Changes between Initial Version and Version 1 of Ticket #15757


Ignore:
Timestamp:
Aug 12, 2024, 11:03:56 AM (15 months ago)
Author:
Eric Pettersen
Comment:

Reported by Prafful Sharma

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #15757

    • Property Component Unassigned → Sessions
    • Property Owner set to Tom Goddard
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → ArrayMemoryError saving molecular surface in session

  • Ticket #15757 – Description

    initial v1  
    353035301x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    35313531
    3532 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3533 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3534 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3535 
    3536 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3537 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3538 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3539 
    3540 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3541 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3542 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3543 
    3544 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3545 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3546 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3547 
    3548 [Repeated 1 time(s)]
    3549 
    3550 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3551 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3552 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3553 
    3554 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3555 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3556 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3557 
    3558 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3559 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3560 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3561 
    3562 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3563 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3564 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3565 
    3566 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3567 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3568 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3569 
    3570 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3571 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3572 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3573 
    3574 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3575 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3576 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3577 
    3578 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3579 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3580 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3581 
    3582 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3583 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3584 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3585 
    3586 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3587 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3588 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3589 
    3590 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3591 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3592 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3593 
    3594 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3595 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3596 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3597 
    3598 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3599 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3600 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3601 
    3602 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3603 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3604 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3605 
    3606 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3607 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3608 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3609 
    3610 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3611 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3612 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3613 
    3614 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3615 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3616 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3617 
    3618 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3619 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3620 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3621 
    3622 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3623 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3624 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3625 
    3626 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3627 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3628 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3629 
    3630 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3631 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3632 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3633 
    3634 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3635 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3636 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3637 
    3638 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3639 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3640 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3641 
    3642 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3643 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3644 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3645 
    3646 QWindowsWindow::setGeometry: Unable to set geometry 1x1+312083438+32764
    3647 (frame: 1x1+312083438+32764) on QWindow/"" on "\\\\.\DISPLAY1". Resulting
    3648 geometry: 1x1+32767+32764 (frame: 1x1+32767+32764) margins: 0, 0, 0, 0) 
    3649 
    3650 QWindowsWindow::setGeometry: Unable to set geometry 1x1-999883248+545 (frame:
    3651 1x1-999883248+545) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3652 1x1-32768+545 (frame: 1x1-32768+545) margins: 0, 0, 0, 0) 
    3653 
    3654 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3655 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3656 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3657 
    3658 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3659 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3660 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3661 
    3662 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3663 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3664 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3665 
    3666 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3667 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3668 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3669 
    3670 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3671 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3672 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3673 
    3674 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3675 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3676 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3677 
    3678 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3679 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3680 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3681 
    3682 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3683 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3684 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3685 
    3686 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3687 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3688 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3689 
    3690 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3691 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3692 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3693 
    3694 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3695 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3696 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3697 
    3698 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3699 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3700 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3701 
    3702 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3703 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3704 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3705 
    3706 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3707 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3708 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3709 
    3710 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3711 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3712 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3713 
    3714 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3715 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3716 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3717 
    3718 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3719 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3720 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3721 
    3722 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3723 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3724 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3725 
    3726 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3727 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3728 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3729 
    3730 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3731 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3732 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3733 
    3734 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3735 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3736 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3737 
    3738 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3739 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3740 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3741 
    3742 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3743 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3744 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3745 
    3746 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3747 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3748 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3749 
    3750 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3751 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3752 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3753 
    3754 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3755 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3756 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3757 
    3758 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3759 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3760 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3761 
    3762 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3763 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3764 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3765 
    3766 QWindowsWindow::setGeometry: Unable to set geometry 1x1-1551177888+32764
    3767 (frame: 1x1-1551177888+32764) on QWindow/"" on "\\\\.\DISPLAY1". Resulting
    3768 geometry: 1x1-32768+32764 (frame: 1x1-32768+32764) margins: 0, 0, 0, 0) 
    3769 
    3770 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3771 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3772 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3773 
    3774 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3775 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3776 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3777 
    3778 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3779 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3780 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3781 
    3782 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3783 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3784 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3785 
    3786 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3787 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3788 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3789 
    3790 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3791 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3792 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3793 
    3794 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3795 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3796 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3797 
    3798 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3799 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3800 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3801 
    3802 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3803 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3804 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3805 
    3806 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3807 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3808 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3809 
    3810 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3811 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3812 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3813 
    3814 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3815 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3816 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3817 
    3818 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3819 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3820 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3821 
    3822 QWindowsWindow::setGeometry: Unable to set geometry 1x1-999883248+545 (frame:
    3823 1x1-999883248+545) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3824 1x1-32768+545 (frame: 1x1-32768+545) margins: 0, 0, 0, 0) 
    3825 
    3826 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3827 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3828 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3829 
    3830 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3831 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3832 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3833 
    3834 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3835 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3836 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3837 
    3838 QWindowsWindow::setGeometry: Unable to set geometry 1x1-999883248+545 (frame:
    3839 1x1-999883248+545) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3840 1x1-32768+545 (frame: 1x1-32768+545) margins: 0, 0, 0, 0) 
    3841 
    3842 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3843 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3844 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3845 
    3846 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3847 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3848 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3849 
    3850 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3851 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3852 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3853 
    3854 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3855 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3856 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3857 
    3858 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3859 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3860 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3861 
    3862 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3863 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3864 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3865 
    3866 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3867 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3868 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3869 
    3870 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3871 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3872 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3873 
    3874 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3875 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3876 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3877 
    3878 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3879 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3880 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3881 
    3882 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3883 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3884 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3885 
    3886 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3887 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3888 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3889 
    3890 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3891 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3892 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3893 
    3894 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3895 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3896 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3897 
    3898 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3899 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3900 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3901 
    3902 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3903 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3904 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3905 
    3906 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3907 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3908 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3909 
    3910 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3911 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3912 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3913 
    3914 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3915 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3916 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3917 
    3918 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3919 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3920 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3921 
    3922 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3923 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3924 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3925 
    3926 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3927 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3928 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3929 
    3930 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3931 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3932 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3933 
    3934 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3935 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3936 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3937 
    3938 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3939 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3940 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3941 
    3942 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3943 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3944 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3945 
    3946 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3947 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3948 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3949 
    3950 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3951 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3952 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3953 
    3954 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3955 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3956 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3957 
    3958 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3959 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3960 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3961 
    3962 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3963 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3964 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3965 
    3966 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3967 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3968 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3969 
    3970 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3971 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3972 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3973 
    3974 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3975 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3976 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3977 
    3978 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475313993+138 (frame:
    3979 1x1+1475313993+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3980 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    3981 
    3982 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    3983 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    3984 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    3985 
    3986 > open "D:/PhD common folder/OneDrive - Indian Institute of
    3987 > Science/Yeast_project/40S_4B/40S_4B_FL.cxs"
    3988 
    3989 Log from Thu Jun 13 18:54:25 2024UCSF ChimeraX version: 1.8.dev202312120034
    3990 (2023-12-12) 
    3991 © 2016-2023 Regents of the University of California. All rights reserved. 
    3992 
    3993 > open "D:\\\PhD common folder\\\OneDrive - Indian Institute of
    3994 > Science\\\Yeast_project\\\40S_4B\\\40S_4B_1-98_RRM_AF3.cxs"
    3995 
    3996 Log from Thu Jun 13 16:35:32 2024 Startup Messages 
    3997 --- 
    3998 warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle 
    3999 
    4000 You can double click a model's Name or ID in the model panel to edit those
    4001 fields 
    4002 UCSF ChimeraX version: 1.8.dev202312120034 (2023-12-12) 
    4003 © 2016-2023 Regents of the University of California. All rights reserved. 
    4004 How to cite UCSF ChimeraX 
    4005 
    4006 > open "D:\PhD common folder\OneDrive - Indian Institute of
    4007 > Science\Jose_TH_43S_PIC\New_RSR_models\PIN_5_real_space_refined.pdb" format
    4008 > pdb
    4009 
    4010 Chain information for PIN_5_real_space_refined.pdb #1 
    4011 --- 
    4012 Chain | Description 
    4013 1 | No description available 
    4014 2 | No description available 
    4015 3 | No description available 
    4016 A | No description available 
    4017 B | No description available 
    4018 C | No description available 
    4019 D | No description available 
    4020 E | No description available 
    4021 F | No description available 
    4022 G | No description available 
    4023 H | No description available 
    4024 I | No description available 
    4025 J | No description available 
    4026 K | No description available 
    4027 L | No description available 
    4028 M | No description available 
    4029 N | No description available 
    4030 O | No description available 
    4031 P | No description available 
    4032 Q | No description available 
    4033 R | No description available 
    4034 S | No description available 
    4035 T | No description available 
    4036 U | No description available 
    4037 V | No description available 
    4038 W | No description available 
    4039 X | No description available 
    4040 Y | No description available 
    4041 Z | No description available 
    4042 a | No description available 
    4043 b | No description available 
    4044 c | No description available 
    4045 d | No description available 
    4046 e | No description available 
    4047 f | No description available 
    4048 g | No description available 
    4049 h | No description available 
    4050 i | No description available 
    4051 j | No description available 
    4052 k | No description available 
    4053 l | No description available 
    4054 m | No description available 
    4055 n | No description available 
    4056 o | No description available 
    4057 p | No description available 
    4058 q | No description available 
    4059 r | No description available 
    4060 
    4061 
    4062 > ui tool show "Show Sequence Viewer"
    4063 
    4064 > sequence chain /2
    4065 
    4066 Alignment identifier is 1/2 
    4067 
    4068 > select /2:1150
    4069 
    4070 22 atoms, 24 bonds, 1 residue, 1 model selected 
    4071 
    4072 > select /2:1150-1157
    4073 
    4074 175 atoms, 196 bonds, 8 residues, 1 model selected 
    4075 
    4076 > select /2:1150
    4077 
    4078 22 atoms, 24 bonds, 1 residue, 1 model selected 
    4079 
    4080 > select /2:1150-1626
    4081 
    4082 10173 atoms, 11370 bonds, 477 residues, 1 model selected 
    4083 
    4084 > select ~sel & ##selected
    4085 
    4086 94063 atoms, 98599 bonds, 9675 residues, 1 model selected 
    4087 
    4088 > delete atoms sel
    4089 
    4090 > delete bonds sel
    4091 
    4092 > select protein
    4093 
    4094 Nothing selected 
    4095 
    4096 > show cartoons
    4097 
    4098 > hide atoms
    4099 
    4100 > set bgColor white
    4101 
    4102 > open "D:/PhD common folder/OneDrive - Indian Institute of
    4103 > Science/Yeast_project/40S_4B/fold_40s_rrna_head_2024_06_12_22_44_model_0.cif"
    4104 
    4105 Chain information for fold_40s_rrna_head_2024_06_12_22_44_model_0.cif #2 
    4106 --- 
    4107 Chain | Description 
    4108 A | . 
    4109 
    4110 
    4111 > ui tool show Matchmaker
    4112 
    4113 > matchmaker #2 to #1
    4114 
    4115 Using Nucleic matrix instead of BLOSUM-62 for matching 
    4116 Parameters 
    4117 --- 
    4118 Chain pairing | bb 
    4119 Alignment algorithm | Needleman-Wunsch 
    4120 Similarity matrix | Nucleic 
    4121 SS fraction | 0.3 
    4122 Gap open (HH/SS/other) | 18/18/6 
    4123 Gap extend | 1 
    4124 SS matrix |  |  | H | S | O 
    4125 ---|---|---|--- 
    4126 H | 6 | -9 | -6 
    4127 S |  | 6 | -6 
    4128 O |  |  | 4 
    4129 Iteration cutoff | 2 
    4130 
    4131 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#1) with
    4132 fold_40s_rrna_head_2024_06_12_22_44_model_0.cif, chain A (#2), sequence
    4133 alignment score = 1887 
    4134 RMSD between 441 pruned atom pairs is 0.742 angstroms; (across all 477 pairs:
    4135 1.140) 
    4136 
    4137 
    4138 > select add #2
    4139 
    4140 10163 atoms, 11360 bonds, 477 residues, 1 model selected 
    4141 
    4142 > hide sel atoms
    4143 
    4144 > select subtract #2
    4145 
    4146 Nothing selected 
    4147 
    4148 > lighting soft
    4149 
    4150 > graphics silhouettes true
    4151 
    4152 > open "D:/PhD common folder/OneDrive - Indian Institute of
    4153 > Science/Yeast_project/40S_4B/New folder/fold_2024_06_13_01_16_model_0.cif"
    4154 
    4155 Chain information for fold_2024_06_13_01_16_model_0.cif #3 
    4156 --- 
    4157 Chain | Description 
    4158 A | . 
    4159 B | . 
    4160 C | . 
    4161 D | . 
    4162 
    4163 
    4164 > ui tool show Matchmaker
    4165 
    4166 > matchmaker #3 to #1
    4167 
    4168 Using Nucleic matrix instead of BLOSUM-62 for matching 
    4169 Parameters 
    4170 --- 
    4171 Chain pairing | bb 
    4172 Alignment algorithm | Needleman-Wunsch 
    4173 Similarity matrix | Nucleic 
    4174 SS fraction | 0.3 
    4175 Gap open (HH/SS/other) | 18/18/6 
    4176 Gap extend | 1 
    4177 SS matrix |  |  | H | S | O 
    4178 ---|---|---|--- 
    4179 H | 6 | -9 | -6 
    4180 S |  | 6 | -6 
    4181 O |  |  | 4 
    4182 Iteration cutoff | 2 
    4183 
    4184 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#1) with
    4185 fold_2024_06_13_01_16_model_0.cif, chain D (#3), sequence alignment score =
    4186 1887 
    4187 RMSD between 451 pruned atom pairs is 0.755 angstroms; (across all 477 pairs:
    4188 1.036) 
    4189 
    4190 
    4191 > matchmaker #3 to #1
    4192 
    4193 Using Nucleic matrix instead of BLOSUM-62 for matching 
    4194 Parameters 
    4195 --- 
    4196 Chain pairing | bb 
    4197 Alignment algorithm | Needleman-Wunsch 
    4198 Similarity matrix | Nucleic 
    4199 SS fraction | 0.3 
    4200 Gap open (HH/SS/other) | 18/18/6 
    4201 Gap extend | 1 
    4202 SS matrix |  |  | H | S | O 
    4203 ---|---|---|--- 
    4204 H | 6 | -9 | -6 
    4205 S |  | 6 | -6 
    4206 O |  |  | 4 
    4207 Iteration cutoff | 2 
    4208 
    4209 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#1) with
    4210 fold_2024_06_13_01_16_model_0.cif, chain D (#3), sequence alignment score =
    4211 1887 
    4212 RMSD between 451 pruned atom pairs is 0.755 angstroms; (across all 477 pairs:
    4213 1.036) 
    4214 
    4215 
    4216 > select add #3
    4217 
    4218 13838 atoms, 15098 bonds, 937 residues, 1 model selected 
    4219 
    4220 > hide sel atoms
    4221 
    4222 > select subtract #3
    4223 
    4224 Nothing selected 
    4225 
    4226 > hide #2 models
    4227 
    4228 > select add #1
    4229 
    4230 10173 atoms, 11370 bonds, 477 residues, 1 model selected 
    4231 
    4232 > show sel cartoons
    4233 
    4234 > hide sel atoms
    4235 
    4236 > surface sel
    4237 
    4238 > hide sel atoms
    4239 
    4240 > surface hidePatches (#!1 & sel)
    4241 
    4242 > open "D:/PhD common folder/OneDrive - Indian Institute of
    4243 > Science/Jose_TH_43S_PIC/New_RSR_models/PIN_5_real_space_refined.pdb"
    4244 
    4245 Chain information for PIN_5_real_space_refined.pdb #4 
    4246 --- 
    4247 Chain | Description 
    4248 1 | No description available 
    4249 2 | No description available 
    4250 3 | No description available 
    4251 A | No description available 
    4252 B | No description available 
    4253 C | No description available 
    4254 D | No description available 
    4255 E | No description available 
    4256 F | No description available 
    4257 G | No description available 
    4258 H | No description available 
    4259 I | No description available 
    4260 J | No description available 
    4261 K | No description available 
    4262 L | No description available 
    4263 M | No description available 
    4264 N | No description available 
    4265 O | No description available 
    4266 P | No description available 
    4267 Q | No description available 
    4268 R | No description available 
    4269 S | No description available 
    4270 T | No description available 
    4271 U | No description available 
    4272 V | No description available 
    4273 W | No description available 
    4274 X | No description available 
    4275 Y | No description available 
    4276 Z | No description available 
    4277 a | No description available 
    4278 b | No description available 
    4279 c | No description available 
    4280 d | No description available 
    4281 e | No description available 
    4282 f | No description available 
    4283 g | No description available 
    4284 h | No description available 
    4285 i | No description available 
    4286 j | No description available 
    4287 k | No description available 
    4288 l | No description available 
    4289 m | No description available 
    4290 n | No description available 
    4291 o | No description available 
    4292 p | No description available 
    4293 q | No description available 
    4294 r | No description available 
    4295 
    4296 
    4297 > select add #4
    4298 
    4299 114409 atoms, 121339 bonds, 10629 residues, 3 models selected 
    4300 
    4301 > select subtract #1
    4302 
    4303 104236 atoms, 109969 bonds, 10152 residues, 2 models selected 
    4304 
    4305 > surface hidePatches sel
    4306 
    4307 > hide sel atoms
    4308 
    4309 > show sel cartoons
    4310 
    4311 > ui tool show Matchmaker
    4312 
    4313 > matchmaker #!4 to #1/2 pairing bs matrix Nucleic
    4314 
    4315 Parameters 
    4316 --- 
    4317 Chain pairing | bs 
    4318 Alignment algorithm | Needleman-Wunsch 
    4319 Similarity matrix | Nucleic 
    4320 SS fraction | 0.3 
    4321 Gap open (HH/SS/other) | 18/18/6 
    4322 Gap extend | 1 
    4323 SS matrix |  |  | H | S | O 
    4324 ---|---|---|--- 
    4325 H | 6 | -9 | -6 
    4326 S |  | 6 | -6 
    4327 O |  |  | 4 
    4328 Iteration cutoff | 2 
    4329 
    4330 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#1) with
    4331 PIN_5_real_space_refined.pdb, chain 2 (#4), sequence alignment score = 5525.6 
    4332 RMSD between 477 pruned atom pairs is 0.000 angstroms; (across all 477 pairs:
    4333 0.000) 
    4334 
    4335 
    4336 > select clear
    4337 
    4338 > color #4 yellow
    4339 
    4340 > select #1/2:1361
    4341 
    4342 20 atoms, 21 bonds, 1 residue, 1 model selected 
    4343 
    4344 > select up
    4345 
    4346 10173 atoms, 11370 bonds, 477 residues, 2 models selected 
    4347 
    4348 > select clear
    4349 
    4350 > select #1/2:1373
    4351 
    4352 20 atoms, 21 bonds, 1 residue, 1 model selected 
    4353 
    4354 > select up
    4355 
    4356 10173 atoms, 11370 bonds, 477 residues, 2 models selected 
    4357 
    4358 > hide #!1 models
    4359 
    4360 > show #!1 models
    4361 
    4362 > hide #!1 models
    4363 
    4364 > hide #3 models
    4365 
    4366 > select add #4/U:47
    4367 
    4368 10180 atoms, 11376 bonds, 478 residues, 3 models selected 
    4369 
    4370 > select up
    4371 
    4372 10332 atoms, 11529 bonds, 497 residues, 3 models selected 
    4373 
    4374 > select up
    4375 
    4376 11018 atoms, 12227 bonds, 583 residues, 3 models selected 
    4377 
    4378 > show #3 models
    4379 
    4380 > hide #3 models
    4381 
    4382 > show #3 models
    4383 
    4384 > hide #3 models
    4385 
    4386 > select add #4/D:126
    4387 
    4388 11025 atoms, 12233 bonds, 584 residues, 3 models selected 
    4389 
    4390 > select up
    4391 
    4392 11150 atoms, 12360 bonds, 600 residues, 3 models selected 
    4393 
    4394 > select up
    4395 
    4396 12792 atoms, 14027 bonds, 810 residues, 3 models selected 
    4397 
    4398 > select up
    4399 
    4400 114409 atoms, 121339 bonds, 10629 residues, 3 models selected 
    4401 
    4402 > select down
    4403 
    4404 12792 atoms, 14027 bonds, 810 residues, 3 models selected 
    4405 
    4406 > show #3 models
    4407 
    4408 > hide #3 models
    4409 
    4410 > select add #4/K:16
    4411 
    4412 12803 atoms, 14038 bonds, 811 residues, 3 models selected 
    4413 
    4414 > select up
    4415 
    4416 12934 atoms, 14172 bonds, 826 residues, 3 models selected 
    4417 
    4418 > select up
    4419 
    4420 13601 atoms, 14858 bonds, 906 residues, 3 models selected 
    4421 
    4422 > select up
    4423 
    4424 114409 atoms, 121339 bonds, 10629 residues, 3 models selected 
    4425 
    4426 > select down
    4427 
    4428 13601 atoms, 14858 bonds, 906 residues, 3 models selected 
    4429 
    4430 > select add #4/2:1333
    4431 
    4432 13621 atoms, 14879 bonds, 907 residues, 3 models selected 
    4433 
    4434 > select up
    4435 
    4436 51413 atoms, 57141 bonds, 2686 residues, 3 models selected 
    4437 
    4438 > select ~sel & ##selected
    4439 
    4440 62996 atoms, 64198 bonds, 7943 residues, 1 model selected 
    4441 
    4442 > hide sel target a
    4443 
    4444 > hide sel cartoons
    4445 
    4446 > select clear
    4447 
    4448 > show #3 models
    4449 
    4450 > open "D:/PhD common folder/OneDrive - Indian Institute of
    4451 > Science/Yeast_project/40S_4B/New folder
    4452 > (2)/fold_2024_06_13_14_34_model_0.cif"
    4453 
    4454 Chain information for fold_2024_06_13_14_34_model_0.cif #5 
    4455 --- 
    4456 Chain | Description 
    4457 A | . 
    4458 B | . 
    4459 C | . 
    4460 D | . 
    4461 E | . 
    4462 
    4463 
    4464 > select #5/C:45@O
    4465 
    4466 1 atom, 1 residue, 1 model selected 
    4467 
    4468 > select #5/C:45@O
    4469 
    4470 1 atom, 1 residue, 1 model selected 
    4471 
    4472 > select clear
    4473 
    4474 > select add #5
    4475 
    4476 14573 atoms, 15847 bonds, 1035 residues, 1 model selected 
    4477 
    4478 > hide sel atoms
    4479 
    4480 > show sel cartoons
    4481 
    4482 > select clear
    4483 
    4484 > color #5 #ff55ffff
    4485 
    4486 > color #5 red
    4487 
    4488 > ui tool show Matchmaker
    4489 
    4490 > matchmaker #5 to #1/2 pairing bs matrix Nucleic
    4491 
    4492 Parameters 
    4493 --- 
    4494 Chain pairing | bs 
    4495 Alignment algorithm | Needleman-Wunsch 
    4496 Similarity matrix | Nucleic 
    4497 SS fraction | 0.3 
    4498 Gap open (HH/SS/other) | 18/18/6 
    4499 Gap extend | 1 
    4500 SS matrix |  |  | H | S | O 
    4501 ---|---|---|--- 
    4502 H | 6 | -9 | -6 
    4503 S |  | 6 | -6 
    4504 O |  |  | 4 
    4505 Iteration cutoff | 2 
    4506 
    4507 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#1) with
    4508 fold_2024_06_13_14_34_model_0.cif, chain E (#5), sequence alignment score =
    4509 1887 
    4510 RMSD between 446 pruned atom pairs is 0.750 angstroms; (across all 477 pairs:
    4511 1.027) 
    4512 
    4513 
    4514 > matchmaker #5 to #1/2 pairing bs matrix Nucleic
    4515 
    4516 Parameters 
    4517 --- 
    4518 Chain pairing | bs 
    4519 Alignment algorithm | Needleman-Wunsch 
    4520 Similarity matrix | Nucleic 
    4521 SS fraction | 0.3 
    4522 Gap open (HH/SS/other) | 18/18/6 
    4523 Gap extend | 1 
    4524 SS matrix |  |  | H | S | O 
    4525 ---|---|---|--- 
    4526 H | 6 | -9 | -6 
    4527 S |  | 6 | -6 
    4528 O |  |  | 4 
    4529 Iteration cutoff | 2 
    4530 
    4531 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#1) with
    4532 fold_2024_06_13_14_34_model_0.cif, chain E (#5), sequence alignment score =
    4533 1887 
    4534 RMSD between 446 pruned atom pairs is 0.750 angstroms; (across all 477 pairs:
    4535 1.027) 
    4536 
    4537 
    4538 > hide #3 models
    4539 
    4540 > select #5/D:61
    4541 
    4542 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4543 
    4544 > select up
    4545 
    4546 30 atoms, 29 bonds, 4 residues, 1 model selected 
    4547 
    4548 > select up
    4549 
    4550 735 atoms, 749 bonds, 98 residues, 1 model selected 
    4551 
    4552 > color sel cyan
    4553 
    4554 > color sel lime
    4555 
    4556 > select clear
    4557 
    4558 > select #5/D:56
    4559 
    4560 5 atoms, 4 bonds, 1 residue, 1 model selected 
    4561 
    4562 > select up
    4563 
    4564 24 atoms, 24 bonds, 3 residues, 1 model selected 
    4565 
    4566 > select up
    4567 
    4568 735 atoms, 749 bonds, 98 residues, 1 model selected 
    4569 
    4570 > select ~sel
    4571 
    4572 152248 atoms, 162895 bonds, 12980 residues, 5 models selected 
    4573 
    4574 > select subtract #1
    4575 
    4576 142075 atoms, 151525 bonds, 12503 residues, 5 models selected 
    4577 
    4578 > select subtract #2
    4579 
    4580 131912 atoms, 140165 bonds, 12026 residues, 3 models selected 
    4581 
    4582 > select subtract #3
    4583 
    4584 118074 atoms, 125067 bonds, 11089 residues, 2 models selected 
    4585 
    4586 > color sel yellow
    4587 
    4588 > select clear
    4589 
    4590 > save "D:/PhD common folder/OneDrive - Indian Institute of
    4591 > Science/Yeast_project/40S_4B/40S_4B_1-98_AF3.cxs"
    4592 
    4593 > open "D:/PhD common folder/OneDrive - Indian Institute of
    4594 > Science/Yeast_project/40S_4B/RRM/fold_rrm_2024_06_13_15_51_model_0.cif"
    4595 
    4596 Chain information for fold_rrm_2024_06_13_15_51_model_0.cif #6 
    4597 --- 
    4598 Chain | Description 
    4599 A | . 
    4600 B | . 
    4601 C | . 
    4602 D | . 
    4603 E | . 
    4604 
    4605 
    4606 > select add #6
    4607 
    4608 14522 atoms, 15797 bonds, 1024 residues, 1 model selected 
    4609 
    4610 > hide sel atoms
    4611 
    4612 > show sel cartoons
    4613 
    4614 > select clear
    4615 
    4616 > ui tool show Matchmaker
    4617 
    4618 > matchmaker #6 to #1/2 pairing bs matrix Nucleic
    4619 
    4620 Parameters 
    4621 --- 
    4622 Chain pairing | bs 
    4623 Alignment algorithm | Needleman-Wunsch 
    4624 Similarity matrix | Nucleic 
    4625 SS fraction | 0.3 
    4626 Gap open (HH/SS/other) | 18/18/6 
    4627 Gap extend | 1 
    4628 SS matrix |  |  | H | S | O 
    4629 ---|---|---|--- 
    4630 H | 6 | -9 | -6 
    4631 S |  | 6 | -6 
    4632 O |  |  | 4 
    4633 Iteration cutoff | 2 
    4634 
    4635 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#1) with
    4636 fold_rrm_2024_06_13_15_51_model_0.cif, chain E (#6), sequence alignment score
    4637 = 1887 
    4638 RMSD between 444 pruned atom pairs is 0.775 angstroms; (across all 477 pairs:
    4639 1.122) 
    4640 
    4641 
    4642 > matchmaker #6 to #1/2 pairing bs matrix Nucleic
    4643 
    4644 Parameters 
    4645 --- 
    4646 Chain pairing | bs 
    4647 Alignment algorithm | Needleman-Wunsch 
    4648 Similarity matrix | Nucleic 
    4649 SS fraction | 0.3 
    4650 Gap open (HH/SS/other) | 18/18/6 
    4651 Gap extend | 1 
    4652 SS matrix |  |  | H | S | O 
    4653 ---|---|---|--- 
    4654 H | 6 | -9 | -6 
    4655 S |  | 6 | -6 
    4656 O |  |  | 4 
    4657 Iteration cutoff | 2 
    4658 
    4659 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#1) with
    4660 fold_rrm_2024_06_13_15_51_model_0.cif, chain E (#6), sequence alignment score
    4661 = 1887 
    4662 RMSD between 444 pruned atom pairs is 0.775 angstroms; (across all 477 pairs:
    4663 1.122) 
    4664 
    4665 
    4666 > matchmaker #6 to #1/2 pairing bs matrix Nucleic
    4667 
    4668 Parameters 
    4669 --- 
    4670 Chain pairing | bs 
    4671 Alignment algorithm | Needleman-Wunsch 
    4672 Similarity matrix | Nucleic 
    4673 SS fraction | 0.3 
    4674 Gap open (HH/SS/other) | 18/18/6 
    4675 Gap extend | 1 
    4676 SS matrix |  |  | H | S | O 
    4677 ---|---|---|--- 
    4678 H | 6 | -9 | -6 
    4679 S |  | 6 | -6 
    4680 O |  |  | 4 
    4681 Iteration cutoff | 2 
    4682 
    4683 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#1) with
    4684 fold_rrm_2024_06_13_15_51_model_0.cif, chain E (#6), sequence alignment score
    4685 = 1887 
    4686 RMSD between 444 pruned atom pairs is 0.775 angstroms; (across all 477 pairs:
    4687 1.122) 
    4688 
    4689 
    4690 > hide #5 models
    4691 
    4692 > show #5 models
    4693 
    4694 > save "D:/PhD common folder/OneDrive - Indian Institute of
    4695 > Science/Yeast_project/40S_4B/40S_4B_1-98_RRM_AF3.cxs"
    4696 
    4697 \u2014\u2014\u2014 End of log from Thu Jun 13 16:35:32 2024 \u2014\u2014\u2014
    4698 
    4699 opened ChimeraX session 
    4700 
    4701 > open "D:/PhD common folder/OneDrive - Indian Institute of
    4702 > Science/Yeast_project/40S_4B/4B_FL/fold_4b_fl_2024_06_13_16_47_model_0.cif"
