Changes between Initial Version and Version 1 of Ticket #15230


Ignore:
Timestamp:
May 16, 2024, 1:39:29 PM (18 months ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #15230

    • Property Cc Tom Goddard added
    • Property Component Unassigned → Core
    • Property Owner set to Eric Pettersen
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → accepted
    • Property Summary ChimeraX bug report submission → Crash in garbage collection

  • Ticket #15230 – Description

    initial v1  
    34893489triangles, 5 residues 
    34903490
    3491 > select up
    3492 
    3493 2300 atoms, 2326 bonds, 153 residues, 2 models selected 
    3494 
    3495 > hide sel surfaces
    3496 
    3497 > select up
    3498 
    3499 4491 atoms, 4538 bonds, 282 residues, 2 models selected 
    3500 
    3501 > hide sel surfaces
    3502 
    3503 Drag select of copy of AF_EFPIWI_EMGTSF1_0.pdb_A SES surface, 629 of 858262
    3504 triangles, 3 residues 
    3505 
    3506 > select #5/B:76
    3507 
    3508 17 atoms, 16 bonds, 1 residue, 1 model selected 
    3509 
    3510 > show sel atoms
    3511 
    3512 > show #7 models
    3513 
    3514 > hide #!5 models
    3515 
    3516 > show #!5 models
    3517 
    3518 > hide #!5 models
    3519 
    3520 > select #7/A:760
    3521 
    3522 15 atoms, 14 bonds, 1 residue, 1 model selected 
    3523 
    3524 > hide sel atoms
    3525 
    3526 > show #!5 models
    3527 
    3528 > hide #!5 models
    3529 
    3530 > show #!5 models
    3531 
    3532 > hide #!5 models
    3533 
    3534 > select #7/B:76
    3535 
    3536 17 atoms, 16 bonds, 1 residue, 1 model selected 
    3537 
    3538 > show sel atoms
    3539 
    3540 > select #7/A:587
    3541 
    3542 11 atoms, 10 bonds, 1 residue, 1 model selected 
    3543 
    3544 > show sel atoms
    3545 
    3546 [Repeated 1 time(s)]
    3547 
    3548 > hide sel atoms
    3549 
    3550 > select #7/A:589
    3551 
    3552 17 atoms, 16 bonds, 1 residue, 1 model selected 
    3553 
    3554 > show sel atoms
    3555 
    3556 > hide sel atoms
    3557 
    3558 > select clear
    3559 
    3560 > hide H
    3561 
    3562 > select clear
    3563 
    3564 > select #7/B:75
    3565 
    3566 16 atoms, 15 bonds, 1 residue, 1 model selected 
    3567 
    3568 > select clear
    3569 
    3570 > select #7/B:76
    3571 
    3572 17 atoms, 16 bonds, 1 residue, 1 model selected 
    3573 
    3574 > hide sel atoms
    3575 
    3576 > select clear
    3577 
    3578 > color #4,7 byhetero
    3579 
    3580 > select clear
    3581 
    3582 > select #7/B:23
    3583 
    3584 24 atoms, 23 bonds, 1 residue, 1 model selected 
    3585 
    3586 > show sel atoms
    3587 
    3588 > select #7/B:6
    3589 
    3590 12 atoms, 11 bonds, 1 residue, 1 model selected 
    3591 
    3592 > show sel atoms
    3593 
    3594 > hide sel atoms
    3595 
    3596 > select #7/B:7
    3597 
    3598 14 atoms, 14 bonds, 1 residue, 1 model selected 
    3599 
    3600 > show sel atoms
    3601 
    3602 > hide sel atoms
    3603 
    3604 > select #7/B:9
    3605 
    3606 15 atoms, 14 bonds, 1 residue, 1 model selected 
    3607 
    3608 > show sel atoms
    3609 
    3610 > hide H
    3611 
    3612 Drag select of 2 atoms, 2 residues, 1 bonds 
    3613 
    3614 > select clear
    3615 
    3616 > select #7/B:23@NH1
    3617 
    3618 1 atom, 1 residue, 1 model selected 
    3619 
    3620 > select add #7/A:575@OE1
    3621 
    3622 2 atoms, 2 residues, 1 model selected 
    3623 
    3624 > distance #7/B:23@NH1 #7/A:575@OE1
    3625 
    3626 Distance between AF_EFPIWI_EMGTSF1_0.pdb #7/B ARG 23 NH1 and /A GLU 575 OE1:
    3627 3.717Å 
    3628 
    3629 > select clear
    3630 
    3631 > select #7/B:9
    3632 
    3633 15 atoms, 14 bonds, 1 residue, 1 model selected 
    3634 
    3635 > hide sel atoms
    3636 
    3637 > show #!2 models
    3638 
    3639 > hide #!2 models
    3640 
    3641 > select #7/B:22
    3642 
    3643 17 atoms, 16 bonds, 1 residue, 1 model selected 
    3644 
    3645 > hide sel atoms
    3646 
    3647 > select #7/A:516
    3648 
    3649 17 atoms, 16 bonds, 1 residue, 1 model selected 
    3650 
    3651 > select #7/A:617@NE
    3652 
    3653 1 atom, 1 residue, 1 model selected 
    3654 
    3655 > select add #7/B:28@OH
    3656 
    3657 2 atoms, 2 residues, 1 model selected 
    3658 
    3659 > distance #7/A:617@NE #7/B:28@OH
    3660 
    3661 Distance between AF_EFPIWI_EMGTSF1_0.pdb #7/A ARG 617 NE and /B TYR 28 OH:
    3662 3.019Å 
    3663 
    3664 > select #7/B:25
    3665 
    3666 24 atoms, 23 bonds, 1 residue, 1 model selected 
    3667 
    3668 > hide sel atoms
    3669 
    3670 > select clear
    3671 
    3672 Drag select of 1 pseudobonds, 8 atoms, 28 residues, 7 bonds 
    3673 
    3674 > select clear
    3675 
    3676 > select #7/A:619
    3677 
    3678 15 atoms, 14 bonds, 1 residue, 1 model selected 
    3679 
    3680 > show sel atoms
    3681 
    3682 > select #7/A:619@OE1
    3683 
    3684 1 atom, 1 residue, 1 model selected 
    3685 
    3686 > view #2 clip false
    3687 
    3688 Drag select of 2 residues 
    3689 
    3690 > select #7/A:619@OE1
    3691 
    3692 1 atom, 1 residue, 1 model selected 
    3693 
    3694 > select add #7/B:35@NZ
    3695 
    3696 2 atoms, 2 residues, 1 model selected 
    3697 
    3698 > distance #7/A:619@OE1 #7/B:35@NZ
    3699 
    3700 Distance between AF_EFPIWI_EMGTSF1_0.pdb #7/A GLU 619 OE1 and /B LYS 35 NZ:
    3701 3.414Å 
    3702 
    3703 > select clear
    3704 
    3705 > select #7/A:619
    3706 
    3707 15 atoms, 14 bonds, 1 residue, 1 model selected 
    3708 
    3709 > select clear
    3710 
    3711 > hide H
    3712 
    3713 > select clear
    3714 
    3715 > distance style color #241f31
    3716 
    3717 [Repeated 2 time(s)]
    3718 
    3719 > distance style color black
    3720 
    3721 [Repeated 2 time(s)]
    3722 
    3723 > ui windowfill toggle
    3724 
    3725 [Repeated 2 time(s)]
    3726 
    3727 > ui tool show Log
    3728 
    3729 > select #7/B:32
    3730 
    3731 22 atoms, 21 bonds, 1 residue, 1 model selected 
    3732 
    3733 > hide sel atoms
    3734 
    3735 > show #3 models
    3736 
    3737 > hide #3 models
    3738 
    3739 > show #3 models
    3740 
    3741 > hide #!4 models
    3742 
    3743 > label @@display
    3744 
    3745 [Repeated 1 time(s)]
    3746 
    3747 > label height 1.5
    3748 
    3749 > save
    3750 > /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/AF_GTSF1_complex_inter.cxs
    3751 
    3752 > hide #!7 models
    3753 
    3754 Drag select of 8 residues 
    3755 
    3756 > hide sel atoms
    3757 
    3758 > select clear
    3759 
    3760 > ui tool show "Model Panel"
    3761 
    3762 > show #!4 models
    3763 
    3764 > select clear
    3765 
    3766 > select #3/B:38
    3767 
    3768 24 atoms, 23 bonds, 1 residue, 1 model selected 
    3769 
    3770 > hide sel atoms
    3771 
    3772 > select #3/A:617
    3773 
    3774 14 atoms, 13 bonds, 1 residue, 1 model selected 
    3775 
    3776 > hide sel atoms
    3777 
    3778 > select clear
    3779 
    3780 > select #3/A:618
    3781 
    3782 21 atoms, 21 bonds, 1 residue, 1 model selected 
    3783 
    3784 > hide sel atoms
    3785 
    3786 > select clear
    3787 
    3788 [Repeated 2 time(s)]
    3789 
    3790 > select #3/B:72
    3791 
    3792 12 atoms, 11 bonds, 1 residue, 1 model selected 
    3793 
    3794 > hide sel atoms
    3795 
    3796 > select clear
    3797 
    3798 > select #3/A:560
    3799 
    3800 22 atoms, 21 bonds, 1 residue, 1 model selected 
    3801 
    3802 > hide sel atoms
    3803 
    3804 > select #3/A:594
    3805 
    3806 17 atoms, 17 bonds, 1 residue, 1 model selected 
    3807 
    3808 > select #3/A:389
    3809 
    3810 19 atoms, 18 bonds, 1 residue, 1 model selected 
    3811 
    3812 > hide sel atoms
    3813 
    3814 > select #3/A:559
    3815 
    3816 14 atoms, 13 bonds, 1 residue, 1 model selected 
    3817 
    3818 > hide sel atoms
    3819 
    3820 > select clear
    3821 
    3822 > select #3/B:112
    3823 
    3824 24 atoms, 25 bonds, 1 residue, 1 model selected 
    3825 
    3826 > hide sel atoms
    3827 
    3828 > select clear
    3829 
    3830 [Repeated 2 time(s)]
    3831 
    3832 > select #3/A:630
    3833 
    3834 20 atoms, 20 bonds, 1 residue, 1 model selected 
