3900 > hide sel atoms
    3901 
    3902 > hide sel cartoons
    3903 
    3904 > select #10/T-Y
    3905 
    3906 20471 atoms, 20720 bonds, 2 pseudobonds, 2649 residues, 2 models selected 
    3907 
    3908 > hide sel cartoons
    3909 
    3910 Drag select of 98 residues 
    3911 
    3912 > select up
    3913 
    3914 910 atoms, 932 bonds, 115 residues, 1 model selected 
    3915 
    3916 > hide sel cartoons
    3917 
    3918 > select #10/Z
    3919 
    3920 467 atoms, 472 bonds, 1 pseudobond, 72 residues, 2 models selected 
    3921 
    3922 > hide sel cartoons
    3923 
    3924 > select clear
    3925 
    3926 > show #!4 models
    3927 
    3928 > color #4 silver models
    3929 
    3930 > color #4 #d6d6d6ff models
    3931 
    3932 > color #4 silver models
    3933 
    3934 > color #4 #c0c0c023 models
    3935 
    3936 > color #4 #c0c0c000 models
    3937 
    3938 > color #4 #c0c0c00e models
    3939 
    3940 > graphics silhouettes true
    3941 
    3942 > graphics silhouettes false
    3943 
    3944 > lighting shadows true intensity 0.5
    3945 
    3946 > lighting shadows false
    3947 
    3948 > lighting shadows true
    3949 
    3950 > lighting soft
    3951 
    3952 > color #4 #c0c0c01b models
    3953 
    3954 > color #4 white models
    3955 
    3956 > color #4 #ffffff25 models
    3957 
    3958 > color #4 #d6d6d6ff models
    3959 
    3960 > color #4 #d6d6d605 models
    3961 
    3962 > color #4 #d6d6d619 models
    3963 
    3964 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    3965 > /Figure 1/Version 2-resubmission/Chimera Session/Figure1_noRvbs'.cxs"
    3966 > includeMaps true
    3967 
    3968 ——— End of log from Thu Dec 12 15:35:36 2024 ———
    3969 
    3970 opened ChimeraX session 
    3971 
    3972 > hide #!4 models
    3973 
    3974 > hide #!10 models
    3975 
    3976 > show #!2 models
    3977 
    3978 > select #2/T-Y,Z
    3979 
    3980 20950 atoms, 21202 bonds, 3 pseudobonds, 2723 residues, 2 models selected 
    3981 
    3982 > hide sel cartoons
    3983 
    3984 > ui mousemode right select
    3985 
    3986 Drag select of 18 residues 
    3987 
    3988 > select up
    3989 
    3990 248 atoms, 246 bonds, 49 residues, 1 model selected 
    3991 
    3992 > select up
    3993 
    3994 651 atoms, 649 bonds, 130 residues, 1 model selected 
    3995 
    3996 > select up
    3997 
    3998 724 atoms, 722 bonds, 140 residues, 1 model selected 
    3999 
    4000 > select up
    4001 
    4002 2940 atoms, 2998 bonds, 427 residues, 1 model selected 
    4003 
    4004 > select down
    4005 
    4006 724 atoms, 722 bonds, 140 residues, 1 model selected 
    4007 
    4008 > hide sel cartoons
    4009 
    4010 [Repeated 1 time(s)]Drag select of 7 residues, 1 pseudobonds 
    4011 
    4012 > select up
    4013 
    4014 120 atoms, 119 bonds, 1 pseudobond, 24 residues, 2 models selected 
    4015 
    4016 > select up
    4017 
    4018 130 atoms, 129 bonds, 1 pseudobond, 26 residues, 2 models selected 
    4019 
    4020 > select up
    4021 
    4022 194 atoms, 194 bonds, 1 pseudobond, 33 residues, 2 models selected 
    4023 
    4024 > select up
    4025 
    4026 1894 atoms, 1922 bonds, 1 pseudobond, 278 residues, 2 models selected 
    4027 
    4028 > select down
    4029 
    4030 194 atoms, 194 bonds, 1 pseudobond, 33 residues, 2 models selected 
    4031 
    4032 > hide sel cartoons
    4033 
    4034 > select #2/Q:1022-1294
    4035 
    4036 1922 atoms, 1967 bonds, 1 pseudobond, 241 residues, 2 models selected 
    4037 
    4038 > color (#!2 & sel) orange
    4039 
    4040 > select #2/L
    4041 
    4042 2862 atoms, 2925 bonds, 1 pseudobond, 364 residues, 2 models selected 
    4043 
    4044 > ui tool show "Color Actions"
    4045 
    4046 > color sel gold
    4047 
    4048 > select clear
    4049 
    4050 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    4051 > Model/WT-0N80Xe-ADPBeF/041924-global-resampleonapo.mrc"
    4052 
    4053 Opened 041924-global-resampleonapo.mrc as #11, grid size 480,480,480, pixel
    4054 0.835, shown at level 0.105, step 2, values float32 
    4055 
    4056 > ui tool show "Color Zone"
    4057 
    4058 > color zone #11 near #2 distance 5.01
    4059 
    4060 > volume splitbyzone #11
    4061 
    4062 Opened 041924-global-resampleonapo.mrc 0 as #12.1, grid size 480,480,480,
    4063 pixel 0.835, shown at level 0.105, step 1, values float32 
    4064 Opened 041924-global-resampleonapo.mrc 1 as #12.2, grid size 480,480,480,
    4065 pixel 0.835, shown at level 0.105, step 1, values float32 
    4066 Opened 041924-global-resampleonapo.mrc 2 as #12.3, grid size 480,480,480,
    4067 pixel 0.835, shown at level 0.105, step 1, values float32 
    4068 Opened 041924-global-resampleonapo.mrc 3 as #12.4, grid size 480,480,480,
    4069 pixel 0.835, shown at level 0.105, step 1, values float32 
    4070 Opened 041924-global-resampleonapo.mrc 4 as #12.5, grid size 480,480,480,
    4071 pixel 0.835, shown at level 0.105, step 1, values float32 
    4072 Opened 041924-global-resampleonapo.mrc 5 as #12.6, grid size 480,480,480,
    4073 pixel 0.835, shown at level 0.105, step 1, values float32 
    4074 Opened 041924-global-resampleonapo.mrc 6 as #12.7, grid size 480,480,480,
    4075 pixel 0.835, shown at level 0.105, step 1, values float32 
    4076 Opened 041924-global-resampleonapo.mrc 7 as #12.8, grid size 480,480,480,
    4077 pixel 0.835, shown at level 0.105, step 1, values float32 
    4078 Opened 041924-global-resampleonapo.mrc 8 as #12.9, grid size 480,480,480,
    4079 pixel 0.835, shown at level 0.105, step 1, values float32 
    4080 Opened 041924-global-resampleonapo.mrc 9 as #12.10, grid size 480,480,480,
    4081 pixel 0.835, shown at level 0.105, step 1, values float32 
    4082 Opened 041924-global-resampleonapo.mrc 10 as #12.11, grid size 480,480,480,
    4083 pixel 0.835, shown at level 0.105, step 1, values float32 
    4084 
    4085 > hide #!12.1 models
    4086 
    4087 > hide #!12.2 models
    4088 
    4089 > hide #!12.9 models
    4090 
    4091 > hide #!12.4 models
    4092 
    4093 > hide #!12.5 models
    4094 
    4095 > hide #!12.6 models
    4096 
    4097 > hide #!12.7 models
    4098 
    4099 > hide #!12.11 models
    4100 
    4101 > hide #!12.3 models
    4102 
    4103 > select #2/Q:1022-1294
    4104 
    4105 1922 atoms, 1967 bonds, 1 pseudobond, 241 residues, 2 models selected 
    4106 
    4107 > hide sel cartoons
    4108 
    4109 > show #!1 models
    4110 
    4111 > hide #!1 models
    4112 
    4113 > hide #!2 models
    4114 
    4115 > hide #!12 models
    4116 
    4117 > show #!2 models
    4118 
    4119 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    4120 > /Figure 1/Version 2-resubmission/Chimera Session/Xl_0N80_model_noRvbs.png"
    4121 > width 3600 height 3420 supersample 3 transparentBackground true
    4122 
    4123 > show #!1 models
    4124 
    4125 > show #!12 models
    4126 
    4127 > show #!6 models
    4128 
    4129 > hide #!2 models
    4130 
    4131 > color #1 white models
    4132 
    4133 > color #1 #ffffff00 models
    4134 
    4135 > graphics silhouettes true
    4136 
    4137 > color #6 white models
    4138 
    4139 > color #6 #ffffff00 models
    4140 
    4141 > color #12 white models
    4142 
    4143 > color #12 #ffffff00 models
    4144 
    4145 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    4146 > /Figure 1/Version 2-resubmission/Chimera Session/Xl_0N80_map_noRvbs.png"
    4147 > width 3600 height 3420 supersample 3 transparentBackground true
    4148 
    4149 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    4150 > /Figure 1/Version 2-resubmission/Chimera Session/Figure1_noRvbs'.cxs"
    4151 > includeMaps true
    4152 
    4153 ——— End of log from Thu Dec 12 17:07:10 2024 ———
    4154 
    4155 opened ChimeraX session 
    4156 
    4157 > close #2-5
    4158 
    4159 > close #1,6-9
    4160 
    4161 > show #!11 models
    4162 
    4163 > close #11-12
    4164 
    4165 > show #!10 models
    4166 
    4167 > graphics silhouettes false
    4168 
    4169 > show surfaces
    4170 
    4171 > select #10/T-Y
    4172 
    4173 20471 atoms, 20720 bonds, 2 pseudobonds, 2649 residues, 2 models selected 
    4174 
    4175 > hide sel surfaces
    4176 
    4177 > select #10/Q:1022-1294
    4178 
    4179 1916 atoms, 1961 bonds, 1 pseudobond, 241 residues, 2 models selected 
    4180 
    4181 > hide sel surfaces
    4182 
    4183 > select #10/z
    4184 
    4185 467 atoms, 472 bonds, 1 pseudobond, 72 residues, 2 models selected 
    4186 
    4187 > hide sel surfaces
    4188 
    4189 > select #10/R,S
    4190 
    4191 4562 atoms, 4675 bonds, 2 pseudobonds, 567 residues, 2 models selected 
    4192 
    4193 > hide sel surfaces
    4194 
    4195 > hide sel cartoons
    4196 
    4197 [Repeated 1 time(s)]
    4198 
    4199 > select #10
    4200 
    4201 55996 atoms, 57633 bonds, 14 pseudobonds, 6600 residues, 15 models selected 
    4202 
    4203 > color (#!10 & sel) light gray
    4204 
    4205 The cached device pixel ratio value was stale on window expose. Please file a
    4206 QTBUG which explains how to reproduce. 
    4207 
    4208 > select #10/Q:0-700
    4209 
    4210 1105 atoms, 1118 bonds, 130 residues, 1 model selected 
    4211 
    4212 > ui tool show "Color Actions"
    4213 
    4214 The cached device pixel ratio value was stale on window expose. Please file a
    4215 QTBUG which explains how to reproduce. 
    4216 
    4217 > color sel fire brick
    4218 
    4219 > transparency (#!10 & sel) 80
    4220 
    4221 > hide sel surfaces
    4222 
    4223 [Repeated 1 time(s)]
    4224 
    4225 > show sel surfaces
    4226 
    4227 [Repeated 1 time(s)]
    4228 
    4229 > select #10/R,S
    4230 
    4231 4562 atoms, 4675 bonds, 2 pseudobonds, 567 residues, 2 models selected 
    4232 
    4233 > hide sel cartoons
    4234 
    4235 > hide sel surfaces
    4236 
    4237 > select up
    4238 
    4239 55996 atoms, 57633 bonds, 12 pseudobonds, 6600 residues, 4 models selected 
    4240 
    4241 > select up
    4242 
    4243 55996 atoms, 57633 bonds, 14 pseudobonds, 6600 residues, 27 models selected 
    4244 
    4245 > select #10/z
    4246 
    4247 467 atoms, 472 bonds, 1 pseudobond, 72 residues, 2 models selected 
    4248 
    4249 > hide sel surfaces
    4250 
    4251 > select #10/Q:1022-1294
    4252 
    4253 1916 atoms, 1961 bonds, 1 pseudobond, 241 residues, 2 models selected 
    4254 
    4255 > hide sel surfaces
    4256 
    4257 [Repeated 1 time(s)]
    4258 
    4259 > select #10/T-Y
    4260 
    4261 20471 atoms, 20720 bonds, 2 pseudobonds, 2649 residues, 2 models selected 
    4262 
    4263 > hide sel surfaces
    4264 
    4265 > transparency (#!10 & sel) 40
    4266 
    4267 > select #10
    4268 
    4269 55996 atoms, 57633 bonds, 14 pseudobonds, 6600 residues, 15 models selected 
    4270 
    4271 > transparency (#!10 & sel) 80
    4272 
    4273 > select clear
    4274 
    4275 > select #10
    4276 
    4277 55996 atoms, 57633 bonds, 14 pseudobonds, 6600 residues, 15 models selected 
    4278 
    4279 > color (#!10 & sel) light gray
    4280 
    4281 > transparency (#!10 & sel) 30
    4282 
    4283 > transparency (#!10 & sel) 80
    4284 
    4285 > hide sel cartoons
    4286 
    4287 > hide sel atoms
    4288 
    4289 > show sel atoms
    4290 
    4291 > hide sel atoms
    4292 
    4293 > show sel surfaces
    4294 
    4295 > show sel cartoons
    4296 
    4297 > select #10/T-Y
    4298 
    4299 20471 atoms, 20720 bonds, 2 pseudobonds, 2649 residues, 2 models selected 
    4300 
    4301 > hide sel surfaces
    4302 
    4303 > hide sel cartoons
    4304 
    4305 > select #10/Q:1022-1294
    4306 
    4307 1916 atoms, 1961 bonds, 1 pseudobond, 241 residues, 2 models selected 
    4308 
    4309 > hide sel cartoons
    4310 
    4311 > hide sel surfaces
    4312 
    4313 > select #10/z
    4314 
    4315 467 atoms, 472 bonds, 1 pseudobond, 72 residues, 2 models selected 
    4316 
    4317 > select #10/z
    4318 
    4319 467 atoms, 472 bonds, 1 pseudobond, 72 residues, 2 models selected 
    4320 
    4321 > hide sel surfaces
    4322 
    4323 > hide sel cartoons
    4324 
    4325 > select #10/R,S
    4326 
    4327 4562 atoms, 4675 bonds, 2 pseudobonds, 567 residues, 2 models selected 
    4328 
    4329 > hide sel surfaces
    4330 
    4331 > hide sel cartoons
    4332 
    4333 > select #10/Q:0-700
    4334 
    4335 1105 atoms, 1118 bonds, 130 residues, 1 model selected 
    4336 
    4337 > color (#!10 & sel) red
    4338 
    4339 > transparency #10/Q:0-700 0 surfaces
    4340 
    4341 > hide sel surfaces
    4342 
    4343 > select #10/Q:700-3000
    4344 
    4345 5289 atoms, 5408 bonds, 3 pseudobonds, 660 residues, 2 models selected 
    4346 
    4347 > hide sel cartoons
    4348 
    4349 > select #10/K,L,M,O
    4350 
    4351 6565 atoms, 6712 bonds, 4 pseudobonds, 829 residues, 3 models selected 
    4352 
    4353 > hide sel cartoons
    4354 
    4355 > select #10/N
    4356 
    4357 5060 atoms, 5173 bonds, 626 residues, 1 model selected 
    4358 
    4359 > hide sel surfaces
    4360 
    4361 > show sel surfaces
    4362 
    4363 > hide sel cartoons
    4364 
    4365 > select clear
    4366 
    4367 > select #10/Q:545, 544, 537, 534, 533, 526, 523 , 482, 483, 487, 490, 504,
    4368 > 505, 512, 515, 522, 523, 526,
    4369 
    4370 Expected a keyword 
    4371 
    4372 > select #10/Q:545, 544, 537, 534, 533, 526, 523, 482, 483, 487, 490, 504,
    4373 > 505, 512, 515, 522, 523, 526,
    4374 
    4375 Expected an objects specifier or a keyword 
    4376 
    4377 > select #10/Q:482, 483, 487, 490, 504, 505, 512, 515, 522, 545, 544, 537,
    4378 > 534, 533, 526, 523,
    4379 
    4380 Expected an objects specifier or a keyword 
    4381 
    4382 > select #10/Q:482, 483, 487, 490, 504, 505, 512, 515, 522, 545, 544, 537,
    4383 > 534, 533, 526, 523
    4384 
    4385 160 atoms, 150 bonds, 16 residues, 1 model selected 
    4386 
    4387 > style sel sphere
    4388 
    4389 Changed 160 atom styles 
    4390 
    4391 > show sel surfaces
    4392 
    4393 > hide sel surfaces
    4394 
    4395 > show sel atoms
    4396 
    4397 > style sel ball
    4398 
    4399 Changed 160 atom styles 
    4400 
    4401 > style sel stick
    4402 
    4403 Changed 160 atom styles 
    4404 
    4405 > select clear
    4406 
    4407 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    4408 > /Figure 1/Version 2-resubmission/Chimera Session/Figure1_HSA.cxs"
    4409 > includeMaps true
    4410 
    4411 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    4412 > /Figure 1/Version 2-resubmission/Chimera Session/Figure1_HSA.cxs"
    4413 
    4414 ——— End of log from Fri Dec 20 14:57:31 2024 ———
    4415 
    4416 opened ChimeraX session 
    4417 
    4418 > ui mousemode right "translate selected models"
    4419 
    4420 > select #10/Q:482, 483, 487, 490, 504, 505, 512, 515, 522, 545, 544, 537,
    4421 > 534, 533, 526, 523
    4422 