    4703 
    4704 Chain information for fold_4b_fl_2024_06_13_16_47_model_0.cif #7 
    4705 --- 
    4706 Chain | Description 
    4707 A | . 
    4708 B | . 
    4709 C | . 
    4710 D | . 
    4711 E | . 
    4712 
    4713 
    4714 > hide #!4 models
    4715 
    4716 > show #!4 models
    4717 
    4718 > hide #5 models
    4719 
    4720 > show #5 models
    4721 
    4722 > hide #5 models
    4723 
    4724 > show #5 models
    4725 
    4726 > hide #5 models
    4727 
    4728 > hide #6 models
    4729 
    4730 > select add #7
    4731 
    4732 17262 atoms, 18592 bonds, 1373 residues, 1 model selected 
    4733 
    4734 > hide sel atoms
    4735 
    4736 > show sel cartoons
    4737 
    4738 > ui tool show Matchmaker
    4739 
    4740 > matchmaker #7 to #1
    4741 
    4742 Using Nucleic matrix instead of BLOSUM-62 for matching 
    4743 Parameters 
    4744 --- 
    4745 Chain pairing | bb 
    4746 Alignment algorithm | Needleman-Wunsch 
    4747 Similarity matrix | Nucleic 
    4748 SS fraction | 0.3 
    4749 Gap open (HH/SS/other) | 18/18/6 
    4750 Gap extend | 1 
    4751 SS matrix |  |  | H | S | O 
    4752 ---|---|---|--- 
    4753 H | 6 | -9 | -6 
    4754 S |  | 6 | -6 
    4755 O |  |  | 4 
    4756 Iteration cutoff | 2 
    4757 
    4758 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#1) with
    4759 fold_4b_fl_2024_06_13_16_47_model_0.cif, chain E (#7), sequence alignment
    4760 score = 1887 
    4761 RMSD between 447 pruned atom pairs is 0.715 angstroms; (across all 477 pairs:
    4762 1.026) 
    4763 
    4764 
    4765 > matchmaker #7 to #1
    4766 
    4767 Using Nucleic matrix instead of BLOSUM-62 for matching 
    4768 Parameters 
    4769 --- 
    4770 Chain pairing | bb 
    4771 Alignment algorithm | Needleman-Wunsch 
    4772 Similarity matrix | Nucleic 
    4773 SS fraction | 0.3 
    4774 Gap open (HH/SS/other) | 18/18/6 
    4775 Gap extend | 1 
    4776 SS matrix |  |  | H | S | O 
    4777 ---|---|---|--- 
    4778 H | 6 | -9 | -6 
    4779 S |  | 6 | -6 
    4780 O |  |  | 4 
    4781 Iteration cutoff | 2 
    4782 
    4783 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#1) with
    4784 fold_4b_fl_2024_06_13_16_47_model_0.cif, chain C (#7), sequence alignment
    4785 score = 3.14629e+230 
    4786 Fewer than 3 residues aligned; cannot match PIN_5_real_space_refined.pdb,
    4787 chain 2 with fold_4b_fl_2024_06_13_16_47_model_0.cif, chain C 
    4788 
    4789 > select clear
    4790 
    4791 > show #5 models
    4792 
    4793 > select #7/D:119
    4794 
    4795 5 atoms, 4 bonds, 1 residue, 1 model selected 
    4796 
    4797 > select up
    4798 
    4799 91 atoms, 93 bonds, 12 residues, 1 model selected 
    4800 
    4801 > select up
    4802 
    4803 3424 atoms, 3494 bonds, 436 residues, 1 model selected 
    4804 
    4805 > color sel red
    4806 
    4807 > select clear
    4808 
    4809 > hide #5 models
    4810 
    4811 > hide #7 models
    4812 
    4813 > show #7 models
    4814 
    4815 > hide #7 models
    4816 
    4817 > show #7 models
    4818 
    4819 > select #7/D:179
    4820 
    4821 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4822 
    4823 > select up
    4824 
    4825 32 atoms, 32 bonds, 4 residues, 1 model selected 
    4826 
    4827 > select up
    4828 
    4829 3424 atoms, 3494 bonds, 436 residues, 1 model selected 
    4830 
    4831 > select ~sel & ##selected
    4832 
    4833 13838 atoms, 15098 bonds, 937 residues, 1 model selected 
    4834 
    4835 > color sel yellow
    4836 
    4837 > select clear
    4838 
    4839 > save "D:/PhD common folder/OneDrive - Indian Institute of
    4840 > Science/Yeast_project/40S_4B/40S_4B_FL.cxs"
    4841 
    4842 \u2014\u2014\u2014 End of log from Thu Jun 13 18:54:25 2024 \u2014\u2014\u2014
    4843 
    4844 opened ChimeraX session 
    4845 
    4846 > graphics silhouettes false
    4847 
    4848 > graphics silhouettes true
    4849 
    4850 > lighting shadows true intensity 0.5
    4851 
    4852 > lighting shadows false
    4853 
    4854 > lighting flat
    4855 
    4856 [Repeated 1 time(s)]
    4857 
    4858 > lighting shadows true intensity 0.5
    4859 
    4860 > graphics silhouettes false
    4861 
    4862 > graphics silhouettes true
    4863 
    4864 > lighting simple
    4865 
    4866 > lighting soft
    4867 
    4868 > hide #!4 models
    4869 
    4870 > select #7/E:149
    4871 
    4872 23 atoms, 25 bonds, 1 residue, 1 model selected 
    4873 
    4874 > select up
    4875 
    4876 10163 atoms, 11360 bonds, 477 residues, 1 model selected 
    4877 
    4878 > select up
    4879 
    4880 17262 atoms, 18592 bonds, 1373 residues, 1 model selected 
    4881 
    4882 > select down
    4883 
    4884 10163 atoms, 11360 bonds, 477 residues, 1 model selected 
    4885 
    4886 > ui tool show "Color Actions"
    4887 
    4888 > color sel wheat
    4889 
    4890 > color sel peach puff
    4891 
    4892 > color sel navajo white
    4893 
    4894 > color sel khaki
    4895 
    4896 > color sel wheat
    4897 
    4898 > select clear
    4899 
    4900 > select #7/C:96
    4901 
    4902 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4903 
    4904 > select up
    4905 
    4906 65 atoms, 65 bonds, 8 residues, 1 model selected 
    4907 
    4908 > select up
    4909 
    4910 936 atoms, 948 bonds, 117 residues, 1 model selected 
    4911 
    4912 > select up
    4913 
    4914 17262 atoms, 18592 bonds, 1373 residues, 1 model selected 
    4915 
    4916 > select down
    4917 
    4918 936 atoms, 948 bonds, 117 residues, 1 model selected 
    4919 
    4920 > ui tool show "Color Actions"
    4921 
    4922 > color sel pale green
    4923 
    4924 > color sel spring green
    4925 
    4926 > color sel lime
    4927 
    4928 > color sel lawn green
    4929 
    4930 > color sel lime green
    4931 
    4932 > color sel spring green
    4933 
    4934 > color sel lime
    4935 
    4936 > select clear
    4937 
    4938 > select #7/D:132
    4939 
    4940 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4941 
    4942 > select up
    4943 
    4944 39 atoms, 38 bonds, 5 residues, 1 model selected 
    4945 
    4946 > select up
    4947 
    4948 3424 atoms, 3494 bonds, 436 residues, 1 model selected 
    4949 
    4950 > color sel magenta
    4951 
    4952 > select clear
    4953 
    4954 > select #7/B:90
    4955 
    4956 11 atoms, 10 bonds, 1 residue, 1 model selected 
    4957 
    4958 > select up
    4959 
    4960 58 atoms, 58 bonds, 7 residues, 1 model selected 
    4961 
    4962 > select up
    4963 
    4964 1847 atoms, 1874 bonds, 237 residues, 1 model selected 
    4965 
    4966 > color sel orange
    4967 
    4968 > select clear
    4969 
    4970 > select #7/A:74
    4971 
    4972 7 atoms, 6 bonds, 1 residue, 1 model selected 
    4973 
    4974 > select up
    4975 
    4976 88 atoms, 89 bonds, 10 residues, 1 model selected 
    4977 
    4978 > select up
    4979 
    4980 892 atoms, 916 bonds, 106 residues, 1 model selected 
    4981 
    4982 > color sel blue
    4983 
    4984 > select clear
    4985 
    4986 > select #7/A:78
    4987 
    4988 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4989 
    4990 > select up
    4991 
    4992 88 atoms, 89 bonds, 10 residues, 1 model selected 
    4993 
    4994 > select up
    4995 
    4996 892 atoms, 916 bonds, 106 residues, 1 model selected 
    4997 
    4998 > ui tool show "Color Actions"
    4999 
    5000 > color sel dodger blue
    5001 
    5002 > color sel royal blue
    5003 
    5004 > select clear
    5005 
    5006 Drag select of 14 residues 
    5007 
    5008 > hide sel target a
    5009 
    5010 > cartoon hide sel
    5011 
    5012 > select clear
    5013 
    5014 Drag select of 22 residues 
    5015 
    5016 > cartoon hide sel
    5017 
    5018 Drag select of 2 residues 
    5019 
    5020 > cartoon hide sel
    5021 
    5022 > select clear
    5023 
    5024 Drag select of 8 residues 
    5025 
    5026 > cartoon hide sel
    5027 
    5028 > select clear
    5029 
    5030 > cartoon style #7 modeHelix tube sides 20
    5031 
    5032 > cartoon style (#7 & coil) xsection oval
    5033 
    5034 > cartoon style #7 xsection barbell modeHelix default
    5035 
    5036 > cartoon style #7 modeHelix tube sides 20
    5037 
    5038 > select #7/D:194
    5039 
    5040 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5041 
    5042 > select up
    5043 
    5044 26 atoms, 27 bonds, 3 residues, 1 model selected 
    5045 
    5046 > select up
    5047 
    5048 3424 atoms, 3494 bonds, 436 residues, 1 model selected 
    5049 
    5050 > cartoon style sel modeHelix tube sides 20
    5051 
    5052 > select clear
    5053 
    5054 > select #7/D:127
    5055 
    5056 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5057 
    5058 > select up
    5059 
    5060 37 atoms, 37 bonds, 5 residues, 1 model selected 
    5061 
    5062 > select clear
    5063 
    5064 > select #7/D:404
    5065 
    5066 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5067 
    5068 > select up
    5069 
    5070 206 atoms, 205 bonds, 27 residues, 1 model selected 
    5071 
    5072 > select up
    5073 
    5074 3424 atoms, 3494 bonds, 436 residues, 1 model selected 
    5075 
    5076 > cartoon style sel xsection oval modeHelix default
    5077 
    5078 > select clear
    5079 
    5080 > select #7/A:13
    5081 
    5082 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5083 
    5084 > select up
    5085 
    5086 131 atoms, 133 bonds, 14 residues, 1 model selected 
    5087 
    5088 > select up
    5089 
    5090 892 atoms, 916 bonds, 106 residues, 1 model selected 
    5091 
    5092 > cartoon style sel modeHelix tube sides 20
    5093 
    5094 > cartoon style sel xsection oval modeHelix default
    5095 
    5096 > ui tool show "Side View"
    5097 
    5098 > select clear
    5099 
    5100 > lighting shadows true intensity 0.5
    5101 
    5102 > select #7/E:101
    5103 
    5104 20 atoms, 21 bonds, 1 residue, 1 model selected 
    5105 
    5106 > select up
    5107 
    5108 10163 atoms, 11360 bonds, 477 residues, 1 model selected 
    5109 
    5110 > surface sel
    5111 
    5112 > select clear
    5113 
    5114 > select #7/E:218@N2
    5115 
    5116 1 atom, 1 residue, 1 model selected 
    5117 
    5118 > select up
    5119 
    5120 23 atoms, 25 bonds, 1 residue, 2 models selected 
    5121 
    5122 > select up
    5123 
    5124 10163 atoms, 11360 bonds, 477 residues, 2 models selected 
    5125 
    5126 > cartoon hide (#!7 & sel)
    5127 
    5128 > select clear
    5129 
    5130 > lighting shadows false
    5131 
    5132 > lighting simple
    5133 
    5134 > lighting flat
    5135 
    5136 > lighting simple
    5137 
    5138 > graphics silhouettes false
    5139 
    5140 > graphics silhouettes true
    5141 
    5142 > lighting full
    5143 
    5144 > lighting shadows false
    5145 
    5146 > lighting shadows true
    5147 
    5148 > lighting shadows false
    5149 
    5150 > lighting shadows true
    5151 
    5152 > graphics silhouettes false
    5153 
    5154 > graphics silhouettes true
    5155 
    5156 > lighting simple
    5157 
    5158 > lighting soft
    5159 
    5160 > lighting simple
    5161 
    5162 > lighting soft
    5163 
    5164 > lighting simple
    5165 
    5166 > lighting soft
    5167 
    5168 > lighting simple
    5169 
    5170 > lighting soft
    5171 
    5172 > lighting simple
    5173 
    5174 > save "D:/PhD common folder/OneDrive - Indian Institute of
    5175 > Science/Yeast_project/40S_4B/3A.png" width 1052 height 585 supersample 3
    5176 
    5177 QWindowsWindow::setGeometry: Unable to set geometry 1x1+312083438+32764
    5178 (frame: 1x1+312083438+32764) on QWindow/"" on "\\\\.\DISPLAY1". Resulting
    5179 geometry: 1x1+32767+32764 (frame: 1x1+32767+32764) margins: 0, 0, 0, 0) 
    5180 
    5181 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    5182 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    5183 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    5184 
    5185 [Repeated 1 time(s)]
    5186 
    5187 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475325705+138 (frame:
    5188 1x1+1475325705+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    5189 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    5190 
    5191 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    5192 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    5193 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    5194 
    5195 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475325705+138 (frame:
    5196 1x1+1475325705+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    5197 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    5198 
    5199 QWindowsWindow::setGeometry: Unable to set geometry 1x1+583780208+546 (frame:
    5200 1x1+583780208+546) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    5201 1x1+32767+546 (frame: 1x1+32767+546) margins: 0, 0, 0, 0) 
    5202 
    5203 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475325705+138 (frame:
    5204 1x1+1475325705+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    5205 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    5206 
    5207 > save "D:/PhD common folder/OneDrive - Indian Institute of
    5208 > Science/Yeast_project/40S_4B/3B.png" width 1052 height 585 supersample 3
    5209 > transparentBackground true
    5210 
    5211 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475325705+138 (frame:
    5212 1x1+1475325705+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    5213 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    5214 
    5215 QWindowsWindow::setGeometry: Unable to set geometry 1x1+47499+0 (frame:
    5216 1x1+47499+0) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    5217 1x1+32767+0 (frame: 1x1+32767+0) margins: 0, 0, 0, 0) 
    5218 
    5219 QWindowsWindow::setGeometry: Unable to set geometry 1x1+1475325705+138 (frame:
    5220 1x1+1475325705+138) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    5221 1x1+32767+138 (frame: 1x1+32767+138) margins: 0, 0, 0, 0) 
    5222 
    5223 [Repeated 2 time(s)]
    5224 
    5225 QWindowsWindow::setGeometry: Unable to set geometry 1x1+47769+0 (frame:
    5226 1x1+47769+0) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    5227 1x1+32767+0 (frame: 1x1+32767+0) margins: 0, 0, 0, 0) 
    5228 
    5229 QWindowsWindow::setGeometry: Unable to set geometry 1x1+47781+0 (frame:
    5230 1x1+47781+0) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    5231 1x1+32767+0 (frame: 1x1+32767+0) margins: 0, 0, 0, 0) 
    5232 
    5233 QWindowsWindow::setGeometry: Unable to set geometry 1x1+47796+0 (frame:
    5234 1x1+47796+0) on QWindow/"" on "\\\\.\DISPLAY1". Resulting geometry:
    5235 1x1+32767+0 (frame: 1x1+32767+0) margins: 0, 0, 0, 0) 
    5236 
    5237 > save "D:/PhD common folder/OneDrive - Indian Institute of
    5238 > Science/Yeast_project/40S_4B/40S_4B_AF_Fig5A.cxs"
    5239 
    5240 \u2014\u2014\u2014 End of log from Fri Aug 9 17:46:46 2024 \u2014\u2014\u2014
    5241 
    5242 opened ChimeraX session 
    5243 
    5244 > close session
    5245 
    5246 > open "D:/PhD common folder/OneDrive - Indian Institute of
    5247 > Science/Yeast_project/40S_4B/fig5C.cxs"
    5248 
    5249 Opened postprocess 1.mrc as #8, grid size 360,360,360, pixel 1.2, shown at
    5250 level 0.004, step 1, values float32 
    5251 Opened emd_17297.map as #9, grid size 400,400,400, pixel 1.06, shown at level
    5252 0.00408, step 2, values float32 
    5253 Log from Fri Aug 9 18:47:29 2024 Startup Messages 
    5254 --- 
    5255 note | available bundle cache has not been initialized yet 
    5256 
    5257 UCSF ChimeraX version: 1.9.dev202407300242 (2024-07-30) 
    5258 © 2016-2024 Regents of the University of California. All rights reserved. 
    5259 How to cite UCSF ChimeraX 
    5260 
    5261 > open "D:\PhD common folder\OneDrive - Indian Institute of
    5262 > Science\Yeast_project\40S_4B\4B_FL\Figure_session.cxs" format session
    5263 
    5264 Opened postprocess 1.mrc as #8, grid size 360,360,360, pixel 1.2, shown at
    5265 level 0.004, step 1, values float32 
    5266 Opened emd_17297.map as #9, grid size 400,400,400, pixel 1.06, shown at level
    5267 0.00408, step 2, values float32 
    5268 Log from Fri Jul 5 12:41:39 2024 Startup Messages 
    5269 --- 
    5270 warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle 
    5271 
    5272 UCSF ChimeraX version: 1.8.dev202312120034 (2023-12-12) 
    5273 © 2016-2023 Regents of the University of California. All rights reserved. 
    5274 How to cite UCSF ChimeraX 
    5275 
    5276 > open "D:\PhD common folder\OneDrive - Indian Institute of
    5277 > Science\Yeast_project\40S_4B\40S_4B_FL_map.cxs" format session
    5278 
    5279 Opened postprocess 1.mrc as #8, grid size 360,360,360, pixel 1.2, shown at
    5280 level 0.004, step 1, values float32 
    5281 Log from Fri Jun 14 15:32:28 2024UCSF ChimeraX version: 1.8.dev202312120034
    5282 (2023-12-12) 
    5283 © 2016-2023 Regents of the University of California. All rights reserved. 
    5284 
    5285 > open "D:\\\PhD common folder\\\OneDrive - Indian Institute of
    5286 > Science\\\Yeast_project\\\40S_4B\\\40S_4B_FL.cxs"
    5287 
    5288 Log from Thu Jun 13 18:54:25 2024UCSF ChimeraX version: 1.8.dev202312120034
    5289 (2023-12-12) 
    5290 © 2016-2023 Regents of the University of California. All rights reserved. 
    5291 
    5292 > open "D:\\\PhD common folder\\\OneDrive - Indian Institute of
    5293 > Science\\\Yeast_project\\\40S_4B\\\40S_4B_1-98_RRM_AF3.cxs"
    5294 
    5295 Log from Thu Jun 13 16:35:32 2024 Startup Messages 
    5296 --- 
    5297 warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle 
    5298 
    5299 You can double click a model's Name or ID in the model panel to edit those
    5300 fields 
    5301 UCSF ChimeraX version: 1.8.dev202312120034 (2023-12-12) 
    5302 © 2016-2023 Regents of the University of California. All rights reserved. 
    5303 How to cite UCSF ChimeraX 
    5304 
    5305 > open "D:\PhD common folder\OneDrive - Indian Institute of
    5306 > Science\Jose_TH_43S_PIC\New_RSR_models\PIN_5_real_space_refined.pdb" format
    5307 > pdb
    5308 
    5309 Chain information for PIN_5_real_space_refined.pdb #1 
    5310 --- 
    5311 Chain | Description 
    5312 1 | No description available 
    5313 2 | No description available 
    5314 3 | No description available 
    5315 A | No description available 
    5316 B | No description available 
    5317 C | No description available 
    5318 D | No description available 
    5319 E | No description available 
    5320 F | No description available 
    5321 G | No description available 
    5322 H | No description available 
    5323 I | No description available 
    5324 J | No description available 
    5325 K | No description available 
    5326 L | No description available 
    5327 M | No description available 
    5328 N | No description available 
    5329 O | No description available 
    5330 P | No description available 
    5331 Q | No description available 
    5332 R | No description available 
    5333 S | No description available 
    5334 T | No description available 
    5335 U | No description available 
    5336 V | No description available 
    5337 W | No description available 
    5338 X | No description available 
    5339 Y | No description available 
    5340 Z | No description available 
    5341 a | No description available 
    5342 b | No description available 
    5343 c | No description available 
    5344 d | No description available 
    5345 e | No description available 
    5346 f | No description available 
    5347 g | No description available 
    5348 h | No description available 
    5349 i | No description available 
    5350 j | No description available 
    5351 k | No description available 
    5352 l | No description available 
    5353 m | No description available 
    5354 n | No description available 
    5355 o | No description available 
    5356 p | No description available 
    5357 q | No description available 
    5358 r | No description available 
    5359 
    5360 
    5361 > ui tool show "Show Sequence Viewer"
    5362 
    5363 > sequence chain /2
    5364 
    5365 Alignment identifier is 1/2 
    5366 
    5367 > select /2:1150
    5368 
    5369 22 atoms, 24 bonds, 1 residue, 1 model selected 
    5370 
    5371 > select /2:1150-1157
    5372 
    5373 175 atoms, 196 bonds, 8 residues, 1 model selected 
    5374 
    5375 > select /2:1150
    5376 
    5377 22 atoms, 24 bonds, 1 residue, 1 model selected 
    5378 
    5379 > select /2:1150-1626
    5380 
    5381 10173 atoms, 11370 bonds, 477 residues, 1 model selected 
    5382 
    5383 > select ~sel & ##selected
    5384 
    5385 94063 atoms, 98599 bonds, 9675 residues, 1 model selected 
    5386 
    5387 > delete atoms sel
    5388 
    5389 > delete bonds sel
    5390 
    5391 > select protein
    5392 
    5393 Nothing selected 
    5394 
    5395 > show cartoons
    5396 
    5397 > hide atoms
    5398 
    5399 > set bgColor white
    5400 
    5401 > open "D:/PhD common folder/OneDrive - Indian Institute of
    5402 > Science/Yeast_project/40S_4B/fold_40s_rrna_head_2024_06_12_22_44_model_0.cif"
    5403 
    5404 Chain information for fold_40s_rrna_head_2024_06_12_22_44_model_0.cif #2 
    5405 --- 
    5406 Chain | Description 
    5407 A | . 
    5408 
    5409 
    5410 > ui tool show Matchmaker
    5411 
    5412 > matchmaker #2 to #1
    5413 
    5414 Using Nucleic matrix instead of BLOSUM-62 for matching 
    5415 Parameters 
    5416 --- 
    5417 Chain pairing | bb 
    5418 Alignment algorithm | Needleman-Wunsch 
    5419 Similarity matrix | Nucleic 
    5420 SS fraction | 0.3 
    5421 Gap open (HH/SS/other) | 18/18/6 
    5422 Gap extend | 1 
    5423 SS matrix |  |  | H | S | O 
    5424 ---|---|---|--- 
    5425 H | 6 | -9 | -6 
    5426 S |  | 6 | -6 
    5427 O |  |  | 4 
    5428 Iteration cutoff | 2 
    5429 
    5430 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#1) with
    5431 fold_40s_rrna_head_2024_06_12_22_44_model_0.cif, chain A (#2), sequence
    5432 alignment score = 1887 
    5433 RMSD between 441 pruned atom pairs is 0.742 angstroms; (across all 477 pairs:
    5434 1.140) 
    5435 
    5436 
    5437 > select add #2
    5438 
    5439 10163 atoms, 11360 bonds, 477 residues, 1 model selected 
    5440 
    5441 > hide sel atoms
    5442 
    5443 > select subtract #2
    5444 
    5445 Nothing selected 
    5446 
    5447 > lighting soft
    5448 
    5449 > graphics silhouettes true
    5450 
    5451 > open "D:/PhD common folder/OneDrive - Indian Institute of
    5452 > Science/Yeast_project/40S_4B/New folder/fold_2024_06_13_01_16_model_0.cif"
    5453 
    5454 Chain information for fold_2024_06_13_01_16_model_0.cif #3 
    5455 --- 
    5456 Chain | Description 
    5457 A | . 
    5458 B | . 
    5459 C | . 
    5460 D | . 
    5461 
    5462 
    5463 > ui tool show Matchmaker
    5464 
    5465 > matchmaker #3 to #1
    5466 
    5467 Using Nucleic matrix instead of BLOSUM-62 for matching 
    5468 Parameters 
    5469 --- 
    5470 Chain pairing | bb 
    5471 Alignment algorithm | Needleman-Wunsch 
    5472 Similarity matrix | Nucleic 
    5473 SS fraction | 0.3 
    5474 Gap open (HH/SS/other) | 18/18/6 
    5475 Gap extend | 1 
    5476 SS matrix |  |  | H | S | O 
    5477 ---|---|---|--- 
    5478 H | 6 | -9 | -6 
    5479 S |  | 6 | -6 
    5480 O |  |  | 4 
    5481 Iteration cutoff | 2 
    5482 
    5483 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#1) with
    5484 fold_2024_06_13_01_16_model_0.cif, chain D (#3), sequence alignment score =
    5485 1887 
    5486 RMSD between 451 pruned atom pairs is 0.755 angstroms; (across all 477 pairs:
    5487 1.036) 
    5488 
    5489 
    5490 > matchmaker #3 to #1
    5491 
    5492 Using Nucleic matrix instead of BLOSUM-62 for matching 
    5493 Parameters 
    5494 --- 
    5495 Chain pairing | bb 
    5496 Alignment algorithm | Needleman-Wunsch 
    5497 Similarity matrix | Nucleic 
    5498 SS fraction | 0.3 
    5499 Gap open (HH/SS/other) | 18/18/6 
    5500 Gap extend | 1 
    5501 SS matrix |  |  | H | S | O 
    5502 ---|---|---|--- 
    5503 H | 6 | -9 | -6 
    5504 S |  | 6 | -6 
    5505 O |  |  | 4 
    5506 Iteration cutoff | 2 
    5507 
    5508 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#1) with
    5509 fold_2024_06_13_01_16_model_0.cif, chain D (#3), sequence alignment score =
    5510 1887 
    5511 RMSD between 451 pruned atom pairs is 0.755 angstroms; (across all 477 pairs:
    5512 1.036) 
    5513 
    5514 
    5515 > select add #3
    5516 
    5517 13838 atoms, 15098 bonds, 937 residues, 1 model selected 
    5518 
    5519 > hide sel atoms
    5520 
    5521 > select subtract #3
    5522 
    5523 Nothing selected 
    5524 
    5525 > hide #2 models
    5526 
    5527 > select add #1
    5528 
    5529 10173 atoms, 11370 bonds, 477 residues, 1 model selected 
    5530 
    5531 > show sel cartoons
    5532 
    5533 > hide sel atoms
    5534 
    5535 > surface sel
    5536 
    5537 > hide sel atoms
    5538 
    5539 > surface hidePatches (#!1 & sel)
    5540 
    5541 > open "D:/PhD common folder/OneDrive - Indian Institute of
    5542 > Science/Jose_TH_43S_PIC/New_RSR_models/PIN_5_real_space_refined.pdb"
    5543 
    5544 Chain information for PIN_5_real_space_refined.pdb #4 
    5545 --- 
    5546 Chain | Description 
    5547 1 | No description available 
    5548 2 | No description available 
    5549 3 | No description available 
    5550 A | No description available 
    5551 B | No description available 
    5552 C | No description available 
    5553 D | No description available 
    5554 E | No description available 
    5555 F | No description available 
    5556 G | No description available 
    5557 H | No description available 
    5558 I | No description available 
    5559 J | No description available 
    5560 K | No description available 
    5561 L | No description available 
    5562 M | No description available 
    5563 N | No description available 
    5564 O | No description available 
    5565 P | No description available 
    5566 Q | No description available 
    5567 R | No description available 
    5568 S | No description available 
    5569 T | No description available 
    5570 U | No description available 
    5571 V | No description available 
    5572 W | No description available 
    5573 X | No description available 
    5574 Y | No description available 
    5575 Z | No description available 
    5576 a | No description available 
    5577 b | No description available 
    5578 c | No description available 
    5579 d | No description available 
    5580 e | No description available 
    5581 f | No description available 
    5582 g | No description available 
    5583 h | No description available 
    5584 i | No description available 
    5585 j | No description available 
    5586 k | No description available 
    5587 l | No description available 
    5588 m | No description available 
    5589 n | No description available 
    5590 o | No description available 
    5591 p | No description available 
    5592 q | No description available 
    5593 r | No description available 
    5594 
    5595 
    5596 > select add #4
    5597 
    5598 114409 atoms, 121339 bonds, 10629 residues, 3 models selected 
    5599 
    5600 > select subtract #1
    5601 
    5602 104236 atoms, 109969 bonds, 10152 residues, 2 models selected 
    5603 
    5604 > surface hidePatches sel
    5605 
    5606 > hide sel atoms
    5607 
    5608 > show sel cartoons
    5609 
    5610 > ui tool show Matchmaker
    5611 
    5612 > matchmaker #!4 to #1/2 pairing bs matrix Nucleic
    5613 
    5614 Parameters 
    5615 --- 
    5616 Chain pairing | bs 
    5617 Alignment algorithm | Needleman-Wunsch 
    5618 Similarity matrix | Nucleic 
    5619 SS fraction | 0.3 
    5620 Gap open (HH/SS/other) | 18/18/6 
    5621 Gap extend | 1 
    5622 SS matrix |  |  | H | S | O 
    5623 ---|---|---|--- 
    5624 H | 6 | -9 | -6 
    5625 S |  | 6 | -6 
    5626 O |  |  | 4 
    5627 Iteration cutoff | 2 
    5628 
    5629 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#1) with
    5630 PIN_5_real_space_refined.pdb, chain 2 (#4), sequence alignment score = 5525.6 
    5631 RMSD between 477 pruned atom pairs is 0.000 angstroms; (across all 477 pairs:
    5632 0.000) 
    5633 
    5634 
    5635 > select clear
    5636 
    5637 > color #4 yellow
    5638 
    5639 > select #1/2:1361
    5640 
    5641 20 atoms, 21 bonds, 1 residue, 1 model selected 
    5642 
    5643 > select up
    5644 
    5645 10173 atoms, 11370 bonds, 477 residues, 2 models selected 
    5646 
    5647 > select clear
    5648 
    5649 > select #1/2:1373
    5650 
    5651 20 atoms, 21 bonds, 1 residue, 1 model selected 
    5652 
    5653 > select up
    5654 
    5655 10173 atoms, 11370 bonds, 477 residues, 2 models selected 
    5656 
    5657 > hide #!1 models
    5658 
    5659 > show #!1 models
    5660 
    5661 > hide #!1 models
    5662 
    5663 > hide #3 models
    5664 
    5665 > select add #4/U:47
    5666 
    5667 10180 atoms, 11376 bonds, 478 residues, 3 models selected 
    5668 
    5669 > select up
    5670 
    5671 10332 atoms, 11529 bonds, 497 residues, 3 models selected 
    5672 
    5673 > select up
    5674 
    5675 11018 atoms, 12227 bonds, 583 residues, 3 models selected 
    5676 
    5677 > show #3 models
    5678 
    5679 > hide #3 models
    5680 
    5681 > show #3 models
    5682 
    5683 > hide #3 models
    5684 
    5685 > select add #4/D:126
    5686 
    5687 11025 atoms, 12233 bonds, 584 residues, 3 models selected 
    5688 
    5689 > select up
    5690 
    5691 11150 atoms, 12360 bonds, 600 residues, 3 models selected 
    5692 
    5693 > select up
    5694 
    5695 12792 atoms, 14027 bonds, 810 residues, 3 models selected 
    5696 
    5697 > select up
    5698 
    5699 114409 atoms, 121339 bonds, 10629 residues, 3 models selected 
    5700 
    5701 > select down
    5702 
    5703 12792 atoms, 14027 bonds, 810 residues, 3 models selected 
    5704 
    5705 > show #3 models
    5706 
    5707 > hide #3 models
    5708 
    5709 > select add #4/K:16
    5710 
    5711 12803 atoms, 14038 bonds, 811 residues, 3 models selected 
    5712 
    5713 > select up
    5714 
    5715 12934 atoms, 14172 bonds, 826 residues, 3 models selected 
    5716 
    5717 > select up
    5718 
    5719 13601 atoms, 14858 bonds, 906 residues, 3 models selected 
    5720 
    5721 > select up
    5722 
    5723 114409 atoms, 121339 bonds, 10629 residues, 3 models selected 
    5724 
    5725 > select down
    5726 
    5727 13601 atoms, 14858 bonds, 906 residues, 3 models selected 
    5728 
    5729 > select add #4/2:1333
    5730 
    5731 13621 atoms, 14879 bonds, 907 residues, 3 models selected 
    5732 
    5733 > select up
    5734 
    5735 51413 atoms, 57141 bonds, 2686 residues, 3 models selected 
    5736 
    5737 > select ~sel & ##selected
    5738 
    5739 62996 atoms, 64198 bonds, 7943 residues, 1 model selected 
    5740 
    5741 > hide sel target a
    5742 
    5743 > hide sel cartoons
    5744 
    5745 > select clear
    5746 
    5747 > show #3 models
    5748 
    5749 > open "D:/PhD common folder/OneDrive - Indian Institute of
    5750 > Science/Yeast_project/40S_4B/New folder
    5751 > (2)/fold_2024_06_13_14_34_model_0.cif"