    3835 
    3836 > ui tool show "Model Panel"
    3837 
    3838 Drag select of 23 residues 
    3839 
    3840 > hide sel atoms
    3841 
    3842 > select clear
    3843 
    3844 > close #3.1
    3845 
    3846 > label @@display
    3847 
    3848 > label height 1.5
    3849 
    3850 > hide #!3 models
    3851 
    3852 > hide #!4 models
    3853 
    3854 > show #!5 models
    3855 
    3856 > ui tool show "Model Panel"
    3857 
    3858 > show #!3 models
    3859 
    3860 > hide #!3 models
    3861 
    3862 > select #5/B:27
    3863 
    3864 14 atoms, 14 bonds, 1 residue, 1 model selected 
    3865 
    3866 > show sel atoms
    3867 
    3868 > show #!3 models
    3869 
    3870 > hide #!3 models
    3871 
    3872 > hide H
    3873 
    3874 > select clear
    3875 
    3876 > show #!7 models
    3877 
    3878 > hide #!5 models
    3879 
    3880 > show #!5 models
    3881 
    3882 > hide #!5 models
    3883 
    3884 > show #!5 models
    3885 
    3886 > hide #!5 models
    3887 
    3888 > hide #!7 models
    3889 
    3890 > show #!5 models
    3891 
    3892 > ui tool show "Model Panel"
    3893 
    3894 > show #!7 models
    3895 
    3896 > hide #!7 models
    3897 
    3898 > hide #!5 surfaces
    3899 
    3900 > show #!3 models
    3901 
    3902 > hide #5.3 models
    3903 
    3904 > hide #!5 models
    3905 
    3906 > hide #!3 models
    3907 
    3908 > show #!7 models
    3909 
    3910 > show #!5 models
    3911 
    3912 > hide #!5 models
    3913 
    3914 > show #!5 models
    3915 
    3916 > hide #!7 models
    3917 
    3918 > ui tool show Distances
    3919 
    3920 > select #5/B:110@OE1
    3921 
    3922 1 atom, 1 residue, 1 model selected 
    3923 
    3924 > select add #5/A:605@NH1
    3925 
    3926 2 atoms, 2 residues, 2 models selected 
    3927 
    3928 > distance #5/B:110@OE1 #5/A:605@NH1
    3929 
    3930 Distance between copy of AF_EFPIWI_EMGTSF1_0.pdb #5/B GLU 110 OE1 and /A ARG
    3931 605 NH1: 2.642Å 
    3932 
    3933 > show #!4 models
    3934 
    3935 > select clear
    3936 
    3937 > select #5/B:112@OE2
    3938 
    3939 1 atom, 1 residue, 1 model selected 
    3940 
    3941 > select add #5/A:711@NZ
    3942 
    3943 2 atoms, 2 residues, 2 models selected 
    3944 
    3945 > distance #5/B:112@OE2 #5/A:711@NZ
    3946 
    3947 Distance between copy of AF_EFPIWI_EMGTSF1_0.pdb #5/B GLU 112 OE2 and /A LYS
    3948 711 NZ: 2.846Å 
    3949 
    3950 > select #5/A:714@NE2
    3951 
    3952 1 atom, 1 residue, 1 model selected 
    3953 
    3954 > select add #5/B:112@OE2
    3955 
    3956 2 atoms, 2 residues, 2 models selected 
    3957 
    3958 > distance #5/A:714@NE2 #5/B:112@OE2
    3959 
    3960 Distance between copy of AF_EFPIWI_EMGTSF1_0.pdb #5/A HIS 714 NE2 and /B GLU
    3961 112 OE2: 3.377Å 
    3962 
    3963 > select clear
    3964 
    3965 > color #4#5.1-2#!5 byhetero
    3966 
    3967 > select clear
    3968 
    3969 > select #5/A:717@NH1
    3970 
    3971 1 atom, 1 residue, 1 model selected 
    3972 
    3973 > select clear
    3974 
    3975 > select #5/A:717@NH1
    3976 
    3977 1 atom, 1 residue, 1 model selected 
    3978 
    3979 > select add #5/B:109@NE1
    3980 
    3981 2 atoms, 2 residues, 2 models selected 
    3982 
    3983 > distance #5/A:717@NH1 #5/B:109@NE1
    3984 
    3985 Distance between copy of AF_EFPIWI_EMGTSF1_0.pdb #5/A ARG 717 NH1 and /B TRP
    3986 109 NE1: 3.454Å 
    3987 
    3988 > select clear
    3989 
    3990 > select #5/A:529@OE1
    3991 
    3992 1 atom, 1 residue, 1 model selected 
    3993 
    3994 > select add #5/B:105@OG
    3995 
    3996 2 atoms, 2 residues, 2 models selected 
    3997 
    3998 > distance #5/A:529@OE1 #5/B:105@OG
    3999 
    4000 Distance between copy of AF_EFPIWI_EMGTSF1_0.pdb #5/A GLU 529 OE1 and /B SER
    4001 105 OG: 2.572Å 
    4002 
    4003 > select clear
    4004 
    4005 > distance style color #241f31
    4006 
    4007 [Repeated 2 time(s)]
    4008 
    4009 > distance style color black
    4010 
    4011 [Repeated 2 time(s)]
    4012 
    4013 > select clear
    4014 
    4015 > select #5/B:113
    4016 
    4017 21 atoms, 21 bonds, 1 residue, 1 model selected 
    4018 
    4019 > hide sel atoms
    4020 
    4021 > select clear
    4022 
    4023 > select #5/A:566@NH2
    4024 
    4025 1 atom, 1 residue, 1 model selected 
    4026 
    4027 > select add #5/B:98@N
    4028 
    4029 2 atoms, 2 residues, 2 models selected 
    4030 
    4031 > distance #5/A:566@NH2 #5/B:98@N
    4032 
    4033 Distance between copy of AF_EFPIWI_EMGTSF1_0.pdb #5/A ARG 566 NH2 and /B THR
    4034 98 N: 3.813Å 
    4035 
    4036 > select clear
    4037 
    4038 > show #!3 models
    4039 
    4040 > hide #2.2 models
    4041 
    4042 > show #2.2 models
    4043 
    4044 > hide #!2 models
    4045 
    4046 > hide #!3 models
    4047 
    4048 > show #!3 models
    4049 
    4050 > hide #3.1 target m
    4051 
    4052 > select #5/A:372
    4053 
    4054 19 atoms, 18 bonds, 1 residue, 1 model selected 
    4055 
    4056 > hide sel atoms
    4057 
    4058 > select up
    4059 
    4060 2 atoms, 1 bond, 1 residue, 1 model selected 
    4061 
    4062 > select up
    4063 
    4064 14 atoms, 14 bonds, 1 residue, 2 models selected 
    4065 
    4066 > hide sel atoms
    4067 
    4068 > select clear
    4069 
    4070 > select #5/A:565
    4071 
    4072 14 atoms, 13 bonds, 1 residue, 1 model selected 
    4073 
    4074 > hide sel atoms
    4075 
    4076 > select up
    4077 
    4078 2 atoms, 1 bond, 1 residue, 1 model selected 
    4079 
    4080 > select up
    4081 
    4082 14 atoms, 14 bonds, 1 residue, 2 models selected 
    4083 
    4084 > hide sel atoms
    4085 
    4086 > select clear
    4087 
    4088 > select #5/A:586
    4089 
    4090 19 atoms, 18 bonds, 1 residue, 1 model selected 
    4091 
    4092 > select #5/B:76
    4093 
    4094 17 atoms, 16 bonds, 1 residue, 1 model selected 
    4095 
    4096 > hide sel atoms
    4097 
    4098 > select #5/B:72@NH2
    4099 
    4100 1 atom, 1 residue, 1 model selected 
    4101 
    4102 > select add #5/A:583@OE2
    4103 
    4104 2 atoms, 2 residues, 2 models selected 
    4105 
    4106 > distance #5/B:72@NH2 #5/A:583@OE2
    4107 
    4108 Distance between copy of AF_EFPIWI_EMGTSF1_0.pdb #5/B ARG 72 NH2 and /A GLU
    4109 583 OE2: 2.628Å 
    4110 
    4111 > select #5/A:583@OE1
    4112 
    4113 1 atom, 1 residue, 1 model selected 
    4114 
    4115 > select add #5/B:72@NH2
    4116 
    4117 2 atoms, 2 residues, 2 models selected 
    4118 
    4119 > distance #5/A:583@OE1 #5/B:72@NH2
    4120 
    4121 Distance between copy of AF_EFPIWI_EMGTSF1_0.pdb #5/A GLU 583 OE1 and /B ARG
    4122 72 NH2: 2.750Å 
    4123 
    4124 > select clear
    4125 
    4126 > hide #!3 models
    4127 
    4128 > select clear
    4129 
    4130 > select #5/B:52@NH1
    4131 
    4132 1 atom, 1 residue, 1 model selected 
    4133 
    4134 > select add #5/A:575@OE1
    4135 
    4136 2 atoms, 2 residues, 2 models selected 
    4137 
    4138 > distance #5/B:52@NH1 #5/A:575@OE1
    4139 
    4140 Distance between copy of AF_EFPIWI_EMGTSF1_0.pdb #5/B ARG 52 NH1 and /A GLU
    4141 575 OE1: 2.707Å 
    4142 
    4143 > select #5/B:52@NH2
    4144 
    4145 1 atom, 1 residue, 1 model selected 
    4146 
    4147 > select add #5/A:575@OE1
    4148 
    4149 2 atoms, 2 residues, 2 models selected 
    4150 
    4151 > distance #5/B:52@NH2 #5/A:575@OE1
    4152 
    4153 Distance between copy of AF_EFPIWI_EMGTSF1_0.pdb #5/B ARG 52 NH2 and /A GLU
    4154 575 OE1: 2.831Å 
    4155 
    4156 > select clear
    4157 
    4158 > distance style color #241f31
    4159 
    4160 [Repeated 2 time(s)]
    4161 
    4162 > distance style color black
    4163 
    4164 [Repeated 2 time(s)]
    4165 
    4166 > select #5/B:28@OH
    4167 
    4168 1 atom, 1 residue, 1 model selected 
    4169 
    4170 > select add #5/A:617@NE
    4171 
    4172 2 atoms, 2 residues, 2 models selected 
    4173 
    4174 > distance #5/B:28@OH #5/A:617@NE
    4175 
    4176 Distance between copy of AF_EFPIWI_EMGTSF1_0.pdb #5/B TYR 28 OH and /A ARG 617
    4177 NE: 3.019Å 
    4178 
    4179 > select clear
    4180 
    4181 > select #5/B:24
    4182 
    4183 22 atoms, 21 bonds, 1 residue, 1 model selected 
    4184 
    4185 > select #5/B:22
    4186 