    4423 160 atoms, 150 bonds, 16 residues, 1 model selected 
    4424 
    4425 > show sel surfaces
    4426 
    4427 > transparency (#!10 & sel) 90
    4428 
    4429 > view matrix models #10,1,0,0,38.985,0,1,0,21.605,0,0,1,42.977
    4430 
    4431 > surface #10/K,L,M,O
    4432 
    4433 > hide sel surfaces
    4434 
    4435 > select #10/K,L,M,O
    4436 
    4437 6565 atoms, 6712 bonds, 4 pseudobonds, 829 residues, 3 models selected 
    4438 
    4439 > hide sel surfaces
    4440 
    4441 > ui mousemode right select
    4442 
    4443 Drag select of 042624-x40-wt-adpbef-withadpbef-final.pdb_N SES surface, 64778
    4444 of 571650 triangles, cap near, 178 of 1639 triangles 
    4445 
    4446 > select up
    4447 
    4448 5060 atoms, 626 residues, 3 models selected 
    4449 
    4450 > select up
    4451 
    4452 55996 atoms, 57633 bonds, 6600 residues, 3 models selected 
    4453 
    4454 > select down
    4455 
    4456 5060 atoms, 626 residues, 26 models selected 
    4457 
    4458 > hide sel surfaces
    4459 
    4460 > select #10/Q:700-2000
    4461 
    4462 5289 atoms, 5408 bonds, 3 pseudobonds, 660 residues, 2 models selected 
    4463 
    4464 > hide sel surfaces
    4465 
    4466 > undo
    4467 
    4468 [Repeated 3 time(s)]
    4469 
    4470 > select #10/Q:700-2000
    4471 
    4472 5289 atoms, 5408 bonds, 3 pseudobonds, 660 residues, 2 models selected 
    4473 
    4474 > show sel cartoons
    4475 
    4476 > select #10/Q:482, 483, 487, 490, 504, 505, 512, 515, 522, 545, 544, 537,
    4477 > 534, 533, 526, 523
    4478 
    4479 160 atoms, 150 bonds, 16 residues, 1 model selected 
    4480 
    4481 > show sel surfaces
    4482 
    4483 > cartoon style (#!10 & sel) xsection oval modeHelix default
    4484 
    4485 > select clear
    4486 
    4487 > select #10/Q
    4488 
    4489 6394 atoms, 6526 bonds, 4 pseudobonds, 790 residues, 2 models selected 
    4490 
    4491 > ui tool show "Color Actions"
    4492 
    4493 > color sel fire brick
    4494 
    4495 > transparency (#!10 & sel) 80
    4496 
    4497 > select clear
    4498 
    4499 > select #I,J,A-H
    4500 
    4501 Expected an objects specifier or a keyword 
    4502 
    4503 > select #10/I,J,A-H
    4504 
    4505 12477 atoms, 13355 bonds, 1 pseudobond, 1067 residues, 2 models selected 
    4506 
    4507 > hide sel surfaces
    4508 
    4509 > nucleotides sel atoms
    4510 
    4511 > style nucleic & sel stick
    4512 
    4513 Changed 6601 atom styles 
    4514 
    4515 > nucleotides sel fill
    4516 
    4517 > style nucleic & sel stick
    4518 
    4519 Changed 6601 atom styles 
    4520 
    4521 > nucleotides sel fill
    4522 
    4523 > style nucleic & sel stick
    4524 
    4525 Changed 6601 atom styles 
    4526 
    4527 > nucleotides sel ladder
    4528 
    4529 > show sel atoms
    4530 
    4531 > undo
    4532 
    4533 > select #10/I,J
    4534 
    4535 6601 atoms, 7404 bonds, 322 residues, 1 model selected 
    4536 
    4537 > nucleotides sel ladder
    4538 
    4539 > show sel atoms
    4540 
    4541 > select clear
    4542 
    4543 > preset cartoons/nucleotides cylinders/stubs
    4544 
    4545 Using preset: Cartoons/Nucleotides / Cylinders/Stubs 
    4546 Changed 49041 atom styles 
    4547 Preset expands to these ChimeraX commands:
    4548 
    4549    
    4550    
    4551     show nucleic
    4552     hide protein|solvent|H
    4553     surf hide
    4554     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    4555     ~worm
    4556     cartoon
    4557     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    4558     cartoon style ~(nucleic|strand) x round
    4559     cartoon style (nucleic|strand) x rect
    4560     cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    4561     cartoon style nucleic x round width 1.6 thick 1.6
    4562     nucleotides stubs
    4563 
    4564  
    4565 
    4566 > undo
    4567 
    4568 > select #10/Q:482, 483, 487, 490, 504, 505, 512, 515, 522, 545, 544, 537,
    4569 > 534, 533, 526, 523
    4570 
    4571 160 atoms, 150 bonds, 16 residues, 1 model selected 
    4572 
    4573 > show sel surfaces
    4574 
    4575 > select clear
    4576 
    4577 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    4578 > Model/WT-0N80Xe-ADPBeF/121124-0n80-xe-wt-adpbef-final-coot-0-pymol-
    4579 > shortdna.pdb"
    4580 
    4581 Chain information for 121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb
    4582 #1 
    4583 --- 
    4584 Chain | Description 
    4585 A | No description available 
    4586 B | No description available 
    4587 C | No description available 
    4588 D | No description available 
    4589 E | No description available 
    4590 F | No description available 
    4591 G | No description available 
    4592 H | No description available 
    4593 I | No description available 
    4594 J | No description available 
    4595 K | No description available 
    4596 L | No description available 
    4597 M | No description available 
    4598 O | No description available 
    4599 Q | No description available 
    4600 R | No description available 
    4601 S | No description available 
    4602 T | No description available 
    4603 U | No description available 
    4604 V | No description available 
    4605 W | No description available 
    4606 X | No description available 
    4607 Y | No description available 
    4608 Z | No description available 
    4609  
    4610 
    4611 > hide #!10 models
    4612 
    4613 > hide #!1 atoms
    4614 
    4615 > show #!1 cartoons
    4616 
    4617 Drag select of 104 residues 
    4618 
    4619 > ui mousemode right select
    4620 
    4621 > ui mousemode right "translate selected models"
    4622 
    4623 > select clear
    4624 
    4625 > ui tool show "Side View"
    4626 
    4627 > show #!10 models
    4628 
    4629 > select add #10
    4630 
    4631 55996 atoms, 57633 bonds, 14 pseudobonds, 6600 residues, 3 models selected 
    4632 
    4633 > ui mousemode right "translate selected models"
    4634 
    4635 > view matrix models #10,1,0,0,7.7309,0,1,0,-1.5622,0,0,1,28.761
    4636 
    4637 > view matrix models #10,1,0,0,21.604,0,1,0,-1.7319,0,0,1,10.905
    4638 
    4639 > select #1/T-Y,R,S,Z
    4640 
    4641 26265 atoms, 26627 bonds, 8 pseudobonds, 3449 residues, 2 models selected 
    4642 
    4643 > hide sel cartoons
    4644 
    4645 > select add #10
    4646 
    4647 82261 atoms, 84260 bonds, 22 pseudobonds, 10049 residues, 5 models selected 
    4648 
    4649 > select add #1
    4650 
    4651 114335 atoms, 117752 bonds, 34 pseudobonds, 13459 residues, 29 models selected 
    4652 
    4653 > view matrix models
    4654 > #10,0.99854,0.0039952,-0.053886,36.374,-0.0072529,0.99815,-0.060394,16.722,0.053545,0.060697,0.99672,-6.6013,#1,0.99854,0.0039952,-0.053886,15.396,-0.0072529,0.99815,-0.060394,19.266,0.053545,0.060697,0.99672,-18.522
    4655 
    4656 > view matrix models
    4657 > #10,0.99854,0.0039952,-0.053886,24.172,-0.0072529,0.99815,-0.060394,14.423,0.053545,0.060697,0.99672,-11.756,#1,0.99854,0.0039952,-0.053886,3.1942,-0.0072529,0.99815,-0.060394,16.967,0.053545,0.060697,0.99672,-23.676
    4658 
    4659 > select subtract #1
    4660 
    4661 55996 atoms, 57633 bonds, 14 pseudobonds, 6600 residues, 27 models selected 
    4662 
    4663 > view matrix models
    4664 > #10,0.99854,0.0039952,-0.053886,19.269,-0.0072529,0.99815,-0.060394,13.67,0.053545,0.060697,0.99672,-14.121
    4665 
    4666 > ui tool show Matchmaker
    4667 
    4668 > matchmaker #10/A to #1/A pairing ss
    4669 
    4670 Parameters 
    4671 --- 
    4672 Chain pairing | ss 
    4673 Alignment algorithm | Needleman-Wunsch 
    4674 Similarity matrix | BLOSUM-62 
    4675 SS fraction | 0.3 
    4676 Gap open (HH/SS/other) | 18/18/6 
    4677 Gap extend | 1 
    4678 SS matrix |  |  | H | S | O 
    4679 ---|---|---|--- 
    4680 H | 6 | -9 | -6 
    4681 S |  | 6 | -6 
    4682 O |  |  | 4 
    4683 Iteration cutoff | 2 
    4684  
    4685 Matchmaker 121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb, chain A
    4686 (#1) with 042624-x40-wt-adpbef-withadpbef-final.pdb, chain A (#10), sequence
    4687 alignment score = 464.5 
    4688 RMSD between 92 pruned atom pairs is 0.625 angstroms; (across all 94 pairs:
    4689 1.166) 
    4690  
    4691 
    4692 > select #1/Q:1022-1294
    4693 
    4694 1922 atoms, 1967 bonds, 1 pseudobond, 241 residues, 2 models selected 
    4695 
    4696 > hide sel cartoons
    4697 
    4698 > select #10/Q:1022-1294
    4699 
    4700 1916 atoms, 1961 bonds, 1 pseudobond, 241 residues, 2 models selected 
    4701 
    4702 > hide sel cartoons
    4703 
    4704 > select #10/I,J-A-H
    4705 
    4706 3300 atoms, 3692 bonds, 161 residues, 1 model selected 
    4707 
    4708 > color (#!10 & sel) light gray
    4709 
    4710 > select #1/I,J-A-H
    4711 
    4712 3873 atoms, 4329 bonds, 190 residues, 1 model selected 
    4713 
    4714 > color sel light gray
    4715 
    4716 > select #1/I,J-A-H
    4717 
    4718 3873 atoms, 4329 bonds, 190 residues, 1 model selected 
    4719 
    4720 > color sel light gray
    4721 
    4722 > select #1/Q
    4723 
    4724 6141 atoms, 6266 bonds, 8 pseudobonds, 758 residues, 2 models selected 
    4725 
    4726 > ui tool show "Color Actions"
    4727 
    4728 > color sel fire brick
    4729 
    4730 > view matrix models
    4731 > #1,0.99854,0.0039952,-0.053886,11.602,-0.0072529,0.99815,-0.060394,23.788,0.053545,0.060697,0.99672,-13.106
    4732 
    4733 > undo
    4734 
    4735 > ui mousemode right select
    4736 
    4737 Drag select of 7 residues 
    4738 
    4739 > select up
    4740 
    4741 7787 atoms, 8735 bonds, 380 residues, 1 model selected 
    4742 
    4743 > select up
    4744 
    4745 58339 atoms, 60119 bonds, 6859 residues, 1 model selected 
    4746 
    4747 > select down
    4748 
    4749 7787 atoms, 8735 bonds, 380 residues, 1 model selected 
    4750 
    4751 > color sel light gray
    4752 
    4753 > nucleotides sel ladder
    4754 
    4755 > show sel atoms
    4756 
    4757 Drag select of 183 residues, 1 pseudobonds 
    4758 
    4759 > select up
    4760 
    4761 2840 atoms, 2860 bonds, 1 pseudobond, 364 residues, 8 models selected 
    4762 
    4763 > select up
    4764 
    4765 7567 atoms, 7659 bonds, 1 pseudobond, 956 residues, 8 models selected 
    4766 
    4767 > color (#!1,10 & sel) light gray
    4768 
    4769 > select up
    4770 
    4771 114335 atoms, 117752 bonds, 12 pseudobonds, 13459 residues, 8 models selected 
    4772 
    4773 > select down
    4774 
    4775 7567 atoms, 7659 bonds, 1 pseudobond, 956 residues, 27 models selected 
    4776 Drag select of 56 residues 
    4777 
    4778 > select up
    4779 
    4780 2398 atoms, 2426 bonds, 304 residues, 6 models selected 
    4781 
    4782 > color (#!1,10 & sel) light gray
    4783 
    4784 Drag select of 12 residues 
    4785 
    4786 > select up
    4787 
    4788 170 atoms, 170 bonds, 21 residues, 3 models selected 
    4789 
    4790 > select up
    4791 
    4792 1286 atoms, 1300 bonds, 162 residues, 3 models selected 
    4793 
    4794 > color (#!1,10 & sel) light gray
    4795 
    4796 Drag select of 27 residues 
    4797 
    4798 > select up
    4799 
    4800 947 atoms, 963 bonds, 118 residues, 4 models selected 
    4801 
    4802 > color (#!1,10 & sel) light gray
    4803 
    4804 > select #1/K,L,M,O
    4805 
    4806 12253 atoms, 12523 bonds, 3 pseudobonds, 1525 residues, 2 models selected 
    4807 
    4808 > hide sel cartoons
    4809 
    4810 [Repeated 1 time(s)]
    4811 
    4812 > select #1/Q:482, 483, 487, 490, 504, 505, 512, 515, 522, 545, 544, 537, 534,
    4813 > 533, 526, 523
    4814 
    4815 160 atoms, 150 bonds, 16 residues, 1 model selected 
    4816 
    4817 > show sel atoms
    4818 
    4819 > style sel stick
    4820 
    4821 Changed 160 atom styles 
    4822 
    4823 > show sel surfaces
    4824 
    4825 > transparency (#!1 & sel) 90
    4826 
    4827 > transparency (#!1 & sel) 80
    4828 
    4829 > select clear
    4830 
    4831 [Repeated 2 time(s)]Drag select of 4 residues, 5 shapes 
    4832 
    4833 > select clear
    4834 
    4835 > ui mousemode right "translate selected models"
    4836 
    4837 > ui mousemode right select
    4838 
    4839 Drag select of 2 residues 
    4840 
    4841 > select up
    4842 
    4843 739 atoms, 750 bonds, 95 residues, 1 model selected 
    4844 
    4845 > color sel light gray
    4846 
    4847 > select clear
    4848 
    4849 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    4850 > /Figure 1/Version 1/Chimera Session V2/HSa.cxs" includeMaps true
    4851 
    4852 Drag select of 4 residues, 2 shapes 
    4853 
    4854 > select clear
    4855 
    4856 > ui mousemode right "translate selected models"
    4857 
    4858 > hide #!10 models
    4859 
    4860 > select #1/K,L,M,O
    4861 
    4862 12253 atoms, 12523 bonds, 3 pseudobonds, 1525 residues, 2 models selected 
    4863 
    4864 > show sel cartoons
    4865 
    4866 > select #1/K
    4867 
    4868 5614 atoms, 5735 bonds, 1 pseudobond, 692 residues, 2 models selected 
    4869 
    4870 > color (#!1 & sel) medium blue
    4871 
    4872 > select #1/L
    4873 
    4874 2862 atoms, 2925 bonds, 1 pseudobond, 364 residues, 2 models selected 
    4875 
    4876 > ui tool show "Color Actions"
    4877 
    4878 > color sel gold
    4879 
    4880 > select #1/M
    4881 
    4882 3430 atoms, 3507 bonds, 1 pseudobond, 429 residues, 2 models selected 
    4883 
    4884 > color sel deep sky blue
    4885 
    4886 > select #1/O
    4887 
    4888 347 atoms, 356 bonds, 40 residues, 1 model selected 
    4889 
    4890 > color sel cornflower blue
    4891 
    4892 > select #1/K,L,M,O
    4893 
    4894 12253 atoms, 12523 bonds, 3 pseudobonds, 1525 residues, 2 models selected 
    4895 
    4896 > show sel surfaces
    4897 
    4898 > transparency (#!1 & sel) 90
    4899 
    4900 > hide sel cartoons
    4901 
    4902 > hide sel surfaces
    4903 
    4904 > view matrix models
    4905 > #1,0.99854,0.0039952,-0.053886,13.787,-0.0072529,0.99815,-0.060394,17.309,0.053545,0.060697,0.99672,-14.708
    4906 
    4907 > select #1/K,L,M,O
    4908 
    4909 12253 atoms, 12523 bonds, 3 pseudobonds, 1525 residues, 2 models selected 
    4910 
    4911 > select #1/K,L,M,O
    4912 
    4913 12253 atoms, 12523 bonds, 3 pseudobonds, 1525 residues, 2 models selected 
    4914 
    4915 > show sel cartoons
    4916 
    4917 > hide sel cartoons
    4918 
    4919 > show sel surfaces
    4920 
    4921 > color (#!1 & sel) light gray
    4922 
    4923 > transparency (#!1 & sel) 90
    4924 
    4925 > select clear
    4926 
    4927 > hide #!1 surfaces
    4928 
    4929 > undo
    4930 
    4931 > select #1/Q:482, 483, 487, 490, 504, 505, 512, 515, 522, 545, 544, 537, 534,
    4932 > 533, 526, 523
    4933 
    4934 160 atoms, 150 bonds, 16 residues, 1 model selected 
    4935 
    4936 > show sel surfaces
    4937 
    4938 > select clear
    4939 
    4940 > cartoon style #1 xsection oval modeHelix default