    5752 
    5753 Chain information for fold_2024_06_13_14_34_model_0.cif #5 
    5754 --- 
    5755 Chain | Description 
    5756 A | . 
    5757 B | . 
    5758 C | . 
    5759 D | . 
    5760 E | . 
    5761 
    5762 
    5763 > select #5/C:45@O
    5764 
    5765 1 atom, 1 residue, 1 model selected 
    5766 
    5767 > select #5/C:45@O
    5768 
    5769 1 atom, 1 residue, 1 model selected 
    5770 
    5771 > select clear
    5772 
    5773 > select add #5
    5774 
    5775 14573 atoms, 15847 bonds, 1035 residues, 1 model selected 
    5776 
    5777 > hide sel atoms
    5778 
    5779 > show sel cartoons
    5780 
    5781 > select clear
    5782 
    5783 > color #5 #ff55ffff
    5784 
    5785 > color #5 red
    5786 
    5787 > ui tool show Matchmaker
    5788 
    5789 > matchmaker #5 to #1/2 pairing bs matrix Nucleic
    5790 
    5791 Parameters 
    5792 --- 
    5793 Chain pairing | bs 
    5794 Alignment algorithm | Needleman-Wunsch 
    5795 Similarity matrix | Nucleic 
    5796 SS fraction | 0.3 
    5797 Gap open (HH/SS/other) | 18/18/6 
    5798 Gap extend | 1 
    5799 SS matrix |  |  | H | S | O 
    5800 ---|---|---|--- 
    5801 H | 6 | -9 | -6 
    5802 S |  | 6 | -6 
    5803 O |  |  | 4 
    5804 Iteration cutoff | 2 
    5805 
    5806 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#1) with
    5807 fold_2024_06_13_14_34_model_0.cif, chain E (#5), sequence alignment score =
    5808 1887 
    5809 RMSD between 446 pruned atom pairs is 0.750 angstroms; (across all 477 pairs:
    5810 1.027) 
    5811 
    5812 
    5813 > matchmaker #5 to #1/2 pairing bs matrix Nucleic
    5814 
    5815 Parameters 
    5816 --- 
    5817 Chain pairing | bs 
    5818 Alignment algorithm | Needleman-Wunsch 
    5819 Similarity matrix | Nucleic 
    5820 SS fraction | 0.3 
    5821 Gap open (HH/SS/other) | 18/18/6 
    5822 Gap extend | 1 
    5823 SS matrix |  |  | H | S | O 
    5824 ---|---|---|--- 
    5825 H | 6 | -9 | -6 
    5826 S |  | 6 | -6 
    5827 O |  |  | 4 
    5828 Iteration cutoff | 2 
    5829 
    5830 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#1) with
    5831 fold_2024_06_13_14_34_model_0.cif, chain E (#5), sequence alignment score =
    5832 1887 
    5833 RMSD between 446 pruned atom pairs is 0.750 angstroms; (across all 477 pairs:
    5834 1.027) 
    5835 
    5836 
    5837 > hide #3 models
    5838 
    5839 > select #5/D:61
    5840 
    5841 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5842 
    5843 > select up
    5844 
    5845 30 atoms, 29 bonds, 4 residues, 1 model selected 
    5846 
    5847 > select up
    5848 
    5849 735 atoms, 749 bonds, 98 residues, 1 model selected 
    5850 
    5851 > color sel cyan
    5852 
    5853 > color sel lime
    5854 
    5855 > select clear
    5856 
    5857 > select #5/D:56
    5858 
    5859 5 atoms, 4 bonds, 1 residue, 1 model selected 
    5860 
    5861 > select up
    5862 
    5863 24 atoms, 24 bonds, 3 residues, 1 model selected 
    5864 
    5865 > select up
    5866 
    5867 735 atoms, 749 bonds, 98 residues, 1 model selected 
    5868 
    5869 > select ~sel
    5870 
    5871 152248 atoms, 162895 bonds, 12980 residues, 5 models selected 
    5872 
    5873 > select subtract #1
    5874 
    5875 142075 atoms, 151525 bonds, 12503 residues, 5 models selected 
    5876 
    5877 > select subtract #2
    5878 
    5879 131912 atoms, 140165 bonds, 12026 residues, 3 models selected 
    5880 
    5881 > select subtract #3
    5882 
    5883 118074 atoms, 125067 bonds, 11089 residues, 2 models selected 
    5884 
    5885 > color sel yellow
    5886 
    5887 > select clear
    5888 
    5889 > save "D:/PhD common folder/OneDrive - Indian Institute of
    5890 > Science/Yeast_project/40S_4B/40S_4B_1-98_AF3.cxs"
    5891 
    5892 > open "D:/PhD common folder/OneDrive - Indian Institute of
    5893 > Science/Yeast_project/40S_4B/RRM/fold_rrm_2024_06_13_15_51_model_0.cif"
    5894 
    5895 Chain information for fold_rrm_2024_06_13_15_51_model_0.cif #6 
    5896 --- 
    5897 Chain | Description 
    5898 A | . 
    5899 B | . 
    5900 C | . 
    5901 D | . 
    5902 E | . 
    5903 
    5904 
    5905 > select add #6
    5906 
    5907 14522 atoms, 15797 bonds, 1024 residues, 1 model selected 
    5908 
    5909 > hide sel atoms
    5910 
    5911 > show sel cartoons
    5912 
    5913 > select clear
    5914 
    5915 > ui tool show Matchmaker
    5916 
    5917 > matchmaker #6 to #1/2 pairing bs matrix Nucleic
    5918 
    5919 Parameters 
    5920 --- 
    5921 Chain pairing | bs 
    5922 Alignment algorithm | Needleman-Wunsch 
    5923 Similarity matrix | Nucleic 
    5924 SS fraction | 0.3 
    5925 Gap open (HH/SS/other) | 18/18/6 
    5926 Gap extend | 1 
    5927 SS matrix |  |  | H | S | O 
    5928 ---|---|---|--- 
    5929 H | 6 | -9 | -6 
    5930 S |  | 6 | -6 
    5931 O |  |  | 4 
    5932 Iteration cutoff | 2 
    5933 
    5934 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#1) with
    5935 fold_rrm_2024_06_13_15_51_model_0.cif, chain E (#6), sequence alignment score
    5936 = 1887 
    5937 RMSD between 444 pruned atom pairs is 0.775 angstroms; (across all 477 pairs:
    5938 1.122) 
    5939 
    5940 
    5941 > matchmaker #6 to #1/2 pairing bs matrix Nucleic
    5942 
    5943 Parameters 
    5944 --- 
    5945 Chain pairing | bs 
    5946 Alignment algorithm | Needleman-Wunsch 
    5947 Similarity matrix | Nucleic 
    5948 SS fraction | 0.3 
    5949 Gap open (HH/SS/other) | 18/18/6 
    5950 Gap extend | 1 
    5951 SS matrix |  |  | H | S | O 
    5952 ---|---|---|--- 
    5953 H | 6 | -9 | -6 
    5954 S |  | 6 | -6 
    5955 O |  |  | 4 
    5956 Iteration cutoff | 2 
    5957 
    5958 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#1) with
    5959 fold_rrm_2024_06_13_15_51_model_0.cif, chain E (#6), sequence alignment score
    5960 = 1887 
    5961 RMSD between 444 pruned atom pairs is 0.775 angstroms; (across all 477 pairs:
    5962 1.122) 
    5963 
    5964 
    5965 > matchmaker #6 to #1/2 pairing bs matrix Nucleic
    5966 
    5967 Parameters 
    5968 --- 
    5969 Chain pairing | bs 
    5970 Alignment algorithm | Needleman-Wunsch 
    5971 Similarity matrix | Nucleic 
    5972 SS fraction | 0.3 
    5973 Gap open (HH/SS/other) | 18/18/6 
    5974 Gap extend | 1 
    5975 SS matrix |  |  | H | S | O 
    5976 ---|---|---|--- 
    5977 H | 6 | -9 | -6 
    5978 S |  | 6 | -6 
    5979 O |  |  | 4 
    5980 Iteration cutoff | 2 
    5981 
    5982 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#1) with
    5983 fold_rrm_2024_06_13_15_51_model_0.cif, chain E (#6), sequence alignment score
    5984 = 1887 
    5985 RMSD between 444 pruned atom pairs is 0.775 angstroms; (across all 477 pairs:
    5986 1.122) 
    5987 
    5988 
    5989 > hide #5 models
    5990 
    5991 > show #5 models
    5992 
    5993 > save "D:/PhD common folder/OneDrive - Indian Institute of
    5994 > Science/Yeast_project/40S_4B/40S_4B_1-98_RRM_AF3.cxs"
    5995 
    5996 \u2014\u2014\u2014 End of log from Thu Jun 13 16:35:32 2024 \u2014\u2014\u2014
    5997 
    5998 opened ChimeraX session 
    5999 
    6000 > open "D:/PhD common folder/OneDrive - Indian Institute of
    6001 > Science/Yeast_project/40S_4B/4B_FL/fold_4b_fl_2024_06_13_16_47_model_0.cif"
    6002 
    6003 Chain information for fold_4b_fl_2024_06_13_16_47_model_0.cif #7 
    6004 --- 
    6005 Chain | Description 
    6006 A | . 
    6007 B | . 
    6008 C | . 
    6009 D | . 
    6010 E | . 
    6011 
    6012 
    6013 > hide #!4 models
    6014 
    6015 > show #!4 models
    6016 
    6017 > hide #5 models
    6018 
    6019 > show #5 models
    6020 
    6021 > hide #5 models
    6022 
    6023 > show #5 models
    6024 
    6025 > hide #5 models
    6026 
    6027 > hide #6 models
    6028 
    6029 > select add #7
    6030 
    6031 17262 atoms, 18592 bonds, 1373 residues, 1 model selected 
    6032 
    6033 > hide sel atoms
    6034 
    6035 > show sel cartoons
    6036 
    6037 > ui tool show Matchmaker
    6038 
    6039 > matchmaker #7 to #1
    6040 
    6041 Using Nucleic matrix instead of BLOSUM-62 for matching 
    6042 Parameters 
    6043 --- 
    6044 Chain pairing | bb 
    6045 Alignment algorithm | Needleman-Wunsch 
    6046 Similarity matrix | Nucleic 
    6047 SS fraction | 0.3 
    6048 Gap open (HH/SS/other) | 18/18/6 
    6049 Gap extend | 1 
    6050 SS matrix |  |  | H | S | O 
    6051 ---|---|---|--- 
    6052 H | 6 | -9 | -6 
    6053 S |  | 6 | -6 
    6054 O |  |  | 4 
    6055 Iteration cutoff | 2 
    6056 
    6057 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#1) with
    6058 fold_4b_fl_2024_06_13_16_47_model_0.cif, chain E (#7), sequence alignment
    6059 score = 1887 
    6060 RMSD between 447 pruned atom pairs is 0.715 angstroms; (across all 477 pairs:
    6061 1.026) 
    6062 
    6063 
    6064 > matchmaker #7 to #1
    6065 
    6066 Using Nucleic matrix instead of BLOSUM-62 for matching 
    6067 Parameters 
    6068 --- 
    6069 Chain pairing | bb 
    6070 Alignment algorithm | Needleman-Wunsch 
    6071 Similarity matrix | Nucleic 
    6072 SS fraction | 0.3 
    6073 Gap open (HH/SS/other) | 18/18/6 
    6074 Gap extend | 1 
    6075 SS matrix |  |  | H | S | O 
    6076 ---|---|---|--- 
    6077 H | 6 | -9 | -6 
    6078 S |  | 6 | -6 
    6079 O |  |  | 4 
    6080 Iteration cutoff | 2 
    6081 
    6082 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#1) with
    6083 fold_4b_fl_2024_06_13_16_47_model_0.cif, chain C (#7), sequence alignment
    6084 score = 3.14629e+230 
    6085 Fewer than 3 residues aligned; cannot match PIN_5_real_space_refined.pdb,
    6086 chain 2 with fold_4b_fl_2024_06_13_16_47_model_0.cif, chain C 
    6087 
    6088 > select clear
    6089 
    6090 > show #5 models
    6091 
    6092 > select #7/D:119
    6093 
    6094 5 atoms, 4 bonds, 1 residue, 1 model selected 
    6095 
    6096 > select up
    6097 
    6098 91 atoms, 93 bonds, 12 residues, 1 model selected 
    6099 
    6100 > select up
    6101 
    6102 3424 atoms, 3494 bonds, 436 residues, 1 model selected 
    6103 
    6104 > color sel red
    6105 
    6106 > select clear
    6107 
    6108 > hide #5 models
    6109 
    6110 > hide #7 models
    6111 
    6112 > show #7 models
    6113 
    6114 > hide #7 models
    6115 
    6116 > show #7 models
    6117 
    6118 > select #7/D:179
    6119 
    6120 6 atoms, 5 bonds, 1 residue, 1 model selected 
    6121 
    6122 > select up
    6123 
    6124 32 atoms, 32 bonds, 4 residues, 1 model selected 
    6125 
    6126 > select up
    6127 
    6128 3424 atoms, 3494 bonds, 436 residues, 1 model selected 
    6129 
    6130 > select ~sel & ##selected
    6131 
    6132 13838 atoms, 15098 bonds, 937 residues, 1 model selected 
    6133 
    6134 > color sel yellow
    6135 
    6136 > select clear
    6137 
    6138 > save "D:/PhD common folder/OneDrive - Indian Institute of
    6139 > Science/Yeast_project/40S_4B/40S_4B_FL.cxs"
    6140 
    6141 \u2014\u2014\u2014 End of log from Thu Jun 13 18:54:25 2024 \u2014\u2014\u2014
    6142 
    6143 opened ChimeraX session 
    6144 
    6145 > open "D:/PhD common folder/OneDrive - Indian Institute of
    6146 > Science/Yeast_project/40S_4B/4B_FL/postprocess.mrc"
    6147 
    6148 Opened postprocess.mrc as #8, grid size 360,360,360, pixel 1.2, shown at level
    6149 0.0128, step 2, values float32 
    6150 
    6151 > volume #8 level 0.005107
    6152 
    6153 > volume #8 level 0.01186
    6154 
    6155 > close #8
    6156 
    6157 > open "D:/PhD common folder/OneDrive - Indian Institute of
    6158 > Science/Yeast_project/40S_4B/4B_FL/postprocess 1.mrc"
    6159 
    6160 Opened postprocess 1.mrc as #8, grid size 360,360,360, pixel 1.2, shown at
    6161 level 0.0117, step 2, values float32 
    6162 
    6163 > select add #7
    6164 
    6165 17262 atoms, 18592 bonds, 1373 residues, 1 model selected 
    6166 
    6167 > select add #4
    6168 
    6169 121498 atoms, 128561 bonds, 11525 residues, 2 models selected 
    6170 
    6171 > select subtract #4
    6172 
    6173 17262 atoms, 18592 bonds, 1373 residues, 1 model selected 
    6174 
    6175 > select add #4
    6176 
    6177 121498 atoms, 128561 bonds, 11525 residues, 2 models selected 
    6178 
    6179 > ui mousemode right "translate selected models"
    6180 
    6181 > view matrix models
    6182 > #4,1,0,0,29.873,0,1,0,-26.112,0,0,1,-4.1724,#7,0.28189,0.89695,-0.3406,208.48,-0.59451,-0.11535,-0.79578,143.74,-0.75306,0.42681,0.50073,170.55
    6183 
    6184 > view matrix models
    6185 > #4,0.82111,0.074806,0.56584,-60.523,0.37786,0.67177,-0.63714,95.401,-0.42778,0.73697,0.52334,8.5864,#7,-0.23912,0.96938,-0.055872,197.7,0.18694,-0.010503,-0.98231,165.67,-0.95282,-0.24534,-0.17871,148.8
    6186 
    6187 > view matrix models
    6188 > #4,0.39428,0.28977,0.87211,-82.164,0.12554,0.92311,-0.36347,36.734,-0.91037,0.25279,0.32759,252.6,#7,-0.71788,0.69246,0.071801,189.85,-0.23969,-0.14901,-0.95935,152.45,-0.65361,-0.7059,0.27294,190.17
    6189 
    6190 > view matrix models
    6191 > #4,0.93276,0.24233,0.26689,-61.721,-0.20029,0.96394,-0.17522,56.548,-0.29973,0.10998,0.94766,39.262,#7,-0.082117,0.92261,-0.3769,192.67,-0.49758,-0.36563,-0.7866,153.89,-0.86352,0.12294,0.48909,169.98
    6192 
    6193 > view matrix models
    6194 > #4,0.90668,0.38695,-0.16792,-3.6645,-0.32198,0.89205,0.31713,0.28806,0.27251,-0.23347,0.9334,5.1958,#7,0.15199,0.69695,-0.70083,194.66,-0.85991,-0.25634,-0.44141,149.71,-0.48729,0.66974,0.56035,177.29
    6195 
    6196 > view matrix models
    6197 > #4,0.83083,0.46289,-0.30895,22.476,-0.33038,0.85698,0.39553,-5.67,0.44785,-0.22655,0.86493,-18.087,#7,0.19167,0.55996,-0.80604,195.51,-0.90046,-0.22637,-0.37138,149.99,-0.39042,0.797,0.46084,174.54
    6198 
    6199 > view matrix models
    6200 > #4,0.81586,0.41377,-0.40394,53.081,-0.43451,0.8996,0.043887,72.529,0.38154,0.13971,0.91373,-95.845,#7,0.28818,0.51166,-0.80942,198.5,-0.69035,-0.47477,-0.5459,155.39,-0.6636,0.7161,0.2164,155.68
    6201 
    6202 > view matrix models
    6203 > #4,0.92225,0.36326,0.13231,-66.698,-0.33704,0.92311,-0.18513,90.197,-0.18939,0.12614,0.97377,7.703,#7,-0.055625,0.84179,-0.53694,182.84,-0.50438,-0.4878,-0.71249,154.45,-0.86169,0.23119,0.45172,165.44
    6204 
    6205 > view matrix models
    6206 > #4,0.90839,0.41625,0.039549,-57.795,-0.40792,0.86146,0.30246,24.934,0.091829,-0.29088,0.95234,48.468,#7,-0.021182,0.78365,-0.62084,182.06,-0.8549,-0.33616,-0.39515,151.25,-0.51836,0.52239,0.67706,181.85
    6207 
    6208 > view matrix models
    6209 > #4,0.84077,0.51864,-0.15529,-28.698,-0.44574,0.82595,0.34513,31.845,0.30726,-0.22096,0.92562,-4.1938,#7,0.04562,0.62803,-0.77685,182.43,-0.87659,-0.34777,-0.33263,152.83,-0.47907,0.69615,0.53466,174.88
    6210 
    6211 > view matrix models
    6212 > #4,0.84077,0.51864,-0.15529,-50.435,-0.44574,0.82595,0.34513,42.879,0.30726,-0.22096,0.92562,-2.874,#7,0.04562,0.62803,-0.77685,160.69,-0.87659,-0.34777,-0.33263,163.86,-0.47907,0.69615,0.53466,176.2
    6213 
    6214 > view matrix models
    6215 > #4,0.89894,0.43035,0.081855,-87.056,-0.41583,0.89706,-0.14958,114.17,-0.1378,0.10043,0.98536,2.6161,#7,-0.064087,0.79161,-0.60766,160.9,-0.53788,-0.54029,-0.64712,166.14,-0.84058,0.28538,0.46042,167.22
    6216 
    6217 > view matrix models
    6218 > #4,0.82294,0.43483,0.36563,-128.34,-0.25543,0.85805,-0.44554,148.79,-0.50747,0.27326,0.8172,70.448,#7,-0.30188,0.84404,-0.44324,156.38,-0.2466,-0.51824,-0.81891,171.07,-0.9209,-0.13791,0.36459,169
    6219 
    6220 > view matrix models
    6221 > #4,0.72434,0.68781,0.047535,-102.66,-0.68702,0.7143,0.13333,154.87,0.057748,-0.12923,0.98993,13.333,#7,-0.24052,0.59065,-0.77025,151.84,-0.71872,-0.64172,-0.26766,176.79,-0.65237,0.48922,0.57886,174.65
    6222 
    6223 > view matrix models
    6224 > #4,0.72434,0.68781,0.047535,-93.022,-0.68702,0.7143,0.13333,168.08,0.057748,-0.12923,0.98993,9.714,#7,-0.24052,0.59065,-0.77025,161.48,-0.71872,-0.64172,-0.26766,190,-0.65237,0.48922,0.57886,171.04
    6225 
    6226 > view matrix models
    6227 > #4,0.72434,0.68781,0.047535,-95.873,-0.68702,0.7143,0.13333,147.08,0.057748,-0.12923,0.98993,29.062,#7,-0.24052,0.59065,-0.77025,158.63,-0.71872,-0.64172,-0.26766,169,-0.65237,0.48922,0.57886,190.38
    6228 
    6229 > view matrix models
    6230 > #4,0.85992,0.49465,-0.12597,-48.976,-0.47438,0.86556,0.16051,68.367,0.18843,-0.078265,0.97896,-5.6566,#7,0.043195,0.66049,-0.74959,166.62,-0.76918,-0.45683,-0.44685,158.7,-0.63758,0.59587,0.4883,185.75
    6231 
    6232 > view matrix models
    6233 > #4,0.82107,0.52004,0.23539,-114.53,-0.48014,0.85219,-0.20793,141.5,-0.30873,0.057706,0.9494,68.51,#7,-0.25498,0.77694,-0.57563,161.58,-0.48539,-0.61771,-0.61873,164.17,-0.83629,0.12164,0.53462,189.05
    6234 
    6235 > ui tool show "Fit in Map"
    6236 
    6237 > fitmap #1 inMap #8
    6238 
    6239 Fit molecule PIN_5_real_space_refined.pdb (#1) to map postprocess 1.mrc (#8)
    6240 using 10173 atoms 
    6241 average map value = 0.01768, steps = 280 
    6242 shifted from previous position = 37.6 
    6243 rotated from previous position = 39.4 degrees 
    6244 atoms outside contour = 1813, contour level = 0.011685 
    6245 
    6246 Position of PIN_5_real_space_refined.pdb (#1) relative to postprocess 1.mrc
    6247 (#8) coordinates: 
    6248 Matrix rotation and translation 
    6249 0.77406817 0.62549730 0.09783453 -108.84656169 
    6250 -0.61873269 0.78014893 -0.09239861 173.02544428 
    6251 -0.13412059 0.01098940 0.99090408 40.92544766 
    6252 Axis 0.08141544 0.18265879 -0.97979962 
    6253 Axis point 198.28970282 243.37991178 0.00000000 
    6254 Rotation angle (degrees) 39.41561211 
    6255 Shift along axis -17.35591133 
    6256 
    6257 
    6258 > volume #8 level 0.008395
    6259 
    6260 > volume #8 level 0.007367
    6261 
    6262 > volume #8 level 0.006339
    6263 
    6264 > volume #8 level 0.005928
    6265 
    6266 > volume #8 level 0.0049
    6267 
    6268 > volume #8 level 0.004694
    6269 
    6270 > volume #8 level 0.004283
    6271 
    6272 > volume #8 level 0.004077
    6273 
    6274 > volume #8 level 0.003872
    6275 
    6276 > volume #8 level 0.004077
    6277 
    6278 > ui tool show "Hide Dust"
    6279 
    6280 > surface dust #8 size 50.34
    6281 
    6282 > view matrix models
    6283 > #4,0.82107,0.52004,0.23539,-116.39,-0.48014,0.85219,-0.20793,141.63,-0.30873,0.057706,0.9494,74.429,#7,-0.25498,0.77694,-0.57563,159.72,-0.48539,-0.61771,-0.61873,164.29,-0.83629,0.12164,0.53462,194.97
    6284 
    6285 > view matrix models
    6286 > #4,0.78554,0.61095,0.098306,-102.93,-0.60821,0.79156,-0.059316,151.7,-0.11405,-0.013196,0.99339,42.954,#7,-0.21581,0.67608,-0.70451,158.32,-0.59736,-0.66215,-0.45245,167.16,-0.77239,0.32321,0.54677,193.9
    6287 
    6288 > fitmap #1 inMap #8
    6289 
    6290 Fit molecule PIN_5_real_space_refined.pdb (#1) to map postprocess 1.mrc (#8)
    6291 using 10173 atoms 
    6292 average map value = 0.01768, steps = 48 
    6293 shifted from previous position = 0.0285 
    6294 rotated from previous position = 0.0236 degrees 
    6295 atoms outside contour = 97, contour level = 0.0040773 
    6296 
    6297 Position of PIN_5_real_space_refined.pdb (#1) relative to postprocess 1.mrc
    6298 (#8) coordinates: 
    6299 Matrix rotation and translation 
    6300 0.77413240 0.62548017 0.09743502 -108.78348482 
    6301 -0.61871031 0.78015823 -0.09246993 173.04062336 
    6302 -0.13385284 0.01129992 0.99093679 40.84496958 
    6303 Axis 0.08172445 0.18215188 -0.97986826 
    6304 Axis point 198.35850392 243.27675668 0.00000000 
    6305 Rotation angle (degrees) 39.41081833 
    6306 Shift along axis -17.39328493 
    6307 
    6308 
    6309 > fitmap #4 inMap #8
    6310 
    6311 Fit molecule PIN_5_real_space_refined.pdb (#4) to map postprocess 1.mrc (#8)
    6312 using 104236 atoms 
    6313 average map value = 0.0104, steps = 108 
    6314 shifted from previous position = 14.3 
    6315 rotated from previous position = 5.98 degrees 
    6316 atoms outside contour = 34631, contour level = 0.0040773 
    6317 
    6318 Position of PIN_5_real_space_refined.pdb (#4) relative to postprocess 1.mrc
    6319 (#8) coordinates: 
    6320 Matrix rotation and translation 
    6321 0.81103895 0.56883502 0.13653773 -110.00386069 
    6322 -0.55348062 0.82172712 -0.13573415 163.72215947 
    6323 -0.18940709 0.03451469 0.98129186 49.38976006 
    6324 Axis 0.14415361 0.27598498 -0.95029050 
    6325 Axis point 220.17547445 262.06246433 0.00000000 
    6326 Rotation angle (degrees) 36.19334027 
    6327 Shift along axis -17.60721577 
    6328 
    6329 
    6330 > fitmap #7 inMap #8
    6331 
    6332 Fit molecule fold_4b_fl_2024_06_13_16_47_model_0.cif (#7) to map postprocess
    6333 1.mrc (#8) using 17262 atoms 
    6334 average map value = 0.01325, steps = 108 
    6335 shifted from previous position = 13 
    6336 rotated from previous position = 1.77 degrees 
    6337 atoms outside contour = 2973, contour level = 0.0040773 
    6338 
    6339 Position of fold_4b_fl_2024_06_13_16_47_model_0.cif (#7) relative to
    6340 postprocess 1.mrc (#8) coordinates: 
    6341 Matrix rotation and translation 
    6342 -0.22927120 0.66107322 -0.71443470 152.80411903 
    6343 -0.57591627 -0.68385311 -0.44795691 178.76428159 
    6344 -0.78470070 0.30875094 0.53751064 191.73888093 
    6345 Axis 0.52122493 0.04839965 -0.85204580 
    6346 Axis point 181.08241586 46.38734422 0.00000000 
    6347 Rotation angle (degrees) 133.45675049 
    6348 Shift along axis -75.07286549 
    6349 
    6350 
    6351 > volume #8 style mesh
    6352 
    6353 > hide #!4 models
    6354 
    6355 > select subtract #4
    6356 
    6357 17262 atoms, 18592 bonds, 1373 residues, 1 model selected 
    6358 
    6359 > select subtract #7
    6360 
    6361 Nothing selected 
    6362 
    6363 > volume #8 style surface
    6364 
    6365 > volume #8 step 1
    6366 
    6367 > volume #8 level 0.0045
    6368 
    6369 > volume #8 level 0.0035
    6370 
    6371 > volume #8 style mesh
    6372 
    6373 > show #!4 models
    6374 
    6375 > volume #8 level 0.0045
    6376 
    6377 > hide #!4 models
    6378 
    6379 > show #!4 models
    6380 
    6381 > hide #!4 models
    6382 
    6383 > show #!4 models
    6384 
    6385 > hide #!4 models
    6386 
    6387 > show #!4 models
    6388 
    6389 > hide #!4 models
    6390 
    6391 > show #!4 models
    6392 
    6393 > close #4
    6394 
    6395 > open "D:/PhD common folder/OneDrive - Indian Institute of
    6396 > Science/Jose_TH_43S_PIC/New_RSR_models/PIN_5_real_space_refined.pdb"
    6397 
    6398 Chain information for PIN_5_real_space_refined.pdb #4 
    6399 --- 
    6400 Chain | Description 
    6401 1 | No description available 