    4187 17 atoms, 16 bonds, 1 residue, 1 model selected 
    4188 
    4189 > hide sel atoms
    4190 
    4191 > select #5/B:24
    4192 
    4193 22 atoms, 21 bonds, 1 residue, 1 model selected 
    4194 
    4195 > show sel atoms
    4196 
    4197 > hide H
    4198 
    4199 > select clear
    4200 
    4201 > select #5/A:586
    4202 
    4203 19 atoms, 18 bonds, 1 residue, 1 model selected 
    4204 
    4205 > hide sel atoms
    4206 
    4207 > select #5/B:73
    4208 
    4209 19 atoms, 18 bonds, 1 residue, 1 model selected 
    4210 
    4211 > hide sel atoms
    4212 
    4213 > select #5/B:49
    4214 
    4215 20 atoms, 20 bonds, 1 residue, 1 model selected 
    4216 
    4217 > hide sel atoms
    4218 
    4219 > select clear
    4220 
    4221 > show #!3 models
    4222 
    4223 > select #5/A:760
    4224 
    4225 15 atoms, 14 bonds, 1 residue, 1 model selected 
    4226 
    4227 > hide sel atoms
    4228 
    4229 > select clear
    4230 
    4231 > hide #!3 models
    4232 
    4233 > select #5/B:91
    4234 
    4235 7 atoms, 6 bonds, 1 residue, 1 model selected 
    4236 
    4237 > show sel atoms
    4238 
    4239 > select #5/B:92
    4240 
    4241 14 atoms, 13 bonds, 1 residue, 1 model selected 
    4242 
    4243 > show sel atoms
    4244 
    4245 > select #5/A:462
    4246 
    4247 19 atoms, 18 bonds, 1 residue, 1 model selected 
    4248 
    4249 > show sel atoms
    4250 
    4251 > select #5/A:461
    4252 
    4253 24 atoms, 23 bonds, 1 residue, 1 model selected 
    4254 
    4255 > show sel atoms
    4256 
    4257 > select #5/A:460
    4258 
    4259 14 atoms, 14 bonds, 1 residue, 1 model selected 
    4260 
    4261 > show sel atoms
    4262 
    4263 Drag select of 18 atoms, 18 bonds, 12 residues 
    4264 
    4265 > select up
    4266 
    4267 294 atoms, 295 bonds, 17 residues, 2 models selected 
    4268 
    4269 > hide sel atoms
    4270 
    4271 > select clear
    4272 
    4273 > select #5/B:91
    4274 
    4275 7 atoms, 6 bonds, 1 residue, 1 model selected 
    4276 
    4277 > show sel atoms
    4278 
    4279 > select #5/B:92
    4280 
    4281 14 atoms, 13 bonds, 1 residue, 1 model selected 
    4282 
    4283 > hide sel atoms
    4284 
    4285 > show #!3 models
    4286 
    4287 > select #5/B:76
    4288 
    4289 17 atoms, 16 bonds, 1 residue, 1 model selected 
    4290 
    4291 > show sel atoms
    4292 
    4293 > hide #!3 models
    4294 
    4295 > select #5/A:571
    4296 
    4297 14 atoms, 13 bonds, 1 residue, 1 model selected 
    4298 
    4299 > show sel atoms
    4300 
    4301 > select #5/A:570
    4302 
    4303 24 atoms, 23 bonds, 1 residue, 1 model selected 
    4304 
    4305 > show sel atoms
    4306 
    4307 > select #5/A:571
    4308 
    4309 14 atoms, 13 bonds, 1 residue, 1 model selected 
    4310 
    4311 > hide sel atoms
    4312 
    4313 > select clear
    4314 
    4315 > hide H
    4316 
    4317 > select #5/B:76@NE2
    4318 
    4319 1 atom, 1 residue, 1 model selected 
    4320 
    4321 > select add #5/A:570@NE
    4322 
    4323 2 atoms, 2 residues, 2 models selected 
    4324 
    4325 > distance #5/B:76@NE2 #5/A:570@NE
    4326 
    4327 Distance between copy of AF_EFPIWI_EMGTSF1_0.pdb #5/B GLN 76 NE2 and /A ARG
    4328 570 NE: 4.166Å 
    4329 
    4330 > select #5/A:587
    4331 
    4332 11 atoms, 10 bonds, 1 residue, 1 model selected 
    4333 
    4334 > show sel atoms
    4335 
    4336 > hide sel atoms
    4337 
    4338 > select clear
    4339 
    4340 > distance style color #241f31
    4341 
    4342 [Repeated 2 time(s)]
    4343 
    4344 > distance style color black
    4345 
    4346 [Repeated 2 time(s)]
    4347 
    4348 > select clear
    4349 
    4350 > select #5/A:574
    4351 
    4352 17 atoms, 16 bonds, 1 residue, 1 model selected 
    4353 
    4354 > show sel atoms
    4355 
    4356 > hide H
    4357 
    4358 > select #5/A:574@OE1
    4359 
    4360 1 atom, 1 residue, 1 model selected 
    4361 
    4362 > select add #5/A:582@ND1
    4363 
    4364 2 atoms, 2 residues, 1 model selected 
    4365 
    4366 > distance #5/A:574@OE1 #5/A:582@ND1
    4367 
    4368 Distance between copy of AF_EFPIWI_EMGTSF1_0.pdb #5/A GLN 574 OE1 and HIS 582
    4369 ND1: 3.433Å 
    4370 
    4371 > select clear
    4372 
    4373 > show #!3 models
    4374 
    4375 > select #3/A:568
    4376 
    4377 17 atoms, 16 bonds, 1 residue, 1 model selected 
    4378 
    4379 > show sel atoms
    4380 
    4381 > hide H
    4382 
    4383 > select #5/A:582
    4384 
    4385 17 atoms, 17 bonds, 1 residue, 1 model selected 
    4386 
    4387 > select #5/A:574
    4388 
    4389 17 atoms, 16 bonds, 1 residue, 1 model selected 
    4390 
    4391 > select #3/A:568
    4392 
    4393 17 atoms, 16 bonds, 1 residue, 1 model selected 
    4394 
    4395 > hide sel atoms
    4396 
    4397 > select clear
    4398 
    4399 > delete label
    4400 
    4401 Missing or invalid "atoms" argument: invalid atoms specifier 
    4402 
    4403 > delete labels
    4404 
    4405 Missing or invalid "atoms" argument: invalid atoms specifier 
    4406 
    4407 > close #2.3
    4408 
    4409 > close #3.1
    4410 
    4411 > close #5.3
    4412 
    4413 > close #7.1
    4414 
    4415 > close #12.2
    4416 
    4417 > close #1.3
    4418 
    4419 > hide #4.1 models
    4420 
    4421 > hide #!5 models
    4422 
    4423 > label @@display
    4424 
    4425 > label height 1.5
    4426 
    4427 > select #3/B:34
    4428 
    4429 19 atoms, 18 bonds, 1 residue, 1 model selected 
    4430 
    4431 > hide sel atoms
    4432 
    4433 > select #3/A:574
    4434 
    4435 19 atoms, 18 bonds, 1 residue, 1 model selected 
    4436 
    4437 > hide sel atoms
    4438 
    4439 > select #3/B:31
    4440 
    4441 14 atoms, 14 bonds, 1 residue, 1 model selected 
    4442 
    4443 > hide sel atoms
    4444 
    4445 > select clear
    4446 
    4447 > ui tool show "Side View"
    4448 
    4449 > ui tool show "Model Panel"
    4450 
    4451 > close #3.1
    4452 
    4453 > label @@display
    4454 
    4455 > label height 1.5
    4456 
    4457 > select #3/B:17
    4458 
    4459 11 atoms, 10 bonds, 1 residue, 1 model selected 
    4460 
    4461 > hide sel atoms
    4462 
    4463 Drag select of 30 residues 
    4464 
    4465 > select up
    4466 
    4467 1085 atoms, 1090 bonds, 66 residues, 1 model selected 
    4468 
    4469 > hide sel atoms
    4470 
    4471 > select clear
    4472 
    4473 > select #3/B:16
    4474 
    4475 17 atoms, 16 bonds, 1 residue, 1 model selected 
    4476 
    4477 > show sel atoms
    4478 
    4479 > select clear
    4480 
    4481 > hide H
    4482 
    4483 > select clear
    4484 
    4485 > select #3/B:37
    4486 
    4487 11 atoms, 10 bonds, 1 residue, 1 model selected 
    4488 
    4489 > hide sel atoms
    4490 
    4491 > select clear
    4492 
    4493 > select #3/B:26
    4494 
    4495 24 atoms, 23 bonds, 1 residue, 1 model selected 
    4496 
    4497 > select #3/B:26
    4498 
    4499 24 atoms, 23 bonds, 1 residue, 1 model selected 
    4500 
    4501 > show sel atoms
    4502 
    4503 > hide H
    4504 
    4505 > select clear
    4506 
    4507 > select #3/B:27
    4508 
    4509 10 atoms, 9 bonds, 1 residue, 1 model selected 
    4510 
    4511 > hide sel atoms
    4512 
    4513 Drag select of 4 atoms, 3 bonds, 19 residues 
    4514 
    4515 > hide sel atoms
    4516 
    4517 > select #3/B:11
    4518 
    4519 14 atoms, 14 bonds, 1 residue, 1 model selected 
    4520 
    4521 > select #3/B:111
    4522 
    4523 19 atoms, 18 bonds, 1 residue, 1 model selected 
    4524 
    4525 > hide sel atoms
    4526 
    4527 > select #3/A:705
    4528 
    4529 19 atoms, 18 bonds, 1 residue, 1 model selected 
    4530 
    4531 > hide sel atoms
    4532 
    4533 > select clear
    4534 
    4535 > select #3/A:703@CA
    4536 
    4537 1 atom, 1 residue, 1 model selected 
    4538 
    4539 > hide sel atoms
    4540 
    4541 > close #2.3
    4542 
    4543 > close #3.1
    4544 
    4545 > select #3/A:703
    4546 
    4547 10 atoms, 9 bonds, 1 residue, 1 model selected 
    4548 
    4549 > hide sel atoms
    4550 
    4551 > select clear
    4552 
    4553 > select #3/A:699
    4554 
    4555 16 atoms, 15 bonds, 1 residue, 1 model selected 
    4556 
    4557 > hide sel atoms
    4558 
    4559 > select clear
    4560 