    4941 
    4942 > cartoon style #1 modeHelix tube sides 20
    4943 
    4944 > cartoon style modeHelix tube radius 1.5
    4945 
    4946 > select #1/I,J
    4947 
    4948 7787 atoms, 8735 bonds, 380 residues, 1 model selected 
    4949 
    4950 > color sel light slate gray
    4951 
    4952 > select clear
    4953 
    4954 > select #1/K,L,M,O
    4955 
    4956 12253 atoms, 12523 bonds, 3 pseudobonds, 1525 residues, 2 models selected 
    4957 
    4958 > show sel cartoons
    4959 
    4960 > transparency #1/K,L,M,O 80 cartoons
    4961 
    4962 > select clear
    4963 
    4964 > graphics silhouettes true
    4965 
    4966 > select #1/K,L,M,O 80 c
    4967 
    4968 Expected a keyword 
    4969 
    4970 > select #1/K,L,M,O
    4971 
    4972 12253 atoms, 12523 bonds, 3 pseudobonds, 1525 residues, 2 models selected 
    4973 
    4974 > color sel cornflower blue
    4975 
    4976 > color sel blue
    4977 
    4978 > color sel medium blue
    4979 
    4980 > color sel cornflower blue
    4981 
    4982 > color sel deep sky blue
    4983 
    4984 > color sel cyan
    4985 
    4986 > color sel cornflower blue
    4987 
    4988 > select clear
    4989 
    4990 > show #!10 models
    4991 
    4992 > select add #10
    4993 
    4994 55996 atoms, 57633 bonds, 14 pseudobonds, 6600 residues, 3 models selected 
    4995 
    4996 > view matrix models
    4997 > #10,0.98483,-0.12885,-0.11623,65.285,0.11868,0.9888,-0.090544,-1.7103,0.1266,0.075375,0.98909,-24.897
    4998 
    4999 > select subtract #10
    5000 
    5001 24 models selected 
    5002 
    5003 > select add #1
    5004 
    5005 58339 atoms, 60119 bonds, 20 pseudobonds, 6859 residues, 6 models selected 
    5006 
    5007 > select add #10
    5008 
    5009 114335 atoms, 117752 bonds, 34 pseudobonds, 13459 residues, 14 models selected 
    5010 
    5011 > select subtract #1
    5012 
    5013 55996 atoms, 57633 bonds, 14 pseudobonds, 6600 residues, 32 models selected 
    5014 
    5015 > select subtract #10
    5016 
    5017 24 models selected 
    5018 
    5019 > hide #!1 models
    5020 
    5021 > show #!1 models
    5022 
    5023 > select #10/K,L,M,O
    5024 
    5025 6565 atoms, 6712 bonds, 4 pseudobonds, 829 residues, 3 models selected 
    5026 
    5027 > show sel cartoons
    5028 
    5029 > select #10/N
    5030 
    5031 5060 atoms, 5173 bonds, 626 residues, 1 model selected 
    5032 
    5033 > show sel cartoons
    5034 
    5035 > select #10/N,K,L,M,O
    5036 
    5037 11625 atoms, 11885 bonds, 4 pseudobonds, 1455 residues, 3 models selected 
    5038 
    5039 > color sel cornflower blue
    5040 
    5041 > transparency #10/N,K,L,M,O 90 cartoons
    5042 
    5043 > select clear
    5044 
    5045 > transparency #1/K,L,M,O 90 cartoons
    5046 
    5047 > select clear
    5048 
    5049 > select #1/ L
    5050 
    5051 2862 atoms, 2925 bonds, 1 pseudobond, 364 residues, 2 models selected 
    5052 
    5053 > color sel gold
    5054 
    5055 > select #10/ L
    5056 
    5057 2824 atoms, 2886 bonds, 1 pseudobond, 361 residues, 2 models selected 
    5058 
    5059 > color sel gold
    5060 
    5061 > select #10/ M
    5062 
    5063 3422 atoms, 3498 bonds, 1 pseudobond, 431 residues, 2 models selected 
    5064 
    5065 > color sel deep sky blue
    5066 
    5067 > color sel cyan
    5068 
    5069 > color sel deep sky blue
    5070 
    5071 > select #1/ M
    5072 
    5073 3430 atoms, 3507 bonds, 1 pseudobond, 429 residues, 2 models selected 
    5074 
    5075 > color sel royal blue
    5076 
    5077 > color sel deep sky blue
    5078 
    5079 > select clear
    5080 
    5081 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    5082 > /Figure 1/Version 1/Chimera Session V2/HSa.cxs" includeMaps true
    5083 
    5084 ——— End of log from Sat Dec 21 18:53:40 2024 ———
    5085 
    5086 opened ChimeraX session 
    5087 
    5088 > select #10/I,J
    5089 
    5090 6601 atoms, 7404 bonds, 322 residues, 1 model selected 
    5091 
    5092 > select clear
    5093 
    5094 > hide #!10 models
    5095 
    5096 > SEL #1/K,L,M,O
    5097 
    5098 Unknown command: SEL #1/K,L,M,O 
    5099 
    5100 > select #1/K,L,M,O
    5101 
    5102 12253 atoms, 12523 bonds, 3 pseudobonds, 1525 residues, 2 models selected 
    5103 
    5104 > hide sel cartoons
    5105 
    5106 > view matrix models
    5107 > #1,0.99854,0.0039952,-0.053886,26.023,-0.0072529,0.99815,-0.060394,15.967,0.053545,0.060697,0.99672,-3.2803
    5108 
    5109 > view matrix models
    5110 > #1,0.99854,0.0039952,-0.053886,42.833,-0.0072529,0.99815,-0.060394,16.012,0.053545,0.060697,0.99672,14.844
    5111 
    5112 > view matrix models
    5113 > #1,0.99854,0.0039952,-0.053886,42.856,-0.0072529,0.99815,-0.060394,15.964,0.053545,0.060697,0.99672,14.815
    5114 
    5115 > view matrix models
    5116 > #1,0.99854,0.0039952,-0.053886,46.079,-0.0072529,0.99815,-0.060394,15.76,0.053545,0.060697,0.99672,17.042
    5117 
    5118 > ui mousemode right "rotate selected models"
    5119 
    5120 > view matrix models
    5121 > #1,0.99848,0.002554,-0.055102,46.617,-0.005834,0.99821,-0.059446,15.308,0.054852,0.059677,0.99671,17.015
    5122 
    5123 > ui mousemode right "translate selected models"
    5124 
    5125 > view matrix models
    5126 > #1,0.99848,0.002554,-0.055102,47.291,-0.005834,0.99821,-0.059446,15.318,0.054852,0.059677,0.99671,17.531
    5127 
    5128 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    5129 > /Figure 1/Version 1/Chimera Session V2/0N80_HSA.png" width 3600 height 2686
    5130 > supersample 3 transparentBackground true
    5131 
    5132 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    5133 > /Figure 1/Version 1/Chimera Session V2/0N80_HSA.png" width 3600 height 2686
    5134 > supersample 3
    5135 
    5136 > hide #!1 models
    5137 
    5138 > show #!10 models
    5139 
    5140 > view matrix models
    5141 > #1,0.99848,0.002554,-0.055102,24.086,-0.005834,0.99821,-0.059446,21.606,0.054852,0.059677,0.99671,7.1292
    5142 
    5143 > view matrix models
    5144 > #1,0.99848,0.002554,-0.055102,5.6807,-0.005834,0.99821,-0.059446,26.158,0.054852,0.059677,0.99671,-1.8649
    5145 
    5146 > view matrix models
    5147 > #1,0.99848,0.002554,-0.055102,-32.619,-0.005834,0.99821,-0.059446,46.065,0.054852,0.059677,0.99671,-2.6764
    5148 
    5149 > view matrix models
    5150 > #1,0.99848,0.002554,-0.055102,-67.761,-0.005834,0.99821,-0.059446,61.29,0.054852,0.059677,0.99671,-8.8338
    5151 
    5152 > select add #10
    5153 
    5154 68249 atoms, 70156 bonds, 17 pseudobonds, 8125 residues, 9 models selected 
    5155 
    5156 > select add #1
    5157 
    5158 114335 atoms, 117752 bonds, 34 pseudobonds, 13459 residues, 33 models selected 
    5159 
    5160 > select subtract #1
    5161 
    5162 55996 atoms, 57633 bonds, 14 pseudobonds, 6600 residues, 32 models selected 
    5163 
    5164 > view matrix models
    5165 > #10,0.98483,-0.12885,-0.11623,37.367,0.11868,0.9888,-0.090544,10.581,0.1266,0.075375,0.98909,-29.439
    5166 
    5167 > select clear
    5168 
    5169 > select #10/K,L,M,O
    5170 
    5171 6565 atoms, 6712 bonds, 4 pseudobonds, 829 residues, 3 models selected 
    5172 
    5173 > hide sel cartoons
    5174 
    5175 > select #10/N
    5176 
    5177 5060 atoms, 5173 bonds, 626 residues, 1 model selected 
    5178 
    5179 > hide sel cartoons
    5180 
    5181 > view matrix models
    5182 > #10,0.98483,-0.12885,-0.11623,20.474,0.11868,0.9888,-0.090544,33.043,0.1266,0.075375,0.98909,-49.921
    5183 
    5184 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    5185 > /Figure 1/Version 1/Chimera Session V2/0N40_HSA.png" width 3600 height 2686
    5186 > supersample 3
    5187 
    5188 > select #10/N,K,L,M,O
    5189 
    5190 11625 atoms, 11885 bonds, 4 pseudobonds, 1455 residues, 3 models selected 
    5191 
    5192 > show sel cartoons
    5193 
    5194 > select clear
    5195 
    5196 > select #10/N,K,L,M,O
    5197 
    5198 11625 atoms, 11885 bonds, 4 pseudobonds, 1455 residues, 3 models selected 
    5199 
    5200 > color (#!10 & sel) gray
    5201 
    5202 > select clear
    5203 
    5204 > show #!1 models
    5205 
    5206 > select add #1
    5207 
    5208 58339 atoms, 60119 bonds, 20 pseudobonds, 6859 residues, 2 models selected 
    5209 
    5210 > view matrix models
    5211 > #1,0.99848,0.002554,-0.055102,-34.947,-0.005834,0.99821,-0.059446,32.857,0.054852,0.059677,0.99671,-30.505
    5212 
    5213 > select subtract #1
    5214 
    5215 5 models selected 
    5216 
    5217 > select #1/A-H
    5218 
    5219 5893 atoms, 5968 bonds, 1 pseudobond, 747 residues, 2 models selected 
    5220 
    5221 > hide sel cartoons
    5222 
    5223 > select #2/A-H
    5224 
    5225 Nothing selected 
    5226 
    5227 > select #10/A-H
    5228 
    5229 5876 atoms, 5951 bonds, 1 pseudobond, 745 residues, 2 models selected 
    5230 
    5231 > hide sel cartoons
    5232 
    5233 > select #10/I,J
    5234 
    5235 6601 atoms, 7404 bonds, 322 residues, 1 model selected 
    5236 
    5237 > ui tool show "Color Actions"
    5238 
    5239 > color sel slate gray
    5240 
    5241 > color sel light slate gray
    5242 
    5243 > color sel light steel blue
    5244 
    5245 [Repeated 1 time(s)]
    5246 
    5247 > color sel light blue
    5248 
    5249 > color sel light steel blue
    5250 
    5251 > color sel light gray
    5252 
    5253 > select clear
    5254 
    5255 > ui mousemode right select
    5256 
    5257 Drag select of 9 residues, 14 shapes 
    5258 
    5259 > select up
    5260 
    5261 6601 atoms, 7404 bonds, 322 residues, 3 models selected 
    5262 
    5263 > select down
    5264 
    5265 185 atoms, 9 residues, 3 models selected 
    5266 
    5267 > hide sel atoms
    5268 
    5269 > select #10/I,J
    5270 
    5271 6601 atoms, 7404 bonds, 322 residues, 1 model selected 
    5272 
    5273 > hide sel atoms
    5274 
    5275 > hide sel cartoons
    5276 
    5277 > select #1/K,L,M,O
    5278 
    5279 12253 atoms, 12523 bonds, 3 pseudobonds, 1525 residues, 2 models selected 
    5280 
    5281 > show sel cartoons
    5282 
    5283 > select clear
    5284 
    5285 > select #1/K,L,M,O
    5286 
    5287 12253 atoms, 12523 bonds, 3 pseudobonds, 1525 residues, 2 models selected 
    5288 
    5289 > hide sel cartoons
    5290 
    5291 > show sel surfaces
    5292 
    5293 > color (#!1 & sel) white
    5294 
    5295 > transparency (#!1 & sel) 100
    5296 
    5297 > select clear
    5298 
    5299 > select #10/N,K,L,M,O
    5300 
    5301 11625 atoms, 11885 bonds, 4 pseudobonds, 1455 residues, 3 models selected 
    5302 
    5303 > hide sel cartoons
    5304 
    5305 > show sel surfaces
    5306 
    5307 > color (#!10 & sel) white
    5308 
    5309 > transparency (#!10 & sel) 100
    5310 
    5311 > select clear
    5312 
    5313 > select #1/Q:482, 483, 487, 490, 504, 505, 512, 515, 522, 545, 544, 537, 534,
    5314 > 533, 526, 523
    5315 
    5316 160 atoms, 150 bonds, 16 residues, 1 model selected 
    5317 
    5318 > transparency (#!1 & sel) 50
    5319 
    5320 > select clear
    5321 
    5322 > select #2/Q:482, 483, 487, 490, 504, 505, 512, 515, 522, 545, 544, 537, 534,
    5323 > 533, 526, 523
    5324 
    5325 Nothing selected 
    5326 
    5327 > transparency 50
    5328 
    5329 > select clear
    5330 
    5331 > lighting soft
    5332 
    5333 > lighting simple
    5334 
    5335 > lighting soft
    5336 
    5337 > lighting full
    5338 
    5339 > lighting flat
    5340 
    5341 > lighting shadows true intensity 0.5
    5342 
    5343 > lighting shadows false
    5344 
    5345 > lighting simple
    5346 
    5347 > lighting soft
    5348 
    5349 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    5350 > /Figure 1/Version 1/Chimera Session V2/HSa.cxs" includeMaps true
    5351 
    5352 ——— End of log from Sat Dec 21 19:42:25 2024 ———
    5353 
    5354 opened ChimeraX session 
    5355 
    5356 > select #10/K,L,M,O
    5357 
    5358 6565 atoms, 6712 bonds, 4 pseudobonds, 829 residues, 3 models selected 
    5359 
    5360 > hide sel atoms
    5361 
    5362 > hide sel cartoons
    5363 
    5364 > hide sel surfaces
    5365 
    5366 > select #10/K,L,M,O,N
    5367 
    5368 11625 atoms, 11885 bonds, 4 pseudobonds, 1455 residues, 3 models selected 
    5369 
    5370 > hide sel surfaces
    5371 
    5372 > select #10/Q:0-700
    5373 
    5374 1105 atoms, 1118 bonds, 130 residues, 1 model selected 
    5375 
    5376 > coulombic sel
    5377 
    5378 The following residues are missing heavy (non-hydrogen) atoms, which may
    5379 result in inaccurate electrostatics: 
    5380 042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q LYS 707 
    5381 042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q ARG 802 
    5382 042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q ASN 804 
    5383 042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q VAL 824 
    5384 042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q ARG 863 
    5385 042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q ARG 865 
    5386 042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q ASP 896 
    5387 042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q GLU 897 
    5388 042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q LYS 947 
    5389 042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q ARG 959 
    5390 042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q ARG 1293 
    5391 042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q LYS 1300 
    5392 042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q ASP 1305 
    5393 042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q ARG 1317 
    5394 042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q LYS 1326 
    5395 042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q MET 1327 
    5396 042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q GLN 1403 
    5397 042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q ARG 1407 
    5398 042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q LEU 1423 
    5399 042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q ILE 1428 
    5400 042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q ARG 1431 
    5401 042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q ARG 1433 
    5402 042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q ARG 1435 
    5403 042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q LYS 1437 
    5404 042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q LYS 1439 
    5405 
    5406 Using Amber 20 recommended default charges and atom types for standard
    5407 residues 
    5408 Coulombic values for 042624-x40-wt-adpbef-withadpbef-final.pdb_Q SES surface
    5409 #10.17: minimum, -21.85, mean -0.46, maximum 18.53 
    5410 To also show corresponding color key, enter the above coulombic command and
    5411 add key true 
    5412 
    5413 > transparency (#!10 & sel) 50
    5414 
    5415 > select clear
    5416 
    5417 > select #10/K,L,M,O,N
    5418 