    6402 2 | No description available 
    6403 3 | No description available 
    6404 A | No description available 
    6405 B | No description available 
    6406 C | No description available 
    6407 D | No description available 
    6408 E | No description available 
    6409 F | No description available 
    6410 G | No description available 
    6411 H | No description available 
    6412 I | No description available 
    6413 J | No description available 
    6414 K | No description available 
    6415 L | No description available 
    6416 M | No description available 
    6417 N | No description available 
    6418 O | No description available 
    6419 P | No description available 
    6420 Q | No description available 
    6421 R | No description available 
    6422 S | No description available 
    6423 T | No description available 
    6424 U | No description available 
    6425 V | No description available 
    6426 W | No description available 
    6427 X | No description available 
    6428 Y | No description available 
    6429 Z | No description available 
    6430 a | No description available 
    6431 b | No description available 
    6432 c | No description available 
    6433 d | No description available 
    6434 e | No description available 
    6435 f | No description available 
    6436 g | No description available 
    6437 h | No description available 
    6438 i | No description available 
    6439 j | No description available 
    6440 k | No description available 
    6441 l | No description available 
    6442 m | No description available 
    6443 n | No description available 
    6444 o | No description available 
    6445 p | No description available 
    6446 q | No description available 
    6447 r | No description available 
    6448 
    6449 
    6450 > select add #7
    6451 
    6452 17262 atoms, 18592 bonds, 1373 residues, 1 model selected 
    6453 
    6454 > select subtract #7
    6455 
    6456 Nothing selected 
    6457 
    6458 > select add #4
    6459 
    6460 104236 atoms, 109969 bonds, 10152 residues, 1 model selected 
    6461 
    6462 > hide sel atoms
    6463 
    6464 > show sel cartoons
    6465 
    6466 > color sel orange
    6467 
    6468 > select clear
    6469 
    6470 > select add #4
    6471 
    6472 104236 atoms, 109969 bonds, 10152 residues, 1 model selected 
    6473 
    6474 > view matrix models #4,1,0,0,-20.338,0,1,0,1.5317,0,0,1,-2.6363
    6475 
    6476 > ui mousemode right "translate selected models"
    6477 
    6478 > view matrix models
    6479 > #4,0.73417,-0.011715,0.67887,-110.65,0.039726,0.99888,-0.025724,-0.60366,-0.67781,0.045854,0.73381,179.35
    6480 
    6481 > view matrix models
    6482 > #4,0.9789,0.11074,-0.17176,-3.8946,-0.04979,0.94437,0.32509,-46.014,0.1982,-0.30968,0.92995,41.92
    6483 
    6484 > view matrix models
    6485 > #4,0.017369,0.56222,-0.82681,227.8,0.33544,0.77573,0.53453,-130.18,0.9419,-0.28663,-0.17512,126.11
    6486 
    6487 > view matrix models
    6488 > #4,-0.12811,0.98357,-0.12718,12.586,0.92087,0.07036,-0.38347,107.6,-0.36822,-0.16624,-0.91476,519.17
    6489 
    6490 > view matrix models
    6491 > #4,0.5569,0.82779,0.068008,-131.09,0.01997,0.068512,-0.99745,419.38,-0.83034,0.55683,0.021623,248.94
    6492 
    6493 > view matrix models
    6494 > #4,0.84123,0.44504,-0.30702,-21.878,-0.53641,0.61579,-0.57712,317.96,-0.067779,0.65018,0.75675,-81.698
    6495 
    6496 > view matrix models
    6497 > #4,0.73797,0.6641,0.11988,-141.84,-0.62927,0.74137,-0.23323,234.59,-0.24376,0.096676,0.965,31.9
    6498 
    6499 > view matrix models
    6500 > #4,0.73797,0.6641,0.11988,-108.61,-0.62927,0.74137,-0.23323,201.59,-0.24376,0.096676,0.965,35.063
    6501 
    6502 > view matrix models
    6503 > #4,0.72535,0.63548,0.26463,-130.83,-0.54471,0.76491,-0.34381,203.26,-0.42091,0.10523,0.90098,82.196
    6504 
    6505 > fitmap #4 inMap #8
    6506 
    6507 Fit molecule PIN_5_real_space_refined.pdb (#4) to map postprocess 1.mrc (#8)
    6508 using 104236 atoms 
    6509 average map value = 0.0104, steps = 216 
    6510 shifted from previous position = 20.7 
    6511 rotated from previous position = 15.2 degrees 
    6512 atoms outside contour = 38093, contour level = 0.0045 
    6513 
    6514 Position of PIN_5_real_space_refined.pdb (#4) relative to postprocess 1.mrc
    6515 (#8) coordinates: 
    6516 Matrix rotation and translation 
    6517 0.81109770 0.56879176 0.13636883 -109.97657823 
    6518 -0.55342535 0.82174938 -0.13582465 163.71638992 
    6519 -0.18931694 0.03469710 0.98130281 49.31254596 
    6520 Axis 0.14440007 0.27579500 -0.95030823 
    6521 Axis point 220.19825708 262.01584691 0.00000000 
    6522 Rotation angle (degrees) 36.18887777 
    6523 Shift along axis -17.59058130 
    6524 
    6525 
    6526 > select clear
    6527 
    6528 > select #4/p:724
    6529 
    6530 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6531 
    6532 > select up
    6533 
    6534 214 atoms, 217 bonds, 24 residues, 1 model selected 
    6535 
    6536 > select up
    6537 
    6538 292 atoms, 298 bonds, 33 residues, 1 model selected 
    6539 
    6540 > select up
    6541 
    6542 5114 atoms, 5246 bonds, 647 residues, 1 model selected 
    6543 
    6544 > select up
    6545 
    6546 104236 atoms, 109969 bonds, 10152 residues, 1 model selected 
    6547 
    6548 > select up
    6549 
    6550 184767 atoms, 198033 bonds, 15475 residues, 9 models selected 
    6551 
    6552 > select down
    6553 
    6554 104236 atoms, 109969 bonds, 10152 residues, 2 models selected 
    6555 
    6556 > select down
    6557 
    6558 5114 atoms, 5246 bonds, 647 residues, 1 model selected 
    6559 
    6560 > delete atoms sel
    6561 
    6562 > delete bonds sel
    6563 
    6564 > select #4/r:88
    6565 
    6566 5 atoms, 4 bonds, 1 residue, 1 model selected 
    6567 
    6568 > select up
    6569 
    6570 42 atoms, 43 bonds, 5 residues, 1 model selected 
    6571 
    6572 > select up
    6573 
    6574 2019 atoms, 2064 bonds, 258 residues, 1 model selected 
    6575 
    6576 > select up
    6577 
    6578 2043 atoms, 2088 bonds, 261 residues, 1 model selected 
    6579 
    6580 > select up
    6581 
    6582 2606 atoms, 2669 bonds, 330 residues, 1 model selected 
    6583 
    6584 > select up
    6585 
    6586 99122 atoms, 104723 bonds, 9505 residues, 1 model selected 
    6587 
    6588 > select down
    6589 
    6590 2606 atoms, 2669 bonds, 330 residues, 1 model selected 
    6591 
    6592 > delete atoms sel
    6593 
    6594 > delete bonds sel
    6595 
    6596 > select #4/o:843
    6597 
    6598 5 atoms, 4 bonds, 1 residue, 1 model selected 
    6599 
    6600 > select up
    6601 
    6602 225 atoms, 224 bonds, 45 residues, 1 model selected 
    6603 
    6604 > select up
    6605 
    6606 280 atoms, 279 bonds, 56 residues, 1 model selected 
    6607 
    6608 > select up
    6609 
    6610 285 atoms, 283 bonds, 57 residues, 1 model selected 
    6611 
    6612 > select up
    6613 
    6614 387 atoms, 385 bonds, 78 residues, 1 model selected 
    6615 
    6616 > select add #4/q:89
    6617 
    6618 396 atoms, 393 bonds, 79 residues, 1 model selected 
    6619 
    6620 > select up
    6621 
    6622 487 atoms, 486 bonds, 89 residues, 1 model selected 
    6623 
    6624 > select up
    6625 
    6626 779 atoms, 784 bonds, 127 residues, 1 model selected 
    6627 
    6628 > delete atoms sel
    6629 
    6630 > delete bonds sel
    6631 
    6632 > select #7/D:158
    6633 
    6634 5 atoms, 4 bonds, 1 residue, 1 model selected 
    6635 
    6636 > select up
    6637 
    6638 44 atoms, 43 bonds, 6 residues, 1 model selected 
    6639 
    6640 > select up
    6641 
    6642 3424 atoms, 3494 bonds, 436 residues, 1 model selected 
    6643 
    6644 > select ~sel & ##selected
    6645 
    6646 13838 atoms, 15098 bonds, 937 residues, 1 model selected 
    6647 
    6648 > hide sel target a
    6649 
    6650 > cartoon hide sel
    6651 
    6652 > volume #8 style surface
    6653 
    6654 > volume #8
    6655 
    6656 > volume #8 style mesh
    6657 
    6658 > volume #8 style surface
    6659 
    6660 > volume #8 level 0.004
    6661 
    6662 > volume #8 style mesh
    6663 
    6664 > save "D:/PhD common folder/OneDrive - Indian Institute of
    6665 > Science/Yeast_project/40S_4B/40S_4B_FL_map.cxs"
    6666 
    6667 \u2014\u2014\u2014 End of log from Fri Jun 14 15:32:28 2024 \u2014\u2014\u2014
    6668 
    6669 opened ChimeraX session 
    6670 
    6671 > open "D:/PhD common folder/OneDrive - Indian Institute of
    6672 > Science/Yeast_project/40S_4B/emd_17297.map.gz"
    6673 
    6674 File reader requires uncompressed file; 'D:/PhD common folder/OneDrive -
    6675 Indian Institute of Science/Yeast_project/40S_4B/emd_17297.map.gz' is
    6676 compressed 
    6677 
    6678 > open "D:/PhD common folder/OneDrive - Indian Institute of
    6679 > Science/Yeast_project/40S_4B/emd_17297.map"
    6680 
    6681 Opened emd_17297.map as #9, grid size 400,400,400, pixel 1.06, shown at level
    6682 0.0109, step 2, values float32 
    6683 
    6684 > hide #!8 models
    6685 
    6686 > hide #!4 models
    6687 
    6688 > hide #7 models
    6689 
    6690 > select add #7
    6691 
    6692 17262 atoms, 18592 bonds, 1373 residues, 1 model selected 
    6693 
    6694 > select subtract #7
    6695 
    6696 Nothing selected 
    6697 
    6698 > volume #9 level 0.002703
    6699 
    6700 > ui tool show "Hide Dust"
    6701 
    6702 > surface dust #9 size 61.82
    6703 
    6704 > open "D:/PhD common folder/OneDrive - Indian Institute of
    6705 > Science/Yeast_project/40S_4B/8oz0.cif"
    6706 
    6707 8oz0.cif title: 
    6708 Structure of a human 48S translation initiation complex with eIF4F and eIF4A
    6709 [more info...] 
    6710 
    6711 Chain information for 8oz0.cif #10 
    6712 --- 
    6713 Chain | Description | UniProt 
    6714 1 3 | Eukaryotic initiation factor 4A-I | IF4A1_HUMAN 1-406 
    6715 2 | Eukaryotic translation initiation factor 4 gamma 1 | IF4G1_HUMAN 196-1599 
    6716 5 | Eukaryotic translation initiation factor 3 subunit E | EIF3E_HUMAN 1-445 
    6717 6 | Eukaryotic translation initiation factor 3 subunit F | EIF3F_HUMAN 1-357 
    6718 7 | Eukaryotic translation initiation factor 3 subunit G | EIF3G_HUMAN 1-320 
    6719 8 | Eukaryotic translation initiation factor 3 subunit H | EIF3H_HUMAN 1-352 
    6720 9 | 60S ribosomal protein L41 | RL41_HUMAN 1-25 
    6721 A | Eukaryotic translation initiation factor 3 subunit A | EIF3A_HUMAN 1-1382 
    6722 B | Eukaryotic translation initiation factor 3 subunit K | EIF3K_HUMAN 1-218 
    6723 C | Eukaryotic translation initiation factor 3 subunit M | EIF3M_HUMAN 1-374 
    6724 D | Eukaryotic translation initiation factor 2 subunit 1 | IF2A_HUMAN 1-315 
    6725 E | Eukaryotic translation initiation factor 2 subunit 3 | IF2G_HUMAN 1-472 
    6726 F | Eukaryotic translation initiation factor 3 subunit I | EIF3I_HUMAN 1-325 
    6727 G | Eukaryotic translation initiation factor 1A, X-chromosomal | IF1AX_HUMAN 1-144 
    6728 H | Eukaryotic translation initiation factor 5 | IF5_HUMAN 1-431 
    6729 I | Eukaryotic translation initiation factor 3 subunit B | EIF3B_HUMAN 1-814 
    6730 J | Eukaryotic translation initiation factor 3 subunit C | EIF3C_HUMAN 1-913 
    6731 K | Eukaryotic translation initiation factor 3 subunit L | EIF3L_HUMAN 1-564 
    6732 L | 40S ribosomal protein S7 | RS7_HUMAN 1-194 
    6733 M | 40S ribosomal protein S27 | RS27_HUMAN 1-84 
    6734 N | 40S ribosomal protein S21 | RS21_HUMAN 1-83 
    6735 O | 40S ribosomal protein S2 | RS2_HUMAN 1-293 
    6736 P | 40S ribosomal protein S3a | RS3A_HUMAN 1-264 
    6737 Q | 40S ribosomal protein SA | RSSA_HUMAN 1-295 
    6738 R | 40S ribosomal protein S26 | RS26_HUMAN 1-115 
    6739 S | 40S ribosomal protein S6 | RS6_HUMAN 1-249 
    6740 T | 40S ribosomal protein S14 | RS14_HUMAN 1-151 
    6741 U | Eukaryotic translation initiation factor 2 subunit 2 | IF2B_HUMAN 1-333 
    6742 V | 40S ribosomal protein S13 | RS13_HUMAN 1-151 
    6743 W | 18S rRNA |   
    6744 X | 40S ribosomal protein S11 | RS11_HUMAN 1-158 
    6745 Y | 40S ribosomal protein S4, X isoform | RS4X_HUMAN 1-263 
    6746 Z | 40S ribosomal protein S9 | RS9_HUMAN 1-194 
    6747 a | 40S ribosomal protein S23 | RS23_HUMAN 1-143 
    6748 b | 40S ribosomal protein S30 | RS30_HUMAN 75-133 
    6749 c | 40S ribosomal protein S15a | RS15A_HUMAN 1-130 
    6750 d | 40S ribosomal protein S8 | RS8_HUMAN 1-208 
    6751 e | 40S ribosomal protein S24 | RS24_HUMAN 1-133 
    6752 f | 40S ribosomal protein S5 | RS5_HUMAN 1-204 
    6753 g | 40S ribosomal protein S16 | RS16_HUMAN 1-146 
    6754 h | 40S ribosomal protein S3 | RS3_HUMAN 1-243 
    6755 i | 40S ribosomal protein S10 | RS10_HUMAN 1-165 
    6756 j | 40S ribosomal protein S15 | RS15_HUMAN 1-145 
    6757 k | Receptor of activated protein C kinase 1 | RACK1_HUMAN 1-317 
    6758 l | 40S ribosomal protein S19 | RS19_HUMAN 1-145 
    6759 m | 40S ribosomal protein S25 | RS25_HUMAN 1-125 
    6760 n | Small ribosomal subunit protein uS13 | RS18_HUMAN 1-151 
    6761 o | 40S ribosomal protein S29 | RS29_HUMAN 1-56 
    6762 p | Ubiquitin-40S ribosomal protein S27a | RS27A_HUMAN 1-156 
    6763 q | 40S ribosomal protein S12 | RS12_HUMAN 1-132 
    6764 s | 40S ribosomal protein S28 | RS28_HUMAN 1-69 
    6765 v | 40S ribosomal protein S17 | RS17_HUMAN 1-135 
    6766 w | 40S ribosomal protein S20 | RS20_HUMAN 1-119 
    6767 x | Eukaryotic translation initiation factor 3 subunit D | EIF3D_HUMAN 1-548 
    6768 y | tRNAiMet |   
    6769 z | mRNA |   
    6770 
    6771 Non-standard residues in 8oz0.cif #10 
    6772 --- 
    6773 5MC \u2014 5-methylcytidine-5'-monophosphate 
    6774 5MU \u2014 5-methyluridine 5'-monophosphate 
    6775 6MZ \u2014 N6-methyladenosine-5'-monophosphate 
    6776 A2M \u2014 2'-O-methyladenosine 5'-(dihydrogen phosphate) 
    6777 C4J \u2014
    6778 (5S)-5-{3-[(3S)-3-amino-3-carboxypropyl]-1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl}-2,5-anhydro-1-O-phosphono-
    6779 L-arabinitol 
    6780 JMH \u2014 3-Methylcytidine- 5'-monophosphate 
    6781 MA6 \u2014 6N-dimethyladenosine-5'-monophoshate 
    6782 MG \u2014 magnesium ion 
    6783 OMC \u2014 O2'-methylycytidine-5'-monophosphate 
    6784 OMG \u2014 O2'-methylguanosine-5'-monophosphate 
    6785 OMU \u2014 O2'-methyluridine 5'-monophosphate 
    6786 UR3 \u2014 3-methyluridine-5'-monophoshate 
    6787 ZN \u2014 zinc ion 
    6788 
    6789 
    6790 > volume #9 style mesh
    6791 
    6792 > show #!10 cartoons
    6793 
    6794 > hide #!10 atoms
    6795 
    6796 > graphics silhouettes false
    6797 
    6798 > graphics silhouettes true
    6799 
    6800 > lighting shadows true intensity 0.5
    6801 
    6802 > lighting shadows false
    6803 
    6804 > graphics silhouettes false
    6805 
    6806 > lighting flat
    6807 
    6808 > lighting full
    6809 
    6810 > lighting soft
    6811 
    6812 > lighting simple
    6813 
    6814 > lighting soft
    6815 
    6816 > graphics silhouettes false
    6817 
    6818 > graphics silhouettes true
    6819 
    6820 > volume #9 level 0.00561
    6821 
    6822 > show #7 models
    6823 
    6824 > hide #!9 models
    6825 
    6826 > hide #!10 models
    6827 
    6828 > select add #7
    6829 
    6830 17262 atoms, 18592 bonds, 1373 residues, 1 model selected 
    6831 
    6832 > show sel cartoons
    6833 
    6834 > select subtract #7
    6835 
    6836 Nothing selected 
    6837 
    6838 > show #!9 models
    6839 
    6840 > show #!10 models
    6841 
    6842 > ui tool show Matchmaker
    6843 
    6844 > matchmaker #7 to #10
    6845 
    6846 Parameters 
    6847 --- 
    6848 Chain pairing | bb 
    6849 Alignment algorithm | Needleman-Wunsch 
    6850 Similarity matrix | BLOSUM-62 
    6851 SS fraction | 0.3 
    6852 Gap open (HH/SS/other) | 18/18/6 
    6853 Gap extend | 1 
    6854 SS matrix |  |  | H | S | O 
    6855 ---|---|---|--- 
    6856 H | 6 | -9 | -6 
    6857 S |  | 6 | -6 
    6858 O |  |  | 4 
    6859 Iteration cutoff | 2 
    6860 
    6861 Matchmaker 8oz0.cif, chain W (#10) with
    6862 fold_4b_fl_2024_06_13_16_47_model_0.cif, chain E (#7), sequence alignment
    6863 score = 2518.7 
    6864 RMSD between 280 pruned atom pairs is 1.217 angstroms; (across all 472 pairs:
    6865 4.015) 
    6866 
    6867 
    6868 > matchmaker #7 to #10
    6869 
    6870 Parameters 
    6871 --- 
    6872 Chain pairing | bb 
    6873 Alignment algorithm | Needleman-Wunsch 
    6874 Similarity matrix | BLOSUM-62 
    6875 SS fraction | 0.3 
    6876 Gap open (HH/SS/other) | 18/18/6 
    6877 Gap extend | 1 
    6878 SS matrix |  |  | H | S | O 
    6879 ---|---|---|--- 
    6880 H | 6 | -9 | -6 
    6881 S |  | 6 | -6 
    6882 O |  |  | 4 
    6883 Iteration cutoff | 2 
    6884 
    6885 Matchmaker 8oz0.cif, chain W (#10) with
    6886 fold_4b_fl_2024_06_13_16_47_model_0.cif, chain E (#7), sequence alignment
    6887 score = 2518.7 
    6888 RMSD between 280 pruned atom pairs is 1.217 angstroms; (across all 472 pairs:
    6889 4.015) 
    6890 
    6891 
    6892 > volume #9 level 0.00408
    6893 
    6894 > hide #!9 models
    6895 
    6896 > color #10 magenta
    6897 
    6898 > show #!9 models
    6899 
    6900 > hide #!9 models
    6901 
    6902 > show #!9 models
    6903 
    6904 > hide #!9 models
    6905 
    6906 > show #!9 models
    6907 
    6908 > hide #!9 models
    6909 
    6910 > hide #!10 models
    6911 
    6912 > select #7/E:207
    6913 
    6914 23 atoms, 25 bonds, 1 residue, 1 model selected 
    6915 
    6916 > select up
    6917 
    6918 10163 atoms, 11360 bonds, 477 residues, 1 model selected 
    6919 
    6920 > ui tool show "Color Actions"
    6921 
    6922 > color sel beige
    6923 
    6924 > color sel wheat
    6925 
    6926 > color sel navajo white
    6927 
    6928 > select clear
    6929 
    6930 > show #!10 models
    6931 
    6932 > hide #!10 models
    6933 
    6934 > select #7/B:25
    6935 
    6936 11 atoms, 11 bonds, 1 residue, 1 model selected 
    6937 
    6938 > select up
    6939 
    6940 188 atoms, 191 bonds, 22 residues, 1 model selected 
    6941 
    6942 > select up
    6943 
    6944 1847 atoms, 1874 bonds, 237 residues, 1 model selected 
    6945 
    6946 > select clear
    6947 
    6948 > select #7/C:34
    6949 
    6950 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6951 
    6952 > select up
    6953 
    6954 130 atoms, 129 bonds, 17 residues, 1 model selected 
    6955 
    6956 > select up
    6957 
    6958 936 atoms, 948 bonds, 117 residues, 1 model selected 
    6959 
    6960 > select up
    6961 
    6962 17262 atoms, 18592 bonds, 1373 residues, 1 model selected 
    6963 
    6964 > select down
    6965 
    6966 936 atoms, 948 bonds, 117 residues, 1 model selected 
    6967 
    6968 > color sel pale green
    6969 
    6970 > color sel medium spring green
    6971 
    6972 > color sel chartreuse
    6973 
    6974 > select clear
    6975 
    6976 > select #7/B:108
    6977 
    6978 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6979 
    6980 > select up
    6981 
    6982 99 atoms, 99 bonds, 13 residues, 1 model selected 
    6983 
    6984 > select up
    6985 
    6986 1847 atoms, 1874 bonds, 237 residues, 1 model selected 
    6987 
    6988 > color sel orange
    6989 
    6990 > color sel peru
    6991 
    6992 > color sel light salmon
    6993 
    6994 > color sel dark salmon
    6995 
    6996 > color sel coral
    6997 
    6998 > select clear
    6999 
    7000 > select #7/E:71
    7001 
    7002 22 atoms, 24 bonds, 1 residue, 1 model selected 
    7003 
    7004 > select up
    7005 
    7006 10163 atoms, 11360 bonds, 477 residues, 1 model selected 
    7007 
    7008 > color sel beige
    7009 
    7010 > select clear
    7011 
    7012 > select #7/D:121
    7013 
    7014 7 atoms, 6 bonds, 1 residue, 1 model selected 
    7015 
    7016 > select up
    7017 
    7018 91 atoms, 93 bonds, 12 residues, 1 model selected 
    7019 
    7020 > select up
    7021 
    7022 3424 atoms, 3494 bonds, 436 residues, 1 model selected 
    7023 
    7024 > color sel magenta
    7025 
    7026 > select clear
    7027 
    7028 > graphics silhouettes false
    7029 
    7030 > lighting shadows true intensity 0.5
    7031 
    7032 > graphics silhouettes true
    7033 
    7034 > ui tool show "Side View"
    7035 
    7036 > save "D:/PhD common folder/OneDrive - Indian Institute of
    7037 > Science/Yeast_project/40S_4B/4B_FL/Fig_5A.jpg" width 957 height 596
    7038 > supersample 3
    7039 
    7040 > ui tool show "Show Sequence Viewer"
    7041 
    7042 > sequence chain #7/D
    7043 
    7044 Alignment identifier is 7/D 
    7045 
    7046 > select #7/D:89
    7047 
    7048 11 atoms, 10 bonds, 1 residue, 1 model selected 
    7049 
    7050 > select #7/D:89-436
    7051 
    7052 2776 atoms, 2834 bonds, 348 residues, 1 model selected 
    7053 
    7054 > cartoon hide sel
    7055 
    7056 > show #!8 models
    7057 
    7058 > show #!1 models
    7059 
    7060 > hide #!1 models
    7061 
    7062 > show #2 models
    7063 
    7064 > hide #2 models
    7065 
    7066 > show #!4 models
    7067 
    7068 > ui tool show Matchmaker
    7069 
    7070 > matchmaker #7 to #4
    7071 
    7072 Parameters 
    7073 --- 
    7074 Chain pairing | bb 
    7075 Alignment algorithm | Needleman-Wunsch 
    7076 Similarity matrix | BLOSUM-62 
    7077 SS fraction | 0.3 
    7078 Gap open (HH/SS/other) | 18/18/6 
    7079 Gap extend | 1 
    7080 SS matrix |  |  | H | S | O 
    7081 ---|---|---|--- 
    7082 H | 6 | -9 | -6 
    7083 S |  | 6 | -6 
    7084 O |  |  | 4 
    7085 Iteration cutoff | 2 
    7086 
    7087 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#4) with
    7088 fold_4b_fl_2024_06_13_16_47_model_0.cif, chain E (#7), sequence alignment
    7089 score = 2881 
    7090 RMSD between 447 pruned atom pairs is 0.715 angstroms; (across all 477 pairs:
    7091 1.026) 
    7092 
    7093 
    7094 > hide #!4 models
    7095 
    7096 > lighting flat
    7097 
    7098 > lighting shadows true intensity 0.5
    7099 
    7100 > graphics silhouettes false
    7101 
    7102 > transparency sel 30
    7103 
    7104 > transparency sel 0
    7105 
    7106 > transparency #8 50
    7107 
    7108 > lighting soft
    7109 
    7110 > graphics silhouettes true
    7111 
    7112 > graphics silhouettes false
    7113 
    7114 > graphics silhouettes true
    7115 
    7116 > lighting simple
    7117 
    7118 > transparency #8 20
    7119 
    7120 > transparency #8 80
    7121 
    7122 > open "D:/PhD common folder/OneDrive - Indian Institute of
    7123 > Science/Yeast_project/40S_4B/8i7j.pdb"
    7124 
    7125 8i7j.pdb title: 