    4561 > select #3/A:617
    4562 
    4563 14 atoms, 13 bonds, 1 residue, 1 model selected 
    4564 
    4565 > select #3/A:616
    4566 
    4567 10 atoms, 9 bonds, 1 residue, 1 model selected 
    4568 
    4569 > hide sel atoms
    4570 
    4571 > select clear
    4572 
    4573 > label @@display
    4574 
    4575 > label height 1.2
    4576 
    4577 > select #3/B:16
    4578 
    4579 17 atoms, 16 bonds, 1 residue, 1 model selected 
    4580 
    4581 > hide sel atoms
    4582 
    4583 > select clear
    4584 
    4585 > save
    4586 > /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/AF_GTSF1_complex_inter.cxs
    4587 
    4588 > hide #!3 models
    4589 
    4590 > show #!5 models
    4591 
    4592 > close #5.3
    4593 
    4594 > label @@display
    4595 
    4596 > label height 1.2
    4597 
    4598 > select #5/A:723
    4599 
    4600 14 atoms, 13 bonds, 1 residue, 1 model selected 
    4601 
    4602 > select #5/B:24
    4603 
    4604 22 atoms, 21 bonds, 1 residue, 1 model selected 
    4605 
    4606 > select #5/B:25
    4607 
    4608 24 atoms, 23 bonds, 1 residue, 1 model selected 
    4609 
    4610 > show #!3 models
    4611 
    4612 > hide #!3 models
    4613 
    4614 > select #5/B:21
    4615 
    4616 16 atoms, 15 bonds, 1 residue, 1 model selected 
    4617 
    4618 > show sel atoms
    4619 
    4620 > hide sel atoms
    4621 
    4622 > select #5/B:22
    4623 
    4624 17 atoms, 16 bonds, 1 residue, 1 model selected 
    4625 
    4626 > show sel atoms
    4627 
    4628 > hide H
    4629 
    4630 > select clear
    4631 
    4632 > select #5/B:24
    4633 
    4634 22 atoms, 21 bonds, 1 residue, 1 model selected 
    4635 
    4636 > hide sel atoms
    4637 
    4638 > select clear
    4639 
    4640 [Repeated 1 time(s)]
    4641 
    4642 > select #5/A:574
    4643 
    4644 17 atoms, 16 bonds, 1 residue, 1 model selected 
    4645 
    4646 > hide sel atoms
    4647 
    4648 > select #5/B:50
    4649 
    4650 14 atoms, 13 bonds, 1 residue, 1 model selected 
    4651 
    4652 > show sel atoms
    4653 
    4654 > hide H
    4655 
    4656 > select #5/A:582@NE2
    4657 
    4658 1 atom, 1 residue, 1 model selected 
    4659 
    4660 > select add #5/B:50@ND2
    4661 
    4662 2 atoms, 2 residues, 2 models selected 
    4663 
    4664 > ui tool show Distances
    4665 
    4666 > distance #5/A:582@NE2 #5/B:50@ND2
    4667 
    4668 Distance between copy of AF_EFPIWI_EMGTSF1_0.pdb #5/A HIS 582 NE2 and /B ASN
    4669 50 ND2: 4.009Å 
    4670 
    4671 > show #4.1 models
    4672 
    4673 > hide #4.1 models
    4674 
    4675 > distance style color #241f31
    4676 
    4677 [Repeated 2 time(s)]
    4678 
    4679 > distance style color black
    4680 
    4681 [Repeated 2 time(s)]
    4682 
    4683 > select clear
    4684 
    4685 > close #5.3
    4686 
    4687 > label @@display
    4688 
    4689 > label height 1.2
    4690 
    4691 > select #5/B:92
    4692 
    4693 14 atoms, 13 bonds, 1 residue, 1 model selected 
    4694 
    4695 > show sel atoms
    4696 
    4697 > select #5/B:93
    4698 
    4699 14 atoms, 13 bonds, 1 residue, 1 model selected 
    4700 
    4701 > show sel atoms
    4702 
    4703 > select #5/A:760
    4704 
    4705 15 atoms, 14 bonds, 1 residue, 1 model selected 
    4706 
    4707 > show sel atoms
    4708 
    4709 > select #5/A:761
    4710 
    4711 19 atoms, 18 bonds, 1 residue, 1 model selected 
    4712 Drag select of 18 atoms, 16 bonds, 28 residues 
    4713 
    4714 > hide sel atoms
    4715 
    4716 > select clear
    4717 
    4718 > select #5/B:92
    4719 
    4720 14 atoms, 13 bonds, 1 residue, 1 model selected 
    4721 
    4722 > hide sel atoms
    4723 
    4724 > select clear
    4725 
    4726 > select #5/A:527
    4727 
    4728 10 atoms, 9 bonds, 1 residue, 1 model selected 
    4729 
    4730 > show sel atoms
    4731 
    4732 > select #5/A:373
    4733 
    4734 20 atoms, 20 bonds, 1 residue, 1 model selected 
    4735 
    4736 > show sel atoms
    4737 
    4738 > select #5/A:374
    4739 
    4740 22 atoms, 21 bonds, 1 residue, 1 model selected 
    4741 
    4742 > show sel atoms
    4743 
    4744 > hide sel atoms
    4745 
    4746 > select #5/A:372
    4747 
    4748 19 atoms, 18 bonds, 1 residue, 1 model selected 
    4749 
    4750 > show sel atoms
    4751 
    4752 > select #5/A:376
    4753 
    4754 11 atoms, 10 bonds, 1 residue, 1 model selected 
    4755 
    4756 > select #5/A:373
    4757 
    4758 20 atoms, 20 bonds, 1 residue, 1 model selected 
    4759 
    4760 > hide sel atoms
    4761 
    4762 > hide H
    4763 
    4764 > select #5/B:80
    4765 
    4766 14 atoms, 13 bonds, 1 residue, 1 model selected 
    4767 
    4768 > show sel atoms
    4769 
    4770 > select #5/A:759
    4771 
    4772 17 atoms, 17 bonds, 1 residue, 1 model selected 
    4773 
    4774 > show sel atoms
    4775 
    4776 > hide sel atoms
    4777 
    4778 > select #5/B:80
    4779 
    4780 14 atoms, 13 bonds, 1 residue, 1 model selected 
    4781 
    4782 > hide sel atoms
    4783 
    4784 > select clear
    4785 
    4786 > save
    4787 > /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/AF_GTSF1_complex_inter.cxs
    4788 
    4789 > ui tool show "Model Panel"
    4790 
    4791 > show #!3 models
    4792 
    4793 > hide #5.3 models
    4794 
    4795 > hide #7.1 models
    4796 
    4797 > hide #3.1 models
    4798 
    4799 > select #3/B:77
    4800 
    4801 19 atoms, 18 bonds, 1 residue, 1 model selected 
    4802 
    4803 > show #3.1 models
    4804 
    4805 > hide #3.1 models
    4806 
    4807 > select /a:26
    4808 
    4809 89 atoms, 87 bonds, 5 residues, 5 models selected 
    4810 
    4811 > view sel
    4812 
    4813 > select /a:26
    4814 
    4815 89 atoms, 87 bonds, 5 residues, 5 models selected 
    4816 
    4817 > view sel
    4818 
    4819 > show #3.1 models
    4820 
    4821 > hide #!3 models
    4822 
    4823 > show #5.3 models
    4824 
    4825 > view sel
    4826 
    4827 > select clear
    4828 
    4829 > save /home/dell/Desktop/image7.png supersample 3
    4830 
    4831 > save /home/dell/Desktop/image8.png supersample 3
    4832 
    4833 > select #5/A:572
    4834 
    4835 10 atoms, 9 bonds, 1 residue, 1 model selected 
    4836 
    4837 > hide sel atoms
    4838 
    4839 > select clear
    4840 
    4841 > close #5.3
    4842 
    4843 > label @@display
    4844 
    4845 > label height 1.2
    4846 
    4847 > select clear
    4848 
    4849 > save /home/dell/Desktop/image9.png supersample 3
    4850 
    4851 > save /home/dell/Desktop/image10.png supersample 3
    4852 
    4853 > hide #!5 models
    4854 
    4855 > show #!3 models
    4856 
    4857 > save /home/dell/Desktop/image11.png supersample 3
    4858 
    4859 > save /home/dell/Desktop/image12.png supersample 3
    4860 
    4861 > select #3/B:111
    4862 
    4863 19 atoms, 18 bonds, 1 residue, 1 model selected 
    4864 
    4865 > color sel lime
    4866 
    4867 > select clear
    4868 
    4869 > hide #5.3 models
    4870 
    4871 > hide #3.1 models
    4872 
    4873 > close #3.1
    4874 
    4875 > select #3/B:107
    4876 
    4877 24 atoms, 25 bonds, 1 residue, 1 model selected 
    4878 
    4879 > select add #3/B:98
    4880 
    4881 48 atoms, 50 bonds, 2 residues, 1 model selected 
    4882 
    4883 > select add #3/B:119
    4884 
    4885 68 atoms, 70 bonds, 3 residues, 1 model selected 
    4886 
    4887 > select add #3/B:121
    4888 
    4889 92 atoms, 95 bonds, 4 residues, 1 model selected 
    4890 
    4891 > label sel text "{0.name} {0.number}{0.insertion_code}"
    4892 
    4893 > label height 1.2
    4894 
    4895 > save /home/dell/Desktop/image13.png supersample 3
    4896 
    4897 > show #!5 models
    4898 
    4899 > hide #!3 models
    4900 
    4901 > close #5.3
    4902 
    4903 > select #5/B:100@CA
    4904 
    4905 1 atom, 1 residue, 1 model selected 
    4906 
    4907 > select add #5/B:109
    4908 
    4909 25 atoms, 25 bonds, 2 residues, 2 models selected 
    4910 
    4911 > label (#!5 & sel) text "{0.name} {0.number}{0.insertion_code}"
    4912 
    4913 > label height 1.2
    4914 
    4915 > select clear
    4916 
    4917 > save /home/dell/Desktop/image14.png supersample 3
    4918 
    4919 > graphics silhouettes true
    4920 
    4921 > show #!3 models
    4922 