    5419 11625 atoms, 11885 bonds, 4 pseudobonds, 1455 residues, 3 models selected 
    5420 
    5421 > show sel cartoons
    5422 
    5423 > select clear
    5424 
    5425 > select #10/Q:0-700
    5426 
    5427 1105 atoms, 1118 bonds, 130 residues, 1 model selected 
    5428 
    5429 > hide sel cartoons
    5430 
    5431 > select #10/Q:0-700
    5432 
    5433 1105 atoms, 1118 bonds, 130 residues, 1 model selected 
    5434 
    5435 > hide sel atoms
    5436 
    5437 > select clear
    5438 
    5439 > transparency 0
    5440 
    5441 > ui tool show "Side View"
    5442 
    5443 > select #1/Q:0-700
    5444 
    5445 957 atoms, 969 bonds, 118 residues, 1 model selected 
    5446 
    5447 > coulombic sel
    5448 
    5449 The following residues are missing heavy (non-hydrogen) atoms, which may
    5450 result in inaccurate electrostatics: 
    5451 121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb #1/Q LYS 707 
    5452 121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb #1/Q ARG 802 
    5453 121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb #1/Q ASN 804 
    5454 121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb #1/Q VAL 824 
    5455 121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb #1/Q ARG 863 
    5456 121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb #1/Q ARG 865 
    5457 121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb #1/Q ASP 896 
    5458 121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb #1/Q GLU 897 
    5459 121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb #1/Q ARG 1008 
    5460 121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb #1/Q LYS 1326 
    5461 121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb #1/Q TRP 1396 
    5462 121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb #1/Q ARG 1431 
    5463 
    5464 Using Amber 20 recommended default charges and atom types for standard
    5465 residues 
    5466 Coulombic values for 121124-0n80-xe-wt-adpbef-final-coot-0-pymol-
    5467 shortdna.pdb_Q SES surface #1.2: minimum, -20.01, mean -0.29, maximum 21.82 
    5468 To also show corresponding color key, enter the above coulombic command and
    5469 add key true 
    5470 
    5471 > select #1/K,L,M,O
    5472 
    5473 12253 atoms, 12523 bonds, 3 pseudobonds, 1525 residues, 2 models selected 
    5474 
    5475 > hide sel surfaces
    5476 
    5477 > show sel cartoons
    5478 
    5479 > select clear
    5480 
    5481 > transparency 10
    5482 
    5483 > transparency 0
    5484 
    5485 > select #1/Q:0-700
    5486 
    5487 957 atoms, 969 bonds, 118 residues, 1 model selected 
    5488 
    5489 > hide sel cartoons
    5490 
    5491 > transparency (#!1 & sel) 10
    5492 
    5493 > hide sel atoms
    5494 
    5495 > select clear
    5496 
    5497 > select #1/K
    5498 
    5499 5614 atoms, 5735 bonds, 1 pseudobond, 692 residues, 2 models selected 
    5500 
    5501 > ui tool show "Color Actions"
    5502 
    5503 > color sel medium blue
    5504 
    5505 > select #1/L
    5506 
    5507 2862 atoms, 2925 bonds, 1 pseudobond, 364 residues, 2 models selected 
    5508 
    5509 > color sel khaki
    5510 
    5511 > select #1/M
    5512 
    5513 3430 atoms, 3507 bonds, 1 pseudobond, 429 residues, 2 models selected 
    5514 
    5515 > color sel deep sky blue
    5516 
    5517 > select #1/O
    5518 
    5519 347 atoms, 356 bonds, 40 residues, 1 model selected 
    5520 
    5521 > color sel dark blue
    5522 
    5523 > select clear
    5524 
    5525 > transparency #1/K,L,M,O 30 cartoons
    5526 
    5527 > transparency #1/K,L,M,O 70 cartoons
    5528 
    5529 > transparency #1/K,L,M,O 80 cartoons
    5530 
    5531 > select clear
    5532 
    5533 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    5534 > /Figure 1/Version 2-resubmission/Chimera Session/HSA_0N80.png" width 3600
    5535 > height 3544 supersample 3
    5536 
    5537 No map chosen to save 
    5538 
    5539 > save /Users/upneet/Desktop/test.jpg width 3600 height 3544 supersample 3
    5540 
    5541 > save /Users/upneet/Desktop/test.tif width 3600 height 3544 supersample 3
    5542 
    5543 > select #1/N
    5544 
    5545 Nothing selected 
    5546 
    5547 > color medium blue
    5548 
    5549 > undo
    5550 
    5551 > select #10/N
    5552 
    5553 5060 atoms, 5173 bonds, 626 residues, 1 model selected 
    5554 
    5555 > color sel medium blue
    5556 
    5557 > select #10/L
    5558 
    5559 2824 atoms, 2886 bonds, 1 pseudobond, 361 residues, 2 models selected 
    5560 
    5561 > color sel khaki
    5562 
    5563 > select #10/O
    5564 
    5565 287 atoms, 296 bonds, 34 residues, 1 model selected 
    5566 
    5567 > color sel deep sky blue
    5568 
    5569 > select #10/M
    5570 
    5571 3422 atoms, 3498 bonds, 1 pseudobond, 431 residues, 2 models selected 
    5572 
    5573 > color sel deep sky blue
    5574 
    5575 > select #10/O
    5576 
    5577 287 atoms, 296 bonds, 34 residues, 1 model selected 
    5578 
    5579 > color sel dark blue
    5580 
    5581 > select clear
    5582 
    5583 > transparency #10/N,L,M,O 80 cartoons
    5584 
    5585 > select clear
    5586 
    5587 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    5588 > /Figure 1/Version 2-resubmission/Chimera Session/HSA_0N40.png" width 3600
    5589 > height 3544 supersample 3
    5590 
    5591 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    5592 > Model/mix-dataset/mix-global-refine.mrc"
    5593 
    5594 Opened mix-global-refine.mrc as #2, grid size 448,448,448, pixel 0.835, shown
    5595 at level 0.00458, step 2, values float32 
    5596 
    5597 > close #2
    5598 
    5599 > open "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    5600 > /Figure 2/Version 2- Resubmission/0_80_ApovsADPBeF_Maps.cxs"
    5601 
    5602 Opened x0_80_ADPBeF_A8-Split.mrc as #1, grid size 480,480,480, pixel 0.835,
    5603 shown at level 0.00261, step 1, values float32 
    5604 Opened x0_80_ADPBeF_Ies2.mrc as #3, grid size 480,480,480, pixel 0.835, shown
    5605 at level 0.348, step 1, values float32 
    5606 Opened 041924-global-resampleonapo.mrc 0 as #5.1, grid size 480,480,480, pixel
    5607 0.835, shown at level 0.221, step 1, values float32 
    5608 Opened 041924-global-resampleonapo.mrc 1 as #5.2, grid size 480,480,480, pixel
    5609 0.835, shown at level 0.238, step 1, values float32 
    5610 Opened 041924-global-resampleonapo.mrc 2 as #5.3, grid size 480,480,480, pixel
    5611 0.835, shown at level 0.221, step 1, values float32 
    5612 Opened 041924-global-resampleonapo.mrc 3 as #5.4, grid size 480,480,480, pixel
    5613 0.835, shown at level 0.221, step 1, values float32 
    5614 Opened 041924-global-resampleonapo.mrc 4 as #5.5, grid size 480,480,480, pixel
    5615 0.835, shown at level 0.221, step 1, values float32 
    5616 Opened 041924-global-resampleonapo.mrc 5 as #5.6, grid size 480,480,480, pixel
    5617 0.835, shown at level 0.221, step 1, values float32 
    5618 Opened 041924-global-resampleonapo.mrc 6 as #5.7, grid size 480,480,480, pixel
    5619 0.835, shown at level 0.221, step 1, values float32 
    5620 Opened 041924-global-resampleonapo.mrc 7 as #5.8, grid size 480,480,480, pixel
    5621 0.835, shown at level 0.221, step 1, values float32 
    5622 Opened 041924-global-resampleonapo.mrc 8 as #5.9, grid size 480,480,480, pixel
    5623 0.835, shown at level 0.235, step 1, values float32 
    5624 Opened 041924-global-resampleonapo.mrc 9 as #5.10, grid size 480,480,480,
    5625 pixel 0.835, shown at level 0.174, step 1, values float32 
    5626 Opened x0_80_ADPBeF_nuc.mrc as #6, grid size 480,480,480, pixel 0.835, shown
    5627 at level 1.44, step 1, values float32 
    5628 Opened y0_80_ADPBeF_Core.mrc as #7, grid size 448,448,448, pixel 0.835, shown
    5629 at level 0.186, step 1, values float32 
    5630 Opened y0_80_ADPBeF_Core-filter.mrc as #8, grid size 256,256,256, pixel 1.67,
    5631 shown at level 0.0143, step 1, values float32 
    5632 Opened y0_80_Apo_A8-split.mrc as #10, grid size 512,512,512, pixel 0.819,
    5633 shown at level 0.0016, step 1, values float32 
    5634 Opened y0_80_Apo_core_nuc.mrc as #11, grid size 512,512,512, pixel 0.819,
    5635 shown at level 0.157, step 1, values float32 
    5636 Opened 122324-x80-apo-a8-split-resample.mrc as #12, grid size 480,480,480,
    5637 pixel 0.835, shown at level 0.00122, step 1, values float32 
    5638 Opened 122324-x80-apo-arp5-resample.mrc as #13, grid size 480,480,480, pixel
    5639 0.835, shown at level 0.0832, step 1, values float32 
    5640 Opened 122324-x80-apo-atpasehighres-resample.mrc as #14, grid size
    5641 480,480,480, pixel 0.835, shown at level 0.0212, step 1, values float32 
    5642 Opened 122324-x80-apo-dna-resample.mrc as #15, grid size 480,480,480, pixel
    5643 0.835, shown at level 0.847, step 1, values float32 
    5644 Opened 122324-x80-apo-grappler-resample.mrc as #16, grid size 480,480,480,
    5645 pixel 0.835, shown at level 0.11, step 1, values float32 
    5646 Opened 122324-x80-apo-histone-resample.mrc as #17, grid size 480,480,480,
    5647 pixel 0.835, shown at level 1.29, step 1, values float32 
    5648 Opened 122324-x80-apo-i2highres-resample.mrc as #18, grid size 480,480,480,
    5649 pixel 0.835, shown at level 0.104, step 1, values float32 
    5650 Opened 122324-x80-apo-rvb-resample.mrc as #20, grid size 480,480,480, pixel
    5651 0.835, shown at level 0.221, step 1, values float32 
    5652 Opened 122324-x80-ies2lowres-resample.mrc as #21, grid size 480,480,480, pixel
    5653 0.835, shown at level 0.00032, step 1, values float32 
    5654 opened ChimeraX session 
    5655 
    5656 > open "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    5657 > /Figure 2/Version 2- Resubmission/0_80_ApovsADPBeF_Maps.cxs"
    5658 
    5659 Opened x0_80_ADPBeF_A8-Split.mrc as #1, grid size 480,480,480, pixel 0.835,
    5660 shown at level 0.00261, step 1, values float32 
    5661 Opened x0_80_ADPBeF_Ies2.mrc as #3, grid size 480,480,480, pixel 0.835, shown
    5662 at level 0.348, step 1, values float32 
    5663 Opened 041924-global-resampleonapo.mrc 0 as #5.1, grid size 480,480,480, pixel
    5664 0.835, shown at level 0.221, step 1, values float32 
    5665 Opened 041924-global-resampleonapo.mrc 1 as #5.2, grid size 480,480,480, pixel
    5666 0.835, shown at level 0.238, step 1, values float32 
    5667 Opened 041924-global-resampleonapo.mrc 2 as #5.3, grid size 480,480,480, pixel
    5668 0.835, shown at level 0.221, step 1, values float32 
    5669 Opened 041924-global-resampleonapo.mrc 3 as #5.4, grid size 480,480,480, pixel
    5670 0.835, shown at level 0.221, step 1, values float32 
    5671 Opened 041924-global-resampleonapo.mrc 4 as #5.5, grid size 480,480,480, pixel
    5672 0.835, shown at level 0.221, step 1, values float32 
    5673 Opened 041924-global-resampleonapo.mrc 5 as #5.6, grid size 480,480,480, pixel
    5674 0.835, shown at level 0.221, step 1, values float32 
    5675 Opened 041924-global-resampleonapo.mrc 6 as #5.7, grid size 480,480,480, pixel
    5676 0.835, shown at level 0.221, step 1, values float32 
    5677 Opened 041924-global-resampleonapo.mrc 7 as #5.8, grid size 480,480,480, pixel
    5678 0.835, shown at level 0.221, step 1, values float32 
    5679 Opened 041924-global-resampleonapo.mrc 8 as #5.9, grid size 480,480,480, pixel
    5680 0.835, shown at level 0.235, step 1, values float32 
    5681 Opened 041924-global-resampleonapo.mrc 9 as #5.10, grid size 480,480,480,
    5682 pixel 0.835, shown at level 0.174, step 1, values float32 
    5683 Opened x0_80_ADPBeF_nuc.mrc as #6, grid size 480,480,480, pixel 0.835, shown
    5684 at level 1.44, step 1, values float32 
    5685 Opened y0_80_ADPBeF_Core.mrc as #7, grid size 448,448,448, pixel 0.835, shown
    5686 at level 0.186, step 1, values float32 
    5687 Opened y0_80_ADPBeF_Core-filter.mrc as #8, grid size 256,256,256, pixel 1.67,
    5688 shown at level 0.0143, step 1, values float32 
    5689 Opened y0_80_Apo_A8-split.mrc as #10, grid size 512,512,512, pixel 0.819,
    5690 shown at level 0.0016, step 1, values float32 
    5691 Opened y0_80_Apo_core_nuc.mrc as #11, grid size 512,512,512, pixel 0.819,
    5692 shown at level 0.157, step 1, values float32 
    5693 Opened 122324-x80-apo-a8-split-resample.mrc as #12, grid size 480,480,480,
    5694 pixel 0.835, shown at level 0.00122, step 1, values float32 
    5695 Opened 122324-x80-apo-arp5-resample.mrc as #13, grid size 480,480,480, pixel
    5696 0.835, shown at level 0.0832, step 1, values float32 
    5697 Opened 122324-x80-apo-atpasehighres-resample.mrc as #14, grid size
    5698 480,480,480, pixel 0.835, shown at level 0.0212, step 1, values float32 
    5699 Opened 122324-x80-apo-dna-resample.mrc as #15, grid size 480,480,480, pixel
    5700 0.835, shown at level 0.847, step 1, values float32 
    5701 Opened 122324-x80-apo-grappler-resample.mrc as #16, grid size 480,480,480,
    5702 pixel 0.835, shown at level 0.11, step 1, values float32 
    5703 Opened 122324-x80-apo-histone-resample.mrc as #17, grid size 480,480,480,
    5704 pixel 0.835, shown at level 1.29, step 1, values float32 
    5705 Opened 122324-x80-apo-i2highres-resample.mrc as #18, grid size 480,480,480,
    5706 pixel 0.835, shown at level 0.104, step 1, values float32 
    5707 Opened 122324-x80-apo-rvb-resample.mrc as #20, grid size 480,480,480, pixel
    5708 0.835, shown at level 0.221, step 1, values float32 
    5709 Opened 122324-x80-ies2lowres-resample.mrc as #21, grid size 480,480,480, pixel
    5710 0.835, shown at level 0.00032, step 1, values float32 
    5711 opened ChimeraX session 
    5712 
    5713 > volume #10 level 0.002171
    5714 
    5715 > volume #10 level 0.002364
    5716 
    5717 > hide #!10 models
    5718 
    5719 > hide #!11 models
    5720 
    5721 > show #!20 models
    5722 
    5723 > show #!21 models
    5724 
    5725 > show #!19 models
    5726 
    5727 > hide #!19 models
    5728 
    5729 > show #!18 models
    5730 
    5731 > show #!17 models
    5732 
    5733 > show #!16 models
    5734 
    5735 > show #!15 models
    5736 
    5737 > show #!14 models
    5738 
    5739 > show #!13 models
    5740 
    5741 > show #!12 models
    5742 
    5743 > hide #!12 models
    5744 
    5745 > hide #!13 models
    5746 
    5747 > hide #!14 models
    5748 
    5749 > hide #!15 models
    5750 
    5751 > hide #!16 models
    5752 
    5753 > hide #!17 models
    5754 
    5755 > hide #!18 models
    5756 
    5757 > hide #!20 models
    5758 
    5759 > hide #!21 models
    5760 
    5761 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    5762 > Model/mix-dataset/mix-global-refine.mrc"
    5763 
    5764 Opened mix-global-refine.mrc as #22, grid size 448,448,448, pixel 0.835, shown
    5765 at level 0.00458, step 2, values float32 
    5766 
    5767 > close #22
    5768 
    5769 
    5770 ===== Log before crash end =====
    5771 
    5772 Log:
    5773 UCSF ChimeraX version: 1.8 (2024-06-10) 
    5774 © 2016-2024 Regents of the University of California. All rights reserved. 