    7126 Yeast 40S-EIF4B - partially open conformation of the 40S head [more info...] 
    7127 
    7128 Chain information for 8i7j.pdb #11 
    7129 --- 
    7130 Chain | Description | UniProt 
    7131 2 | RNA (1780-mer) |   
    7132 A | 40S ribosomal protein S0 | RSSA_KLULA 1-254 
    7133 B | 40S ribosomal protein S1 | RS3A_KLULA 1-255 
    7134 C | KLLA0F09812P | Q6CKL3_KLULA 1-259 
    7135 D | KLLA0D08305P | Q6CRK7_KLULA 1-237 
    7136 E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 1-261 
    7137 F | KLLA0D10659P | Q6CRA3_KLULA 1-227 
    7138 G | 40S ribosomal protein S6 | RS6_KLULC 1-236 
    7139 H | 40S ribosomal protein S7 | Q6CTD6_KLULA 1-190 
    7140 I | 40S ribosomal protein S8 | Q6CMG3_KLULA 1-201 
    7141 J | KLLA0E23673P | Q6CM18_KLULA 1-188 
    7142 K | KLLA0B08173P | Q6CVZ5_KLULA 1-106 
    7143 L | KLLA0A10483P | Q6CX80_KLULA 1-156 
    7144 M | 40S ribosomal protein S12 | Q6CLU4_KLULA 1-134 
    7145 N | KLLA0F18040P | Q6CJK0_KLULA 1-151 
    7146 O | RP59 | RS14_KLULC 1-137 
    7147 P | KLLA0F07843P | Q6CKV4_KLULA 1-142 
    7148 Q | 40S ribosomal protein S16 | RS16_KLULC 1-143 
    7149 R | KLLA0B01474P | Q6CWU3_KLULA 1-136 
    7150 S | KLLA0B01562P | Q6CWT9_KLULA 1-146 
    7151 T | KLLA0A07194P | Q6CXM0_KLULA 1-144 
    7152 U | KLLA0F25542P | Q6CIM1_KLULA 4-120 
    7153 V | 40S ribosomal protein S21 | RS21_KLULC 1-87 
    7154 W | KLLA0B07931P | Q6CW06_KLULA 1-130 
    7155 X | KLLA0B11231P | F2Z602_KLULA 1-145 
    7156 Y | 40S ribosomal protein S24 | Q6CU44_KLULA 1-135 
    7157 Z | 40S ribosomal protein S25 | Q6CW78_KLULA 1-108 
    7158 a | 40S ribosomal protein S26 | Q6CS01_KLULA 1-119 
    7159 b | 40S ribosomal protein S27 | Q6CNL2_KLULA 1-82 
    7160 c | S33 | RS28_KLULC 1-67 
    7161 d | 40S ribosomal protein S29 | RS29_KLULC 1-56 
    7162 e | 40S ribosomal protein S30 | Q6CUH5_KLULA 1-63 
    7163 f | ubiquitin-40S ribosomal protein S27A | RS27A_KLULC 1-150 
    7164 g | KLLA0E12277P | Q6CNI7_KLULA 1-326 
    7165 h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25 
    7166 
    7167 Non-standard residues in 8i7j.pdb #11 
    7168 --- 
    7169 MG \u2014 magnesium ion 
    7170 ZN \u2014 zinc ion 
    7171 
    7172 
    7173 > select add #11
    7174 
    7175 79075 atoms, 84250 bonds, 12 pseudobonds, 7007 residues, 3 models selected 
    7176 
    7177 > select add #7
    7178 
    7179 93561 atoms, 100008 bonds, 12 pseudobonds, 8032 residues, 3 models selected 
    7180 
    7181 > select subtract #7
    7182 
    7183 76299 atoms, 81416 bonds, 12 pseudobonds, 6659 residues, 2 models selected 
    7184 
    7185 > show sel cartoons
    7186 
    7187 > hide sel atoms
    7188 
    7189 > select clear
    7190 
    7191 > hide #7 models
    7192 
    7193 > ui tool show "Fit in Map"
    7194 
    7195 > fitmap #11 inMap #8
    7196 
    7197 Fit molecule 8i7j.pdb (#11) to map postprocess 1.mrc (#8) using 76299 atoms 
    7198 average map value = 0.01715, steps = 124 
    7199 shifted from previous position = 6.85 
    7200 rotated from previous position = 9.78 degrees 
    7201 atoms outside contour = 4764, contour level = 0.004 
    7202 
    7203 Position of 8i7j.pdb (#11) relative to postprocess 1.mrc (#8) coordinates: 
    7204 Matrix rotation and translation 
    7205 0.99574639 -0.08528090 0.03487557 11.36946753 
    7206 0.08939706 0.98586789 -0.14167806 8.39268741 
    7207 -0.02230027 0.14419319 0.98929825 -24.08267778 
    7208 Axis 0.84114773 0.16823422 0.51397252 
    7209 Axis point 0.00000000 165.31387249 44.41337612 
    7210 Rotation angle (degrees) 9.78370709 
    7211 Shift along axis -1.40249549 
    7212 
    7213 
    7214 > ui tool show Matchmaker
    7215 
    7216 > matchmaker #7 to #11
    7217 
    7218 Parameters 
    7219 --- 
    7220 Chain pairing | bb 
    7221 Alignment algorithm | Needleman-Wunsch 
    7222 Similarity matrix | BLOSUM-62 
    7223 SS fraction | 0.3 
    7224 Gap open (HH/SS/other) | 18/18/6 
    7225 Gap extend | 1 
    7226 SS matrix |  |  | H | S | O 
    7227 ---|---|---|--- 
    7228 H | 6 | -9 | -6 
    7229 S |  | 6 | -6 
    7230 O |  |  | 4 
    7231 Iteration cutoff | 2 
    7232 
    7233 Matchmaker 8i7j.pdb, chain 2 (#11) with
    7234 fold_4b_fl_2024_06_13_16_47_model_0.cif, chain E (#7), sequence alignment
    7235 score = 2911.1 
    7236 RMSD between 374 pruned atom pairs is 1.206 angstroms; (across all 477 pairs:
    7237 1.708) 
    7238 
    7239 
    7240 > matchmaker #7 to #11
    7241 
    7242 Parameters 
    7243 --- 
    7244 Chain pairing | bb 
    7245 Alignment algorithm | Needleman-Wunsch 
    7246 Similarity matrix | BLOSUM-62 
    7247 SS fraction | 0.3 
    7248 Gap open (HH/SS/other) | 18/18/6 
    7249 Gap extend | 1 
    7250 SS matrix |  |  | H | S | O 
    7251 ---|---|---|--- 
    7252 H | 6 | -9 | -6 
    7253 S |  | 6 | -6 
    7254 O |  |  | 4 
    7255 Iteration cutoff | 2 
    7256 
    7257 Matchmaker 8i7j.pdb, chain 2 (#11) with
    7258 fold_4b_fl_2024_06_13_16_47_model_0.cif, chain E (#7), sequence alignment
    7259 score = 2911.1 
    7260 RMSD between 374 pruned atom pairs is 1.206 angstroms; (across all 477 pairs:
    7261 1.708) 
    7262 
    7263 
    7264 > show #7 models
    7265 
    7266 > hide #!11 models
    7267 
    7268 > transparency #8 90
    7269 
    7270 > transparency #8 95
    7271 
    7272 > transparency #8 99
    7273 
    7274 > save "D:/PhD common folder/OneDrive - Indian Institute of
    7275 > Science/Yeast_project/40S_4B/4B_FL/Figure_session.cxs"
    7276 
    7277 \u2014\u2014\u2014 End of log from Fri Jul 5 12:41:39 2024 \u2014\u2014\u2014
    7278 
    7279 opened ChimeraX session 
    7280 
    7281 > select #7/A:103
    7282 
    7283 4 atoms, 3 bonds, 1 residue, 1 model selected 
    7284 
    7285 > select up
    7286 
    7287 107 atoms, 108 bonds, 14 residues, 1 model selected 
    7288 
    7289 > select up
    7290 
    7291 892 atoms, 916 bonds, 106 residues, 1 model selected 
    7292 
    7293 > ui tool show "Color Actions"
    7294 
    7295 > color sel royal blue
    7296 
    7297 > select clear
    7298 
    7299 > select #7/E:361
    7300 
    7301 23 atoms, 25 bonds, 1 residue, 1 model selected 
    7302 
    7303 > select up
    7304 
    7305 10163 atoms, 11360 bonds, 477 residues, 1 model selected 
    7306 
    7307 > ui tool show "Color Actions"
    7308 
    7309 > color sel wheat
    7310 
    7311 > select clear
    7312 
    7313 > volume #8 style surface
    7314 
    7315 > select add #8
    7316 
    7317 2 models selected 
    7318 
    7319 > ui tool show "Color Actions"
    7320 
    7321 > color sel wheat
    7322 
    7323 > transparency #8.1 90
    7324 
    7325 > select clear
    7326 
    7327 > transparency #7-8 80
    7328 
    7329 > ui tool show "Color Zone"
    7330 
    7331 > select #7/D:28
    7332 
    7333 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7334 
    7335 > select up
    7336 
    7337 51 atoms, 52 bonds, 6 residues, 1 model selected 
    7338 
    7339 > select up
    7340 
    7341 3424 atoms, 3494 bonds, 436 residues, 1 model selected 
    7342 
    7343 > color zone #8 near sel distance 7.2
    7344 
    7345 > color zone #8 near sel distance 7.1
    7346 
    7347 > color zone #8 near sel distance 7
    7348 
    7349 > color zone #8 near sel distance 6.9
    7350 
    7351 > color zone #8 near sel distance 6.8
    7352 
    7353 > color zone #8 near sel distance 6.7
    7354 
    7355 > color zone #8 near sel distance 6.6
    7356 
    7357 > color zone #8 near sel distance 6.5
    7358 
    7359 > color zone #8 near sel distance 6.4
    7360 
    7361 > color zone #8 near sel distance 6.3
    7362 
    7363 > color zone #8 near sel distance 6.2
    7364 
    7365 > color zone #8 near sel distance 6.1
    7366 
    7367 > color zone #8 near sel distance 6
    7368 
    7369 > color zone #8 near sel distance 5.9
    7370 
    7371 > color zone #8 near sel distance 5.8
    7372 
    7373 > color zone #8 near sel distance 5.7
    7374 
    7375 > color zone #8 near sel distance 5.6
    7376 
    7377 > color zone #8 near sel distance 5.5
    7378 
    7379 > color zone #8 near sel distance 5.4
    7380 
    7381 > color zone #8 near sel distance 5.3
    7382 
    7383 > color zone #8 near sel distance 5.2
    7384 
    7385 > color zone #8 near sel distance 5.1
    7386 
    7387 > color zone #8 near sel distance 5
    7388 
    7389 > color zone #8 near sel distance 4.9
    7390 
    7391 > color zone #8 near sel distance 4.8
    7392 
    7393 > color zone #8 near sel distance 4.7
    7394 
    7395 > color zone #8 near sel distance 4.6
    7396 
    7397 > color zone #8 near sel distance 4.5
    7398 
    7399 > color zone #8 near sel distance 4.4
    7400 
    7401 > color zone #8 near sel distance 4.3
    7402 
    7403 > color zone #8 near sel distance 4.2
    7404 
    7405 > color zone #8 near sel distance 4.1
    7406 
    7407 > color zone #8 near sel distance 4
    7408 
    7409 > color zone #8 near sel distance 3.9
    7410 
    7411 > color zone #8 near sel distance 3.8
    7412 
    7413 > color zone #8 near sel distance 3.7
    7414 
    7415 > color zone #8 near sel distance 3.6
    7416 
    7417 > color zone #8 near sel distance 3.5
    7418 
    7419 > color zone #8 near sel distance 3.4
    7420 
    7421 > color zone #8 near sel distance 3.3
    7422 
    7423 > color zone #8 near sel distance 3.2
    7424 
    7425 > color zone #8 near sel distance 3.1
    7426 
    7427 > color zone #8 near sel distance 3
    7428 
    7429 > color zone #8 near sel distance 2.9
    7430 
    7431 > color zone #8 near sel distance 2.8
    7432 
    7433 > color zone #8 near sel distance 2.7
    7434 
    7435 > color zone #8 near sel distance 2.6
    7436 
    7437 > color zone #8 near sel distance 2.5
    7438 
    7439 > color zone #8 near sel distance 2.4
    7440 
    7441 > color zone #8 near sel distance 2.3
    7442 
    7443 > color zone #8 near sel distance 2.2
    7444 
    7445 > color zone #8 near sel distance 2.1
    7446 
    7447 > color zone #8 near sel distance 2
    7448 
    7449 > color zone #8 near sel distance 1.9
    7450 
    7451 > color zone #8 near sel distance 1.8
    7452 
    7453 > select clear
    7454 
    7455 No atoms selected for color zoning 
    7456 
    7457 [Repeated 7 time(s)]
    7458 
    7459 > color single #8
    7460 
    7461 > select clear
    7462 
    7463 > hide #!8 models
    7464 
    7465 > select #7/D:56
    7466 
    7467 5 atoms, 4 bonds, 1 residue, 1 model selected 
    7468 
    7469 > select up
    7470 
    7471 68 atoms, 68 bonds, 9 residues, 1 model selected 
    7472 
    7473 > select up
    7474 
    7475 3424 atoms, 3494 bonds, 436 residues, 1 model selected 
    7476 
    7477 > show sel cartoons
    7478 
    7479 > select clear
    7480 
    7481 > ui tool show "Show Sequence Viewer"
    7482 
    7483 > sequence chain #7/D
    7484 
    7485 Alignment identifier is 7/D 
    7486 
    7487 > select #7/D:80
    7488 
    7489 7 atoms, 7 bonds, 1 residue, 1 model selected 
    7490 
    7491 > select #7/D:80-280
    7492 
    7493 1571 atoms, 1608 bonds, 201 residues, 1 model selected 
    7494 
    7495 > delete atoms sel
    7496 
    7497 > delete bonds sel
    7498 
    7499 > select #7/D:281
    7500 
    7501 11 atoms, 10 bonds, 1 residue, 1 model selected 
    7502 
    7503 > select #7/D:281-419
    7504 
    7505 1124 atoms, 1143 bonds, 139 residues, 1 model selected 
    7506 
    7507 > select #7/D:436
    7508 
    7509 10 atoms, 9 bonds, 1 residue, 1 model selected 
    7510 
    7511 > select #7/D:386-436
    7512 
    7513 402 atoms, 403 bonds, 51 residues, 1 model selected 
    7514 
    7515 > select #7/D:436
    7516 
    7517 10 atoms, 9 bonds, 1 residue, 1 model selected 
    7518 
    7519 > select #7/D:281-436
    7520 
    7521 1257 atoms, 1278 bonds, 156 residues, 1 model selected 
    7522 
    7523 > delete atoms sel
    7524 
    7525 > delete bonds sel
    7526 
    7527 > show #!8 models
    7528 
    7529 > select #7/D:29
    7530 
    7531 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7532 
    7533 > select up
    7534 
    7535 51 atoms, 52 bonds, 6 residues, 1 model selected 
    7536 
    7537 > select up
    7538 
    7539 596 atoms, 606 bonds, 79 residues, 1 model selected 
    7540 
    7541 > color zone #8 near sel distance 1.2
    7542 
    7543 > color zone #8 near sel distance 1.31
    7544 
    7545 > color zone #8 near sel distance 2.19
    7546 
    7547 > color zone #8 near sel distance 2.29
    7548 
    7549 > color zone #8 near sel distance 2.39
    7550 
    7551 > color zone #8 near sel distance 2.49
    7552 
    7553 > color zone #8 near sel distance 2.59
    7554 
    7555 > color zone #8 near sel distance 2.69
    7556 
    7557 > color zone #8 near sel distance 2.79
    7558 
    7559 > color zone #8 near sel distance 2.89
    7560 
    7561 > color zone #8 near sel distance 2.99
    7562 
    7563 > color zone #8 near sel distance 2.89
    7564 
    7565 > color zone #8 near sel distance 2.79
    7566 
    7567 > color zone #8 near sel distance 2.69
    7568 
    7569 > color zone #8 near sel distance 2.59
    7570 
    7571 > color zone #8 near sel distance 2.49
    7572 
    7573 > color zone #8 near sel distance 2.39
    7574 
    7575 > color zone #8 near sel distance 2.29
    7576 
    7577 > color zone #8 near sel distance 2.19
    7578 
    7579 > color zone #8 near sel distance 2.09
    7580 
    7581 > color zone #8 near sel distance 1.99
    7582 
    7583 > color zone #8 near sel distance 1.89
    7584 
    7585 > color zone #8 near sel distance 1.79
    7586 
    7587 > select clear
    7588 
    7589 > select #8
    7590 
    7591 3 models selected 
    7592 
    7593 > select clear
    7594 
    7595 > select #7/D:21
    7596 
    7597 7 atoms, 6 bonds, 1 residue, 1 model selected 
    7598 
    7599 > select up
    7600 
    7601 26 atoms, 26 bonds, 3 residues, 1 model selected 
    7602 
    7603 > select up
    7604 
    7605 596 atoms, 606 bonds, 79 residues, 1 model selected 
    7606 
    7607 > hide #!8 models
    7608 
    7609 > select subtract #7/D:1
    7610 
    7611 588 atoms, 598 bonds, 78 residues, 1 model selected 
    7612 
    7613 > select subtract #7/D:2
    7614 
    7615 583 atoms, 593 bonds, 77 residues, 1 model selected 
    7616 
    7617 > select subtract #7/D:3
    7618 
    7619 576 atoms, 585 bonds, 76 residues, 1 model selected 
    7620 
    7621 > select subtract #7/D:4
    7622 
    7623 569 atoms, 577 bonds, 75 residues, 1 model selected 
    7624 
    7625 > select subtract #7/D:5
    7626 
    7627 560 atoms, 568 bonds, 74 residues, 1 model selected 
    7628 
    7629 > select subtract #7/D:6
    7630 
    7631 551 atoms, 559 bonds, 73 residues, 1 model selected 
    7632 
    7633 > select subtract #7/D:7
    7634 
    7635 544 atoms, 552 bonds, 72 residues, 1 model selected 
    7636 
    7637 > show #!8 models
    7638 
    7639 > color zone #8 near sel distance 1.79
    7640 
    7641 > color zone #8 near sel distance 1.89
    7642 
    7643 > color zone #8 near sel distance 1.99
    7644 
    7645 > color zone #8 near sel distance 2.09
    7646 
    7647 > color zone #8 near sel distance 2.19
    7648 
    7649 > color zone #8 near sel distance 2.29
    7650 
    7651 > color zone #8 near sel distance 2.39
    7652 
    7653 > color zone #8 near sel distance 2.49
    7654 
    7655 > color zone #8 near sel distance 2.59
    7656 
    7657 > color zone #8 near sel distance 2.69
    7658 
    7659 > select clear
    7660 
    7661 > hide #!7 models
    7662 
    7663 > show #!7 models
    7664 
    7665 > color single #8
    7666 
    7667 [Repeated 1 time(s)]
    7668 
    7669 No atoms selected for color zoning 
    7670 
    7671 [Repeated 2 time(s)]
    7672 
    7673 > select #7/D:9
    7674 
    7675 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7676 
    7677 > select up
    7678 
    7679 34 atoms, 33 bonds, 4 residues, 1 model selected 
    7680 
    7681 > select up
    7682 
    7683 596 atoms, 606 bonds, 79 residues, 1 model selected 
    7684 
    7685 > hide #!8 models
    7686 
    7687 > select subtract #7/D:1
    7688 
    7689 588 atoms, 598 bonds, 78 residues, 1 model selected 
    7690 
    7691 > select subtract #7/D:2
    7692 
    7693 583 atoms, 593 bonds, 77 residues, 1 model selected 
    7694 
    7695 > select subtract #7/D:3
    7696 
    7697 576 atoms, 585 bonds, 76 residues, 1 model selected 
    7698 
    7699 > select subtract #7/D:4
    7700 
    7701 569 atoms, 577 bonds, 75 residues, 1 model selected 
    7702 
    7703 > select add #7/E:228
    7704 
    7705 589 atoms, 598 bonds, 76 residues, 1 model selected 
    7706 
    7707 > select subtract #7/E:228
    7708 
    7709 569 atoms, 577 bonds, 75 residues, 1 model selected 
    7710 
    7711 > select subtract #7/D:5
    7712 
    7713 560 atoms, 568 bonds, 74 residues, 1 model selected 
    7714 
    7715 > select subtract #7/D:6
    7716 
    7717 551 atoms, 559 bonds, 73 residues, 1 model selected 
    7718 
    7719 > select subtract #7/D:7
    7720 
    7721 544 atoms, 552 bonds, 72 residues, 1 model selected 
    7722 
    7723 > show #!8 models
    7724 
    7725 > color zone #8 near sel distance 2.69
    7726 
    7727 > hide #!7 models
    7728 
    7729 > color zone #8 near sel distance 2.59
    7730 
    7731 > color zone #8 near sel distance 2.49
    7732 
    7733 > color zone #8 near sel distance 2.39
    7734 
    7735 > color zone #8 near sel distance 2.49
    7736 
    7737 > color zone #8 near sel distance 2.59
    7738 
    7739 > color zone #8 near sel distance 2.69
    7740 
    7741 > color zone #8 near sel distance 2.79
    7742 
    7743 > color zone #8 near sel distance 2.89
    7744 
    7745 > color zone #8 near sel distance 2.99
    7746 
    7747 > color zone #8 near sel distance 3.09
    7748 
    7749 > color zone #8 near sel distance 3.19
    7750 
    7751 > color zone #8 near sel distance 3.29
    7752 
    7753 > color zone #8 near sel distance 3.39
    7754 
    7755 > color zone #8 near sel distance 3.49
    7756 
    7757 > color zone #8 near sel distance 3.59
    7758 
    7759 > color zone #8 near sel distance 3.69
    7760 
    7761 > color zone #8 near sel distance 3.79
    7762 
    7763 > color single #8
    7764 
    7765 > show #!7 models
    7766 
    7767 > select clear
    7768 
    7769 [Repeated 1 time(s)]
    7770 
    7771 > select #7/C:1
    7772 
    7773 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7774 
    7775 > select add #7/C:2
    7776 
    7777 14 atoms, 12 bonds, 2 residues, 1 model selected 
    7778 
    7779 > select add #7/C:3
    7780 
    7781 23 atoms, 20 bonds, 3 residues, 1 model selected 
    7782 
    7783 > select add #7/C:4
    7784 
    7785 30 atoms, 26 bonds, 4 residues, 1 model selected 
    7786 
    7787 > select add #7/C:5
    7788 
    7789 39 atoms, 34 bonds, 5 residues, 1 model selected 
    7790 
    7791 > select add #7/C:6
    7792 
    7793 48 atoms, 42 bonds, 6 residues, 1 model selected 
    7794 
    7795 > select add #7/C:7
    7796 
    7797 57 atoms, 50 bonds, 7 residues, 1 model selected 
    7798 
    7799 > select add #7/C:8
    7800 
    7801 63 atoms, 55 bonds, 8 residues, 1 model selected 
    7802 
    7803 > select add #7/C:9
    7804 
    7805 72 atoms, 63 bonds, 9 residues, 1 model selected 
    7806 
    7807 > select add #7/C:10
    7808 
    7809 81 atoms, 71 bonds, 10 residues, 1 model selected 
    7810 
    7811 > select add #7/C:11
    7812 
    7813 90 atoms, 79 bonds, 11 residues, 1 model selected 
    7814 
    7815 > hide sel cartoons
    7816 
    7817 > select #7/C:12
    7818 
    7819 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7820 
    7821 > select clear
    7822 
    7823 > select #7/C:12
    7824 
    7825 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7826 
    7827 > select clear
    7828 
    7829 [Repeated 1 time(s)]
    7830 
    7831 > select #7/C:12
    7832 
    7833 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7834 
    7835 > select clear
    7836 
    7837 [Repeated 1 time(s)]
    7838 
    7839 > select #7/C:12
    7840 
    7841 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7842 
    7843 > select clear
    7844 
    7845 [Repeated 1 time(s)]
    7846 
    7847 > select #7/C:12
    7848 
    7849 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7850 
    7851 > select clear
    7852 
    7853 > hide #!8 models
    7854 
    7855 > select #7/C:12
    7856 
    7857 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7858 
    7859 > select add #7/C:13
    7860 
    7861 18 atoms, 16 bonds, 2 residues, 1 model selected 
    7862 
    7863 > select add #7/C:14
    7864 
    7865 25 atoms, 22 bonds, 3 residues, 1 model selected 
    7866 
    7867 > select add #7/C:15
    7868 
    7869 32 atoms, 28 bonds, 4 residues, 1 model selected 
    7870 
    7871 > select add #7/C:16
    7872 
    7873 40 atoms, 35 bonds, 5 residues, 1 model selected 
    7874 
    7875 > hide sel cartoons
    7876 
    7877 > select #7/B:237
    7878 
    7879 6 atoms, 5 bonds, 1 residue, 1 model selected 
    7880 Drag select of 9 residues 
    7881 
    7882 > hide sel cartoons
    7883 
    7884 > select #7/B:228
    7885 
    7886 7 atoms, 6 bonds, 1 residue, 1 model selected 
    7887 
    7888 > select add #7/B:227
    7889 
    7890 14 atoms, 13 bonds, 2 residues, 1 model selected 
    7891 
    7892 > select add #7/B:226
    7893 
    7894 25 atoms, 23 bonds, 3 residues, 1 model selected 
    7895 
    7896 > select add #7/B:225
    7897 
    7898 37 atoms, 35 bonds, 4 residues, 1 model selected 
    7899 
    7900 > select add #7/B:224
    7901 
    7902 45 atoms, 42 bonds, 5 residues, 1 model selected 
    7903 
    7904 > hide sel atoms
    7905 
    7906 > hide sel cartoons
    7907 
    7908 > select #7/B:223
    7909 
    7910 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7911 
    7912 > select add #7/B:222
    7913 
    7914 16 atoms, 14 bonds, 2 residues, 1 model selected 
    7915 
    7916 > select add #7/B:221
    7917 
    7918 22 atoms, 19 bonds, 3 residues, 1 model selected 
    7919 
    7920 > select add #7/B:220
    7921 
    7922 29 atoms, 26 bonds, 4 residues, 1 model selected 
    7923 
    7924 > hide sel cartoons
    7925 
    7926 > show #!8 models
    7927 
    7928 > select clear
    7929 
    7930 [Repeated 1 time(s)]
    7931 
    7932 > select #7/A:106
    7933 
    7934 13 atoms, 13 bonds, 1 residue, 1 model selected 
    7935 
    7936 > select add #7/A:105
    7937 
    7938 22 atoms, 21 bonds, 2 residues, 1 model selected 
    7939 
    7940 > select add #7/A:104
    7941 
    7942 31 atoms, 29 bonds, 3 residues, 1 model selected 
    7943 
    7944 > select add #7/A:103
    7945 
    7946 35 atoms, 32 bonds, 4 residues, 1 model selected 
    7947 
    7948 > select add #7/A:102
    7949 
    7950 44 atoms, 40 bonds, 5 residues, 1 model selected 
    7951 
    7952 > hide sel cartoons
    7953 
    7954 > select clear
    7955 
    7956 > cartoon style #7-8 modeHelix tube sides 20
    7957 
    7958 > show #!1 models
    7959 
    7960 > hide #!1 models
    7961 
    7962 > show #!4 models
    7963 
    7964 > hide #!4 models
    7965 
    7966 > show #!10 models
    7967 
    7968 > hide #!10 models
    7969 
    7970 > show #!11 models
    7971 
    7972 > select add #11
    7973 
    7974 76299 atoms, 81416 bonds, 12 pseudobonds, 6659 residues, 2 models selected 
    7975 
    7976 > ui tool show "Color Actions"
    7977 
    7978 > color sel wheat
    7979 
    7980 > select clear
    7981 
    7982 > hide #!7 models
    7983 
    7984 > color zone #8 near #11 distance 3.79
    7985 
    7986 > color single #8
    7987 
    7988 > hide #!11 models
    7989 
    7990 > show #!7 models
    7991 
    7992 > hide #!8 models
    7993 
    7994 > select #7/D:58
    7995 
    7996 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7997 
    7998 > select up
    7999 
    8000 68 atoms, 68 bonds, 9 residues, 1 model selected 
    8001 
    8002 > select up
    8003 
    8004 596 atoms, 606 bonds, 79 residues, 1 model selected 
    8005 
    8006 > select subtract #7/D:1
    8007 
    8008 588 atoms, 598 bonds, 78 residues, 1 model selected 
    8009 
    8010 > select subtract #7/D:2
    8011 
    8012 583 atoms, 593 bonds, 77 residues, 1 model selected 
    8013 
    8014 > select subtract #7/D:3
    8015 
    8016 576 atoms, 585 bonds, 76 residues, 1 model selected 
    8017 
    8018 > select subtract #7/D:4
    8019 
    8020 569 atoms, 577 bonds, 75 residues, 1 model selected 
    8021 
    8022 > select subtract #7/D:5
    8023 
    8024 560 atoms, 568 bonds, 74 residues, 1 model selected 
    8025 
    8026 > select subtract #7/D:6
    8027 
    8028 551 atoms, 559 bonds, 73 residues, 1 model selected 
    8029 
    8030 > select subtract #7/D:7
    8031 
    8032 544 atoms, 552 bonds, 72 residues, 1 model selected 
    8033 
    8034 > select subtract #7/D:8
    8035 
    8036 537 atoms, 545 bonds, 71 residues, 1 model selected 
    8037 
    8038 > select subtract #7/D:9
    8039 
    8040 528 atoms, 536 bonds, 70 residues, 1 model selected 
    8041 
    8042 > select add #7/D:9
    8043 
    8044 537 atoms, 544 bonds, 71 residues, 1 model selected 
    8045 
    8046 > show #!8 models
    8047 
    8048 > color zone #8 near sel distance 3.79
    8049 
    8050 > color zone #8 near sel distance 3.69
    8051 
    8052 > color zone #8 near sel distance 3.59
    8053 
    8054 > color zone #8 near sel distance 3.49
    8055 
    8056 > color zone #8 near sel distance 3.39
    8057 
    8058 > color zone #8 near sel distance 3.29
    8059 
    8060 > color zone #8 near sel distance 3.19
    8061 
    8062 > color zone #8 near sel distance 3.09
    8063 
    8064 > hide #!8 models
    8065 
    8066 > select subtract #7/D:54
    8067 
    8068 532 atoms, 538 bonds, 70 residues, 1 model selected 
    8069 
    8070 > select subtract #7/D:53
    8071 
    8072 524 atoms, 530 bonds, 69 residues, 1 model selected 
    8073 
    8074 > select subtract #7/D:55
    8075 
    8076 514 atoms, 519 bonds, 68 residues, 1 model selected 
    8077 
    8078 > select subtract #7/D:57
    8079 
    8080 505 atoms, 509 bonds, 67 residues, 1 model selected 
    8081 
    8082 > select subtract #7/D:56
    8083 
    8084 500 atoms, 505 bonds, 66 residues, 1 model selected 
    8085 
    8086 > select subtract #7/D:58
    8087 
    8088 492 atoms, 497 bonds, 65 residues, 1 model selected 
    8089 
    8090 > select subtract #7/D:52
    8091 
    8092 483 atoms, 488 bonds, 64 residues, 1 model selected 
    8093 
    8094 > select subtract #7/D:51
    8095 
    8096 477 atoms, 482 bonds, 63 residues, 1 model selected 
    8097 
    8098 > select subtract #7/D:50
    8099 
    8100 469 atoms, 474 bonds, 62 residues, 1 model selected 
    8101 
    8102 > color zone #8 near sel distance 3.09
    8103 
    8104 > show #!8 models
    8105 
    8106 > color zone #8 near sel distance 2.99
    8107 
    8108 > color zone #8 near sel distance 2.89
    8109 
    8110 > color zone #8 near sel distance 2.79
    8111 
    8112 > hide #!7 models
    8113 
    8114 > show #!7 models
    8115 
    8116 > hide #!7 models
    8117 
    8118 > open C:/ProgramData/ChimeraX/h28.png
    8119 
    8120 Opened multi-channel map h28.png as #12, 3 channels, grid size 1196,741,1,
    8121 pixel 1, shown at step 1, values uint8 
    8122 
    8123 > close #12
    8124 
    8125 > open "D:/PhD common folder/OneDrive - Indian Institute of
    8126 > Science/iso4E_crystallization/Alphafold3_predictions/rep1_trj.pdb"
    8127 
    8128 Summary of feedback from opening D:/PhD common folder/OneDrive - Indian
    8129 Institute of Science/iso4E_crystallization/Alphafold3_predictions/rep1_trj.pdb 
    8130 --- 
    8131 warnings | Ignored bad PDB record found on line 1 
    8132 REMARK GENERATED BY TRJCONV 
    8133 
    8134 Ignored bad PDB record found on line 3 
    8135 REMARK THIS IS A SIMULATION BOX 
    8136 
    8137 Ignored bad PDB record found on line 2792 
    8138 REMARK GENERATED BY TRJCONV 
    8139 
    8140 Ignored bad PDB record found on line 2794 
    8141 REMARK THIS IS A SIMULATION BOX 
    8142 
    8143 Ignored bad PDB record found on line 5583 
    8144 REMARK GENERATED BY TRJCONV 
    8145 
    8146 797 messages similar to the above omitted 
    8147 
    8148 rep1_trj.pdb title: 
    8149 Protein in water t= 0.00000 step= 0 [more info...] 
    8150 
    8151 Chain information for rep1_trj.pdb 
    8152 --- 
    8153 Chain | Description 
    8154 12.1/? 12.2/? 12.3/? 12.4/? 12.5/? 12.6/? 12.7/? 12.8/? 12.9/? 12.10/? 12.11/? 12.12/? 12.13/? 12.14/? 12.15/? 12.16/? 12.17/? 12.18/? 12.19/? 12.20/? 12.21/? 12.22/? 12.23/? 12.24/? 12.25/? 12.26/? 12.27/? 12.28/? 12.29/? 12.30/? 12.31/? 12.32/? 12.33/? 12.34/? 12.35/? 12.36/? 12.37/? 12.38/? 12.39/? 12.40/? 12.41/? 12.42/? 12.43/? 12.44/? 12.45/? 12.46/? 12.47/? 12.48/? 12.49/? 12.50/? 12.51/? 12.52/? 12.53/? 12.54/? 12.55/? 12.56/? 12.57/? 12.58/? 12.59/? 12.60/? 12.61/? 12.62/? 12.63/? 12.64/? 12.65/? 12.66/? 12.67/? 12.68/? 12.69/? 12.70/? 12.71/? 12.72/? 12.73/? 12.74/? 12.75/? 12.76/? 12.77/? 12.78/? 12.79/? 12.80/? 12.81/? 12.82/? 12.83/? 12.84/? 12.85/? 12.86/? 12.87/? 12.88/? 12.89/? 12.90/? 12.91/? 12.92/? 12.93/? 12.94/? 12.95/? 12.96/? 12.97/? 12.98/? 12.99/? 12.100/? 12.101/? 12.102/? 12.103/? 12.104/? 12.105/? 12.106/? 12.107/? 12.108/? 12.109/? 12.110/? 12.111/? 12.112/? 12.113/? 12.114/? 12.115/? 12.116/? 12.117/? 12.118/? 12.119/? 12.120/? 12.121/? 12.122/? 12.123/? 12.124/? 12.125/? 12.126/? 12.127/? 12.128/? 12.129/? 12.130/? 12.131/? 12.132/? 12.133/? 12.134/? 12.135/? 12.136/? 12.137/? 12.138/? 12.139/? 12.140/? 12.141/? 12.142/? 12.143/? 12.144/? 12.145/? 12.146/? 12.147/? 12.148/? 12.149/? 12.150/? 12.151/? 12.152/? 12.153/? 12.154/? 12.155/? 12.156/? 12.157/? 12.158/? 12.159/? 12.160/? 12.161/? 12.162/? 12.163/? 12.164/? 12.165/? 12.166/? 12.167/? 12.168/? 12.169/? 12.170/? 12.171/? 12.172/? 12.173/? 12.174/? 12.175/? 12.176/? 12.177/? 12.178/? 12.179/? 12.180/? 12.181/? 12.182/? 12.183/? 12.184/? 12.185/? 12.186/? 12.187/? 12.188/? 12.189/? 12.190/? 12.191/? 12.192/? 12.193/? 12.194/? 12.195/? 12.196/? 12.197/? 12.198/? 12.199/? 12.200/? 12.201/? 12.202/? 12.203/? 12.204/? 12.205/? 12.206/? 12.207/? 12.208/? 12.209/? 12.210/? 12.211/? 12.212/? 12.213/? 12.214/? 12.215/? 12.216/? 12.217/? 12.218/? 12.219/? 12.220/? 12.221/? 12.222/? 12.223/? 12.224/? 12.225/? 12.226/? 12.227/? 12.228/? 12.229/? 12.230/? 12.231/? 12.232/? 12.233/? 12.234/? 12.235/? 12.236/? 12.237/? 12.238/? 12.239/? 12.240/? 12.241/? 12.242/? 12.243/? 12.244/? 12.245/? 12.246/? 12.247/? 12.248/? 12.249/? 12.250/? 12.251/? 12.252/? 12.253/? 12.254/? 12.255/? 12.256/? 12.257/? 12.258/? 12.259/? 12.260/? 12.261/? 12.262/? 12.263/? 12.264/? 12.265/? 12.266/? 12.267/? 12.268/? 12.269/? 12.270/? 12.271/? 12.272/? 12.273/? 12.274/? 12.275/? 12.276/? 12.277/? 12.278/? 12.279/? 12.280/? 12.281/? 12.282/? 12.283/? 12.284/? 12.285/? 12.286/? 12.287/? 12.288/? 12.289/? 12.290/? 12.291/? 12.292/? 12.293/? 12.294/? 12.295/? 12.296/? 12.297/? 12.298/? 12.299/? 12.300/? 12.301/? 12.302/? 12.303/? 12.304/? 12.305/? 12.306/? 12.307/? 12.308/? 12.309/? 12.310/? 12.311/? 12.312/? 12.313/? 12.314/? 12.315/? 12.316/? 12.317/? 12.318/? 12.319/? 12.320/? 12.321/? 12.322/? 12.323/? 12.324/? 12.325/? 12.326/? 12.327/? 12.328/? 12.329/? 12.330/? 12.331/? 12.332/? 12.333/? 12.334/? 12.335/? 12.336/? 12.337/? 12.338/? 12.339/? 12.340/? 12.341/? 12.342/? 12.343/? 12.344/? 12.345/? 12.346/? 12.347/? 12.348/? 12.349/? 12.350/? 12.351/? 12.352/? 12.353/? 12.354/? 12.355/? 12.356/? 12.357/? 12.358/? 12.359/? 12.360/? 12.361/? 12.362/? 12.363/? 12.364/? 12.365/? 12.366/? 12.367/? 12.368/? 12.369/? 12.370/? 12.371/? 12.372/? 12.373/? 12.374/? 12.375/? 12.376/? 12.377/? 12.378/? 12.379/? 12.380/? 12.381/? 12.382/? 12.383/? 12.384/? 12.385/? 12.386/? 12.387/? 12.388/? 12.389/? 12.390/? 12.391/? 12.392/? 12.393/? 12.394/? 12.395/? 12.396/? 12.397/? 12.398/? 12.399/? 12.400/? 12.401/? | No description available 
    8155 
    8156 
    8157 > close #12
    8158 
    8159 > open "D:/PhD common folder/OneDrive - Indian Institute of
    8160 > Science/AF-Q9BY44-F1-model_v4.pdb"
    8161 
    8162 AF-Q9BY44-F1-model_v4.pdb title: 
    8163 Alphafold monomer V2.0 prediction for eukaryotic translation initiation factor
    8164 2A (Q9BY44) [more info...] 