    4923 > hide #5.3 models
    4924 
    4925 > show #5.3 models
    4926 
    4927 > hide #!5 models
    4928 
    4929 > open /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/AF_LZQ.pdb
    4930 
    4931 Chain information for AF_LZQ.pdb #6 
    4932 --- 
    4933 Chain | Description 
    4934 A | No description available 
    4935 B | No description available 
    4936  
    4937 
    4938 > ui tool show Matchmaker
    4939 
    4940 > matchmaker #6 to #1
    4941 
    4942 Parameters 
    4943 --- 
    4944 Chain pairing | bb 
    4945 Alignment algorithm | Needleman-Wunsch 
    4946 Similarity matrix | BLOSUM-62 
    4947 SS fraction | 0.3 
    4948 Gap open (HH/SS/other) | 18/18/6 
    4949 Gap extend | 1 
    4950 SS matrix |  |  | H | S | O 
    4951 ---|---|---|--- 
    4952 H | 6 | -9 | -6 
    4953 S |  | 6 | -6 
    4954 O |  |  | 4 
    4955 Iteration cutoff | 2 
    4956  
    4957 Matchmaker ranked_0.pdb, chain A (#1) with AF_LZQ.pdb, chain A (#6), sequence
    4958 alignment score = 3969.7 
    4959 RMSD between 756 pruned atom pairs is 0.696 angstroms; (across all 763 pairs:
    4960 0.724) 
    4961  
    4962 
    4963 > view clip false
    4964 
    4965 > ui tool show Log
    4966 
    4967 > save
    4968 > /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/AF_GTSF1_complex_inter.cxs
    4969 
    4970 ——— End of log from Fri Apr 12 21:01:49 2024 ———
    4971 
    4972 opened ChimeraX session 
    4973 
    4974 > show #!2 models
    4975 
    4976 > hide #!2 models
    4977 
    4978 > close #2
    4979 
    4980 > show #!5 models
    4981 
    4982 > hide #!5 models
    4983 
    4984 > open
    4985 > /home/dell/shen_data/Alpha.Pred./AF3/fold_2024_05_09_2zn_2mg_model_0.cif
    4986 
    4987 Chain information for fold_2024_05_09_2zn_2mg_model_0.cif #2 
    4988 --- 
    4989 Chain | Description 
    4990 A | . 
    4991 B | . 
    4992 G | . 
    4993 H | . 
    4994  
    4995 
    4996 > ui tool show Matchmaker
    4997 
    4998 > matchmaker #!5 to #12
    4999 
    5000 Parameters 
    5001 --- 
    5002 Chain pairing | bb 
    5003 Alignment algorithm | Needleman-Wunsch 
    5004 Similarity matrix | BLOSUM-62 
    5005 SS fraction | 0.3 
    5006 Gap open (HH/SS/other) | 18/18/6 
    5007 Gap extend | 1 
    5008 SS matrix |  |  | H | S | O 
    5009 ---|---|---|--- 
    5010 H | 6 | -9 | -6 
    5011 S |  | 6 | -6 
    5012 O |  |  | 4 
    5013 Iteration cutoff | 2 
    5014  
    5015 Matchmaker RT_MILI_26nt_2-coot-0.pdb, chain A (#12) with copy of
    5016 AF_EFPIWI_EMGTSF1_0.pdb, chain A (#5), sequence alignment score = 1683.8 
    5017 RMSD between 345 pruned atom pairs is 1.267 angstroms; (across all 745 pairs:
    5018 5.311) 
    5019  
    5020 
    5021 > matchmaker #2 to #12
    5022 
    5023 Parameters 
    5024 --- 
    5025 Chain pairing | bb 
    5026 Alignment algorithm | Needleman-Wunsch 
    5027 Similarity matrix | BLOSUM-62 
    5028 SS fraction | 0.3 
    5029 Gap open (HH/SS/other) | 18/18/6 
    5030 Gap extend | 1 
    5031 SS matrix |  |  | H | S | O 
    5032 ---|---|---|--- 
    5033 H | 6 | -9 | -6 
    5034 S |  | 6 | -6 
    5035 O |  |  | 4 
    5036 Iteration cutoff | 2 
    5037  
    5038 Matchmaker RT_MILI_26nt_2-coot-0.pdb, chain A (#12) with
    5039 fold_2024_05_09_2zn_2mg_model_0.cif, chain A (#2), sequence alignment score =
    5040 3250 
    5041 RMSD between 350 pruned atom pairs is 1.105 angstroms; (across all 751 pairs:
    5042 5.938) 
    5043  
    5044 
    5045 > matchmaker #2 to #12
    5046 
    5047 Parameters 
    5048 --- 
    5049 Chain pairing | bb 
    5050 Alignment algorithm | Needleman-Wunsch 
    5051 Similarity matrix | BLOSUM-62 
    5052 SS fraction | 0.3 
    5053 Gap open (HH/SS/other) | 18/18/6 
    5054 Gap extend | 1 
    5055 SS matrix |  |  | H | S | O 
    5056 ---|---|---|--- 
    5057 H | 6 | -9 | -6 
    5058 S |  | 6 | -6 
    5059 O |  |  | 4 
    5060 Iteration cutoff | 2 
    5061  
    5062 Matchmaker RT_MILI_26nt_2-coot-0.pdb, chain A (#12) with
    5063 fold_2024_05_09_2zn_2mg_model_0.cif, chain A (#2), sequence alignment score =
    5064 3250 
    5065 RMSD between 350 pruned atom pairs is 1.105 angstroms; (across all 751 pairs:
    5066 5.938) 
    5067  
    5068 
    5069 > hide #6 models
    5070 
    5071 > show #6 models
    5072 
    5073 > hide #6 models
    5074 
    5075 > show #6 models
    5076 
    5077 > close #6
    5078 
    5079 > ui mousemode right select
    5080 
    5081 > select #2/A:564
    5082 
    5083 11 atoms, 10 bonds, 1 residue, 1 model selected 
    5084 
    5085 > show sel atoms
    5086 
    5087 > select #2/B:80
    5088 
    5089 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5090 
    5091 > show sel atoms
    5092 
    5093 > select #2/B:83
    5094 
    5095 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5096 
    5097 > show sel atoms
    5098 
    5099 > hide sel atoms
    5100 
    5101 > select #2/B:84
    5102 
    5103 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5104 
    5105 > show sel atoms
    5106 
    5107 > select #2/A:562
    5108 
    5109 12 atoms, 12 bonds, 1 residue, 1 model selected 
    5110 
    5111 > show sel atoms
    5112 
    5113 > select #2/A:584
    5114 
    5115 4 atoms, 3 bonds, 1 residue, 1 model selected 
    5116 
    5117 > select #2/A:588
    5118 
    5119 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5120 
    5121 > show sel atoms
    5122 
    5123 > select #2/A:587
    5124 
    5125 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5126 
    5127 > show sel atoms
    5128 
    5129 > view sel
    5130 
    5131 > select #3/A:580
    5132 
    5133 19 atoms, 18 bonds, 1 residue, 1 model selected 
    5134 
    5135 > hide sel atoms
    5136 
    5137 > ui mousemode right distance
    5138 
    5139 > distance #2/B:84@NE2 #2/A:562@OH
    5140 
    5141 Distance between fold_2024_05_09_2zn_2mg_model_0.cif #2/B GLN 84 NE2 and /A
    5142 TYR 562 OH: 4.915Å 
    5143 
    5144 > show #4.1 models
    5145 
    5146 > ui mousemode right select
    5147 
    5148 > select #2/B:87
    5149 
    5150 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5151 
    5152 > show sel atoms
    5153 
    5154 > select #2/A:755
    5155 
    5156 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5157 
    5158 > show sel atoms
    5159 
    5160 > select #2/B:83
    5161 
    5162 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5163 
    5164 > show sel atoms
    5165 
    5166 > select #2/B:87
    5167 
    5168 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5169 
    5170 > hide sel atoms
    5171 
    5172 > select #3/B:83
    5173 
    5174 14 atoms, 13 bonds, 1 residue, 1 model selected 
    5175 
    5176 > select #2/B:83
    5177 
    5178 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5179 
    5180 > ui mousemode right distance
    5181 
    5182 > distance #2/A:755@NE2 #2/B:83@OD1
    5183 
    5184 Distance between fold_2024_05_09_2zn_2mg_model_0.cif #2/A GLN 755 NE2 and /B
    5185 ASN 83 OD1: 4.282Å 
    5186 
    5187 > ui mousemode right select
    5188 
    5189 > select #2/B:86
    5190 
    5191 11 atoms, 10 bonds, 1 residue, 1 model selected 
    5192 
    5193 > select #3/B:87
    5194 
    5195 14 atoms, 13 bonds, 1 residue, 1 model selected 
    5196 
    5197 > select #2/B:87
    5198 
    5199 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5200 
    5201 > show sel atoms
    5202 
    5203 > select #2/B:87@ND2
    5204 
    5205 1 atom, 1 residue, 1 model selected 
    5206 
    5207 > ui mousemode right distance
    5208 
    5209 > distance #2/A:755@NE2 #2/B:87@ND2
    5210 
    5211 Distance between fold_2024_05_09_2zn_2mg_model_0.cif #2/A GLN 755 NE2 and /B
    5212 ASN 87 ND2: 4.819Å 
    5213 
    5214 > ui mousemode right select
    5215 
    5216 > select #2/A:754
    5217 
    5218 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5219 
    5220 > select #2/A:756
    5221 
    5222 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5223 
    5224 > select #3/B:86
    5225 
    5226 24 atoms, 23 bonds, 1 residue, 1 model selected 
    5227 
    5228 > hide #!3 models
    5229 
    5230 > select #2/A:754
    5231 
    5232 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5233 
    5234 > select #2/B:88
    5235 
    5236 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5237 