    5775 
    5776 > open "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    5777 > /Figure 2/Version 2- Resubmission/0_80_ApovsADPBeF_Maps.cxs"
    5778 
    5779 Opened x0_80_ADPBeF_A8-Split.mrc as #1, grid size 480,480,480, pixel 0.835,
    5780 shown at level 0.00261, step 1, values float32 
    5781 Opened x0_80_ADPBeF_Ies2.mrc as #3, grid size 480,480,480, pixel 0.835, shown
    5782 at level 0.348, step 1, values float32 
    5783 Opened 041924-global-resampleonapo.mrc 0 as #5.1, grid size 480,480,480, pixel
    5784 0.835, shown at level 0.221, step 1, values float32 
    5785 Opened 041924-global-resampleonapo.mrc 1 as #5.2, grid size 480,480,480, pixel
    5786 0.835, shown at level 0.238, step 1, values float32 
    5787 Opened 041924-global-resampleonapo.mrc 2 as #5.3, grid size 480,480,480, pixel
    5788 0.835, shown at level 0.221, step 1, values float32 
    5789 Opened 041924-global-resampleonapo.mrc 3 as #5.4, grid size 480,480,480, pixel
    5790 0.835, shown at level 0.221, step 1, values float32 
    5791 Opened 041924-global-resampleonapo.mrc 4 as #5.5, grid size 480,480,480, pixel
    5792 0.835, shown at level 0.221, step 1, values float32 
    5793 Opened 041924-global-resampleonapo.mrc 5 as #5.6, grid size 480,480,480, pixel
    5794 0.835, shown at level 0.221, step 1, values float32 
    5795 Opened 041924-global-resampleonapo.mrc 6 as #5.7, grid size 480,480,480, pixel
    5796 0.835, shown at level 0.221, step 1, values float32 
    5797 Opened 041924-global-resampleonapo.mrc 7 as #5.8, grid size 480,480,480, pixel
    5798 0.835, shown at level 0.221, step 1, values float32 
    5799 Opened 041924-global-resampleonapo.mrc 8 as #5.9, grid size 480,480,480, pixel
    5800 0.835, shown at level 0.235, step 1, values float32 
    5801 Opened 041924-global-resampleonapo.mrc 9 as #5.10, grid size 480,480,480,
    5802 pixel 0.835, shown at level 0.174, step 1, values float32 
    5803 Opened x0_80_ADPBeF_nuc.mrc as #6, grid size 480,480,480, pixel 0.835, shown
    5804 at level 1.44, step 1, values float32 
    5805 Opened y0_80_ADPBeF_Core.mrc as #7, grid size 448,448,448, pixel 0.835, shown
    5806 at level 0.186, step 1, values float32 
    5807 Opened y0_80_ADPBeF_Core-filter.mrc as #8, grid size 256,256,256, pixel 1.67,
    5808 shown at level 0.0143, step 1, values float32 
    5809 Opened y0_80_Apo_A8-split.mrc as #10, grid size 512,512,512, pixel 0.819,
    5810 shown at level 0.0016, step 1, values float32 
    5811 Opened y0_80_Apo_core_nuc.mrc as #11, grid size 512,512,512, pixel 0.819,
    5812 shown at level 0.157, step 1, values float32 
    5813 Opened 122324-x80-apo-a8-split-resample.mrc as #12, grid size 480,480,480,
    5814 pixel 0.835, shown at level 0.00122, step 1, values float32 
    5815 Opened 122324-x80-apo-arp5-resample.mrc as #13, grid size 480,480,480, pixel
    5816 0.835, shown at level 0.0832, step 1, values float32 
    5817 Opened 122324-x80-apo-atpasehighres-resample.mrc as #14, grid size
    5818 480,480,480, pixel 0.835, shown at level 0.0212, step 1, values float32 
    5819 Opened 122324-x80-apo-dna-resample.mrc as #15, grid size 480,480,480, pixel
    5820 0.835, shown at level 0.847, step 1, values float32 
    5821 Opened 122324-x80-apo-grappler-resample.mrc as #16, grid size 480,480,480,
    5822 pixel 0.835, shown at level 0.11, step 1, values float32 
    5823 Opened 122324-x80-apo-histone-resample.mrc as #17, grid size 480,480,480,
    5824 pixel 0.835, shown at level 1.29, step 1, values float32 
    5825 Opened 122324-x80-apo-i2highres-resample.mrc as #18, grid size 480,480,480,
    5826 pixel 0.835, shown at level 0.104, step 1, values float32 
    5827 Opened 122324-x80-apo-rvb-resample.mrc as #20, grid size 480,480,480, pixel
    5828 0.835, shown at level 0.221, step 1, values float32 
    5829 Opened 122324-x80-ies2lowres-resample.mrc as #21, grid size 480,480,480, pixel
    5830 0.835, shown at level 0.00032, step 1, values float32 
    5831 Log from Mon Dec 30 10:55:42 2024UCSF ChimeraX version: 1.8 (2024-06-10) 
    5832 © 2016-2024 Regents of the University of California. All rights reserved. 
    5833 
    5834 > open "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    5835 > /Figure 2/Version 2- Resubmission/0_80_ApovsADPBeF_Maps.cxs"
    5836 
    5837 Opened x0_80_ADPBeF_A8-Split.mrc as #1, grid size 480,480,480, pixel 0.835,
    5838 shown at level 0.00261, step 1, values float32 
    5839 Opened x0_80_ADPBeF_Ies2.mrc as #3, grid size 480,480,480, pixel 0.835, shown
    5840 at level 0.348, step 1, values float32 
    5841 Opened 041924-global-resampleonapo.mrc 0 as #5.1, grid size 480,480,480, pixel
    5842 0.835, shown at level 0.221, step 1, values float32 
    5843 Opened 041924-global-resampleonapo.mrc 1 as #5.2, grid size 480,480,480, pixel
    5844 0.835, shown at level 0.238, step 1, values float32 
    5845 Opened 041924-global-resampleonapo.mrc 2 as #5.3, grid size 480,480,480, pixel
    5846 0.835, shown at level 0.221, step 1, values float32 
    5847 Opened 041924-global-resampleonapo.mrc 3 as #5.4, grid size 480,480,480, pixel
    5848 0.835, shown at level 0.221, step 1, values float32 
    5849 Opened 041924-global-resampleonapo.mrc 4 as #5.5, grid size 480,480,480, pixel
    5850 0.835, shown at level 0.221, step 1, values float32 
    5851 Opened 041924-global-resampleonapo.mrc 5 as #5.6, grid size 480,480,480, pixel
    5852 0.835, shown at level 0.221, step 1, values float32 
    5853 Opened 041924-global-resampleonapo.mrc 6 as #5.7, grid size 480,480,480, pixel
    5854 0.835, shown at level 0.221, step 1, values float32 
    5855 Opened 041924-global-resampleonapo.mrc 7 as #5.8, grid size 480,480,480, pixel
    5856 0.835, shown at level 0.221, step 1, values float32 
    5857 Opened 041924-global-resampleonapo.mrc 8 as #5.9, grid size 480,480,480, pixel
    5858 0.835, shown at level 0.235, step 1, values float32 
    5859 Opened 041924-global-resampleonapo.mrc 9 as #5.10, grid size 480,480,480,
    5860 pixel 0.835, shown at level 0.174, step 1, values float32 
    5861 Opened x0_80_ADPBeF_nuc.mrc as #6, grid size 480,480,480, pixel 0.835, shown
    5862 at level 1.44, step 1, values float32 
    5863 Opened y0_80_ADPBeF_Core.mrc as #7, grid size 448,448,448, pixel 0.835, shown
    5864 at level 0.167, step 2, values float32 
    5865 Opened y0_80_ADPBeF_Core-filter.mrc as #8, grid size 256,256,256, pixel 1.67,
    5866 shown at level 0.0143, step 1, values float32 
    5867 Opened y0_80_Apo_A8-split.mrc as #10, grid size 512,512,512, pixel 0.819,
    5868 shown at level 0.000899, step 1, values float32 
    5869 Opened y0_80_Apo_core_nuc.mrc as #11, grid size 512,512,512, pixel 0.819,
    5870 shown at level 0.147, step 1, values float32 
    5871 Opened 122324-x80-apo-a8-split-resample.mrc as #12, grid size 480,480,480,
    5872 pixel 0.835, shown at level 0.00122, step 1, values float32 
    5873 Opened 122324-x80-apo-arp5-resample.mrc as #13, grid size 480,480,480, pixel
    5874 0.835, shown at level 0.0832, step 1, values float32 
    5875 Opened 122324-x80-apo-atpasehighres-resample.mrc as #14, grid size
    5876 480,480,480, pixel 0.835, shown at level 0.0212, step 1, values float32 
    5877 Opened 122324-x80-apo-dna-resample.mrc as #15, grid size 480,480,480, pixel
    5878 0.835, shown at level 0.847, step 1, values float32 
    5879 Opened 122324-x80-apo-grappler-resample.mrc as #16, grid size 480,480,480,
    5880 pixel 0.835, shown at level 0.11, step 1, values float32 
    5881 Opened 122324-x80-apo-histone-resample.mrc as #17, grid size 480,480,480,
    5882 pixel 0.835, shown at level 1.29, step 1, values float32 
    5883 Opened 122324-x80-apo-i2highres-resample.mrc as #18, grid size 480,480,480,
    5884 pixel 0.835, shown at level 0.104, step 1, values float32 
    5885 Opened 122324-x80-apo-rvb-resample.mrc as #20, grid size 480,480,480, pixel
    5886 0.835, shown at level 0.221, step 1, values float32 
    5887 Opened 122324-x80-ies2lowres-resample.mrc as #21, grid size 480,480,480, pixel
    5888 0.835, shown at level 0.00032, step 1, values float32 
    5889 Log from Mon Dec 30 10:34:25 2024UCSF ChimeraX version: 1.8 (2024-06-10) 
    5890 © 2016-2024 Regents of the University of California. All rights reserved. 
    5891 
    5892 > open "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    5893 > /Figure 2/Version 2- Resubmission/0_80_ApovsADPBeF_Maps.cxs"
    5894 
    5895 Opened x0_80_ADPBeF_A8-Split.mrc as #1, grid size 480,480,480, pixel 0.835,
    5896 shown at level 0.00375, step 1, values float32 
    5897 Opened x0_80_ADPBeF_Ies2.mrc as #3, grid size 480,480,480, pixel 0.835, shown
    5898 at level 0.348, step 1, values float32 
    5899 Opened 041924-global-resampleonapo.mrc 0 as #5.1, grid size 480,480,480, pixel
    5900 0.835, shown at level 0.221, step 1, values float32 
    5901 Opened 041924-global-resampleonapo.mrc 1 as #5.2, grid size 480,480,480, pixel
    5902 0.835, shown at level 0.238, step 1, values float32 
    5903 Opened 041924-global-resampleonapo.mrc 2 as #5.3, grid size 480,480,480, pixel
    5904 0.835, shown at level 0.221, step 1, values float32 
    5905 Opened 041924-global-resampleonapo.mrc 3 as #5.4, grid size 480,480,480, pixel
    5906 0.835, shown at level 0.221, step 1, values float32 
    5907 Opened 041924-global-resampleonapo.mrc 4 as #5.5, grid size 480,480,480, pixel
    5908 0.835, shown at level 0.221, step 1, values float32 
    5909 Opened 041924-global-resampleonapo.mrc 5 as #5.6, grid size 480,480,480, pixel
    5910 0.835, shown at level 0.221, step 1, values float32 
    5911 Opened 041924-global-resampleonapo.mrc 6 as #5.7, grid size 480,480,480, pixel
    5912 0.835, shown at level 0.221, step 1, values float32 
    5913 Opened 041924-global-resampleonapo.mrc 7 as #5.8, grid size 480,480,480, pixel
    5914 0.835, shown at level 0.221, step 1, values float32 
    5915 Opened 041924-global-resampleonapo.mrc 8 as #5.9, grid size 480,480,480, pixel
    5916 0.835, shown at level 0.235, step 1, values float32 
    5917 Opened 041924-global-resampleonapo.mrc 9 as #5.10, grid size 480,480,480,
    5918 pixel 0.835, shown at level 0.174, step 1, values float32 
    5919 Opened x0_80_ADPBeF_nuc.mrc as #6, grid size 480,480,480, pixel 0.835, shown
    5920 at level 1.44, step 1, values float32 
    5921 Opened y0_80_ADPBeF_Core.mrc as #7, grid size 448,448,448, pixel 0.835, shown
    5922 at level 0.167, step 2, values float32 
    5923 Opened y0_80_ADPBeF_Core-filter.mrc as #8, grid size 256,256,256, pixel 1.67,
    5924 shown at level 0.0143, step 1, values float32 
    5925 Opened y0_80_Apo_A8-split.mrc as #10, grid size 512,512,512, pixel 0.819,
    5926 shown at level 0.000444, step 2, values float32 
    5927 Opened y0_80_Apo_core_nuc.mrc as #11, grid size 512,512,512, pixel 0.819,
    5928 shown at level 0.0802, step 2, values float32 
    5929 Opened 122324-x80-apo-a8-split-resample.mrc as #12, grid size 480,480,480,
    5930 pixel 0.835, shown at level 0.000239, step 2, values float32 
    5931 Opened 122324-x80-apo-arp5-resample.mrc as #13, grid size 480,480,480, pixel
    5932 0.835, shown at level 0.000123, step 2, values float32 
    5933 Opened 122324-x80-apo-atpasehighres-resample.mrc as #14, grid size
    5934 480,480,480, pixel 0.835, shown at level 0.000139, step 2, values float32 
    5935 Opened 122324-x80-apo-dna-resample.mrc as #15, grid size 480,480,480, pixel
    5936 0.835, shown at level 0.000354, step 2, values float32 
    5937 Opened 122324-x80-apo-grappler-resample.mrc as #16, grid size 480,480,480,
    5938 pixel 0.835, shown at level 3.54e-05, step 2, values float32 
    5939 Opened 122324-x80-apo-histone-resample.mrc as #17, grid size 480,480,480,
    5940 pixel 0.835, shown at level 0.000232, step 2, values float32 
    5941 Opened 122324-x80-apo-i2highres-resample.mrc as #18, grid size 480,480,480,
    5942 pixel 0.835, shown at level 3.03e-06, step 2, values float32 
    5943 Opened 122324-x80-apo-rvb-resample.mrc as #20, grid size 480,480,480, pixel
    5944 0.835, shown at level 7.73e-05, step 2, values float32 
    5945 Opened 122324-x80-ies2lowres-resample.mrc as #21, grid size 480,480,480, pixel
    5946 0.835, shown at level 2.62e-07, step 2, values float32 
    5947 Log from Sun Dec 29 17:47:13 2024UCSF ChimeraX version: 1.8 (2024-06-10) 
    5948 © 2016-2024 Regents of the University of California. All rights reserved. 
    5949 
    5950 > open "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    5951 > /Figure 1/Version 2-resubmission/Chimera Session/Figure1.cxs"
    5952 
    5953 Opened 121124-a8-split_xl080.mrc as #1, grid size 480,480,480, pixel 0.835,
    5954 shown at level 0.00375, step 1, values float32 
    5955 Opened ies2-x80-lowres.mrc as #3, grid size 480,480,480, pixel 0.835, shown at
    5956 level 0.348, step 1, values float32 
    5957 Opened 041924-global-resampleonapo.mrc 0 as #5.1, grid size 480,480,480, pixel
    5958 0.835, shown at level 0.221, step 1, values float32 
    5959 Opened 041924-global-resampleonapo.mrc 1 as #5.2, grid size 480,480,480, pixel
    5960 0.835, shown at level 0.238, step 1, values float32 
    5961 Opened 041924-global-resampleonapo.mrc 2 as #5.3, grid size 480,480,480, pixel
    5962 0.835, shown at level 0.221, step 1, values float32 
    5963 Opened 041924-global-resampleonapo.mrc 3 as #5.4, grid size 480,480,480, pixel
    5964 0.835, shown at level 0.221, step 1, values float32 
    5965 Opened 041924-global-resampleonapo.mrc 4 as #5.5, grid size 480,480,480, pixel
    5966 0.835, shown at level 0.221, step 1, values float32 
    5967 Opened 041924-global-resampleonapo.mrc 5 as #5.6, grid size 480,480,480, pixel
    5968 0.835, shown at level 0.221, step 1, values float32 
    5969 Opened 041924-global-resampleonapo.mrc 6 as #5.7, grid size 480,480,480, pixel
    5970 0.835, shown at level 0.221, step 1, values float32 
    5971 Opened 041924-global-resampleonapo.mrc 7 as #5.8, grid size 480,480,480, pixel
    5972 0.835, shown at level 0.221, step 1, values float32 
    5973 Opened 041924-global-resampleonapo.mrc 8 as #5.9, grid size 480,480,480, pixel
    5974 0.835, shown at level 0.235, step 1, values float32 
    5975 Opened 041924-global-resampleonapo.mrc 9 as #5.10, grid size 480,480,480,
    5976 pixel 0.835, shown at level 0.174, step 1, values float32 
    5977 Opened 041924-nuc-resampleonapo_xl080.mrc as #6, grid size 480,480,480, pixel
    5978 0.835, shown at level 1.44, step 1, values float32 
    5979 Opened 121124-a8-split_Xl040.mrc as #4, grid size 448,448,448, pixel 0.831,
    5980 shown at level 0.00268, step 1, values float32 
    5981 Opened onlyies2-lowres-Xl040.mrc as #7, grid size 448,448,448, pixel 0.831,
    5982 shown at level 0.0519, step 1, values float32 
    5983 Opened onlynuc_Xl040.mrc as #8, grid size 448,448,448, pixel 0.831, shown at
    5984 level 0.411, step 1, values float32 
    5985 Opened inocore_Xl040.mrc as #9, grid size 448,448,448, pixel 0.831, shown at
    5986 level 0.218, step 1, values float32 
    5987 Log from Sat Dec 28 15:21:23 2024UCSF ChimeraX version: 1.8 (2024-06-10) 
    5988 © 2016-2024 Regents of the University of California. All rights reserved. 