    8165 
    8166 Chain information for AF-Q9BY44-F1-model_v4.pdb #12 
    8167 --- 
    8168 Chain | Description | UniProt 
    8169 A | eukaryotic translation initiation factor 2A | EIF2A_HUMAN 1-585 
    8170 
    8171 
    8172 > ui mousemode right "translate selected models"
    8173 
    8174 > view matrix models
    8175 > #7,-0.23218,0.69779,-0.67763,283.76,-0.55434,-0.66738,-0.4973,235.63,-0.79925,0.26017,0.54176,224.32
    8176 
    8177 > view matrix models
    8178 > #7,-0.23218,0.69779,-0.67763,348.82,-0.55434,-0.66738,-0.4973,267.66,-0.79925,0.26017,0.54176,245.29
    8179 
    8180 > select add #12
    8181 
    8182 5055 atoms, 5183 bonds, 647 residues, 2 models selected 
    8183 
    8184 > view matrix models
    8185 > #7,-0.23218,0.69779,-0.67763,536.12,-0.55434,-0.66738,-0.4973,348.46,-0.79925,0.26017,0.54176,292.21,#12,1,0,0,187.29,0,1,0,80.808,0,0,1,46.916
    8186 
    8187 > select clear
    8188 
    8189 Drag select of 30 residues 
    8190 
    8191 > select ~sel & ##selected
    8192 
    8193 4349 atoms, 4471 bonds, 555 residues, 1 model selected 
    8194 
    8195 > delete atoms sel
    8196 
    8197 > delete bonds sel
    8198 
    8199 > color single #8
    8200 
    8201 > show #!7 models
    8202 
    8203 > hide #!7 models
    8204 
    8205 > show #!7 models
    8206 
    8207 > show #12#!7 cartoons
    8208 
    8209 > select add #7
    8210 
    8211 14434 atoms, 15704 bonds, 1016 residues, 1 model selected 
    8212 
    8213 > show sel cartoons
    8214 
    8215 > close session
    8216 
    8217 > open "D:\PhD common folder\OneDrive - Indian Institute of
    8218 > Science\Yeast_project\40S_4B\4B_FL\Figure_session.cxs" format session
    8219 
    8220 Opened postprocess 1.mrc as #8, grid size 360,360,360, pixel 1.2, shown at
    8221 level 0.004, step 1, values float32 
    8222 Opened emd_17297.map as #9, grid size 400,400,400, pixel 1.06, shown at level
    8223 0.00408, step 2, values float32 
    8224 Log from Fri Jul 5 12:41:39 2024 Startup Messages 
    8225 --- 
    8226 warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle 
    8227 
    8228 UCSF ChimeraX version: 1.8.dev202312120034 (2023-12-12) 
    8229 © 2016-2023 Regents of the University of California. All rights reserved. 
    8230 How to cite UCSF ChimeraX 
    8231 
    8232 > open "D:\PhD common folder\OneDrive - Indian Institute of
    8233 > Science\Yeast_project\40S_4B\40S_4B_FL_map.cxs" format session
    8234 
    8235 Opened postprocess 1.mrc as #8, grid size 360,360,360, pixel 1.2, shown at
    8236 level 0.004, step 1, values float32 
    8237 Log from Fri Jun 14 15:32:28 2024UCSF ChimeraX version: 1.8.dev202312120034
    8238 (2023-12-12) 
    8239 © 2016-2023 Regents of the University of California. All rights reserved. 
    8240 
    8241 > open "D:\\\PhD common folder\\\OneDrive - Indian Institute of
    8242 > Science\\\Yeast_project\\\40S_4B\\\40S_4B_FL.cxs"
    8243 
    8244 Log from Thu Jun 13 18:54:25 2024UCSF ChimeraX version: 1.8.dev202312120034
    8245 (2023-12-12) 
    8246 © 2016-2023 Regents of the University of California. All rights reserved. 
    8247 
    8248 > open "D:\\\PhD common folder\\\OneDrive - Indian Institute of
    8249 > Science\\\Yeast_project\\\40S_4B\\\40S_4B_1-98_RRM_AF3.cxs"
    8250 
    8251 Log from Thu Jun 13 16:35:32 2024 Startup Messages 
    8252 --- 
    8253 warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle 
    8254 
    8255 You can double click a model's Name or ID in the model panel to edit those
    8256 fields 
    8257 UCSF ChimeraX version: 1.8.dev202312120034 (2023-12-12) 
    8258 © 2016-2023 Regents of the University of California. All rights reserved. 
    8259 How to cite UCSF ChimeraX 
    8260 
    8261 > open "D:\PhD common folder\OneDrive - Indian Institute of
    8262 > Science\Jose_TH_43S_PIC\New_RSR_models\PIN_5_real_space_refined.pdb" format
    8263 > pdb
    8264 
    8265 Chain information for PIN_5_real_space_refined.pdb #1 
    8266 --- 
    8267 Chain | Description 
    8268 1 | No description available 
    8269 2 | No description available 
    8270 3 | No description available 
    8271 A | No description available 
    8272 B | No description available 
    8273 C | No description available 
    8274 D | No description available 
    8275 E | No description available 
    8276 F | No description available 
    8277 G | No description available 
    8278 H | No description available 
    8279 I | No description available 
    8280 J | No description available 
    8281 K | No description available 
    8282 L | No description available 
    8283 M | No description available 
    8284 N | No description available 
    8285 O | No description available 
    8286 P | No description available 
    8287 Q | No description available 
    8288 R | No description available 
    8289 S | No description available 
    8290 T | No description available 
    8291 U | No description available 
    8292 V | No description available 
    8293 W | No description available 
    8294 X | No description available 
    8295 Y | No description available 
    8296 Z | No description available 
    8297 a | No description available 
    8298 b | No description available 
    8299 c | No description available 
    8300 d | No description available 
    8301 e | No description available 
    8302 f | No description available 
    8303 g | No description available 
    8304 h | No description available 
    8305 i | No description available 
    8306 j | No description available 
    8307 k | No description available 
    8308 l | No description available 
    8309 m | No description available 
    8310 n | No description available 
    8311 o | No description available 
    8312 p | No description available 
    8313 q | No description available 
    8314 r | No description available 
    8315 
    8316 
    8317 > ui tool show "Show Sequence Viewer"
    8318 
    8319 > sequence chain /2
    8320 
    8321 Alignment identifier is 1/2 
    8322 
    8323 > select /2:1150
    8324 
    8325 22 atoms, 24 bonds, 1 residue, 1 model selected 
    8326 
    8327 > select /2:1150-1157
    8328 
    8329 175 atoms, 196 bonds, 8 residues, 1 model selected 
    8330 
    8331 > select /2:1150
    8332 
    8333 22 atoms, 24 bonds, 1 residue, 1 model selected 
    8334 
    8335 > select /2:1150-1626
    8336 
    8337 10173 atoms, 11370 bonds, 477 residues, 1 model selected 
    8338 
    8339 > select ~sel & ##selected
    8340 
    8341 94063 atoms, 98599 bonds, 9675 residues, 1 model selected 
    8342 
    8343 > delete atoms sel
    8344 
    8345 > delete bonds sel
    8346 
    8347 > select protein
    8348 
    8349 Nothing selected 
    8350 
    8351 > show cartoons
    8352 
    8353 > hide atoms
    8354 
    8355 > set bgColor white
    8356 
    8357 > open "D:/PhD common folder/OneDrive - Indian Institute of
    8358 > Science/Yeast_project/40S_4B/fold_40s_rrna_head_2024_06_12_22_44_model_0.cif"
    8359 
    8360 Chain information for fold_40s_rrna_head_2024_06_12_22_44_model_0.cif #2 
    8361 --- 
    8362 Chain | Description 
    8363 A | . 
    8364 
    8365 
    8366 > ui tool show Matchmaker
    8367 
    8368 > matchmaker #2 to #1
    8369 
    8370 Using Nucleic matrix instead of BLOSUM-62 for matching 
    8371 Parameters 
    8372 --- 
    8373 Chain pairing | bb 
    8374 Alignment algorithm | Needleman-Wunsch 
    8375 Similarity matrix | Nucleic 
    8376 SS fraction | 0.3 
    8377 Gap open (HH/SS/other) | 18/18/6 
    8378 Gap extend | 1 
    8379 SS matrix |  |  | H | S | O 
    8380 ---|---|---|--- 
    8381 H | 6 | -9 | -6 
    8382 S |  | 6 | -6 
    8383 O |  |  | 4 
    8384 Iteration cutoff | 2 
    8385 
    8386 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#1) with
    8387 fold_40s_rrna_head_2024_06_12_22_44_model_0.cif, chain A (#2), sequence
    8388 alignment score = 1887 
    8389 RMSD between 441 pruned atom pairs is 0.742 angstroms; (across all 477 pairs:
    8390 1.140) 
    8391 
    8392 
    8393 > select add #2
    8394 
    8395 10163 atoms, 11360 bonds, 477 residues, 1 model selected 
    8396 
    8397 > hide sel atoms
    8398 
    8399 > select subtract #2
    8400 
    8401 Nothing selected 
    8402 
    8403 > lighting soft
    8404 
    8405 > graphics silhouettes true
    8406 
    8407 > open "D:/PhD common folder/OneDrive - Indian Institute of
    8408 > Science/Yeast_project/40S_4B/New folder/fold_2024_06_13_01_16_model_0.cif"
    8409 
    8410 Chain information for fold_2024_06_13_01_16_model_0.cif #3 
    8411 --- 
    8412 Chain | Description 
    8413 A | . 
    8414 B | . 
    8415 C | . 
    8416 D | . 
    8417 
    8418 
    8419 > ui tool show Matchmaker
    8420 
    8421 > matchmaker #3 to #1
    8422 
    8423 Using Nucleic matrix instead of BLOSUM-62 for matching 
    8424 Parameters 
    8425 --- 
    8426 Chain pairing | bb 
    8427 Alignment algorithm | Needleman-Wunsch 
    8428 Similarity matrix | Nucleic 
    8429 SS fraction | 0.3 
    8430 Gap open (HH/SS/other) | 18/18/6 
    8431 Gap extend | 1 
    8432 SS matrix |  |  | H | S | O 
    8433 ---|---|---|--- 
    8434 H | 6 | -9 | -6 
    8435 S |  | 6 | -6 
    8436 O |  |  | 4 
    8437 Iteration cutoff | 2 
    8438 
    8439 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#1) with
    8440 fold_2024_06_13_01_16_model_0.cif, chain D (#3), sequence alignment score =
    8441 1887 
    8442 RMSD between 451 pruned atom pairs is 0.755 angstroms; (across all 477 pairs:
    8443 1.036) 
    8444 
    8445 
    8446 > matchmaker #3 to #1
    8447 
    8448 Using Nucleic matrix instead of BLOSUM-62 for matching 
    8449 Parameters 
    8450 --- 
    8451 Chain pairing | bb 
    8452 Alignment algorithm | Needleman-Wunsch 
    8453 Similarity matrix | Nucleic 
    8454 SS fraction | 0.3 
    8455 Gap open (HH/SS/other) | 18/18/6 
    8456 Gap extend | 1 
    8457 SS matrix |  |  | H | S | O 
    8458 ---|---|---|--- 
    8459 H | 6 | -9 | -6 
    8460 S |  | 6 | -6 
    8461 O |  |  | 4 
    8462 Iteration cutoff | 2 
    8463 
    8464 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#1) with
    8465 fold_2024_06_13_01_16_model_0.cif, chain D (#3), sequence alignment score =
    8466 1887 
    8467 RMSD between 451 pruned atom pairs is 0.755 angstroms; (across all 477 pairs:
    8468 1.036) 
    8469 
    8470 
    8471 > select add #3
    8472 
    8473 13838 atoms, 15098 bonds, 937 residues, 1 model selected 
    8474 
    8475 > hide sel atoms
    8476 
    8477 > select subtract #3
    8478 
    8479 Nothing selected 
    8480 
    8481 > hide #2 models
    8482 
    8483 > select add #1
    8484 
    8485 10173 atoms, 11370 bonds, 477 residues, 1 model selected 
    8486 
    8487 > show sel cartoons
    8488 
    8489 > hide sel atoms
    8490 
    8491 > surface sel
    8492 
    8493 > hide sel atoms
    8494 
    8495 > surface hidePatches (#!1 & sel)
    8496 
    8497 > open "D:/PhD common folder/OneDrive - Indian Institute of
    8498 > Science/Jose_TH_43S_PIC/New_RSR_models/PIN_5_real_space_refined.pdb"
    8499 
    8500 Chain information for PIN_5_real_space_refined.pdb #4 
    8501 --- 
    8502 Chain | Description 
    8503 1 | No description available 
    8504 2 | No description available 
    8505 3 | No description available 
    8506 A | No description available 
    8507 B | No description available 
    8508 C | No description available 
    8509 D | No description available 
    8510 E | No description available 
    8511 F | No description available 
    8512 G | No description available 
    8513 H | No description available 
    8514 I | No description available 
    8515 J | No description available 
    8516 K | No description available 
    8517 L | No description available 
    8518 M | No description available 
    8519 N | No description available 
    8520 O | No description available 
    8521 P | No description available 
    8522 Q | No description available 
    8523 R | No description available 
    8524 S | No description available 
    8525 T | No description available 
    8526 U | No description available 
    8527 V | No description available 
    8528 W | No description available 
    8529 X | No description available 
    8530 Y | No description available 
    8531 Z | No description available 
    8532 a | No description available 
    8533 b | No description available 
    8534 c | No description available 
    8535 d | No description available 
    8536 e | No description available 
    8537 f | No description available 
    8538 g | No description available 
    8539 h | No description available 
    8540 i | No description available 
    8541 j | No description available 
    8542 k | No description available 
    8543 l | No description available 
    8544 m | No description available 
    8545 n | No description available 
    8546 o | No description available 
    8547 p | No description available 
    8548 q | No description available 
    8549 r | No description available 
    8550 
    8551 
    8552 > select add #4
    8553 
    8554 114409 atoms, 121339 bonds, 10629 residues, 3 models selected 
    8555 
    8556 > select subtract #1
    8557 
    8558 104236 atoms, 109969 bonds, 10152 residues, 2 models selected 
    8559 
    8560 > surface hidePatches sel
    8561 
    8562 > hide sel atoms
    8563 
    8564 > show sel cartoons
    8565 
    8566 > ui tool show Matchmaker
    8567 
    8568 > matchmaker #!4 to #1/2 pairing bs matrix Nucleic
    8569 
    8570 Parameters 
    8571 --- 
    8572 Chain pairing | bs 
    8573 Alignment algorithm | Needleman-Wunsch 
    8574 Similarity matrix | Nucleic 
    8575 SS fraction | 0.3 
    8576 Gap open (HH/SS/other) | 18/18/6 
    8577 Gap extend | 1 
    8578 SS matrix |  |  | H | S | O 
    8579 ---|---|---|--- 
    8580 H | 6 | -9 | -6 
    8581 S |  | 6 | -6 
    8582 O |  |  | 4 
    8583 Iteration cutoff | 2 
    8584 
    8585 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#1) with
    8586 PIN_5_real_space_refined.pdb, chain 2 (#4), sequence alignment score = 5525.6 
    8587 RMSD between 477 pruned atom pairs is 0.000 angstroms; (across all 477 pairs:
    8588 0.000) 
    8589 
    8590 
    8591 > select clear
    8592 
    8593 > color #4 yellow
    8594 
    8595 > select #1/2:1361
    8596 
    8597 20 atoms, 21 bonds, 1 residue, 1 model selected 
    8598 
    8599 > select up
    8600 
    8601 10173 atoms, 11370 bonds, 477 residues, 2 models selected 
    8602 
    8603 > select clear
    8604 
    8605 > select #1/2:1373
    8606 
    8607 20 atoms, 21 bonds, 1 residue, 1 model selected 
    8608 
    8609 > select up
    8610 
    8611 10173 atoms, 11370 bonds, 477 residues, 2 models selected 
    8612 
    8613 > hide #!1 models
    8614 
    8615 > show #!1 models
    8616 
    8617 > hide #!1 models
    8618 
    8619 > hide #3 models
    8620 
    8621 > select add #4/U:47
    8622 
    8623 10180 atoms, 11376 bonds, 478 residues, 3 models selected 
    8624 
    8625 > select up
    8626 
    8627 10332 atoms, 11529 bonds, 497 residues, 3 models selected 
    8628 
    8629 > select up
    8630 
    8631 11018 atoms, 12227 bonds, 583 residues, 3 models selected 
    8632 
    8633 > show #3 models
    8634 
    8635 > hide #3 models
    8636 
    8637 > show #3 models
    8638 
    8639 > hide #3 models
    8640 
    8641 > select add #4/D:126
    8642 
    8643 11025 atoms, 12233 bonds, 584 residues, 3 models selected 
    8644 
    8645 > select up
    8646 
    8647 11150 atoms, 12360 bonds, 600 residues, 3 models selected 
    8648 
    8649 > select up
    8650 
    8651 12792 atoms, 14027 bonds, 810 residues, 3 models selected 
    8652 
    8653 > select up
    8654 
    8655 114409 atoms, 121339 bonds, 10629 residues, 3 models selected 
    8656 
    8657 > select down
    8658 
    8659 12792 atoms, 14027 bonds, 810 residues, 3 models selected 
    8660 
    8661 > show #3 models
    8662 
    8663 > hide #3 models
    8664 
    8665 > select add #4/K:16
    8666 
    8667 12803 atoms, 14038 bonds, 811 residues, 3 models selected 
    8668 
    8669 > select up
    8670 
    8671 12934 atoms, 14172 bonds, 826 residues, 3 models selected 
    8672 
    8673 > select up
    8674 
    8675 13601 atoms, 14858 bonds, 906 residues, 3 models selected 
    8676 
    8677 > select up
    8678 
    8679 114409 atoms, 121339 bonds, 10629 residues, 3 models selected 
    8680 
    8681 > select down
    8682 
    8683 13601 atoms, 14858 bonds, 906 residues, 3 models selected 
    8684 
    8685 > select add #4/2:1333
    8686 
    8687 13621 atoms, 14879 bonds, 907 residues, 3 models selected 
    8688 
    8689 > select up
    8690 
    8691 51413 atoms, 57141 bonds, 2686 residues, 3 models selected 
    8692 
    8693 > select ~sel & ##selected
    8694 
    8695 62996 atoms, 64198 bonds, 7943 residues, 1 model selected 
    8696 
    8697 > hide sel target a
    8698 
    8699 > hide sel cartoons
    8700 
    8701 > select clear
    8702 
    8703 > show #3 models
    8704 
    8705 > open "D:/PhD common folder/OneDrive - Indian Institute of
    8706 > Science/Yeast_project/40S_4B/New folder
    8707 > (2)/fold_2024_06_13_14_34_model_0.cif"
    8708 
    8709 Chain information for fold_2024_06_13_14_34_model_0.cif #5 
    8710 --- 
    8711 Chain | Description 
    8712 A | . 
    8713 B | . 
    8714 C | . 
    8715 D | . 
    8716 E | . 
    8717 
    8718 
    8719 > select #5/C:45@O
    8720 
    8721 1 atom, 1 residue, 1 model selected 
    8722 
    8723 > select #5/C:45@O
    8724 
    8725 1 atom, 1 residue, 1 model selected 
    8726 
    8727 > select clear
    8728 
    8729 > select add #5
    8730 
    8731 14573 atoms, 15847 bonds, 1035 residues, 1 model selected 
    8732 
    8733 > hide sel atoms
    8734 
    8735 > show sel cartoons
    8736 
    8737 > select clear
    8738 
    8739 > color #5 #ff55ffff
    8740 
    8741 > color #5 red
    8742 
    8743 > ui tool show Matchmaker
    8744 
    8745 > matchmaker #5 to #1/2 pairing bs matrix Nucleic
    8746 
    8747 Parameters 
    8748 --- 
    8749 Chain pairing | bs 
    8750 Alignment algorithm | Needleman-Wunsch 
    8751 Similarity matrix | Nucleic 
    8752 SS fraction | 0.3 
    8753 Gap open (HH/SS/other) | 18/18/6 
    8754 Gap extend | 1 
    8755 SS matrix |  |  | H | S | O 
    8756 ---|---|---|--- 
    8757 H | 6 | -9 | -6 
    8758 S |  | 6 | -6 
    8759 O |  |  | 4 
    8760 Iteration cutoff | 2 
    8761 
    8762 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#1) with
    8763 fold_2024_06_13_14_34_model_0.cif, chain E (#5), sequence alignment score =
    8764 1887 
    8765 RMSD between 446 pruned atom pairs is 0.750 angstroms; (across all 477 pairs:
    8766 1.027) 
    8767 
    8768 
    8769 > matchmaker #5 to #1/2 pairing bs matrix Nucleic
    8770 
    8771 Parameters 
    8772 --- 
    8773 Chain pairing | bs 
    8774 Alignment algorithm | Needleman-Wunsch 
    8775 Similarity matrix | Nucleic 
    8776 SS fraction | 0.3 
    8777 Gap open (HH/SS/other) | 18/18/6 
    8778 Gap extend | 1 
    8779 SS matrix |  |  | H | S | O 
    8780 ---|---|---|--- 
    8781 H | 6 | -9 | -6 
    8782 S |  | 6 | -6 
    8783 O |  |  | 4 
    8784 Iteration cutoff | 2 
    8785 
    8786 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#1) with
    8787 fold_2024_06_13_14_34_model_0.cif, chain E (#5), sequence alignment score =
    8788 1887 
    8789 RMSD between 446 pruned atom pairs is 0.750 angstroms; (across all 477 pairs:
    8790 1.027) 
    8791 
    8792 
    8793 > hide #3 models
    8794 
    8795 > select #5/D:61
    8796 
    8797 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8798 
    8799 > select up
    8800 
    8801 30 atoms, 29 bonds, 4 residues, 1 model selected 
    8802 
    8803 > select up
    8804 
    8805 735 atoms, 749 bonds, 98 residues, 1 model selected 
    8806 
    8807 > color sel cyan
    8808 
    8809 > color sel lime
    8810 
    8811 > select clear
    8812 
    8813 > select #5/D:56
    8814 
    8815 5 atoms, 4 bonds, 1 residue, 1 model selected 
    8816 
    8817 > select up
    8818 
    8819 24 atoms, 24 bonds, 3 residues, 1 model selected 
    8820 
    8821 > select up
    8822 
    8823 735 atoms, 749 bonds, 98 residues, 1 model selected 
    8824 
    8825 > select ~sel
    8826 
    8827 152248 atoms, 162895 bonds, 12980 residues, 5 models selected 
    8828 
    8829 > select subtract #1
    8830 
    8831 142075 atoms, 151525 bonds, 12503 residues, 5 models selected 
    8832 
    8833 > select subtract #2
    8834 
    8835 131912 atoms, 140165 bonds, 12026 residues, 3 models selected 
    8836 
    8837 > select subtract #3
    8838 
    8839 118074 atoms, 125067 bonds, 11089 residues, 2 models selected 
    8840 
    8841 > color sel yellow
    8842 
    8843 > select clear
    8844 
    8845 > save "D:/PhD common folder/OneDrive - Indian Institute of
    8846 > Science/Yeast_project/40S_4B/40S_4B_1-98_AF3.cxs"
    8847 
    8848 > open "D:/PhD common folder/OneDrive - Indian Institute of
    8849 > Science/Yeast_project/40S_4B/RRM/fold_rrm_2024_06_13_15_51_model_0.cif"
    8850 
    8851 Chain information for fold_rrm_2024_06_13_15_51_model_0.cif #6 
    8852 --- 
    8853 Chain | Description 
    8854 A | . 
    8855 B | . 
    8856 C | . 
    8857 D | . 
    8858 E | . 
    8859 
    8860 
    8861 > select add #6
    8862 
    8863 14522 atoms, 15797 bonds, 1024 residues, 1 model selected 
    8864 
    8865 > hide sel atoms
    8866 
    8867 > show sel cartoons
    8868 
    8869 > select clear
    8870 
    8871 > ui tool show Matchmaker
    8872 
    8873 > matchmaker #6 to #1/2 pairing bs matrix Nucleic
    8874 
    8875 Parameters 
    8876 --- 
    8877 Chain pairing | bs 
    8878 Alignment algorithm | Needleman-Wunsch 
    8879 Similarity matrix | Nucleic 
    8880 SS fraction | 0.3 
    8881 Gap open (HH/SS/other) | 18/18/6 
    8882 Gap extend | 1 
    8883 SS matrix |  |  | H | S | O 
    8884 ---|---|---|--- 
    8885 H | 6 | -9 | -6 
    8886 S |  | 6 | -6 
    8887 O |  |  | 4 
    8888 Iteration cutoff | 2 
    8889 
    8890 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#1) with
    8891 fold_rrm_2024_06_13_15_51_model_0.cif, chain E (#6), sequence alignment score
    8892 = 1887 
    8893 RMSD between 444 pruned atom pairs is 0.775 angstroms; (across all 477 pairs:
    8894 1.122) 
    8895 
    8896 
    8897 > matchmaker #6 to #1/2 pairing bs matrix Nucleic
    8898 
    8899 Parameters 
    8900 --- 
    8901 Chain pairing | bs 
    8902 Alignment algorithm | Needleman-Wunsch 
    8903 Similarity matrix | Nucleic 
    8904 SS fraction | 0.3 
    8905 Gap open (HH/SS/other) | 18/18/6 
    8906 Gap extend | 1 
    8907 SS matrix |  |  | H | S | O 
    8908 ---|---|---|--- 
    8909 H | 6 | -9 | -6 
    8910 S |  | 6 | -6 
    8911 O |  |  | 4 
    8912 Iteration cutoff | 2 
    8913 
    8914 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#1) with
    8915 fold_rrm_2024_06_13_15_51_model_0.cif, chain E (#6), sequence alignment score
    8916 = 1887 
    8917 RMSD between 444 pruned atom pairs is 0.775 angstroms; (across all 477 pairs:
    8918 1.122) 
    8919 
    8920 
    8921 > matchmaker #6 to #1/2 pairing bs matrix Nucleic
    8922 
    8923 Parameters 
    8924 --- 
    8925 Chain pairing | bs 
    8926 Alignment algorithm | Needleman-Wunsch 
    8927 Similarity matrix | Nucleic 
    8928 SS fraction | 0.3 
    8929 Gap open (HH/SS/other) | 18/18/6 
    8930 Gap extend | 1 
    8931 SS matrix |  |  | H | S | O 
    8932 ---|---|---|--- 
    8933 H | 6 | -9 | -6 
    8934 S |  | 6 | -6 
    8935 O |  |  | 4 
    8936 Iteration cutoff | 2 
    8937 
    8938 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#1) with
    8939 fold_rrm_2024_06_13_15_51_model_0.cif, chain E (#6), sequence alignment score
    8940 = 1887 
    8941 RMSD between 444 pruned atom pairs is 0.775 angstroms; (across all 477 pairs:
    8942 1.122) 
    8943 
    8944 
    8945 > hide #5 models
    8946 
    8947 > show #5 models
    8948 
    8949 > save "D:/PhD common folder/OneDrive - Indian Institute of
    8950 > Science/Yeast_project/40S_4B/40S_4B_1-98_RRM_AF3.cxs"
    8951 
    8952 \u2014\u2014\u2014 End of log from Thu Jun 13 16:35:32 2024 \u2014\u2014\u2014
    8953 
    8954 opened ChimeraX session 
    8955 
    8956 > open "D:/PhD common folder/OneDrive - Indian Institute of
    8957 > Science/Yeast_project/40S_4B/4B_FL/fold_4b_fl_2024_06_13_16_47_model_0.cif"