    5238 > show sel cartoons
    5239 
    5240 [Repeated 1 time(s)]
    5241 
    5242 > select #2/B:87
    5243 
    5244 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5245 
    5246 > show #!3 models
    5247 
    5248 > select #2/B:73
    5249 
    5250 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5251 
    5252 > show sel atoms
    5253 
    5254 > select #2/A:623
    5255 
    5256 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5257 
    5258 > select #2/A:577
    5259 
    5260 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5261 
    5262 > show sel atoms
    5263 
    5264 > select #2/B:53
    5265 
    5266 11 atoms, 11 bonds, 1 residue, 1 model selected 
    5267 
    5268 > select #2/B:54
    5269 
    5270 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5271 
    5272 > show sel atoms
    5273 
    5274 > hide #!3 models
    5275 
    5276 > ui mousemode right distance
    5277 
    5278 > distance #2/B:54@ND2 #2/B:73@OD2
    5279 
    5280 Distance between fold_2024_05_09_2zn_2mg_model_0.cif #2/B ASN 54 ND2 and ASP
    5281 73 OD2: 2.824Å 
    5282 
    5283 > distance #2/A:564@NH2 #2/B:80@OD2
    5284 
    5285 Distance between fold_2024_05_09_2zn_2mg_model_0.cif #2/A ARG 564 NH2 and /B
    5286 ASP 80 OD2: 2.210Å 
    5287 
    5288 > show #!3 models
    5289 
    5290 > ui mousemode right select
    5291 
    5292 > select #3/B:77
    5293 
    5294 19 atoms, 18 bonds, 1 residue, 1 model selected 
    5295 
    5296 > select #2/B:76
    5297 
    5298 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5299 
    5300 > select clear
    5301 
    5302 > select #3/B:88
    5303 
    5304 19 atoms, 18 bonds, 1 residue, 1 model selected 
    5305 
    5306 > select #2/B:88
    5307 
    5308 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5309 
    5310 > select #2/B:87
    5311 
    5312 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5313 
    5314 > select #2/A:584
    5315 
    5316 4 atoms, 3 bonds, 1 residue, 1 model selected 
    5317 
    5318 > select #2/A:588
    5319 
    5320 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5321 
    5322 > select #2/A:587@NZ
    5323 
    5324 1 atom, 1 residue, 1 model selected 
    5325 
    5326 > ui mousemode right distance
    5327 
    5328 > distance #2/B:84@OE1 #2/A:587@NZ
    5329 
    5330 Distance between fold_2024_05_09_2zn_2mg_model_0.cif #2/B GLN 84 OE1 and /A
    5331 LYS 587 NZ: 5.090Å 
    5332 
    5333 > ~distance #2/B:84@OE1 #2/A:587@NZ
    5334 
    5335 > ~distance #2/B:84@NE2 #2/A:562@OH
    5336 
    5337 > ~distance #2/A:755@NE2 #2/B:87@ND2
    5338 
    5339 > ui mousemode right select
    5340 
    5341 > select #3/A:754
    5342 
    5343 19 atoms, 18 bonds, 1 residue, 1 model selected 
    5344 
    5345 > select #2/A:755
    5346 
    5347 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5348 
    5349 > select clear
    5350 
    5351 > save
    5352 > /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/AF_GTSF1_complex_inter.cxs
    5353 
    5354 > ui mousemode right distance
    5355 
    5356 > ~distance #2/A:755@NE2 #2/B:83@OD1
    5357 
    5358 > ui mousemode right zoom
    5359 
    5360 > view clip false
    5361 
    5362 > show #!12 models
    5363 
    5364 > hide #!12 models
    5365 
    5366 > hide #2 models
    5367 
    5368 > show #2 models
    5369 
    5370 > hide #2 models
    5371 
    5372 > show #2 models
    5373 
    5374 > hide #2 models
    5375 
    5376 > show #2 models
    5377 
    5378 > hide #2 models
    5379 
    5380 > open
    5381 > /home/dell/shen_data/PIWI/PIWIL2/mismatch/fold_2024_05_09_ter_8nt_model_0.cif
    5382 
    5383 Chain information for fold_2024_05_09_ter_8nt_model_0.cif #6 
    5384 --- 
    5385 Chain | Description 
    5386 A | . 
    5387 D | . 
    5388 E | . 
    5389  
    5390 
    5391 > ui tool show Matchmaker
    5392 
    5393 > matchmaker #6 to #1
    5394 
    5395 Parameters 
    5396 --- 
    5397 Chain pairing | bb 
    5398 Alignment algorithm | Needleman-Wunsch 
    5399 Similarity matrix | BLOSUM-62 
    5400 SS fraction | 0.3 
    5401 Gap open (HH/SS/other) | 18/18/6 
    5402 Gap extend | 1 
    5403 SS matrix |  |  | H | S | O 
    5404 ---|---|---|--- 
    5405 H | 6 | -9 | -6 
    5406 S |  | 6 | -6 
    5407 O |  |  | 4 
    5408 Iteration cutoff | 2 
    5409  
    5410 Matchmaker ranked_0.pdb, chain A (#1) with
    5411 fold_2024_05_09_ter_8nt_model_0.cif, chain A (#6), sequence alignment score =
    5412 3931.3 
    5413 RMSD between 515 pruned atom pairs is 0.856 angstroms; (across all 763 pairs:
    5414 2.912) 
    5415  
    5416 
    5417 > matchmaker #6 to #1
    5418 
    5419 Parameters 
    5420 --- 
    5421 Chain pairing | bb 
    5422 Alignment algorithm | Needleman-Wunsch 
    5423 Similarity matrix | BLOSUM-62 
    5424 SS fraction | 0.3 
    5425 Gap open (HH/SS/other) | 18/18/6 
    5426 Gap extend | 1 
    5427 SS matrix |  |  | H | S | O 
    5428 ---|---|---|--- 
    5429 H | 6 | -9 | -6 
    5430 S |  | 6 | -6 
    5431 O |  |  | 4 
    5432 Iteration cutoff | 2 
    5433  
    5434 Matchmaker ranked_0.pdb, chain A (#1) with
    5435 fold_2024_05_09_ter_8nt_model_0.cif, chain A (#6), sequence alignment score =
    5436 3931.3 
    5437 RMSD between 515 pruned atom pairs is 0.856 angstroms; (across all 763 pairs:
    5438 2.912) 
    5439  
    5440 
    5441 > hide #!3 models
    5442 
    5443 > show #2 models
    5444 
    5445 > hide #2 models
    5446 
    5447 > show #2 models
    5448 
    5449 > show #!1 models
    5450 
    5451 > hide #!1 models
    5452 
    5453 > show #!5 models
    5454 
    5455 > hide #!5 models
    5456 
    5457 > show #!12 models
    5458 
    5459 > hide #!12 models
    5460 
    5461 > show #!3 models
    5462 
    5463 > hide #6 models
    5464 
    5465 > ui mousemode right select
    5466 
    5467 > select #3/A:365
    5468 
    5469 19 atoms, 18 bonds, 1 residue, 1 model selected 
    5470 
    5471 > show sel atoms
    5472 
    5473 > select #2/A:367
    5474 
    5475 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5476 
    5477 > select #2/A:366
    5478 
    5479 11 atoms, 10 bonds, 1 residue, 1 model selected 
    5480 
    5481 > show sel atoms
    5482 
    5483 > select #2/A:365
    5484 
    5485 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5486 
    5487 > select #3/A:521
    5488 
    5489 7 atoms, 6 bonds, 1 residue, 1 model selected 
    5490 
    5491 > select #2/A:522
    5492 
    5493 7 atoms, 6 bonds, 1 residue, 1 model selected 
    5494 
    5495 > show sel atoms
    5496 
    5497 > view sel
    5498 
    5499 > select clear
    5500 
    5501 > select #3/A:388
    5502 
    5503 19 atoms, 18 bonds, 1 residue, 1 model selected 
    5504 
    5505 > select #2/A:388
    5506 
    5507 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5508 
    5509 > show sel atoms
    5510 
    5511 > label sel text "{0.name} {0.number}{0.insertion_code}"
    5512 
    5513 > select #2/A:368
    5514 
    5515 7 atoms, 6 bonds, 1 residue, 1 model selected 
    5516 
    5517 > select #2/A:369
    5518 
    5519 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5520 
    5521 > select #3/A:521
    5522 
    5523 7 atoms, 6 bonds, 1 residue, 1 model selected 
    5524 
    5525 > select #2/A:520
    5526 
    5527 14 atoms, 15 bonds, 1 residue, 1 model selected 
    5528 
    5529 > show sel atoms
    5530 
    5531 > select #2/A:518
    5532 
    5533 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5534 
    5535 > select clear
    5536 
    5537 > select #2/A:519
    5538 
    5539 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5540 
    5541 > show sel atoms
    5542 
    5543 Drag select of 14 atoms, 7 residues, 15 bonds 
    5544 
    5545 > hide sel atoms
    5546 
    5547 > select clear
    5548 
    5549 [Repeated 1 time(s)]
    5550 
    5551 > label @@display
    5552 
    5553 > select #2/A:522
    5554 
    5555 7 atoms, 6 bonds, 1 residue, 1 model selected 
    5556 
    5557 > hide sel atoms
    5558 
    5559 > select clear
    5560 
    5561 > select #2/A:521
    5562 
    5563 4 atoms, 3 bonds, 1 residue, 1 model selected 
    5564 
    5565 > ~label sel residues
    5566 
    5567 > select clear
    5568 
    5569 [Repeated 1 time(s)]
    5570 
    5571 > ui mousemode right "move label"
    5572 