    5989 
    5990 > open "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    5991 > /Figure 1/Version 2-resubmission/Chimera Session/Figure1.cxs"
    5992 
    5993 Opened 121124-a8-split_xl080.mrc as #1, grid size 480,480,480, pixel 0.835,
    5994 shown at level 0.00375, step 1, values float32 
    5995 Opened ies2-x80-lowres.mrc as #3, grid size 480,480,480, pixel 0.835, shown at
    5996 level 0.348, step 1, values float32 
    5997 Opened 041924-global-resampleonapo.mrc 0 as #5.1, grid size 480,480,480, pixel
    5998 0.835, shown at level 0.221, step 1, values float32 
    5999 Opened 041924-global-resampleonapo.mrc 1 as #5.2, grid size 480,480,480, pixel
    6000 0.835, shown at level 0.238, step 1, values float32 
    6001 Opened 041924-global-resampleonapo.mrc 2 as #5.3, grid size 480,480,480, pixel
    6002 0.835, shown at level 0.221, step 1, values float32 
    6003 Opened 041924-global-resampleonapo.mrc 3 as #5.4, grid size 480,480,480, pixel
    6004 0.835, shown at level 0.221, step 1, values float32 
    6005 Opened 041924-global-resampleonapo.mrc 4 as #5.5, grid size 480,480,480, pixel
    6006 0.835, shown at level 0.221, step 1, values float32 
    6007 Opened 041924-global-resampleonapo.mrc 5 as #5.6, grid size 480,480,480, pixel
    6008 0.835, shown at level 0.221, step 1, values float32 
    6009 Opened 041924-global-resampleonapo.mrc 6 as #5.7, grid size 480,480,480, pixel
    6010 0.835, shown at level 0.221, step 1, values float32 
    6011 Opened 041924-global-resampleonapo.mrc 7 as #5.8, grid size 480,480,480, pixel
    6012 0.835, shown at level 0.221, step 1, values float32 
    6013 Opened 041924-global-resampleonapo.mrc 8 as #5.9, grid size 480,480,480, pixel
    6014 0.835, shown at level 0.235, step 1, values float32 
    6015 Opened 041924-global-resampleonapo.mrc 9 as #5.10, grid size 480,480,480,
    6016 pixel 0.835, shown at level 0.174, step 1, values float32 
    6017 Opened 041924-nuc-resampleonapo_xl080.mrc as #6, grid size 480,480,480, pixel
    6018 0.835, shown at level 1.44, step 1, values float32 
    6019 Opened 121124-a8-split_Xl040.mrc as #4, grid size 448,448,448, pixel 0.831,
    6020 shown at level 0.0026, step 1, values float32 
    6021 Opened onlyies2-lowres-Xl040.mrc as #7, grid size 448,448,448, pixel 0.831,
    6022 shown at level 0.0519, step 1, values float32 
    6023 Opened onlynuc_Xl040.mrc as #8, grid size 448,448,448, pixel 0.831, shown at
    6024 level 0.411, step 1, values float32 
    6025 Opened inocore_Xl040.mrc as #9, grid size 448,448,448, pixel 0.831, shown at
    6026 level 0.218, step 1, values float32 
    6027 Log from Thu Dec 12 15:18:18 2024 Startup Messages 
    6028 --- 
    6029 warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr bundle with that from OME-Zarr bundle 
    6030 Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
    6031 that from NMRSTAR bundle 
    6032  
    6033 UCSF ChimeraX version: 1.7.1 (2024-01-23) 
    6034 © 2016-2023 Regents of the University of California. All rights reserved. 
    6035 How to cite UCSF ChimeraX 
    6036 
    6037 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    6038 > Model/wtINO80-0N80-Yeast-Apo/121124-a8-split.mrc"
    6039 
    6040 Opened 121124-a8-split.mrc as #1, grid size 512,512,512, pixel 0.819, shown at
    6041 level 0.000444, step 2, values float32 
    6042 
    6043 > set bgColor white
    6044 
    6045 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    6046 > Model/wtINO80-0N80-Yeast-Apo/120524-inocore-nuc-3.16A.mrc"
    6047 
    6048 Opened 120524-inocore-nuc-3.16A.mrc as #2, grid size 512,512,512, pixel 0.819,
    6049 shown at level 0.0802, step 2, values float32 
    6050 
    6051 > volume #1 step 1
    6052 
    6053 > volume #2 step 1
    6054 
    6055 > volume #1 level 0.001846
    6056 
    6057 > surface dust #1 size 8.19
    6058 
    6059 > surface dust #2 size 8.19
    6060 
    6061 > volume #2 level 0.1187
    6062 
    6063 > volume #1 level 0.002828
    6064 
    6065 > volume #2 level 0.1524
    6066 
    6067 > volume #2 level 0.1596
    6068 
    6069 > volume #2 level 0.1741
    6070 
    6071 > color #2 silver models
    6072 
    6073 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    6074 > Model/wtINO80-0N80-Yeast-Apo/120524-final-ino80-0y80-apo-512box.pdb"
    6075 
    6076 Chain information for 120524-final-ino80-0y80-apo-512box.pdb #3 
    6077 --- 
    6078 Chain | Description 
    6079 A E | No description available 
    6080 B F | No description available 
    6081 C | No description available 
    6082 D H | No description available 
    6083 G | No description available 
    6084 I | No description available 
    6085 J | No description available 
    6086 K | No description available 
    6087 L | No description available 
    6088 M | No description available 
    6089 O | No description available 
    6090 Q | No description available 
    6091 R | No description available 
    6092 S | No description available 
    6093 T | No description available 
    6094 U | No description available 
    6095 V | No description available 
    6096 W | No description available 
    6097 X | No description available 
    6098 Y | No description available 
    6099 Z | No description available 
    6100  
    6101 
    6102 > volume #1 level 0.003126
    6103 
    6104 > hide #!1 models
    6105 
    6106 > hide #!2 models
    6107 
    6108 > hide atoms
    6109 
    6110 > show cartoons
    6111 
    6112 > select #3/A-H,T-Y
    6113 
    6114 26415 atoms, 26739 bonds, 2 pseudobonds, 3403 residues, 2 models selected 
    6115 
    6116 > ui tool show "Color Actions"
    6117 
    6118 > color sel light gray
    6119 
    6120 > select #3/I,J
    6121 
    6122 7702 atoms, 8638 bonds, 1 pseudobond, 376 residues, 2 models selected 
    6123 
    6124 > color sel slate gray
    6125 
    6126 > show sel atoms
    6127 
    6128 > hide sel atoms
    6129 
    6130 > nucleotides sel atoms
    6131 
    6132 > style nucleic & sel stick
    6133 
    6134 Changed 7702 atom styles 
    6135 
    6136 > nucleotides sel ladder
    6137 
    6138 > show sel atoms
    6139 
    6140 > select #3/Q
    6141 
    6142 6141 atoms, 6266 bonds, 8 pseudobonds, 758 residues, 2 models selected 
    6143 
    6144 > color sel fire brick
    6145 
    6146 > select #3/Z
    6147 
    6148 464 atoms, 469 bonds, 1 pseudobond, 72 residues, 2 models selected 
    6149 
    6150 > color sel fire brick
    6151 
    6152 > color sel orange
    6153 
    6154 > select #3/R,S
    6155 
    6156 4527 atoms, 4639 bonds, 2 pseudobonds, 570 residues, 2 models selected 
    6157 
    6158 > color sel medium sea green
    6159 
    6160 > select #3/K
    6161 
    6162 5092 atoms, 5206 bonds, 628 residues, 1 model selected 
    6163 
    6164 > color sel medium blue
    6165 
    6166 > select #3/L
    6167 
    6168 2856 atoms, 2919 bonds, 1 pseudobond, 363 residues, 2 models selected 
    6169 
    6170 > color sel gold
    6171 
    6172 > select #3/M
    6173 
    6174 3454 atoms, 3531 bonds, 1 pseudobond, 433 residues, 2 models selected 
    6175 
    6176 > color sel deep sky blue
    6177 
    6178 > select #3/N
    6179 
    6180 Nothing selected 
    6181 
    6182 > color dim gray
    6183 
    6184 > undo
    6185 
    6186 > select #3/O
    6187 
    6188 287 atoms, 296 bonds, 34 residues, 1 model selected 
    6189 
    6190 > color sel dim gray
    6191 
    6192 > select clear
    6193 
    6194 > show #!2 models
    6195 
    6196 > show #!1 models
    6197 
    6198 > ui tool show "Color Zone"
    6199 
    6200 > color zone #1 near #3 distance 4.91
    6201 
    6202 > color zone #1 near #3 distance 4.81
    6203 
    6204 > color zone #1 near #3 distance 4.71
    6205 
    6206 > color zone #1 near #3 distance 4.61
    6207 
    6208 > color zone #1 near #3 distance 4.51
    6209 
    6210 > color zone #1 near #3 distance 4.41
    6211 
    6212 > color zone #1 near #3 distance 4.31
    6213 
    6214 > color zone #1 near #3 distance 4.21
    6215 
    6216 > color zone #1 near #3 distance 4.11
    6217 
    6218 > color zone #1 near #3 distance 4.01
    6219 
    6220 > color zone #1 near #3 distance 3.91
    6221 
    6222 > color zone #1 near #3 distance 3.81
    6223 
    6224 > color zone #1 near #3 distance 3.71
    6225 
    6226 > color zone #1 near #3 distance 3.61
    6227 
    6228 > color zone #1 near #3 distance 3.51
    6229 
    6230 > color zone #1 near #3 distance 3.41
    6231 
    6232 > color zone #1 near #3 distance 3.83
    6233 
    6234 > color zone #1 near #3 distance 9.39
    6235 
    6236 > color zone #1 near #3 distance 1
    6237 
    6238 > color zone #1 near #3 distance 10
    6239 
    6240 [Repeated 1 time(s)]
    6241 
    6242 > volume #1 level 0.00344
    6243 
    6244 > color zone #2 near #3 distance 4.91
    6245 
    6246 > volume #1 level 0.003283
    6247 
    6248 > lighting simple
    6249 
    6250 > lighting soft
    6251 
    6252 > lighting simple
    6253 
    6254 > lighting soft
    6255 
    6256 > ui tool show "Side View"
    6257 
    6258 > hide #!3 models
    6259 
    6260 > color #1 #b2b2b224 models
    6261 
    6262 > color #1 #b2b2b297 models
    6263 
    6264 > color #1 #b2b2b296 models
    6265 
    6266 > undo
    6267 
    6268 [Repeated 4 time(s)]
    6269 
    6270 > color zone #1 near #3 distance 10
    6271 
    6272 > volume #2 level 0.1046
    6273 
    6274 > volume #2 level 0.1313
    6275 
    6276 > volume #2 level 0.1607
    6277 
    6278 > volume #2 level 0.118
    6279 
    6280 > volume #2 level 0.1287
    6281 
    6282 > volume #2 level 0.15
    6283 
    6284 > volume #2 level 0.1634
    6285 
    6286 No map chosen to save 
    6287 
    6288 > save /Users/upneet/Desktop/test.png width 3600 height 2697 supersample 3
    6289 > transparentBackground true
    6290 
    6291 > hide #!2 models
    6292 
    6293 > hide #!1 models
    6294 
    6295 > show #!3 models
    6296 
    6297 > hide #!3 models
    6298 
    6299 > show #!1 models
    6300 
    6301 > show #!3 models
    6302 
    6303 > hide #!1 models
    6304 
    6305 > show #!1 models
    6306 
    6307 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    6308 > Model/WT-0N80Xe-ADPBeF/121124-a8-split.mrc"
    6309 
    6310 Opened 121124-a8-split.mrc as #4, grid size 480,480,480, pixel 0.835, shown at
    6311 level 0.000837, step 2, values float32 
    6312 
    6313 > volume #4 level 0.003553
    6314 
    6315 > volume #4 step 1
    6316 
    6317 > hide #!3 models
    6318 
    6319 > hide #!4 models
    6320 
    6321 > hide #!1 models
    6322 
    6323 > show #!4 models
    6324 
    6325 > volume #4 level 0.003726
    6326 
    6327 > volume #4 level 0.003661
    6328 
    6329 > color #4 silver models
    6330 
    6331 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    6332 > Model/INO-40yeastnuc-ADPBeF/121124-a8-split.mrc"
    6333 
    6334 Opened 121124-a8-split.mrc as #5, grid size 480,480,480, pixel 0.835, shown at
    6335 level 4.83e-07, step 2, values float32 
    6336 
    6337 > volume #5 level 0.003775
    6338 
    6339 > volume #5 level 0.003851
    6340 
    6341 > hide #!4 models
    6342 
    6343 > hide #!5 models
    6344 
    6345 > show #!3 models
    6346 
    6347 > select ::name="ARG"
    6348 
    6349 3893 atoms, 3559 bonds, 362 residues, 1 model selected 
    6350 
    6351 > ui mousemode right select
    6352 
    6353 > select clear
    6354 
    6355 Drag select of 1 residues 
    6356 
    6357 > show sel surfaces
    6358 
    6359 > hide sel surfaces
    6360 
    6361 > style sel stick
    6362 
    6363 Changed 11 atom styles 
    6364 
    6365 > show sel atoms
    6366 
    6367 > color sel byhetero
    6368 
    6369 > hide #!3 models
    6370 
    6371 > show #!1 models
    6372 
    6373 > show #!2 models
    6374 
    6375 > close #1-5
    6376 
    6377 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    6378 > Model/WT-0N80Xe-ADPBeF/121124-a8-split.mrc"
    6379 
    6380 Opened 121124-a8-split.mrc as #1, grid size 480,480,480, pixel 0.835, shown at
    6381 level 4.88e-06, step 2, values float32 
    6382 
    6383 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    6384 > Model/WT-0N80Xe-ADPBeF/121124-0n80-xe-wt-adpbef-final-coot-0-pymol-
    6385 > shortdna.pdb"
    6386 
    6387 Chain information for 121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb
    6388 #2 
    6389 --- 
    6390 Chain | Description 
    6391 A | No description available 
    6392 B | No description available 
    6393 C | No description available 
    6394 D | No description available 
    6395 E | No description available 
    6396 F | No description available 
    6397 G | No description available 
    6398 H | No description available 
    6399 I | No description available 
    6400 J | No description available 
    6401 K | No description available 
    6402 L | No description available 
    6403 M | No description available 
    6404 O | No description available 
    6405 Q | No description available 
    6406 R | No description available 
    6407 S | No description available 
    6408 T | No description available 
    6409 U | No description available 
    6410 V | No description available 
    6411 W | No description available 
    6412 X | No description available 
    6413 Y | No description available 
    6414 Z | No description available 
    6415  
    6416 
    6417 > hide atoms
    6418 
    6419 > show cartoons
    6420 
    6421 > volume #1 step 1
    6422 
    6423 > volume #1 level 0.004082
    6424 
    6425 > hide #!2 models
    6426 
    6427 > show #!2 models
    6428 
    6429 > hide #!1 models
    6430 
    6431 > color #2/Q firebrick
    6432 
    6433 > color #2/Q firebrick, #2/R,S seagreen
    6434 
    6435 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    6436 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    6437 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    6438 
    6439 > color #2/Q firebrick
    6440 
    6441 > color #2/R,S medium seagreen
    6442 
    6443 > color #2/T-Y, A-H grey
    6444 
    6445 > color #2/T-Y, A-H lightr grey
    6446 
    6447 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    6448 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    6449 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    6450 
    6451 > color #2/T-Y, A-H light grey
    6452 
    6453 > color #2/Z orange
    6454 
    6455 > color #2/k medium blue
    6456 
    6457 > color #2/L gold
    6458 
    6459 > color #2/N deep skyblue
    6460 
    6461 > color #2/M deep skyblue
    6462 
    6463 [Repeated 1 time(s)]
    6464 
    6465 > color #2/O grey
    6466 
    6467 > color #2/I,J slate blue
    6468 
    6469 > color #2/I,J slate grey
    6470 
    6471 > select #2/I,J
    6472 
    6473 7787 atoms, 8735 bonds, 380 residues, 1 model selected 
    6474 
    6475 > nucleotides sel ladder
    6476 
    6477 > show sel atoms
    6478 
    6479 > select clear
    6480 
    6481 [Repeated 2 time(s)]
    6482 
    6483 > show #!1 models
    6484 
    6485 > ui tool show "Color Zone"
    6486 
    6487 > color zone #1 near #2 distance 5.01
    6488 
    6489 > color zone #1 near #2 distance 5.19
    6490 
    6491 > color zone #1 near #2 distance 11.56
    6492 
    6493 > color zone #1 near #2 distance 11.7
    6494 
    6495 [Repeated 1 time(s)]
    6496 
    6497 > color zone #1 near #2 distance 1
    6498 
    6499 > color zone #1 near #2 distance 10
    6500 
    6501 [Repeated 1 time(s)]
    6502 
    6503 > color zone #1 near #2 distance 1
    6504 
    6505 > color zone #1 near #2 distance 15
    6506 
    6507 [Repeated 1 time(s)]
    6508 
    6509 > volume #1 level 0.004276
    6510 
    6511 > volume #1 level 0.004216
    6512 
    6513 > volume #1 level 0.003992
    6514 
    6515 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    6516 > Model/WT-0N80Xe-ADPBeF/ies2-x80-lowres.mrc"
    6517 
    6518 Opened ies2-x80-lowres.mrc as #3, grid size 480,480,480, pixel 0.835, shown at
    6519 level 5.64e-05, step 2, values float32 
    6520 
    6521 > volume #3 step 1
    6522 
    6523 > volume #3 level 0.3484
    6524 
    6525 > hide #!3 models
    6526 
    6527 > volume #1 level 0.003664
    6528 
    6529 > surface dust #1 size 8.35
    6530 
    6531 > volume #1 level 0.003843
    6532 
    6533 > volume #1 level 0.003873