    8958 
    8959 Chain information for fold_4b_fl_2024_06_13_16_47_model_0.cif #7 
    8960 --- 
    8961 Chain | Description 
    8962 A | . 
    8963 B | . 
    8964 C | . 
    8965 D | . 
    8966 E | . 
    8967 
    8968 
    8969 > hide #!4 models
    8970 
    8971 > show #!4 models
    8972 
    8973 > hide #5 models
    8974 
    8975 > show #5 models
    8976 
    8977 > hide #5 models
    8978 
    8979 > show #5 models
    8980 
    8981 > hide #5 models
    8982 
    8983 > hide #6 models
    8984 
    8985 > select add #7
    8986 
    8987 17262 atoms, 18592 bonds, 1373 residues, 1 model selected 
    8988 
    8989 > hide sel atoms
    8990 
    8991 > show sel cartoons
    8992 
    8993 > ui tool show Matchmaker
    8994 
    8995 > matchmaker #7 to #1
    8996 
    8997 Using Nucleic matrix instead of BLOSUM-62 for matching 
    8998 Parameters 
    8999 --- 
    9000 Chain pairing | bb 
    9001 Alignment algorithm | Needleman-Wunsch 
    9002 Similarity matrix | Nucleic 
    9003 SS fraction | 0.3 
    9004 Gap open (HH/SS/other) | 18/18/6 
    9005 Gap extend | 1 
    9006 SS matrix |  |  | H | S | O 
    9007 ---|---|---|--- 
    9008 H | 6 | -9 | -6 
    9009 S |  | 6 | -6 
    9010 O |  |  | 4 
    9011 Iteration cutoff | 2 
    9012 
    9013 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#1) with
    9014 fold_4b_fl_2024_06_13_16_47_model_0.cif, chain E (#7), sequence alignment
    9015 score = 1887 
    9016 RMSD between 447 pruned atom pairs is 0.715 angstroms; (across all 477 pairs:
    9017 1.026) 
    9018 
    9019 
    9020 > matchmaker #7 to #1
    9021 
    9022 Using Nucleic matrix instead of BLOSUM-62 for matching 
    9023 Parameters 
    9024 --- 
    9025 Chain pairing | bb 
    9026 Alignment algorithm | Needleman-Wunsch 
    9027 Similarity matrix | Nucleic 
    9028 SS fraction | 0.3 
    9029 Gap open (HH/SS/other) | 18/18/6 
    9030 Gap extend | 1 
    9031 SS matrix |  |  | H | S | O 
    9032 ---|---|---|--- 
    9033 H | 6 | -9 | -6 
    9034 S |  | 6 | -6 
    9035 O |  |  | 4 
    9036 Iteration cutoff | 2 
    9037 
    9038 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#1) with
    9039 fold_4b_fl_2024_06_13_16_47_model_0.cif, chain C (#7), sequence alignment
    9040 score = 3.14629e+230 
    9041 Fewer than 3 residues aligned; cannot match PIN_5_real_space_refined.pdb,
    9042 chain 2 with fold_4b_fl_2024_06_13_16_47_model_0.cif, chain C 
    9043 
    9044 > select clear
    9045 
    9046 > show #5 models
    9047 
    9048 > select #7/D:119
    9049 
    9050 5 atoms, 4 bonds, 1 residue, 1 model selected 
    9051 
    9052 > select up
    9053 
    9054 91 atoms, 93 bonds, 12 residues, 1 model selected 
    9055 
    9056 > select up
    9057 
    9058 3424 atoms, 3494 bonds, 436 residues, 1 model selected 
    9059 
    9060 > color sel red
    9061 
    9062 > select clear
    9063 
    9064 > hide #5 models
    9065 
    9066 > hide #7 models
    9067 
    9068 > show #7 models
    9069 
    9070 > hide #7 models
    9071 
    9072 > show #7 models
    9073 
    9074 > select #7/D:179
    9075 
    9076 6 atoms, 5 bonds, 1 residue, 1 model selected 
    9077 
    9078 > select up
    9079 
    9080 32 atoms, 32 bonds, 4 residues, 1 model selected 
    9081 
    9082 > select up
    9083 
    9084 3424 atoms, 3494 bonds, 436 residues, 1 model selected 
    9085 
    9086 > select ~sel & ##selected
    9087 
    9088 13838 atoms, 15098 bonds, 937 residues, 1 model selected 
    9089 
    9090 > color sel yellow
    9091 
    9092 > select clear
    9093 
    9094 > save "D:/PhD common folder/OneDrive - Indian Institute of
    9095 > Science/Yeast_project/40S_4B/40S_4B_FL.cxs"
    9096 
    9097 \u2014\u2014\u2014 End of log from Thu Jun 13 18:54:25 2024 \u2014\u2014\u2014
    9098 
    9099 opened ChimeraX session 
    9100 
    9101 > open "D:/PhD common folder/OneDrive - Indian Institute of
    9102 > Science/Yeast_project/40S_4B/4B_FL/postprocess.mrc"
    9103 
    9104 Opened postprocess.mrc as #8, grid size 360,360,360, pixel 1.2, shown at level
    9105 0.0128, step 2, values float32 
    9106 
    9107 > volume #8 level 0.005107
    9108 
    9109 > volume #8 level 0.01186
    9110 
    9111 > close #8
    9112 
    9113 > open "D:/PhD common folder/OneDrive - Indian Institute of
    9114 > Science/Yeast_project/40S_4B/4B_FL/postprocess 1.mrc"
    9115 
    9116 Opened postprocess 1.mrc as #8, grid size 360,360,360, pixel 1.2, shown at
    9117 level 0.0117, step 2, values float32 
    9118 
    9119 > select add #7
    9120 
    9121 17262 atoms, 18592 bonds, 1373 residues, 1 model selected 
    9122 
    9123 > select add #4
    9124 
    9125 121498 atoms, 128561 bonds, 11525 residues, 2 models selected 
    9126 
    9127 > select subtract #4
    9128 
    9129 17262 atoms, 18592 bonds, 1373 residues, 1 model selected 
    9130 
    9131 > select add #4
    9132 
    9133 121498 atoms, 128561 bonds, 11525 residues, 2 models selected 
    9134 
    9135 > ui mousemode right "translate selected models"
    9136 
    9137 > view matrix models
    9138 > #4,1,0,0,29.873,0,1,0,-26.112,0,0,1,-4.1724,#7,0.28189,0.89695,-0.3406,208.48,-0.59451,-0.11535,-0.79578,143.74,-0.75306,0.42681,0.50073,170.55
    9139 
    9140 > view matrix models
    9141 > #4,0.82111,0.074806,0.56584,-60.523,0.37786,0.67177,-0.63714,95.401,-0.42778,0.73697,0.52334,8.5864,#7,-0.23912,0.96938,-0.055872,197.7,0.18694,-0.010503,-0.98231,165.67,-0.95282,-0.24534,-0.17871,148.8
    9142 
    9143 > view matrix models
    9144 > #4,0.39428,0.28977,0.87211,-82.164,0.12554,0.92311,-0.36347,36.734,-0.91037,0.25279,0.32759,252.6,#7,-0.71788,0.69246,0.071801,189.85,-0.23969,-0.14901,-0.95935,152.45,-0.65361,-0.7059,0.27294,190.17
    9145 
    9146 > view matrix models
    9147 > #4,0.93276,0.24233,0.26689,-61.721,-0.20029,0.96394,-0.17522,56.548,-0.29973,0.10998,0.94766,39.262,#7,-0.082117,0.92261,-0.3769,192.67,-0.49758,-0.36563,-0.7866,153.89,-0.86352,0.12294,0.48909,169.98
    9148 
    9149 > view matrix models
    9150 > #4,0.90668,0.38695,-0.16792,-3.6645,-0.32198,0.89205,0.31713,0.28806,0.27251,-0.23347,0.9334,5.1958,#7,0.15199,0.69695,-0.70083,194.66,-0.85991,-0.25634,-0.44141,149.71,-0.48729,0.66974,0.56035,177.29
    9151 
    9152 > view matrix models
    9153 > #4,0.83083,0.46289,-0.30895,22.476,-0.33038,0.85698,0.39553,-5.67,0.44785,-0.22655,0.86493,-18.087,#7,0.19167,0.55996,-0.80604,195.51,-0.90046,-0.22637,-0.37138,149.99,-0.39042,0.797,0.46084,174.54
    9154 
    9155 > view matrix models
    9156 > #4,0.81586,0.41377,-0.40394,53.081,-0.43451,0.8996,0.043887,72.529,0.38154,0.13971,0.91373,-95.845,#7,0.28818,0.51166,-0.80942,198.5,-0.69035,-0.47477,-0.5459,155.39,-0.6636,0.7161,0.2164,155.68
    9157 
    9158 > view matrix models
    9159 > #4,0.92225,0.36326,0.13231,-66.698,-0.33704,0.92311,-0.18513,90.197,-0.18939,0.12614,0.97377,7.703,#7,-0.055625,0.84179,-0.53694,182.84,-0.50438,-0.4878,-0.71249,154.45,-0.86169,0.23119,0.45172,165.44
    9160 
    9161 > view matrix models
    9162 > #4,0.90839,0.41625,0.039549,-57.795,-0.40792,0.86146,0.30246,24.934,0.091829,-0.29088,0.95234,48.468,#7,-0.021182,0.78365,-0.62084,182.06,-0.8549,-0.33616,-0.39515,151.25,-0.51836,0.52239,0.67706,181.85
    9163 
    9164 > view matrix models
    9165 > #4,0.84077,0.51864,-0.15529,-28.698,-0.44574,0.82595,0.34513,31.845,0.30726,-0.22096,0.92562,-4.1938,#7,0.04562,0.62803,-0.77685,182.43,-0.87659,-0.34777,-0.33263,152.83,-0.47907,0.69615,0.53466,174.88
    9166 
    9167 > view matrix models
    9168 > #4,0.84077,0.51864,-0.15529,-50.435,-0.44574,0.82595,0.34513,42.879,0.30726,-0.22096,0.92562,-2.874,#7,0.04562,0.62803,-0.77685,160.69,-0.87659,-0.34777,-0.33263,163.86,-0.47907,0.69615,0.53466,176.2
    9169 
    9170 > view matrix models
    9171 > #4,0.89894,0.43035,0.081855,-87.056,-0.41583,0.89706,-0.14958,114.17,-0.1378,0.10043,0.98536,2.6161,#7,-0.064087,0.79161,-0.60766,160.9,-0.53788,-0.54029,-0.64712,166.14,-0.84058,0.28538,0.46042,167.22
    9172 
    9173 > view matrix models
    9174 > #4,0.82294,0.43483,0.36563,-128.34,-0.25543,0.85805,-0.44554,148.79,-0.50747,0.27326,0.8172,70.448,#7,-0.30188,0.84404,-0.44324,156.38,-0.2466,-0.51824,-0.81891,171.07,-0.9209,-0.13791,0.36459,169
    9175 
    9176 > view matrix models
    9177 > #4,0.72434,0.68781,0.047535,-102.66,-0.68702,0.7143,0.13333,154.87,0.057748,-0.12923,0.98993,13.333,#7,-0.24052,0.59065,-0.77025,151.84,-0.71872,-0.64172,-0.26766,176.79,-0.65237,0.48922,0.57886,174.65
    9178 
    9179 > view matrix models
    9180 > #4,0.72434,0.68781,0.047535,-93.022,-0.68702,0.7143,0.13333,168.08,0.057748,-0.12923,0.98993,9.714,#7,-0.24052,0.59065,-0.77025,161.48,-0.71872,-0.64172,-0.26766,190,-0.65237,0.48922,0.57886,171.04
    9181 
    9182 > view matrix models
    9183 > #4,0.72434,0.68781,0.047535,-95.873,-0.68702,0.7143,0.13333,147.08,0.057748,-0.12923,0.98993,29.062,#7,-0.24052,0.59065,-0.77025,158.63,-0.71872,-0.64172,-0.26766,169,-0.65237,0.48922,0.57886,190.38
    9184 
    9185 > view matrix models
    9186 > #4,0.85992,0.49465,-0.12597,-48.976,-0.47438,0.86556,0.16051,68.367,0.18843,-0.078265,0.97896,-5.6566,#7,0.043195,0.66049,-0.74959,166.62,-0.76918,-0.45683,-0.44685,158.7,-0.63758,0.59587,0.4883,185.75
    9187 
    9188 > view matrix models
    9189 > #4,0.82107,0.52004,0.23539,-114.53,-0.48014,0.85219,-0.20793,141.5,-0.30873,0.057706,0.9494,68.51,#7,-0.25498,0.77694,-0.57563,161.58,-0.48539,-0.61771,-0.61873,164.17,-0.83629,0.12164,0.53462,189.05
    9190 
    9191 > ui tool show "Fit in Map"
    9192 
    9193 > fitmap #1 inMap #8
    9194 
    9195 Fit molecule PIN_5_real_space_refined.pdb (#1) to map postprocess 1.mrc (#8)
    9196 using 10173 atoms 
    9197 average map value = 0.01768, steps = 280 
    9198 shifted from previous position = 37.6 
    9199 rotated from previous position = 39.4 degrees 
    9200 atoms outside contour = 1813, contour level = 0.011685 
    9201 
    9202 Position of PIN_5_real_space_refined.pdb (#1) relative to postprocess 1.mrc
    9203 (#8) coordinates: 
    9204 Matrix rotation and translation 
    9205 0.77406817 0.62549730 0.09783453 -108.84656169 
    9206 -0.61873269 0.78014893 -0.09239861 173.02544428 
    9207 -0.13412059 0.01098940 0.99090408 40.92544766 
    9208 Axis 0.08141544 0.18265879 -0.97979962 
    9209 Axis point 198.28970282 243.37991178 0.00000000 
    9210 Rotation angle (degrees) 39.41561211 
    9211 Shift along axis -17.35591133 
    9212 
    9213 
    9214 > volume #8 level 0.008395
    9215 
    9216 > volume #8 level 0.007367
    9217 
    9218 > volume #8 level 0.006339
    9219 
    9220 > volume #8 level 0.005928
    9221 
    9222 > volume #8 level 0.0049
    9223 
    9224 > volume #8 level 0.004694
    9225 
    9226 > volume #8 level 0.004283
    9227 
    9228 > volume #8 level 0.004077
    9229 
    9230 > volume #8 level 0.003872
    9231 
    9232 > volume #8 level 0.004077
    9233 
    9234 > ui tool show "Hide Dust"
    9235 
    9236 > surface dust #8 size 50.34
    9237 
    9238 > view matrix models
    9239 > #4,0.82107,0.52004,0.23539,-116.39,-0.48014,0.85219,-0.20793,141.63,-0.30873,0.057706,0.9494,74.429,#7,-0.25498,0.77694,-0.57563,159.72,-0.48539,-0.61771,-0.61873,164.29,-0.83629,0.12164,0.53462,194.97
    9240 
    9241 > view matrix models
    9242 > #4,0.78554,0.61095,0.098306,-102.93,-0.60821,0.79156,-0.059316,151.7,-0.11405,-0.013196,0.99339,42.954,#7,-0.21581,0.67608,-0.70451,158.32,-0.59736,-0.66215,-0.45245,167.16,-0.77239,0.32321,0.54677,193.9
    9243 
    9244 > fitmap #1 inMap #8
    9245 
    9246 Fit molecule PIN_5_real_space_refined.pdb (#1) to map postprocess 1.mrc (#8)
    9247 using 10173 atoms 
    9248 average map value = 0.01768, steps = 48 
    9249 shifted from previous position = 0.0285 
    9250 rotated from previous position = 0.0236 degrees 
    9251 atoms outside contour = 97, contour level = 0.0040773 
    9252 
    9253 Position of PIN_5_real_space_refined.pdb (#1) relative to postprocess 1.mrc
    9254 (#8) coordinates: 
    9255 Matrix rotation and translation 
    9256 0.77413240 0.62548017 0.09743502 -108.78348482 
    9257 -0.61871031 0.78015823 -0.09246993 173.04062336 
    9258 -0.13385284 0.01129992 0.99093679 40.84496958 
    9259 Axis 0.08172445 0.18215188 -0.97986826 
    9260 Axis point 198.35850392 243.27675668 0.00000000 
    9261 Rotation angle (degrees) 39.41081833 
    9262 Shift along axis -17.39328493 
    9263 
    9264 
    9265 > fitmap #4 inMap #8
    9266 
    9267 Fit molecule PIN_5_real_space_refined.pdb (#4) to map postprocess 1.mrc (#8)
    9268 using 104236 atoms 
    9269 average map value = 0.0104, steps = 108 
    9270 shifted from previous position = 14.3 
    9271 rotated from previous position = 5.98 degrees 
    9272 atoms outside contour = 34631, contour level = 0.0040773 
    9273 
    9274 Position of PIN_5_real_space_refined.pdb (#4) relative to postprocess 1.mrc
    9275 (#8) coordinates: 
    9276 Matrix rotation and translation 
    9277 0.81103895 0.56883502 0.13653773 -110.00386069 
    9278 -0.55348062 0.82172712 -0.13573415 163.72215947 
    9279 -0.18940709 0.03451469 0.98129186 49.38976006 
    9280 Axis 0.14415361 0.27598498 -0.95029050 
    9281 Axis point 220.17547445 262.06246433 0.00000000 
    9282 Rotation angle (degrees) 36.19334027 
    9283 Shift along axis -17.60721577 
    9284 
    9285 
    9286 > fitmap #7 inMap #8
    9287 
    9288 Fit molecule fold_4b_fl_2024_06_13_16_47_model_0.cif (#7) to map postprocess
    9289 1.mrc (#8) using 17262 atoms 
    9290 average map value = 0.01325, steps = 108 
    9291 shifted from previous position = 13 
    9292 rotated from previous position = 1.77 degrees 
    9293 atoms outside contour = 2973, contour level = 0.0040773 
    9294 
    9295 Position of fold_4b_fl_2024_06_13_16_47_model_0.cif (#7) relative to
    9296 postprocess 1.mrc (#8) coordinates: 
    9297 Matrix rotation and translation 
    9298 -0.22927120 0.66107322 -0.71443470 152.80411903 
    9299 -0.57591627 -0.68385311 -0.44795691 178.76428159 
    9300 -0.78470070 0.30875094 0.53751064 191.73888093 
    9301 Axis 0.52122493 0.04839965 -0.85204580 
    9302 Axis point 181.08241586 46.38734422 0.00000000 
    9303 Rotation angle (degrees) 133.45675049 
    9304 Shift along axis -75.07286549 
    9305 
    9306 
    9307 > volume #8 style mesh
    9308 
    9309 > hide #!4 models
    9310 
    9311 > select subtract #4
    9312 
    9313 17262 atoms, 18592 bonds, 1373 residues, 1 model selected 
    9314 
    9315 > select subtract #7
    9316 
    9317 Nothing selected 
    9318 
    9319 > volume #8 style surface
    9320 
    9321 > volume #8 step 1
    9322 
    9323 > volume #8 level 0.0045
    9324 
    9325 > volume #8 level 0.0035
    9326 
    9327 > volume #8 style mesh
    9328 
    9329 > show #!4 models
    9330 
    9331 > volume #8 level 0.0045
    9332 
    9333 > hide #!4 models
    9334 
    9335 > show #!4 models
    9336 
    9337 > hide #!4 models
    9338 
    9339 > show #!4 models
    9340 
    9341 > hide #!4 models
    9342 
    9343 > show #!4 models
    9344 
    9345 > hide #!4 models
    9346 
    9347 > show #!4 models
    9348 
    9349 > close #4
    9350 
    9351 > open "D:/PhD common folder/OneDrive - Indian Institute of
    9352 > Science/Jose_TH_43S_PIC/New_RSR_models/PIN_5_real_space_refined.pdb"
    9353 
    9354 Chain information for PIN_5_real_space_refined.pdb #4 
    9355 --- 
    9356 Chain | Description 
    9357 1 | No description available 
    9358 2 | No description available 
    9359 3 | No description available 
    9360 A | No description available 
    9361 B | No description available 
    9362 C | No description available 
    9363 D | No description available 
    9364 E | No description available 
    9365 F | No description available 
    9366 G | No description available 
    9367 H | No description available 
    9368 I | No description available 
    9369 J | No description available 
    9370 K | No description available 
    9371 L | No description available 
    9372 M | No description available 
    9373 N | No description available 
    9374 O | No description available 
    9375 P | No description available 
    9376 Q | No description available 
    9377 R | No description available 
    9378 S | No description available 
    9379 T | No description available 
    9380 U | No description available 
    9381 V | No description available 
    9382 W | No description available 
    9383 X | No description available 
    9384 Y | No description available 
    9385 Z | No description available 
    9386 a | No description available 
    9387 b | No description available 
    9388 c | No description available 
    9389 d | No description available 
    9390 e | No description available 
    9391 f | No description available 
    9392 g | No description available 
    9393 h | No description available 
    9394 i | No description available 
    9395 j | No description available 
    9396 k | No description available 
    9397 l | No description available 
    9398 m | No description available 
    9399 n | No description available 
    9400 o | No description available 
    9401 p | No description available 
    9402 q | No description available 
    9403 r | No description available 
    9404 
    9405 
    9406 > select add #7
    9407 
    9408 17262 atoms, 18592 bonds, 1373 residues, 1 model selected 
    9409 
    9410 > select subtract #7
    9411 
    9412 Nothing selected 
    9413 
    9414 > select add #4
    9415 
    9416 104236 atoms, 109969 bonds, 10152 residues, 1 model selected 
    9417 
    9418 > hide sel atoms
    9419 
    9420 > show sel cartoons
    9421 
    9422 > color sel orange
    9423 
    9424 > select clear
    9425 
    9426 > select add #4
    9427 
    9428 104236 atoms, 109969 bonds, 10152 residues, 1 model selected 
    9429 
    9430 > view matrix models #4,1,0,0,-20.338,0,1,0,1.5317,0,0,1,-2.6363
    9431 
    9432 > ui mousemode right "translate selected models"
    9433 
    9434 > view matrix models
    9435 > #4,0.73417,-0.011715,0.67887,-110.65,0.039726,0.99888,-0.025724,-0.60366,-0.67781,0.045854,0.73381,179.35
    9436 
    9437 > view matrix models
    9438 > #4,0.9789,0.11074,-0.17176,-3.8946,-0.04979,0.94437,0.32509,-46.014,0.1982,-0.30968,0.92995,41.92
    9439 
    9440 > view matrix models
    9441 > #4,0.017369,0.56222,-0.82681,227.8,0.33544,0.77573,0.53453,-130.18,0.9419,-0.28663,-0.17512,126.11
    9442 
    9443 > view matrix models
    9444 > #4,-0.12811,0.98357,-0.12718,12.586,0.92087,0.07036,-0.38347,107.6,-0.36822,-0.16624,-0.91476,519.17
    9445 
    9446 > view matrix models
    9447 > #4,0.5569,0.82779,0.068008,-131.09,0.01997,0.068512,-0.99745,419.38,-0.83034,0.55683,0.021623,248.94
    9448 
    9449 > view matrix models
    9450 > #4,0.84123,0.44504,-0.30702,-21.878,-0.53641,0.61579,-0.57712,317.96,-0.067779,0.65018,0.75675,-81.698
    9451 
    9452 > view matrix models
    9453 > #4,0.73797,0.6641,0.11988,-141.84,-0.62927,0.74137,-0.23323,234.59,-0.24376,0.096676,0.965,31.9
    9454 
    9455 > view matrix models
    9456 > #4,0.73797,0.6641,0.11988,-108.61,-0.62927,0.74137,-0.23323,201.59,-0.24376,0.096676,0.965,35.063
    9457 
    9458 > view matrix models
    9459 > #4,0.72535,0.63548,0.26463,-130.83,-0.54471,0.76491,-0.34381,203.26,-0.42091,0.10523,0.90098,82.196
    9460 
    9461 > fitmap #4 inMap #8
    9462 
    9463 Fit molecule PIN_5_real_space_refined.pdb (#4) to map postprocess 1.mrc (#8)
    9464 using 104236 atoms 
    9465 average map value = 0.0104, steps = 216 
    9466 shifted from previous position = 20.7 
    9467 rotated from previous position = 15.2 degrees 
    9468 atoms outside contour = 38093, contour level = 0.0045 
    9469 
    9470 Position of PIN_5_real_space_refined.pdb (#4) relative to postprocess 1.mrc
    9471 (#8) coordinates: 
    9472 Matrix rotation and translation 
    9473 0.81109770 0.56879176 0.13636883 -109.97657823 
    9474 -0.55342535 0.82174938 -0.13582465 163.71638992 
    9475 -0.18931694 0.03469710 0.98130281 49.31254596 
    9476 Axis 0.14440007 0.27579500 -0.95030823 
    9477 Axis point 220.19825708 262.01584691 0.00000000 
    9478 Rotation angle (degrees) 36.18887777 
    9479 Shift along axis -17.59058130 
    9480 
    9481 
    9482 > select clear
    9483 
    9484 > select #4/p:724
    9485 
    9486 8 atoms, 7 bonds, 1 residue, 1 model selected 
    9487 
    9488 > select up
    9489 
    9490 214 atoms, 217 bonds, 24 residues, 1 model selected 
    9491 
    9492 > select up
    9493 
    9494 292 atoms, 298 bonds, 33 residues, 1 model selected 
    9495 
    9496 > select up
    9497 
    9498 5114 atoms, 5246 bonds, 647 residues, 1 model selected 
    9499 
    9500 > select up
    9501 
    9502 104236 atoms, 109969 bonds, 10152 residues, 1 model selected 
    9503 
    9504 > select up
    9505 
    9506 184767 atoms, 198033 bonds, 15475 residues, 9 models selected 
    9507 
    9508 > select down
    9509 
    9510 104236 atoms, 109969 bonds, 10152 residues, 2 models selected 
    9511 
    9512 > select down
    9513 
    9514 5114 atoms, 5246 bonds, 647 residues, 1 model selected 
    9515 
    9516 > delete atoms sel
    9517 
    9518 > delete bonds sel
    9519 
    9520 > select #4/r:88
    9521 
    9522 5 atoms, 4 bonds, 1 residue, 1 model selected 
    9523 
    9524 > select up
    9525 
    9526 42 atoms, 43 bonds, 5 residues, 1 model selected 
    9527 
    9528 > select up
    9529 
    9530 2019 atoms, 2064 bonds, 258 residues, 1 model selected 
    9531 
    9532 > select up
    9533 
    9534 2043 atoms, 2088 bonds, 261 residues, 1 model selected 
    9535 
    9536 > select up
    9537 
    9538 2606 atoms, 2669 bonds, 330 residues, 1 model selected 
    9539 
    9540 > select up
    9541 
    9542 99122 atoms, 104723 bonds, 9505 residues, 1 model selected 
    9543 
    9544 > select down
    9545 
    9546 2606 atoms, 2669 bonds, 330 residues, 1 model selected 
    9547 
    9548 > delete atoms sel
    9549 
    9550 > delete bonds sel
    9551 
    9552 > select #4/o:843
    9553 
    9554 5 atoms, 4 bonds, 1 residue, 1 model selected 
    9555 
    9556 > select up
    9557 
    9558 225 atoms, 224 bonds, 45 residues, 1 model selected 
    9559 
    9560 > select up
    9561 
    9562 280 atoms, 279 bonds, 56 residues, 1 model selected 
    9563 
    9564 > select up
    9565 
    9566 285 atoms, 283 bonds, 57 residues, 1 model selected 
    9567 
    9568 > select up
    9569 
    9570 387 atoms, 385 bonds, 78 residues, 1 model selected 
    9571 
    9572 > select add #4/q:89
    9573 
    9574 396 atoms, 393 bonds, 79 residues, 1 model selected 
    9575 
    9576 > select up
    9577 
    9578 487 atoms, 486 bonds, 89 residues, 1 model selected 
    9579 
    9580 > select up
    9581 
    9582 779 atoms, 784 bonds, 127 residues, 1 model selected 
    9583 
    9584 > delete atoms sel
    9585 
    9586 > delete bonds sel
    9587 
    9588 > select #7/D:158
    9589 
    9590 5 atoms, 4 bonds, 1 residue, 1 model selected 
    9591 
    9592 > select up
    9593 
    9594 44 atoms, 43 bonds, 6 residues, 1 model selected 
    9595 
    9596 > select up
    9597 
    9598 3424 atoms, 3494 bonds, 436 residues, 1 model selected 
    9599 
    9600 > select ~sel & ##selected
    9601 
    9602 13838 atoms, 15098 bonds, 937 residues, 1 model selected 
    9603 
    9604 > hide sel target a
    9605 
    9606 > cartoon hide sel
    9607 
    9608 > volume #8 style surface
    9609 
    9610 > volume #8
    9611 
    9612 > volume #8 style mesh
    9613 
    9614 > volume #8 style surface
    9615 
    9616 > volume #8 level 0.004
    9617 
    9618 > volume #8 style mesh
    9619 
    9620 > save "D:/PhD common folder/OneDrive - Indian Institute of
    9621 > Science/Yeast_project/40S_4B/40S_4B_FL_map.cxs"
    9622 
    9623 \u2014\u2014\u2014 End of log from Fri Jun 14 15:32:28 2024 \u2014\u2014\u2014
    9624 
    9625 opened ChimeraX session 
    9626 
    9627 > open "D:/PhD common folder/OneDrive - Indian Institute of
    9628 > Science/Yeast_project/40S_4B/emd_17297.map.gz"
    9629 
    9630 File reader requires uncompressed file; 'D:/PhD common folder/OneDrive -
    9631 Indian Institute of Science/Yeast_project/40S_4B/emd_17297.map.gz' is
    9632 compressed 
    9633 
    9634 > open "D:/PhD common folder/OneDrive - Indian Institute of
    9635 > Science/Yeast_project/40S_4B/emd_17297.map"
    9636 
    9637 Opened emd_17297.map as #9, grid size 400,400,400, pixel 1.06, shown at level
    9638 0.0109, step 2, values float32 
    9639 
    9640 > hide #!8 models
    9641 
    9642 > hide #!4 models
    9643 
    9644 > hide #7 models
    9645 
    9646 > select add #7
    9647 
    9648 17262 atoms, 18592 bonds, 1373 residues, 1 model selected 
    9649 
    9650 > select subtract #7
    9651 
    9652 Nothing selected 
    9653 
    9654 > volume #9 level 0.002703
    9655 
    9656 > ui tool show "Hide Dust"
    9657 
    9658 > surface dust #9 size 61.82
    9659 
    9660 > open "D:/PhD common folder/OneDrive - Indian Institute of
    9661 > Science/Yeast_project/40S_4B/8oz0.cif"
    9662 
    9663 8oz0.cif title: 
    9664 Structure of a human 48S translation initiation complex with eIF4F and eIF4A
    9665 [more info...] 