    5573 > ui mousemode right select
    5574 
    5575 Drag select of 3 atoms, 8 residues, 2 bonds 
    5576 
    5577 > select clear
    5578 
    5579 Drag select of 5 atoms, 4 residues, 4 bonds 
    5580 
    5581 > hide sel atoms
    5582 
    5583 > select clear
    5584 
    5585 > ui tool show "Side View"
    5586 
    5587 > select clear
    5588 
    5589 > save /home/dell/Desktop/image1.png supersample 3
    5590 
    5591 > select #3/A:525
    5592 
    5593 14 atoms, 14 bonds, 1 residue, 1 model selected 
    5594 
    5595 > show sel atoms
    5596 
    5597 > view sel
    5598 
    5599 > select #2/A:712
    5600 
    5601 11 atoms, 10 bonds, 1 residue, 1 model selected 
    5602 
    5603 > show sel atoms
    5604 
    5605 > select #2/A:709
    5606 
    5607 10 atoms, 10 bonds, 1 residue, 1 model selected 
    5608 
    5609 > show sel atoms
    5610 
    5611 > select #2/B:107
    5612 
    5613 14 atoms, 15 bonds, 1 residue, 1 model selected 
    5614 
    5615 > show sel atoms
    5616 
    5617 > select #2/A:525
    5618 
    5619 7 atoms, 7 bonds, 1 residue, 1 model selected 
    5620 
    5621 > show sel cartoons
    5622 
    5623 > show sel atoms
    5624 
    5625 > select #2/A:713
    5626 
    5627 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5628 
    5629 > show sel atoms
    5630 
    5631 > select #2/A:526
    5632 
    5633 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5634 
    5635 > show sel atoms
    5636 
    5637 > select ~sel & ##selected
    5638 
    5639 8570 atoms, 8871 bonds, 2 pseudobonds, 985 residues, 2 models selected 
    5640 
    5641 > hide H
    5642 
    5643 > select clear
    5644 
    5645 > select #2/B:105
    5646 
    5647 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5648 
    5649 > show sel atoms
    5650 
    5651 > rename #2 2zn_2mg_model_0.cif
    5652 
    5653 > rename #6 ter_8nt_model_0.cif
    5654 
    5655 > show #!5 models
    5656 
    5657 > hide #!5 models
    5658 
    5659 > close #5
    5660 
    5661 > close #7
    5662 
    5663 > close #12
    5664 
    5665 > hide #!3 models
    5666 
    5667 Drag select of 29 atoms, 11 residues, 30 bonds 
    5668 
    5669 > select clear
    5670 
    5671 > select #2/B:111
    5672 
    5673 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5674 
    5675 > select clear
    5676 
    5677 > select #2/B:110
    5678 
    5679 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5680 
    5681 > select #2/B:111
    5682 
    5683 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5684 
    5685 > show sel atoms
    5686 
    5687 Drag select of 4 residues 
    5688 
    5689 > select up
    5690 
    5691 70 atoms, 73 bonds, 7 residues, 1 model selected 
    5692 
    5693 > select up
    5694 
    5695 1337 atoms, 1374 bonds, 167 residues, 1 model selected 
    5696 
    5697 > select up
    5698 
    5699 8578 atoms, 8878 bonds, 986 residues, 1 model selected 
    5700 
    5701 > select up
    5702 
    5703 45389 atoms, 46262 bonds, 21 pseudobonds, 3645 residues, 5 models selected 
    5704 
    5705 > select down
    5706 
    5707 8578 atoms, 8878 bonds, 986 residues, 3 models selected 
    5708 
    5709 > select down
    5710 
    5711 1337 atoms, 1374 bonds, 167 residues, 1 model selected 
    5712 
    5713 > color sel magenta
    5714 
    5715 > color sel byhetero
    5716 
    5717 > select clear
    5718 
    5719 > show target m
    5720 
    5721 > hide #!1 models
    5722 
    5723 > hide #!6 models
    5724 
    5725 > hide #!3 models
    5726 
    5727 > view #3 clip false
    5728 
    5729 > close #3.1
    5730 
    5731 > close #2.1
    5732 
    5733 > show #3 models
    5734 
    5735 > select #2/B:98
    5736 
    5737 14 atoms, 15 bonds, 1 residue, 1 model selected 
    5738 
    5739 > show sel atoms
    5740 
    5741 > select #2/A:364
    5742 
    5743 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5744 
    5745 > show sel atoms
    5746 
    5747 > select #2/B:100
    5748 
    5749 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5750 
    5751 > show sel atoms
    5752 
    5753 > select #2/A:367
    5754 
    5755 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5756 
    5757 > show sel atoms
    5758 
    5759 > hide sel atoms
    5760 
    5761 > select #2/A:716
    5762 
    5763 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5764 
    5765 > show sel atoms
    5766 
    5767 > hide sel atoms
    5768 
    5769 > mlp sel
    5770 
    5771 Map values for surface "2zn_2mg_model_0.cif_A SES surface": minimum -30.51,
    5772 mean -4.508, maximum 23.12 
    5773 To also show corresponding color key, enter the above mlp command and add key
    5774 true 
    5775 
    5776 > mlp sel
    5777 
    5778 Map values for surface "2zn_2mg_model_0.cif_A SES surface": minimum -30.51,
    5779 mean -4.508, maximum 23.12 
    5780 To also show corresponding color key, enter the above mlp command and add key
    5781 true 
    5782 
    5783 > select clear
    5784 
    5785 Drag select of 71 residues, 1 shapes 
    5786 
    5787 > select up
    5788 
    5789 935 atoms, 308 bonds, 72 residues, 3 models selected 
    5790 
    5791 > select up
    5792 
    5793 2213 atoms, 2296 bonds, 160 residues, 3 models selected 
    5794 
    5795 > select up
    5796 
    5797 19061 atoms, 19404 bonds, 1552 residues, 3 models selected 
    5798 
    5799 > select up
    5800 
    5801 23554 atoms, 24030 bonds, 1916 residues, 3 models selected 
    5802 
    5803 > select down
    5804 
    5805 19061 atoms, 19404 bonds, 1552 residues, 3 models selected 
    5806 
    5807 > mlp sel
    5808 
    5809 Map values for surface "copy of ranked_0.pdb_A SES surface": minimum -28.98,
    5810 mean -3.606, maximum 24.24 
    5811 Map values for surface "2zn_2mg_model_0.cif_A SES surface": minimum -30.51,
    5812 mean -4.508, maximum 23.12 
    5813 To also show corresponding color key, enter the above mlp command and add key
    5814 true 
    5815 
    5816 > transparency (#!2-3 & sel) 50
    5817 
    5818 > select #2/A:716@CD
    5819 
    5820 1 atom, 1 residue, 1 model selected 
    5821 Drag select of copy of ranked_0.pdb_A SES surface, 37220 of 833356 triangles,
    5822 2zn_2mg_model_0.cif_A SES surface, 22056 of 657748 triangles, 58 atoms, 126
    5823 residues, 49 bonds, 1 pseudobonds, 14 shapes 
    5824 
    5825 > close #2.1
    5826 
    5827 > close #3.1
    5828 
    5829 > mlp sel
    5830 
    5831 Map values for surface "copy of ranked_0.pdb_A SES surface": minimum -28.98,
    5832 mean -3.606, maximum 24.24 
    5833 Map values for surface "copy of ranked_0.pdb_B SES surface": minimum -28.26,
    5834 mean -3.591, maximum 22.8 
    5835 Map values for surface "2zn_2mg_model_0.cif_A SES surface": minimum -30.51,
    5836 mean -4.508, maximum 23.12 
    5837 Map values for surface "2zn_2mg_model_0.cif_B SES surface": minimum -28.54,
    5838 mean -4.628, maximum 23.24 
    5839 To also show corresponding color key, enter the above mlp command and add key
    5840 true 
    5841 
    5842 > select #3/B:105@CG
    5843 
    5844 1 atom, 1 residue, 1 model selected 
    5845 
    5846 > select #3/B:105@HB2
    5847 
    5848 1 atom, 1 residue, 1 model selected 
    5849 
    5850 > select up
    5851 
    5852 15 atoms, 14 bonds, 1 residue, 2 models selected 
    5853 
    5854 > select up
    5855 
    5856 271 atoms, 274 bonds, 19 residues, 2 models selected 
    5857 
    5858 > surface hidePatches (#!3 & sel)
    5859 
    5860 > select #3/B:107@HD1
    5861 
    5862 1 atom, 1 residue, 1 model selected 
    5863 
    5864 > select up
    5865 
    5866 24 atoms, 25 bonds, 1 residue, 2 models selected 
    5867 
    5868 > surface hidePatches (#!3 & sel)
    5869 
    5870 > select #2/B:105@CG
    5871 
    5872 1 atom, 1 residue, 1 model selected 
    5873 
    5874 > select up
    5875 
    5876 9 atoms, 8 bonds, 1 residue, 2 models selected 
    5877 
    5878 > select up
    5879 
    5880 134 atoms, 137 bonds, 17 residues, 2 models selected 
    5881 
    5882 > select up
    5883 
    5884 1337 atoms, 1374 bonds, 167 residues, 2 models selected 
    5885 
    5886 > hide sel surfaces
    5887 
    5888 > select #2/A:526
    5889 
    5890 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5891 
    5892 > mlp sel
    5893 