    6534 
    6535 > ui tool show "Side View"
    6536 
    6537 > volume #1 level 0.003754
    6538 
    6539 > volume #1 level 0.003664
    6540 
    6541 > surface dust #1 size 8.35
    6542 
    6543 > volume #1 level 0.003754
    6544 
    6545 > select #2/L
    6546 
    6547 2862 atoms, 2925 bonds, 1 pseudobond, 364 residues, 2 models selected 
    6548 
    6549 > ui tool show "Color Actions"
    6550 
    6551 > color sel sandy brown
    6552 
    6553 > color zone #1 near #2 distance 15
    6554 
    6555 > color sel navajo white
    6556 
    6557 > color zone #1 near #2 distance 15
    6558 
    6559 > hide #!1 models
    6560 
    6561 > show #!1 models
    6562 
    6563 > color sel goldenrod
    6564 
    6565 > color zone #1 near #2 distance 15
    6566 
    6567 > color sel orange
    6568 
    6569 > color zone #1 near #2 distance 15
    6570 
    6571 > color (#!2 & sel) #ffd479ff
    6572 
    6573 > color zone #1 near #2 distance 15
    6574 
    6575 > color (#!2 & sel) #ffd778ff
    6576 
    6577 > color (#!2 & sel) #ffd87aff
    6578 
    6579 > color (#!2 & sel) #ffdb82ff
    6580 
    6581 > color (#!2 & sel) #ffdc89ff
    6582 
    6583 > color (#!2 & sel) #ffe296ff
    6584 
    6585 > color (#!2 & sel) #ffe396ff
    6586 
    6587 > color (#!2 & sel) #ffea91ff
    6588 
    6589 > color (#!2 & sel) #ffe482ff
    6590 
    6591 > color (#!2 & sel) #ffe077ff
    6592 
    6593 > color (#!2 & sel) #ffe370ff
    6594 
    6595 > color (#!2 & sel) #ffea6cff
    6596 
    6597 > color (#!2 & sel) #fff26aff
    6598 
    6599 > color (#!2 & sel) #fff36aff
    6600 
    6601 > color (#!2 & sel) #fff36dff
    6602 
    6603 > color (#!2 & sel) #fff475ff
    6604 
    6605 > color zone #1 near #2 distance 15
    6606 
    6607 > hide #!1 models
    6608 
    6609 > show #!1 models
    6610 
    6611 > hide #!1 models
    6612 
    6613 > show #!1 models
    6614 
    6615 > select #2/O
    6616 
    6617 347 atoms, 356 bonds, 40 residues, 1 model selected 
    6618 
    6619 > color sel #011993ff
    6620 
    6621 > color zone #1 near #2 distance 15
    6622 
    6623 > color sel #9437ffff
    6624 
    6625 > color zone #1 near #2 distance 15
    6626 
    6627 > color sel #76d6ffff
    6628 
    6629 > color zone #1 near #2 distance 15
    6630 
    6631 > color sel #79b8ffff
    6632 
    6633 > color zone #1 near #2 distance 15
    6634 
    6635 > color sel #00fdffff
    6636 
    6637 > color sel #73fdffff
    6638 
    6639 > color zone #1 near #2 distance 15
    6640 
    6641 > color sel #ffd479ff
    6642 
    6643 > color zone #1 near #2 distance 15
    6644 
    6645 > color sel #011993ff
    6646 
    6647 > color sel #005493ff
    6648 
    6649 > color zone #1 near #2 distance 15
    6650 
    6651 > select clear
    6652 
    6653 > select #2/Z
    6654 
    6655 467 atoms, 472 bonds, 1 pseudobond, 72 residues, 2 models selected 
    6656 
    6657 > color (#!2 & sel) #ff2600ff
    6658 
    6659 > color (#!2 & sel) #ff7e79ff
    6660 
    6661 > select clear
    6662 
    6663 > select #2/M
    6664 
    6665 3430 atoms, 3507 bonds, 1 pseudobond, 429 residues, 2 models selected 
    6666 
    6667 > select #2/L
    6668 
    6669 2862 atoms, 2925 bonds, 1 pseudobond, 364 residues, 2 models selected 
    6670 
    6671 > select #2/L
    6672 
    6673 2862 atoms, 2925 bonds, 1 pseudobond, 364 residues, 2 models selected 
    6674 
    6675 > select #2/K
    6676 
    6677 5614 atoms, 5735 bonds, 1 pseudobond, 692 residues, 2 models selected 
    6678 
    6679 > ui tool show "Color Actions"
    6680 
    6681 > color sel cornflower blue
    6682 
    6683 > color zone #1 near #2 distance 15
    6684 
    6685 > color sel royal blue
    6686 
    6687 > color zone #1 near #2 distance 15
    6688 
    6689 > select #2/M
    6690 
    6691 3430 atoms, 3507 bonds, 1 pseudobond, 429 residues, 2 models selected 
    6692 
    6693 > ui tool show "Color Actions"
    6694 
    6695 > color sel light pink
    6696 
    6697 > color zone #1 near #2 distance 15
    6698 
    6699 > color sel plum
    6700 
    6701 > color zone #1 near #2 distance 15
    6702 
    6703 > color sel pink
    6704 
    6705 > color zone #1 near #2 distance 15
    6706 
    6707 > color sel light pink
    6708 
    6709 > color zone #1 near #2 distance 15
    6710 
    6711 > hide #!1 models
    6712 
    6713 > cartoon style (#!2 & sel) modeHelix tube sides 20
    6714 
    6715 > cartoon style modeHelix tube radius 1.5
    6716 
    6717 > select clear
    6718 
    6719 > show #!1 models
    6720 
    6721 > select #2/L
    6722 
    6723 2862 atoms, 2925 bonds, 1 pseudobond, 364 residues, 2 models selected 
    6724 
    6725 > select #2/K
    6726 
    6727 5614 atoms, 5735 bonds, 1 pseudobond, 692 residues, 2 models selected 
    6728 
    6729 > ui tool show "Color Actions"
    6730 
    6731 > color sel cornflower blue
    6732 
    6733 > color sel blue
    6734 
    6735 > color zone #1 near #2 distance 15
    6736 
    6737 > color sel medium blue
    6738 
    6739 > color zone #1 near #2 distance 15
    6740 
    6741 > select #2/M
    6742 
    6743 3430 atoms, 3507 bonds, 1 pseudobond, 429 residues, 2 models selected 
    6744 
    6745 > ui tool show "Color Actions"
    6746 
    6747 > color sel deep sky blue
    6748 
    6749 > color zone #1 near #2 distance 15
    6750 
    6751 > select clear
    6752 
    6753 > hide #!1 models
    6754 
    6755 > show #!1 models
    6756 
    6757 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    6758 > Model/WT-0N80Xe-ADPBeF/041924-global-resampleonapo.mrc"
    6759 
    6760 Opened 041924-global-resampleonapo.mrc as #4, grid size 480,480,480, pixel
    6761 0.835, shown at level 0.105, step 2, values float32 
    6762 
    6763 > volume #4 step 1
    6764 
    6765 > volume #4 level 0.1559
    6766 
    6767 > volume #4 level 0.2387
    6768 
    6769 > volume #4 level 0.3295
    6770 
    6771 > volume #4 level 0.2569
    6772 
    6773 > volume #4 level 0.2205
    6774 
    6775 > color zone #4 near #2 distance 5.01
    6776 
    6777 > hide #!2 models
    6778 
    6779 > lighting soft
    6780 
    6781 > lighting simple
    6782 
    6783 > lighting soft
    6784 
    6785 > volume splitbyzone #4
    6786 
    6787 Opened 041924-global-resampleonapo.mrc 0 as #5.1, grid size 480,480,480, pixel
    6788 0.835, shown at level 0.221, step 1, values float32 
    6789 Opened 041924-global-resampleonapo.mrc 1 as #5.2, grid size 480,480,480, pixel
    6790 0.835, shown at level 0.221, step 1, values float32 
    6791 Opened 041924-global-resampleonapo.mrc 2 as #5.3, grid size 480,480,480, pixel
    6792 0.835, shown at level 0.221, step 1, values float32 
    6793 Opened 041924-global-resampleonapo.mrc 3 as #5.4, grid size 480,480,480, pixel
    6794 0.835, shown at level 0.221, step 1, values float32 
    6795 Opened 041924-global-resampleonapo.mrc 4 as #5.5, grid size 480,480,480, pixel
    6796 0.835, shown at level 0.221, step 1, values float32 
    6797 Opened 041924-global-resampleonapo.mrc 5 as #5.6, grid size 480,480,480, pixel
    6798 0.835, shown at level 0.221, step 1, values float32 
    6799 Opened 041924-global-resampleonapo.mrc 6 as #5.7, grid size 480,480,480, pixel
    6800 0.835, shown at level 0.221, step 1, values float32 
    6801 Opened 041924-global-resampleonapo.mrc 7 as #5.8, grid size 480,480,480, pixel
    6802 0.835, shown at level 0.221, step 1, values float32 
    6803 Opened 041924-global-resampleonapo.mrc 8 as #5.9, grid size 480,480,480, pixel
    6804 0.835, shown at level 0.221, step 1, values float32 
    6805 Opened 041924-global-resampleonapo.mrc 9 as #5.10, grid size 480,480,480,
    6806 pixel 0.835, shown at level 0.221, step 1, values float32 
    6807 
    6808 > hide #!5 models
    6809 
    6810 > show #!5 models
    6811 
    6812 > hide #!5.2 models
    6813 
    6814 > show #!5.2 models
    6815 
    6816 > hide #!5.3 models
    6817 
    6818 > hide #5.2.1 models
    6819 
    6820 > show #5.2.1 models
    6821 
    6822 > volume #5.2 level 0.2383
    6823 
    6824 > volume #5.8 level 0.2205
    6825 
    6826 > volume #5.9 level 0.2241
    6827 
    6828 > volume #5.10 level 0.164
    6829 
    6830 > volume #5.10 level 0.174
    6831 
    6832 > surface dust #1 size 8.35
    6833 
    6834 > surface dust #5.1 size 8.35
    6835 
    6836 > surface dust #5.2 size 8.35
    6837 
    6838 > surface dust #5.4 size 8.35
    6839 
    6840 > surface dust #5.5 size 8.35
    6841 
    6842 > surface dust #5.6 size 8.35
    6843 
    6844 > surface dust #5.7 size 8.35
    6845 
    6846 > surface dust #5.8 size 8.35
    6847 
    6848 > surface dust #5.9 size 8.35
    6849 
    6850 > surface dust #5.10 size 8.35
    6851 
    6852 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    6853 > Model/WT-0N80Xe-ADPBeF/041924-nuc-resampleonapo.mrc"
    6854 
    6855 Opened 041924-nuc-resampleonapo.mrc as #6, grid size 480,480,480, pixel 0.835,
    6856 shown at level 0.188, step 2, values float32 
    6857 
    6858 > color zone #6 near #2 distance 5.01
    6859 
    6860 > surface dust #1 size 8.35
    6861 
    6862 > surface dust #5.1 size 8.35
    6863 
    6864 > surface dust #5.2 size 8.35
    6865 
    6866 > surface dust #5.4 size 8.35
    6867 
    6868 > surface dust #5.5 size 8.35
    6869 
    6870 > surface dust #5.6 size 8.35
    6871 
    6872 > surface dust #5.7 size 8.35
    6873 
    6874 > surface dust #5.8 size 8.35
    6875 
    6876 > surface dust #5.9 size 8.35
    6877 
    6878 > surface dust #5.10 size 8.35
    6879 
    6880 > surface dust #6 size 8.35
    6881 
    6882 > volume #6 step 1
    6883 
    6884 > volume #6 level 0.7474
    6885 
    6886 > volume #6 level 0.9057
    6887 
    6888 > color zone #6 near #2 distance 5.01
    6889 
    6890 [Repeated 1 time(s)]
    6891 
    6892 > volume #6 level 1.127
    6893 
    6894 > volume #6 level 1.233
    6895 
    6896 > color zone #6 near #2 distance 5.11
    6897 
    6898 > color zone #6 near #2 distance 5.21
    6899 
    6900 > color zone #6 near #2 distance 5.31
    6901 
    6902 > color zone #6 near #2 distance 5.41
    6903 
    6904 > color zone #6 near #2 distance 5.51
    6905 
    6906 > color zone #6 near #2 distance 5.61
    6907 
    6908 > color zone #6 near #2 distance 5.71
    6909 
    6910 > color zone #6 near #2 distance 5.81
    6911 
    6912 > color zone #6 near #2 distance 5.91
    6913 
    6914 > color zone #6 near #2 distance 6.01
    6915 
    6916 > color zone #6 near #2 distance 6.11
    6917 
    6918 > color zone #6 near #2 distance 6.21
    6919 
    6920 > volume #6 level 1.444
    6921 
    6922 > volume #5.9 level 0.2348
    6923 
    6924 > show #!3 models
    6925 
    6926 > color zone #3 near #2 distance 5.01
    6927 
    6928 > select clear
    6929 
    6930 > save /Users/upneet/Desktop/test.png width 3600 height 2671 supersample 3
    6931 > transparentBackground true
    6932 
    6933 > close #4
    6934 
    6935 > rename #5 "041924-global-resampleonapo_xl080.mrc split"
    6936 
    6937 > rename #6 041924-nuc-resampleonapo_xl080.mrc
    6938 
    6939 > rename #1 121124-a8-split_xl080.mrc
    6940 
    6941 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    6942 > Model/INO-40Xenuc-ADPBe/121124-a8-split.mrc"
    6943 
    6944 Opened 121124-a8-split.mrc as #4, grid size 448,448,448, pixel 0.831, shown at
    6945 level 0.0002, step 2, values float32 
    6946 
    6947 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    6948 > Model/INO-40Xenuc-ADPBe/onlyies2-lowres.mrc"
    6949 
    6950 Opened onlyies2-lowres.mrc as #7, grid size 448,448,448, pixel 0.831, shown at
    6951 level 2.07e-05, step 2, values float32 
    6952 
    6953 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    6954 > Model/INO-40Xenuc-ADPBe/onlynuc.mrc"
    6955 
    6956 Opened onlynuc.mrc as #8, grid size 448,448,448, pixel 0.831, shown at level
    6957 9.79e-05, step 2, values float32 
    6958 
    6959 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    6960 > Model/INO-40Xenuc-ADPBe/inocore.mrc"
    6961 
    6962 Opened inocore.mrc as #9, grid size 448,448,448, pixel 0.831, shown at level
    6963 3.68e-05, step 2, values float32 
    6964 
    6965 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    6966 > Model/INO-40Xenuc-ADPBe/nuc-resample.mrc"
    6967 
    6968 Opened nuc-resample.mrc as #10, grid size 448,448,448, pixel 0.831, shown at
    6969 level 0.326, step 2, values float32 
    6970 
    6971 > surface dust #1 size 8.35
    6972 
    6973 > surface dust #3 size 8.35
    6974 
    6975 > surface dust #5.1 size 8.35
    6976 
    6977 > surface dust #5.2 size 8.35
    6978 
    6979 > surface dust #5.4 size 8.35
    6980 
    6981 > surface dust #5.5 size 8.35
    6982 
    6983 > surface dust #5.6 size 8.35
    6984 
    6985 > surface dust #5.7 size 8.35
    6986 
    6987 > surface dust #5.8 size 8.35
    6988 
    6989 > surface dust #5.9 size 8.35
    6990 
    6991 > surface dust #5.10 size 8.35
    6992 
    6993 > surface dust #6 size 8.35
    6994 
    6995 > surface dust #4 size 8.31
    6996 
    6997 > surface dust #7 size 8.31
    6998 
    6999 > surface dust #8 size 8.31
    7000 
    7001 > surface dust #9 size 8.31
    7002 
    7003 > surface dust #10 size 8.31
    7004 
    7005 > hide #!7 models
    7006 
    7007 > hide #!8 models
    7008 
    7009 > hide #!9 models
    7010 
    7011 > hide #!10 models
    7012 
    7013 > rename #7 onlyies2-lowres-Xl040.mrc
    7014 
    7015 > rename #8 onlynuc_Xl040.mrc
    7016 
    7017 > rename #9 inocore_Xl040.mrc
    7018 
    7019 > rename #10 nuc-resample_Xl040.mrc
    7020 
    7021 > surface dust #1 size 8.35
    7022 
    7023 > surface dust #3 size 8.35
    7024 
    7025 > surface dust #5.1 size 8.35
    7026 
    7027 > surface dust #5.2 size 8.35
    7028 
    7029 > surface dust #5.4 size 8.35
    7030 
    7031 > surface dust #5.5 size 8.35
    7032 
    7033 > surface dust #5.6 size 8.35
    7034 
    7035 > surface dust #5.7 size 8.35
    7036 
    7037 > surface dust #5.8 size 8.35
    7038 
    7039 > surface dust #5.9 size 8.35
    7040 
    7041 > surface dust #5.10 size 8.35
    7042 
    7043 > surface dust #6 size 8.35
    7044 
    7045 > surface dust #4 size 8.31
    7046 
    7047 > surface dust #10 size 8.31
    7048 
    7049 > volume #7 step 1
    7050 
    7051 > volume #8 step 1
    7052 
    7053 > volume #9 step 1
    7054 
    7055 > volume #10 step 1
    7056 
    7057 > volume #7 level 0.00766
    7058 
    7059 > volume #7 level 0.04253
    7060 
    7061 > volume #8 level 0.1849
    7062 
    7063 > volume #9 level 0.1834
    7064 
    7065 > hide #!1 models
    7066 
    7067 > hide #!3 models
    7068 
    7069 > hide #!4 models
    7070 
    7071 > hide #!5 models
    7072 
    7073 > hide #!6 models
    7074 
    7075 > show #!4 models
    7076 
    7077 > hide #!4 models
    7078 
    7079 > volume #10 level 0.6999
    7080 
    7081 > volume #8 level 0.4115
    7082 
    7083 > volume #7 level 0.05194
    7084 
    7085 > volume #9 level 0.2181
    7086 
    7087 > surface dust #7 size 8.31
    7088 
    7089 > surface dust #8 size 8.31
    7090 
    7091 > surface dust #9 size 8.31
    7092 
    7093 > show #!4 models
    7094 
    7095 > volume #4 step 1
    7096 
    7097 > volume #4 level 0.002465
    7098 
    7099 > lighting simple
    7100 
    7101 > lighting soft
    7102 
    7103 > volume #4 level 0.0026
    7104 
    7105 > close #10
    7106 
    7107 > rename #4 121124-a8-split_Xl040.mrc
    7108 
    7109 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    7110 > Model/Final-withADPBeF/042624-x40-wt-adpbef-withadpbef-final.pdb"
    7111 
    7112 Chain information for 042624-x40-wt-adpbef-withadpbef-final.pdb #10 
    7113 --- 
    7114 Chain | Description 
    7115 A | No description available 
    7116 B | No description available 
    7117 C G | No description available 
    7118 D | No description available 
    7119 E | No description available 
    7120 F | No description available 
    7121 H | No description available 
    7122 I | No description available 
    7123 J | No description available 
    7124 L | No description available 
    7125 M | No description available 
    7126 N | No description available 
    7127 O | No description available 
    7128 Q | No description available 