    9666 
    9667 Chain information for 8oz0.cif #10 
    9668 --- 
    9669 Chain | Description | UniProt 
    9670 1 3 | Eukaryotic initiation factor 4A-I | IF4A1_HUMAN 1-406 
    9671 2 | Eukaryotic translation initiation factor 4 gamma 1 | IF4G1_HUMAN 196-1599 
    9672 5 | Eukaryotic translation initiation factor 3 subunit E | EIF3E_HUMAN 1-445 
    9673 6 | Eukaryotic translation initiation factor 3 subunit F | EIF3F_HUMAN 1-357 
    9674 7 | Eukaryotic translation initiation factor 3 subunit G | EIF3G_HUMAN 1-320 
    9675 8 | Eukaryotic translation initiation factor 3 subunit H | EIF3H_HUMAN 1-352 
    9676 9 | 60S ribosomal protein L41 | RL41_HUMAN 1-25 
    9677 A | Eukaryotic translation initiation factor 3 subunit A | EIF3A_HUMAN 1-1382 
    9678 B | Eukaryotic translation initiation factor 3 subunit K | EIF3K_HUMAN 1-218 
    9679 C | Eukaryotic translation initiation factor 3 subunit M | EIF3M_HUMAN 1-374 
    9680 D | Eukaryotic translation initiation factor 2 subunit 1 | IF2A_HUMAN 1-315 
    9681 E | Eukaryotic translation initiation factor 2 subunit 3 | IF2G_HUMAN 1-472 
    9682 F | Eukaryotic translation initiation factor 3 subunit I | EIF3I_HUMAN 1-325 
    9683 G | Eukaryotic translation initiation factor 1A, X-chromosomal | IF1AX_HUMAN 1-144 
    9684 H | Eukaryotic translation initiation factor 5 | IF5_HUMAN 1-431 
    9685 I | Eukaryotic translation initiation factor 3 subunit B | EIF3B_HUMAN 1-814 
    9686 J | Eukaryotic translation initiation factor 3 subunit C | EIF3C_HUMAN 1-913 
    9687 K | Eukaryotic translation initiation factor 3 subunit L | EIF3L_HUMAN 1-564 
    9688 L | 40S ribosomal protein S7 | RS7_HUMAN 1-194 
    9689 M | 40S ribosomal protein S27 | RS27_HUMAN 1-84 
    9690 N | 40S ribosomal protein S21 | RS21_HUMAN 1-83 
    9691 O | 40S ribosomal protein S2 | RS2_HUMAN 1-293 
    9692 P | 40S ribosomal protein S3a | RS3A_HUMAN 1-264 
    9693 Q | 40S ribosomal protein SA | RSSA_HUMAN 1-295 
    9694 R | 40S ribosomal protein S26 | RS26_HUMAN 1-115 
    9695 S | 40S ribosomal protein S6 | RS6_HUMAN 1-249 
    9696 T | 40S ribosomal protein S14 | RS14_HUMAN 1-151 
    9697 U | Eukaryotic translation initiation factor 2 subunit 2 | IF2B_HUMAN 1-333 
    9698 V | 40S ribosomal protein S13 | RS13_HUMAN 1-151 
    9699 W | 18S rRNA |   
    9700 X | 40S ribosomal protein S11 | RS11_HUMAN 1-158 
    9701 Y | 40S ribosomal protein S4, X isoform | RS4X_HUMAN 1-263 
    9702 Z | 40S ribosomal protein S9 | RS9_HUMAN 1-194 
    9703 a | 40S ribosomal protein S23 | RS23_HUMAN 1-143 
    9704 b | 40S ribosomal protein S30 | RS30_HUMAN 75-133 
    9705 c | 40S ribosomal protein S15a | RS15A_HUMAN 1-130 
    9706 d | 40S ribosomal protein S8 | RS8_HUMAN 1-208 
    9707 e | 40S ribosomal protein S24 | RS24_HUMAN 1-133 
    9708 f | 40S ribosomal protein S5 | RS5_HUMAN 1-204 
    9709 g | 40S ribosomal protein S16 | RS16_HUMAN 1-146 
    9710 h | 40S ribosomal protein S3 | RS3_HUMAN 1-243 
    9711 i | 40S ribosomal protein S10 | RS10_HUMAN 1-165 
    9712 j | 40S ribosomal protein S15 | RS15_HUMAN 1-145 
    9713 k | Receptor of activated protein C kinase 1 | RACK1_HUMAN 1-317 
    9714 l | 40S ribosomal protein S19 | RS19_HUMAN 1-145 
    9715 m | 40S ribosomal protein S25 | RS25_HUMAN 1-125 
    9716 n | Small ribosomal subunit protein uS13 | RS18_HUMAN 1-151 
    9717 o | 40S ribosomal protein S29 | RS29_HUMAN 1-56 
    9718 p | Ubiquitin-40S ribosomal protein S27a | RS27A_HUMAN 1-156 
    9719 q | 40S ribosomal protein S12 | RS12_HUMAN 1-132 
    9720 s | 40S ribosomal protein S28 | RS28_HUMAN 1-69 
    9721 v | 40S ribosomal protein S17 | RS17_HUMAN 1-135 
    9722 w | 40S ribosomal protein S20 | RS20_HUMAN 1-119 
    9723 x | Eukaryotic translation initiation factor 3 subunit D | EIF3D_HUMAN 1-548 
    9724 y | tRNAiMet |   
    9725 z | mRNA |   
    9726 
    9727 Non-standard residues in 8oz0.cif #10 
    9728 --- 
    9729 5MC \u2014 5-methylcytidine-5'-monophosphate 
    9730 5MU \u2014 5-methyluridine 5'-monophosphate 
    9731 6MZ \u2014 N6-methyladenosine-5'-monophosphate 
    9732 A2M \u2014 2'-O-methyladenosine 5'-(dihydrogen phosphate) 
    9733 C4J \u2014
    9734 (5S)-5-{3-[(3S)-3-amino-3-carboxypropyl]-1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl}-2,5-anhydro-1-O-phosphono-
    9735 L-arabinitol 
    9736 JMH \u2014 3-Methylcytidine- 5'-monophosphate 
    9737 MA6 \u2014 6N-dimethyladenosine-5'-monophoshate 
    9738 MG \u2014 magnesium ion 
    9739 OMC \u2014 O2'-methylycytidine-5'-monophosphate 
    9740 OMG \u2014 O2'-methylguanosine-5'-monophosphate 
    9741 OMU \u2014 O2'-methyluridine 5'-monophosphate 
    9742 UR3 \u2014 3-methyluridine-5'-monophoshate 
    9743 ZN \u2014 zinc ion 
    9744 
    9745 
    9746 > volume #9 style mesh
    9747 
    9748 > show #!10 cartoons
    9749 
    9750 > hide #!10 atoms
    9751 
    9752 > graphics silhouettes false
    9753 
    9754 > graphics silhouettes true
    9755 
    9756 > lighting shadows true intensity 0.5
    9757 
    9758 > lighting shadows false
    9759 
    9760 > graphics silhouettes false
    9761 
    9762 > lighting flat
    9763 
    9764 > lighting full
    9765 
    9766 > lighting soft
    9767 
    9768 > lighting simple
    9769 
    9770 > lighting soft
    9771 
    9772 > graphics silhouettes false
    9773 
    9774 > graphics silhouettes true
    9775 
    9776 > volume #9 level 0.00561
    9777 
    9778 > show #7 models
    9779 
    9780 > hide #!9 models
    9781 
    9782 > hide #!10 models
    9783 
    9784 > select add #7
    9785 
    9786 17262 atoms, 18592 bonds, 1373 residues, 1 model selected 
    9787 
    9788 > show sel cartoons
    9789 
    9790 > select subtract #7
    9791 
    9792 Nothing selected 
    9793 
    9794 > show #!9 models
    9795 
    9796 > show #!10 models
    9797 
    9798 > ui tool show Matchmaker
    9799 
    9800 > matchmaker #7 to #10
    9801 
    9802 Parameters 
    9803 --- 
    9804 Chain pairing | bb 
    9805 Alignment algorithm | Needleman-Wunsch 
    9806 Similarity matrix | BLOSUM-62 
    9807 SS fraction | 0.3 
    9808 Gap open (HH/SS/other) | 18/18/6 
    9809 Gap extend | 1 
    9810 SS matrix |  |  | H | S | O 
    9811 ---|---|---|--- 
    9812 H | 6 | -9 | -6 
    9813 S |  | 6 | -6 
    9814 O |  |  | 4 
    9815 Iteration cutoff | 2 
    9816 
    9817 Matchmaker 8oz0.cif, chain W (#10) with
    9818 fold_4b_fl_2024_06_13_16_47_model_0.cif, chain E (#7), sequence alignment
    9819 score = 2518.7 
    9820 RMSD between 280 pruned atom pairs is 1.217 angstroms; (across all 472 pairs:
    9821 4.015) 
    9822 
    9823 
    9824 > matchmaker #7 to #10
    9825 
    9826 Parameters 
    9827 --- 
    9828 Chain pairing | bb 
    9829 Alignment algorithm | Needleman-Wunsch 
    9830 Similarity matrix | BLOSUM-62 
    9831 SS fraction | 0.3 
    9832 Gap open (HH/SS/other) | 18/18/6 
    9833 Gap extend | 1 
    9834 SS matrix |  |  | H | S | O 
    9835 ---|---|---|--- 
    9836 H | 6 | -9 | -6 
    9837 S |  | 6 | -6 
    9838 O |  |  | 4 
    9839 Iteration cutoff | 2 
    9840 
    9841 Matchmaker 8oz0.cif, chain W (#10) with
    9842 fold_4b_fl_2024_06_13_16_47_model_0.cif, chain E (#7), sequence alignment
    9843 score = 2518.7 
    9844 RMSD between 280 pruned atom pairs is 1.217 angstroms; (across all 472 pairs:
    9845 4.015) 
    9846 
    9847 
    9848 > volume #9 level 0.00408
    9849 
    9850 > hide #!9 models
    9851 
    9852 > color #10 magenta
    9853 
    9854 > show #!9 models
    9855 
    9856 > hide #!9 models
    9857 
    9858 > show #!9 models
    9859 
    9860 > hide #!9 models
    9861 
    9862 > show #!9 models
    9863 
    9864 > hide #!9 models
    9865 
    9866 > hide #!10 models
    9867 
    9868 > select #7/E:207
    9869 
    9870 23 atoms, 25 bonds, 1 residue, 1 model selected 
    9871 
    9872 > select up
    9873 
    9874 10163 atoms, 11360 bonds, 477 residues, 1 model selected 
    9875 
    9876 > ui tool show "Color Actions"
    9877 
    9878 > color sel beige
    9879 
    9880 > color sel wheat
    9881 
    9882 > color sel navajo white
    9883 
    9884 > select clear
    9885 
    9886 > show #!10 models
    9887 
    9888 > hide #!10 models
    9889 
    9890 > select #7/B:25
    9891 
    9892 11 atoms, 11 bonds, 1 residue, 1 model selected 
    9893 
    9894 > select up
    9895 
    9896 188 atoms, 191 bonds, 22 residues, 1 model selected 
    9897 
    9898 > select up
    9899 
    9900 1847 atoms, 1874 bonds, 237 residues, 1 model selected 
    9901 
    9902 > select clear
    9903 
    9904 > select #7/C:34
    9905 
    9906 7 atoms, 6 bonds, 1 residue, 1 model selected 
    9907 
    9908 > select up
    9909 
    9910 130 atoms, 129 bonds, 17 residues, 1 model selected 
    9911 
    9912 > select up
    9913 
    9914 936 atoms, 948 bonds, 117 residues, 1 model selected 
    9915 
    9916 > select up
    9917 
    9918 17262 atoms, 18592 bonds, 1373 residues, 1 model selected 
    9919 
    9920 > select down
    9921 
    9922 936 atoms, 948 bonds, 117 residues, 1 model selected 
    9923 
    9924 > color sel pale green
    9925 
    9926 > color sel medium spring green
    9927 
    9928 > color sel chartreuse
    9929 
    9930 > select clear
    9931 
    9932 > select #7/B:108
    9933 
    9934 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9935 
    9936 > select up
    9937 
    9938 99 atoms, 99 bonds, 13 residues, 1 model selected 
    9939 
    9940 > select up
    9941 
    9942 1847 atoms, 1874 bonds, 237 residues, 1 model selected 
    9943 
    9944 > color sel orange
    9945 
    9946 > color sel peru
    9947 
    9948 > color sel light salmon
    9949 
    9950 > color sel dark salmon
    9951 
    9952 > color sel coral
    9953 
    9954 > select clear
    9955 
    9956 > select #7/E:71
    9957 
    9958 22 atoms, 24 bonds, 1 residue, 1 model selected 
    9959 
    9960 > select up
    9961 
    9962 10163 atoms, 11360 bonds, 477 residues, 1 model selected 
    9963 
    9964 > color sel beige
    9965 
    9966 > select clear
    9967 
    9968 > select #7/D:121
    9969 
    9970 7 atoms, 6 bonds, 1 residue, 1 model selected 
    9971 
    9972 > select up
    9973 
    9974 91 atoms, 93 bonds, 12 residues, 1 model selected 
    9975 
    9976 > select up
    9977 
    9978 3424 atoms, 3494 bonds, 436 residues, 1 model selected 
    9979 
    9980 > color sel magenta
    9981 
    9982 > select clear
    9983 
    9984 > graphics silhouettes false
    9985 
    9986 > lighting shadows true intensity 0.5
    9987 
    9988 > graphics silhouettes true
    9989 
    9990 > ui tool show "Side View"
    9991 
    9992 > save "D:/PhD common folder/OneDrive - Indian Institute of
    9993 > Science/Yeast_project/40S_4B/4B_FL/Fig_5A.jpg" width 957 height 596
    9994 > supersample 3
    9995 
    9996 > ui tool show "Show Sequence Viewer"
    9997 
    9998 > sequence chain #7/D
    9999 
    10000 Alignment identifier is 7/D 
    10001 
    10002 > select #7/D:89
    10003 
    10004 11 atoms, 10 bonds, 1 residue, 1 model selected 
    10005 
    10006 > select #7/D:89-436
    10007 
    10008 2776 atoms, 2834 bonds, 348 residues, 1 model selected 
    10009 
    10010 > cartoon hide sel
    10011 
    10012 > show #!8 models
    10013 
    10014 > show #!1 models
    10015 
    10016 > hide #!1 models
    10017 
    10018 > show #2 models
    10019 
    10020 > hide #2 models
    10021 
    10022 > show #!4 models
    10023 
    10024 > ui tool show Matchmaker
    10025 
    10026 > matchmaker #7 to #4
    10027 
    10028 Parameters 
    10029 --- 
    10030 Chain pairing | bb 
    10031 Alignment algorithm | Needleman-Wunsch 
    10032 Similarity matrix | BLOSUM-62 
    10033 SS fraction | 0.3 
    10034 Gap open (HH/SS/other) | 18/18/6 
    10035 Gap extend | 1 
    10036 SS matrix |  |  | H | S | O 
    10037 ---|---|---|--- 
    10038 H | 6 | -9 | -6 
    10039 S |  | 6 | -6 
    10040 O |  |  | 4 
    10041 Iteration cutoff | 2 
    10042 
    10043 Matchmaker PIN_5_real_space_refined.pdb, chain 2 (#4) with
    10044 fold_4b_fl_2024_06_13_16_47_model_0.cif, chain E (#7), sequence alignment
    10045 score = 2881 
    10046 RMSD between 447 pruned atom pairs is 0.715 angstroms; (across all 477 pairs:
    10047 1.026) 
    10048 
    10049 
    10050 > hide #!4 models
    10051 
    10052 > lighting flat
    10053 
    10054 > lighting shadows true intensity 0.5
    10055 
    10056 > graphics silhouettes false
    10057 
    10058 > transparency sel 30
    10059 
    10060 > transparency sel 0
    10061 
    10062 > transparency #8 50
    10063 
    10064 > lighting soft
    10065 
    10066 > graphics silhouettes true
    10067 
    10068 > graphics silhouettes false
    10069 
    10070 > graphics silhouettes true
    10071 
    10072 > lighting simple
    10073 
    10074 > transparency #8 20
    10075 
    10076 > transparency #8 80
    10077 
    10078 > open "D:/PhD common folder/OneDrive - Indian Institute of
    10079 > Science/Yeast_project/40S_4B/8i7j.pdb"
    10080 
    10081 8i7j.pdb title: 
    10082 Yeast 40S-EIF4B - partially open conformation of the 40S head [more info...] 
    10083 
    10084 Chain information for 8i7j.pdb #11 
    10085 --- 
    10086 Chain | Description | UniProt 
    10087 2 | RNA (1780-mer) |   
    10088 A | 40S ribosomal protein S0 | RSSA_KLULA 1-254 
    10089 B | 40S ribosomal protein S1 | RS3A_KLULA 1-255 
    10090 C | KLLA0F09812P | Q6CKL3_KLULA 1-259 
    10091 D | KLLA0D08305P | Q6CRK7_KLULA 1-237 
    10092 E | 40S ribosomal protein S4 | Q6CWJ2_KLULA 1-261 
    10093 F | KLLA0D10659P | Q6CRA3_KLULA 1-227 
    10094 G | 40S ribosomal protein S6 | RS6_KLULC 1-236 
    10095 H | 40S ribosomal protein S7 | Q6CTD6_KLULA 1-190 
    10096 I | 40S ribosomal protein S8 | Q6CMG3_KLULA 1-201 
    10097 J | KLLA0E23673P | Q6CM18_KLULA 1-188 
    10098 K | KLLA0B08173P | Q6CVZ5_KLULA 1-106 
    10099 L | KLLA0A10483P | Q6CX80_KLULA 1-156 
    10100 M | 40S ribosomal protein S12 | Q6CLU4_KLULA 1-134 
    10101 N | KLLA0F18040P | Q6CJK0_KLULA 1-151 
    10102 O | RP59 | RS14_KLULC 1-137 
    10103 P | KLLA0F07843P | Q6CKV4_KLULA 1-142 
    10104 Q | 40S ribosomal protein S16 | RS16_KLULC 1-143 
    10105 R | KLLA0B01474P | Q6CWU3_KLULA 1-136 
    10106 S | KLLA0B01562P | Q6CWT9_KLULA 1-146 
    10107 T | KLLA0A07194P | Q6CXM0_KLULA 1-144 
    10108 U | KLLA0F25542P | Q6CIM1_KLULA 4-120 
    10109 V | 40S ribosomal protein S21 | RS21_KLULC 1-87 
    10110 W | KLLA0B07931P | Q6CW06_KLULA 1-130 
    10111 X | KLLA0B11231P | F2Z602_KLULA 1-145 
    10112 Y | 40S ribosomal protein S24 | Q6CU44_KLULA 1-135 
    10113 Z | 40S ribosomal protein S25 | Q6CW78_KLULA 1-108 
    10114 a | 40S ribosomal protein S26 | Q6CS01_KLULA 1-119 
    10115 b | 40S ribosomal protein S27 | Q6CNL2_KLULA 1-82 
    10116 c | S33 | RS28_KLULC 1-67 
    10117 d | 40S ribosomal protein S29 | RS29_KLULC 1-56 
    10118 e | 40S ribosomal protein S30 | Q6CUH5_KLULA 1-63 
    10119 f | ubiquitin-40S ribosomal protein S27A | RS27A_KLULC 1-150 
    10120 g | KLLA0E12277P | Q6CNI7_KLULA 1-326 
    10121 h | 60S ribosomal protein L41-A | RL41A_YEAST 1-25 
    10122 
    10123 Non-standard residues in 8i7j.pdb #11 
    10124 --- 
    10125 MG \u2014 magnesium ion 
    10126 ZN \u2014 zinc ion 
    10127 
    10128 
    10129 > select add #11
    10130 
    10131 79075 atoms, 84250 bonds, 12 pseudobonds, 7007 residues, 3 models selected 
    10132 
    10133 > select add #7
    10134 
    10135 93561 atoms, 100008 bonds, 12 pseudobonds, 8032 residues, 3 models selected 
    10136 
    10137 > select subtract #7
    10138 
    10139 76299 atoms, 81416 bonds, 12 pseudobonds, 6659 residues, 2 models selected 
    10140 
    10141 > show sel cartoons
    10142 
    10143 > hide sel atoms
    10144 
    10145 > select clear
    10146 
    10147 > hide #7 models
    10148 
    10149 > ui tool show "Fit in Map"
    10150 
    10151 > fitmap #11 inMap #8
    10152 
    10153 Fit molecule 8i7j.pdb (#11) to map postprocess 1.mrc (#8) using 76299 atoms 
    10154 average map value = 0.01715, steps = 124 
    10155 shifted from previous position = 6.85 
    10156 rotated from previous position = 9.78 degrees 
    10157 atoms outside contour = 4764, contour level = 0.004 
    10158 
    10159 Position of 8i7j.pdb (#11) relative to postprocess 1.mrc (#8) coordinates: 
    10160 Matrix rotation and translation 
    10161 0.99574639 -0.08528090 0.03487557 11.36946753 
    10162 0.08939706 0.98586789 -0.14167806 8.39268741 
    10163 -0.02230027 0.14419319 0.98929825 -24.08267778 
    10164 Axis 0.84114773 0.16823422 0.51397252 
    10165 Axis point 0.00000000 165.31387249 44.41337612 
    10166 Rotation angle (degrees) 9.78370709 
    10167 Shift along axis -1.40249549 
    10168 
    10169 
    10170 > ui tool show Matchmaker
    10171 
    10172 > matchmaker #7 to #11
    10173 
    10174 Parameters 
    10175 --- 
    10176 Chain pairing | bb 
    10177 Alignment algorithm | Needleman-Wunsch 
    10178 Similarity matrix | BLOSUM-62 
    10179 SS fraction | 0.3 
    10180 Gap open (HH/SS/other) | 18/18/6 
    10181 Gap extend | 1 
    10182 SS matrix |  |  | H | S | O 
    10183 ---|---|---|--- 
    10184 H | 6 | -9 | -6 
    10185 S |  | 6 | -6 
    10186 O |  |  | 4 
    10187 Iteration cutoff | 2 
    10188 
    10189 Matchmaker 8i7j.pdb, chain 2 (#11) with
    10190 fold_4b_fl_2024_06_13_16_47_model_0.cif, chain E (#7), sequence alignment
    10191 score = 2911.1 
    10192 RMSD between 374 pruned atom pairs is 1.206 angstroms; (across all 477 pairs:
    10193 1.708) 
    10194 
    10195 
    10196 > matchmaker #7 to #11
    10197 
    10198 Parameters 
    10199 --- 
    10200 Chain pairing | bb 
    10201 Alignment algorithm | Needleman-Wunsch 
    10202 Similarity matrix | BLOSUM-62 
    10203 SS fraction | 0.3 
    10204 Gap open (HH/SS/other) | 18/18/6 
    10205 Gap extend | 1 
    10206 SS matrix |  |  | H | S | O 
    10207 ---|---|---|--- 
    10208 H | 6 | -9 | -6 
    10209 S |  | 6 | -6 
    10210 O |  |  | 4 
    10211 Iteration cutoff | 2 
    10212 
    10213 Matchmaker 8i7j.pdb, chain 2 (#11) with
    10214 fold_4b_fl_2024_06_13_16_47_model_0.cif, chain E (#7), sequence alignment
    10215 score = 2911.1 
    10216 RMSD between 374 pruned atom pairs is 1.206 angstroms; (across all 477 pairs:
    10217 1.708) 
    10218 
    10219 
    10220 > show #7 models
    10221 
    10222 > hide #!11 models
    10223 
    10224 > transparency #8 90
    10225 
    10226 > transparency #8 95
    10227 
    10228 > transparency #8 99
    10229 
    10230 > save "D:/PhD common folder/OneDrive - Indian Institute of
    10231 > Science/Yeast_project/40S_4B/4B_FL/Figure_session.cxs"
    10232 
    10233 \u2014\u2014\u2014 End of log from Fri Jul 5 12:41:39 2024 \u2014\u2014\u2014
    10234 
    10235 opened ChimeraX session 
    10236 
    10237 > volume #8 style surface
    10238 
    10239 > select add #8
    10240 
    10241 2 models selected 
    10242 
    10243 > ui tool show "Color Actions"
    10244 
    10245 > color sel wheat
    10246 
    10247 > transparency #8.1 80
    10248 
    10249 > select clear
    10250 
    10251 > select #8
    10252 
    10253 2 models selected 
    10254 
    10255 > select clear
    10256 
    10257 > select #8
    10258 
    10259 2 models selected 
    10260 
    10261 > select clear
    10262 
    10263 > hide #!8 models
    10264 
    10265 > select #7/A:9
    10266 
    10267 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10268 
    10269 > select up
    10270 
    10271 131 atoms, 133 bonds, 14 residues, 1 model selected 
    10272 
    10273 > select up
    10274 
    10275 892 atoms, 916 bonds, 106 residues, 1 model selected 
    10276 
    10277 > ui tool show "Color Actions"
    10278 
    10279 > color sel royal blue
    10280 
    10281 > select clear
    10282 
    10283 > select #7/E:399
    10284 
    10285 22 atoms, 24 bonds, 1 residue, 1 model selected 
    10286 
    10287 > select up
    10288 
    10289 10163 atoms, 11360 bonds, 477 residues, 1 model selected 
    10290 
    10291 > ui tool show "Color Actions"
    10292 
    10293 > color sel wheat
    10294 
    10295 > select clear
    10296 
    10297 Drag select of 8 residues 
    10298 
    10299 > hide sel cartoons
    10300 
    10301 Drag select of 13 residues 
    10302 
    10303 > hide sel cartoons
    10304 
    10305 Drag select of 16 residues 
    10306 
    10307 > hide sel cartoons
    10308 
    10309 > save "D:/PhD common folder/OneDrive - Indian Institute of
    10310 > Science/Yeast_project/40S_4B/fig5C.cxs"
    10311 
    10312 \u2014\u2014\u2014 End of log from Fri Aug 9 18:47:29 2024 \u2014\u2014\u2014
    10313 
    10314 opened ChimeraX session 
    10315 
    10316 > show #!8 models
    10317 
    10318 > hide #!8 models
    10319 
    10320 > select #7/E:101
    10321 
    10322 20 atoms, 21 bonds, 1 residue, 1 model selected 
    10323 
    10324 > select up
    10325 
    10326 10163 atoms, 11360 bonds, 477 residues, 1 model selected 
    10327 
    10328 > show #!8 models
    10329 
    10330 > select up
    10331 
    10332 17262 atoms, 18592 bonds, 1373 residues, 1 model selected 
    10333 
    10334 > select up
    10335 
    10336 374177 atoms, 397981 bonds, 34825 residues, 13 models selected 
    10337 
    10338 > select up
    10339 
    10340 374177 atoms, 397981 bonds, 34825 residues, 14 models selected 
    10341 
    10342 > select up
    10343 
    10344 374177 atoms, 397981 bonds, 34825 residues, 14 models selected 
    10345 
    10346 > select down
    10347 
    10348 374177 atoms, 397981 bonds, 34825 residues, 14 models selected 
    10349 
    10350 > select down
    10351 
    10352 17262 atoms, 18592 bonds, 1373 residues, 2 models selected 
    10353 
    10354 > select down
    10355 
    10356 10163 atoms, 11360 bonds, 477 residues, 1 model selected 
    10357 
    10358 > select down
    10359 
    10360 20 atoms, 21 bonds, 1 residue, 1 model selected 
    10361 
    10362 > cartoon sel transparency 0.5
    10363 
    10364 Expected a keyword 
    10365 
    10366 > select transparency 0.5
    10367 
    10368 Expected an objects specifier or a keyword 
    10369 
    10370 > ui tool show "Side View"
    10371 
    10372 > save "D:/PhD common folder/OneDrive - Indian Institute of
    10373 > Science/Yeast_project/40S_4B/4B_NTD_in_density.png" width 957 height 585
    10374 > supersample 3 transparentBackground true
    10375 
    10376 > transparency sel 70
    10377 
    10378 > select clear
    10379 
    10380 > select #8
    10381 
    10382 3 models selected 
    10383 
    10384 > select clear
    10385 
    10386 > hide #!8 models
    10387 
    10388 > select #7/E:398
    10389 
    10390 20 atoms, 21 bonds, 1 residue, 1 model selected 
    10391 
    10392 > select up
    10393 
    10394 10163 atoms, 11360 bonds, 477 residues, 1 model selected 
    10395 
    10396 > cartoon hide sel
    10397 
    10398 > show #!8 models
    10399 
    10400 > hide #!8 models
    10401 
    10402 Drag select of 21 residues 
    10403 
    10404 > hide sel cartoons
    10405 
    10406 > show #!8 models
    10407 
    10408 > save "D:/PhD common folder/OneDrive - Indian Institute of
    10409 > Science/Yeast_project/40S_4B/4B_NTD_in_density.png" width 957 height 585
    10410 > supersample 3
    10411 
    10412 > save "D:/PhD common folder/OneDrive - Indian Institute of
    10413 > Science/Yeast_project/40S_4B/fig5C_.cxs"
    10414 
    10415 > close session
    10416 
    10417 > open "D:\PhD common folder\OneDrive - Indian Institute of
    10418 > Science\Yeast_project\40S_4B\4B_FL\Fig_S4.cxs" format session
    10419 
    10420 Opened postprocess 1.mrc as #8, grid size 360,360,360, pixel 1.2, shown at
    10421 level 0.00593, step 1, values float32 
    10422 Opened emd_17297.map as #9, grid size 400,400,400, pixel 1.06, shown at level
    10423 0.004, step 2, values float32 
    10424 Log from Fri Jul 5 17:37:19 2024 Startup Messages 
    10425 --- 
    10426 warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle 
    10427 
    10428 UCSF ChimeraX version: 1.8.dev202312120034 (2023-12-12) 
    10429 © 2016-2023 Regents of the University of California. All rights reserved. 
    10430 How to cite UCSF ChimeraX 
    10431 
    10432 > open "D:\PhD common folder\OneDrive - Indian Institute of
    10433 > Science\Yeast_project\40S_4B\40S_4B_FL_map.cxs" format session
    10434 
    10435 Opened postprocess 1.mrc as #8, grid size 360,360,360, pixel 1.2, shown at
    10436 level 0.004, step 1, values float32 
    10437 Log from Fri Jun 14 15:32:28 2024UCSF ChimeraX version: 1.8.dev202312120034
    10438 (2023-12-12) 
    10439 © 2016-2023 Regents of the University of California. All rights reserved. 
    10440 
    10441 > open "D:\\\PhD common folder\\\OneDrive - Indian Institute of
    10442 > Science\\\Yeast_project\\\40S_4B\\\40S_4B_FL.cxs"
    10443 
    10444 Log from Thu Jun 13 18:54:25 2024UCSF ChimeraX version: 1.8.dev202312120034
    10445 (2023-12-12) 
    10446 © 2016-2023 Regents of the University of California. All rights reserved. 
    10447 
    10448 > open "D:\\\PhD common folder\\\OneDrive - Indian Institute of
    10449 > Science\\\Yeast_project\\\40S_4B\\\40S_4B_1-98_RRM_AF3.cxs"
    10450 
    10451 Log from Thu Jun 13 16:35:32 2024 Startup Messages 
    10452 --- 
    10453 warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle 
    10454 
    10455 You can double click a model's Name or ID in the model panel to edit those
    10456 fields 
    10457 UCSF ChimeraX version: 1.8.dev202312120034 (2023-12-12) 
    10458 © 2016-2023 Regents of the University of California. All rights reserved. 
    10459 How to cite UCSF ChimeraX 
    10460 
    10461 > open "D:\PhD common folder\OneDrive - Indian Institute of
    10462 > Science\Jose_TH_43S_PIC\New_RSR_models\PIN_5_real_space_refined.pdb" format
    10463 > pdb
    10464 
    10465 Chain information for PIN_5_real_space_refined.pdb #1 
    10466 --- 
    10467 Chain | Description 
    10468 1 | No description available 
    10469 2 | No description available 
    10470 3 | No description available 
    10471 A | No description available 
    10472 B | No description available 
    10473 C | No description available 
    10474 D | No description available 
    10475 E | No description available 
    10476 F | No description available 
    10477 G | No description available 
    10478 H | No description available 
    10479 I | No description available 
    10480 J | No description available 
    10481 K | No description available 
    10482 L | No description available 
    10483 M | No description available 
    10484 N | No description available 
    10485 O | No description available 
    10486 P | No description available 
    10487 Q | No description available 
    10488 R | No description available 
    10489 S | No description available 
    10490 T | No description available 
    10491 U | No description available 
    10492 V | No description available 
    10493 W | No description available 
    10494 X | No description available 
    10495 Y | No description available 
    10496 Z | No description available 
    10497 a | No description available 
    10498 b | No description available 
    10499 c | No description available 
    10500 d | No description available 
    10501 e | No description available 
    10502 f | No description available 
    10503 g | No description available 
    10504 h | No description available 
    10505 i | No description available 
    10506 j | No description available 
    10507 k | No description available 
    10508 l | No description available 
    10509 m | No description available 
    10510 n | No description available 
    10511 o | No description available 
    10512 p | No description available 
    10513 q | No description available 
    10514 r | No description available 
    10515 
     3532[deleted to fit within ticket size limits]
    105163533
    105173534> ui tool show "Show Sequence Viewer"