    7129 R | No description available 
    7130 S | No description available 
    7131 T | No description available 
    7132 U | No description available 
    7133 V | No description available 
    7134 W | No description available 
    7135 X | No description available 
    7136 Y | No description available 
    7137 Z | No description available 
    7138  
    7139 
    7140 > hide #!10 cartoons
    7141 
    7142 > hide #!10 atoms
    7143 
    7144 > show #!10 cartoons
    7145 
    7146 > hide #!7 models
    7147 
    7148 > hide #!8 models
    7149 
    7150 > hide #!9 models
    7151 
    7152 > hide #!10 models
    7153 
    7154 > hide #!4 models
    7155 
    7156 > show #!10 models
    7157 
    7158 > color #10/Q firebrick
    7159 
    7160 Drag select of 808 residues 
    7161 
    7162 > color #10/R,S medium seagreen
    7163 
    7164 > color #10/T-Y,A-H medium seagreen
    7165 
    7166 > color #10/T-Y,A-H light gray
    7167 
    7168 > select clear
    7169 
    7170 > color #10/T-Y,I,J light slate gray
    7171 
    7172 > color #10/I,J light slate gray
    7173 
    7174 > nucleotides #!10 ladder
    7175 
    7176 > show #!10 atoms
    7177 
    7178 > undo
    7179 
    7180 > select #10/I,J
    7181 
    7182 6601 atoms, 7404 bonds, 322 residues, 1 model selected 
    7183 
    7184 > show sel atoms
    7185 
    7186 > select clear
    7187 
    7188 > select #10/K
    7189 
    7190 32 atoms, 32 bonds, 2 pseudobonds, 3 residues, 2 models selected 
    7191 
    7192 > color #10/N medium blue
    7193 
    7194 [Repeated 1 time(s)]
    7195 
    7196 > select #10/L
    7197 
    7198 2824 atoms, 2886 bonds, 1 pseudobond, 361 residues, 2 models selected 
    7199 
    7200 > ui tool show "Color Actions"
    7201 
    7202 > color sel sandy brown
    7203 
    7204 > color sel goldenrod
    7205 
    7206 [Repeated 1 time(s)]
    7207 
    7208 > show #!2 models
    7209 
    7210 > cartoon style (#!10 & sel) modeHelix tube sides 20
    7211 
    7212 > select up
    7213 
    7214 55996 atoms, 57633 bonds, 12 pseudobonds, 6600 residues, 2 models selected 
    7215 
    7216 > select up
    7217 
    7218 55996 atoms, 57633 bonds, 14 pseudobonds, 6600 residues, 3 models selected 
    7219 
    7220 > select up
    7221 
    7222 55996 atoms, 57633 bonds, 14 pseudobonds, 6600 residues, 3 models selected 
    7223 
    7224 > select up
    7225 
    7226 114335 atoms, 117752 bonds, 14 pseudobonds, 13459 residues, 19 models selected 
    7227 
    7228 > select down
    7229 
    7230 55996 atoms, 57633 bonds, 14 pseudobonds, 6600 residues, 3 models selected 
    7231 
    7232 > select down
    7233 
    7234 14 pseudobonds, 2 models selected 
    7235 
    7236 > cartoon style modeHelix tube radius 1.5
    7237 
    7238 > select #10/Z
    7239 
    7240 467 atoms, 472 bonds, 1 pseudobond, 72 residues, 2 models selected 
    7241 
    7242 > color sel salmon
    7243 
    7244 [Repeated 1 time(s)]
    7245 
    7246 > color sel dark salmon
    7247 
    7248 > color sel salmon
    7249 
    7250 > select #10/L
    7251 
    7252 2824 atoms, 2886 bonds, 1 pseudobond, 361 residues, 2 models selected 
    7253 
    7254 > color (#!10 & sel) #ffd479ff
    7255 
    7256 > color (#!10 & sel) #feff80ff
    7257 
    7258 [Repeated 1 time(s)]
    7259 
    7260 > select clear
    7261 
    7262 > select #10/M
    7263 
    7264 3422 atoms, 3498 bonds, 1 pseudobond, 431 residues, 2 models selected 
    7265 
    7266 > color sel deep sky blue
    7267 
    7268 > select #10/O\
    7269 
    7270 Nothing selected 
    7271 
    7272 > select #10/O
    7273 
    7274 287 atoms, 296 bonds, 34 residues, 1 model selected 
    7275 
    7276 > color sel royal blue
    7277 
    7278 > color sel #2163a6ff
    7279 
    7280 [Repeated 1 time(s)]
    7281 
    7282 > select clear
    7283 
    7284 > hide #!2 models
    7285 
    7286 > show #!9 models
    7287 
    7288 > show #!8 models
    7289 
    7290 > show #!4 models
    7291 
    7292 > show #!7 models
    7293 
    7294 > ui tool show "Color Zone"
    7295 
    7296 > color zone #4 near #10 distance 4.99
    7297 
    7298 > color zone #4 near #10 distance 1
    7299 
    7300 > color zone #4 near #10 distance 10
    7301 
    7302 > color zone #7 near #10 distance 4.99
    7303 
    7304 > color zone #8 near #10 distance 4.99
    7305 
    7306 > color zone #9 near #10 distance 4.99
    7307 
    7308 > hide #!4 models
    7309 
    7310 > show #!4 models
    7311 
    7312 > hide #!10 models
    7313 
    7314 > ui tool show "Side View"
    7315 
    7316 > show #!2 models
    7317 
    7318 > hide #!2 models
    7319 
    7320 > show #!1 models
    7321 
    7322 > hide #!1 models
    7323 
    7324 > show #!6 models
    7325 
    7326 > hide #!6 models
    7327 
    7328 > show #!5 models
    7329 
    7330 > hide #!5 models
    7331 
    7332 > show #!1 models
    7333 
    7334 > hide #!7 models
    7335 
    7336 > hide #!8 models
    7337 
    7338 > hide #!9 models
    7339 
    7340 > hide #!4 models
    7341 
    7342 > show #!3 models
    7343 
    7344 > show #!4 models
    7345 
    7346 > hide #!4 models
    7347 
    7348 > show #!5 models
    7349 
    7350 > show #!6 models
    7351 
    7352 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    7353 > /Figure 1/Version 2/xl_080_map.png" width 3600 height 2934 supersample 3
    7354 > transparentBackground true
    7355 
    7356 > hide #!1 models
    7357 
    7358 > hide #!3 models
    7359 
    7360 > hide #!5 models
    7361 
    7362 > hide #!6 models
    7363 
    7364 > show #!8 models
    7365 
    7366 > show #!9 models
    7367 
    7368 > show #!7 models
    7369 
    7370 > show #!4 models
    7371 
    7372 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    7373 > /Figure 1/Version 2/xl_040_map.png" width 3600 height 2934 supersample 3
    7374 > transparentBackground true
    7375 
    7376 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    7377 > /Figure 1/Version 2-resubmission/Chimera Session/Figure1.cxs" includeMaps
    7378 > true
    7379 
    7380 > show #!10 models
    7381 
    7382 > select #10/L
    7383 
    7384 2824 atoms, 2886 bonds, 1 pseudobond, 361 residues, 2 models selected 
    7385 
    7386 > ui tool show "Color Actions"
    7387 
    7388 > color sel gold
    7389 
    7390 [Repeated 1 time(s)]
    7391 
    7392 > color zone #9 near #10 distance 4.99
    7393 
    7394 > color zone #4 near #10 distance 10
    7395 
    7396 > select clear
    7397 
    7398 > hide #!10 models
    7399 
    7400 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    7401 > /Figure 1/Version 2-resubmission/Chimera Session/Xl_0N40_map.png" width 3600
    7402 > height 2700 supersample 3 transparentBackground true
    7403 
    7404 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    7405 > /Figure 1/Version 2-resubmission/Chimera Session/Xl_0N40_map.png" width 3600
    7406 > height 2700 supersample 4 transparentBackground true
    7407 
    7408 > select clear
    7409 
    7410 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    7411 > /Figure 1/Version 2-resubmission/Chimera Session/Xl_0N40_map.png" width 3600
    7412 > height 2700 supersample 1 transparentBackground true
    7413 
    7414 > graphics silhouettes true
    7415 
    7416 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    7417 > /Figure 1/Version 2-resubmission/Chimera Session/Xl_0N40_map.png" width 3600
    7418 > height 2700 supersample 3 transparentBackground true
    7419 
    7420 > graphics silhouettes false
    7421 
    7422 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    7423 > /Figure 1/Version 2-resubmission/Chimera Session/Xl_0N40_map.png" width 3600
    7424 > height 2700 supersample 3 transparentBackground true
    7425 
    7426 > hide #!4 models
    7427 
    7428 > hide #!7 models
    7429 
    7430 > hide #!8 models
    7431 
    7432 > hide #!9 models
    7433 
    7434 > show #!1 models
    7435 
    7436 > show #!3 models
    7437 
    7438 > show #!5 models
    7439 
    7440 > show #!6 models
    7441 
    7442 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    7443 > /Figure 1/Version 2-resubmission/Chimera Session/Xl_0N80_map.png" width 3600
    7444 > height 2700 supersample 3 transparentBackground true
    7445 
    7446 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    7447 > /Figure 1/Version 2-resubmission/Chimera Session/Figure1.cxs" includeMaps
    7448 > true
    7449 
    7450 ——— End of log from Thu Dec 12 15:18:18 2024 ———
    7451 
    7452 opened ChimeraX session 
    7453 
    7454 Cell requested for row 0 is out of bounds for table with 20 rows! Resizing
    7455 table model. 
    7456 
    7457 > hide #!1 models
    7458 
    7459 > hide #!3 models
    7460 
    7461 > hide #!5 models
    7462 
    7463 > hide #!6 models
    7464 
    7465 > show #!7 models
    7466 
    7467 > show #!8 models
    7468 
    7469 > show #!9 models
    7470 
    7471 > show #!10 models
    7472 
    7473 > show #!4 models
    7474 
    7475 > surface dust #4 size 8.31
    7476 
    7477 > surface dust #7 size 8.31
    7478 
    7479 > surface dust #8 size 8.31
    7480 
    7481 > surface dust #9 size 8.31
    7482 
    7483 > volume #4 level 0.002924
    7484 
    7485 > volume #4 level 0.002769
    7486 
    7487 > volume #4 level 0.00284
    7488 
    7489 > volume #4 level 0.002896
    7490 
    7491 > volume #4 level 0.002685
    7492 
    7493 > select #10/L
    7494 
    7495 2824 atoms, 2886 bonds, 1 pseudobond, 361 residues, 2 models selected 
    7496 
    7497 > ui tool show "Color Actions"
    7498 
    7499 > color sel khaki
    7500 
    7501 > ui tool show "Color Zone"
    7502 
    7503 > color zone #4 near #10 distance 10
    7504 
    7505 > show #!1 models
    7506 
    7507 > color (#!10 & sel) #ffff86ff
    7508 
    7509 > select #10/L
    7510 
    7511 2824 atoms, 2886 bonds, 1 pseudobond, 361 residues, 2 models selected 
    7512 
    7513 > color zone #4 near #10 distance 10
    7514 
    7515 > select clear
    7516 
    7517 > hide #!1 models
    7518 
    7519 > hide #!7 models
    7520 
    7521 > show #!7 models
    7522 
    7523 > hide #!7 models
    7524 
    7525 > show #!7 models
    7526 
    7527 > hide #!10 models
    7528 
    7529 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    7530 > /Figure 1/Version 2-resubmission/Chimera Session/Xl_0N40_map.png" width 3600
    7531 > height 3398 supersample 3 transparentBackground true
    7532 
    7533 > save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
    7534 > /Figure 1/Version 2-resubmission/Chimera Session/Figure1.cxs" includeMaps
    7535 > true
    7536 
    7537 ——— End of log from Sat Dec 28 15:21:23 2024 ———
    7538 
    7539 opened ChimeraX session 
    7540 
    7541 > show #!1 models
    7542 
    7543 > show #!2 models
    7544 
    7545 > show #!3 models
    7546 
    7547 > show #!5 models
    7548 
    7549 > hide #!5 models
    7550 
    7551 > show #!6 models
    7552 
    7553 > hide #!6 models
    7554 
    7555 > hide #!1 models
    7556 
    7557 > hide #!2 models
    7558 
    7559 > hide #!3 models
    7560 
    7561 > hide #!4 models
    7562 
    7563 > hide #!7 models
    7564 
    7565 > hide #!8 models
    7566 
    7567 > hide #!9 models
    7568 
    7569 > close #4,7-10
    7570 
    7571 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    7572 > Model/INO-80Yeastnuc-ADPBeF/20231226-wt-y80nuc-adpbef-inocore-
    7573 > nuc_real_space_refined_009-coot-1.pdb"
    7574 
    7575 Chain information for 20231226-wt-y80nuc-adpbef-inocore-
    7576 nuc_real_space_refined_009-coot-1.pdb #4 
    7577 --- 
    7578 Chain | Description 
    7579 C | No description available 
    7580 D | No description available 
    7581 E h | No description available 
    7582 F j | No description available 
    7583 G | No description available 
    7584 H | No description available 
    7585 K | No description available 
    7586 L | No description available 
    7587 Q | No description available 
    7588 R | No description available 
    7589 S | No description available 
    7590 T | No description available 
    7591 U | No description available 
    7592 V | No description available 
    7593 W | No description available 
    7594 X | No description available 
    7595 Y | No description available 
    7596 Z | No description available 
    7597  
    7598 
    7599 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    7600 > Model/INO-80Yeastnuc-ADPBeF/1x448-global-cryosparc-refine-unsharp-
    7601 > align-2.91A.mrc"
    7602 
    7603 Opened 1x448-global-cryosparc-refine-unsharp-align-2.91A.mrc as #7, grid size
    7604 448,448,448, pixel 0.835, shown at level 0.167, step 2, values float32 
    7605 
    7606 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    7607 > Model/INO-80Yeastnuc-ADPBeF/filter.mrc"
    7608 
    7609 Opened filter.mrc as #8, grid size 256,256,256, pixel 1.67, shown at level
    7610 0.0143, step 1, values float32 
    7611 
    7612 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    7613 > Model/wtINO80-0N80-Yeast-Apo/121124-0n80-ye-wt-apo-final-coot-0-pymol.pdb"
    7614 
    7615 Chain information for 121124-0n80-ye-wt-apo-final-coot-0-pymol.pdb #9 
    7616 --- 
    7617 Chain | Description 
    7618 A E | No description available 
    7619 B F | No description available 
    7620 C | No description available 
    7621 D H | No description available 
    7622 G | No description available 
    7623 I | No description available 
    7624 J | No description available 
    7625 K | No description available 
    7626 L | No description available 
    7627 M | No description available 
    7628 O | No description available 
    7629 Q | No description available 
    7630 R | No description available 
    7631 S | No description available 
    7632 T | No description available 
    7633 U | No description available 
    7634 V | No description available 
    7635 W | No description available 
    7636 X | No description available 
    7637 Y | No description available 
    7638 Z | No description available 
    7639  
    7640 
    7641 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    7642 > Model/wtINO80-0N80-Yeast-Apo/121124-a8-split.mrc"
    7643 
    7644 Opened 121124-a8-split.mrc as #10, grid size 512,512,512, pixel 0.819, shown
    7645 at level 0.000444, step 2, values float32 
    7646 
    7647 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    7648 > Model/wtINO80-0N80-Yeast-Apo/120524-inocore-nuc-3.16A.mrc"
    7649 
    7650 Opened 120524-inocore-nuc-3.16A.mrc as #11, grid size 512,512,512, pixel
    7651 0.819, shown at level 0.0802, step 2, values float32 
    7652 
    7653 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    7654 > Model/wtINO80-0N80-Xe-Apo/122324-x80-apo-a8-split-resample.mrc"
    7655 
    7656 Opened 122324-x80-apo-a8-split-resample.mrc as #12, grid size 480,480,480,
    7657 pixel 0.835, shown at level 0.000239, step 2, values float32 
    7658 
    7659 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    7660 > Model/wtINO80-0N80-Xe-Apo/122324-x80-apo-arp5-resample.mrc"
    7661 
    7662 Opened 122324-x80-apo-arp5-resample.mrc as #13, grid size 480,480,480, pixel
    7663 0.835, shown at level 0.000123, step 2, values float32 
    7664 
    7665 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    7666 > Model/wtINO80-0N80-Xe-Apo/122324-x80-apo-atpasehighres-resample.mrc"
    7667 
    7668 Opened 122324-x80-apo-atpasehighres-resample.mrc as #14, grid size
    7669 480,480,480, pixel 0.835, shown at level 0.000139, step 2, values float32 
    7670 
    7671 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    7672 > Model/wtINO80-0N80-Xe-Apo/122324-x80-apo-dna-resample.mrc"
    7673 
    7674 Opened 122324-x80-apo-dna-resample.mrc as #15, grid size 480,480,480, pixel
    7675 0.835, shown at level 0.000354, step 2, values float32 
    7676 
    7677 > open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
    7678 > Model/wtINO80-0N80-Xe-Apo/122324-x80-apo-grappler-resample.mrc"
    7679 
    7680 Opened 122324-x80-apo-grappler-resample.mrc as #16, grid size 480,480,480,
    7681 pixel 0.835, shown at level 3.54e-05, step 2, values float32 
     1156[deleted to fit within ticket limits]
    76821157
    76831158> open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and