    5894 Map values for surface "2zn_2mg_model_0.cif_A SES surface": minimum -30.51,
    5895 mean -4.508, maximum 23.12 
    5896 To also show corresponding color key, enter the above mlp command and add key
    5897 true 
    5898 
    5899 > select #3/A:709@O
    5900 
    5901 1 atom, 1 residue, 1 model selected 
    5902 
    5903 > view sel
    5904 
    5905 > select clear
    5906 
    5907 > hide #!2-3 surfaces
    5908 
    5909 > close #2.1-2
    5910 
    5911 > close #3.1-2
    5912 
    5913 > select clear
    5914 
    5915 > select #3/B:107
    5916 
    5917 24 atoms, 25 bonds, 1 residue, 1 model selected 
    5918 
    5919 > view sel
    5920 
    5921 > hide #3 models
    5922 
    5923 Drag select of 51 atoms, 22 residues, 47 bonds 
    5924 
    5925 > select add #2/B:110
    5926 
    5927 198 atoms, 54 bonds, 24 residues, 1 model selected 
    5928 
    5929 > select subtract #2/B:111
    5930 
    5931 194 atoms, 51 bonds, 23 residues, 1 model selected 
    5932 
    5933 > select add #2/B:111
    5934 
    5935 202 atoms, 58 bonds, 24 residues, 1 model selected 
    5936 
    5937 > select subtract #2/B:108
    5938 
    5939 194 atoms, 58 bonds, 23 residues, 1 model selected 
    5940 
    5941 > select add #2/B:108
    5942 
    5943 202 atoms, 65 bonds, 24 residues, 1 model selected 
    5944 
    5945 > select subtract #2/B:104
    5946 
    5947 194 atoms, 65 bonds, 23 residues, 1 model selected 
    5948 
    5949 > select subtract #2/B:105
    5950 
    5951 185 atoms, 60 bonds, 22 residues, 1 model selected 
    5952 
    5953 > select subtract #2/B:106
    5954 
    5955 177 atoms, 60 bonds, 21 residues, 1 model selected 
    5956 
    5957 > select subtract #2/B:107
    5958 
    5959 163 atoms, 48 bonds, 20 residues, 1 model selected 
    5960 
    5961 > select subtract #2/B:108
    5962 
    5963 155 atoms, 41 bonds, 19 residues, 1 model selected 
    5964 
    5965 > select subtract #2/B:109
    5966 
    5967 146 atoms, 41 bonds, 18 residues, 1 model selected 
    5968 
    5969 > select subtract #2/B:110
    5970 
    5971 138 atoms, 34 bonds, 17 residues, 1 model selected 
    5972 
    5973 > select subtract #2/B:111
    5974 
    5975 130 atoms, 27 bonds, 16 residues, 1 model selected 
    5976 
    5977 > mlp sel
    5978 
    5979 Map values for surface "2zn_2mg_model_0.cif_A SES surface": minimum -30.51,
    5980 mean -4.508, maximum 23.12 
    5981 To also show corresponding color key, enter the above mlp command and add key
    5982 true 
    5983 
    5984 > close #2.1
    5985 
    5986 > show sel surfaces
    5987 
    5988 > mlp sel
    5989 
    5990 Map values for surface "2zn_2mg_model_0.cif_A SES surface": minimum -30.51,
    5991 mean -4.508, maximum 23.12 
    5992 To also show corresponding color key, enter the above mlp command and add key
    5993 true 
    5994 
    5995 > close #2.1
    5996 
    5997 Drag select of 52 atoms, 25 residues, 48 bonds 
    5998 
    5999 > label @@display
    6000 
    6001 > select clear
    6002 
    6003 > select #2/A:525
    6004 
    6005 7 atoms, 7 bonds, 1 residue, 1 model selected 
    6006 
    6007 > select add #2/A:526
    6008 
    6009 15 atoms, 14 bonds, 2 residues, 1 model selected 
    6010 
    6011 > color sel red
    6012 
    6013 > color sel byhetero
    6014 
    6015 > select clear
    6016 
    6017 > select #2/A:709
    6018 
    6019 10 atoms, 10 bonds, 1 residue, 1 model selected 
    6020 
    6021 > color sel red
    6022 
    6023 > color sel byhetero
    6024 
    6025 > select clear
    6026 
    6027 Drag select of 49 atoms, 22 residues, 46 bonds 
    6028 
    6029 > select clear
    6030 
    6031 Drag select of 4 residues 
    6032 
    6033 > select up
    6034 
    6035 204 atoms, 211 bonds, 24 residues, 1 model selected 
    6036 
    6037 > select clear
    6038 
    6039 Drag select of 49 atoms, 30 residues, 47 bonds 
    6040 
    6041 > mlp sel
    6042 
    6043 Map values for surface "2zn_2mg_model_0.cif_A SES surface": minimum -30.51,
    6044 mean -4.508, maximum 23.12 
    6045 Map values for surface "2zn_2mg_model_0.cif_B SES surface": minimum -28.54,
    6046 mean -4.628, maximum 23.24 
    6047 To also show corresponding color key, enter the above mlp command and add key
    6048 true 
    6049 
    6050 > select clear
    6051 
    6052 > select #2/B:104
    6053 
    6054 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6055 
    6056 > select up
    6057 
    6058 134 atoms, 137 bonds, 17 residues, 2 models selected 
    6059 
    6060 > select up
    6061 
    6062 1337 atoms, 1374 bonds, 167 residues, 2 models selected 
    6063 
    6064 > hide sel surfaces
    6065 
    6066 > select clear
    6067 
    6068 Drag select of 2zn_2mg_model_0.cif_A SES surface, 1092 of 657748 triangles, 20
    6069 atoms, 24 residues, 18 bonds 
    6070 
    6071 > show sel surfaces
    6072 
    6073 > select #2/B:98@CA
    6074 
    6075 1 atom, 1 residue, 1 model selected 
    6076 
    6077 > select up
    6078 
    6079 14 atoms, 15 bonds, 1 residue, 2 models selected 
    6080 
    6081 > select up
    6082 
    6083 134 atoms, 137 bonds, 17 residues, 2 models selected 
    6084 
    6085 > select up
    6086 
    6087 1337 atoms, 1374 bonds, 167 residues, 2 models selected 
    6088 
    6089 > hide sel surfaces
    6090 
    6091 > transparency (#!2 & sel) 50
    6092 
    6093 > select clear
    6094 
    6095 > transparency #2,4 50
    6096 
    6097 > hide #2.3 models
    6098 
    6099 > hide #2.2 models
    6100 
    6101 > show #2.2 models
    6102 
    6103 > close #2.3
    6104 
    6105 > transparency #2,4 70
    6106 
    6107 > select #2/A:526@CD1
    6108 
    6109 1 atom, 1 residue, 1 model selected 
    6110 
    6111 > select #2/B:107
    6112 
    6113 14 atoms, 15 bonds, 1 residue, 1 model selected 
    6114 
    6115 > view sel
    6116 
    6117 [Repeated 1 time(s)]
    6118 
    6119 > ui mousemode right "move label"
    6120 
    6121 > color #2.1 black models
    6122 
    6123 > ui mousemode right select
    6124 
    6125 > select clear
    6126 
    6127 > save /home/dell/Desktop/image2.png supersample 3
    6128 
    6129 > hide #!2 surfaces
    6130 
    6131 > select clear
    6132 
    6133 > save /home/dell/Desktop/image3.png supersample 3
    6134 
    6135 > view sel
    6136 
    6137 > select clear
    6138 
    6139 > ui mousemode right "move label"
    6140 
    6141 > ui mousemode right distance
    6142 
    6143 > distance #2/A:364@ND2 #2/B:100@SG
    6144 
    6145 Distance between 2zn_2mg_model_0.cif #2/A ASN 364 ND2 and /B CYS 100 SG:
    6146 3.349Å 
    6147 
    6148 > color #2.1 black models
    6149 
    6150 > save /home/dell/Desktop/image4.png supersample 3
    6151 
    6152 > open
    6153 > /home/dell/shen_data/PIWI/PIWIL2/RT_STRUCTURE_4.12/412_MILI_26nt_1/412_26NT_1-coot-8.pdb
    6154 
    6155 Summary of feedback from opening
    6156 /home/dell/shen_data/PIWI/PIWIL2/RT_STRUCTURE_4.12/412_MILI_26nt_1/412_26NT_1-coot-8.pdb 
    6157 --- 
    6158 warning | Start residue of secondary structure not found: SHEET 1 A 2 THR A
    6159 220 LEU A 224 0 
    6160  
    6161 Chain information for 412_26NT_1-coot-8.pdb #5 
    6162 --- 
    6163 Chain | Description 
    6164 A | No description available 
    6165 B | No description available 
    6166 C | No description available 
    6167  
    6168 
    6169 > ui tool show Matchmaker
    6170 
    6171 > matchmaker #!5 to #2
    6172 
    6173 Parameters 
    6174 --- 
    6175 Chain pairing | bb 
    6176 Alignment algorithm | Needleman-Wunsch 
    6177 Similarity matrix | BLOSUM-62 
    6178 SS fraction | 0.3 
    6179 Gap open (HH/SS/other) | 18/18/6 
    6180 Gap extend | 1 
    6181 SS matrix |  |  | H | S | O 
    6182 ---|---|---|--- 
    6183 H | 6 | -9 | -6 
    6184 S |  | 6 | -6 
    6185 O |  |  | 4 
    6186 Iteration cutoff | 2 
    6187  
    6188 Matchmaker 2zn_2mg_model_0.cif, chain A (#2) with 412_26NT_1-coot-8.pdb, chain
    6189 A (#5), sequence alignment score = 3383.2 
    6190 RMSD between 418 pruned atom pairs is 1.088 angstroms; (across all 736 pairs:
    6191 4.016) 
    6192  
    6193 
    6194 > matchmaker #!5 to #2
    6195 
    6196 Parameters 
    6197 --- 
    6198 Chain pairing | bb 
    6199 Alignment algorithm | Needleman-Wunsch 
    6200 Similarity matrix | BLOSUM-62 
    6201 SS fraction | 0.3 
    6202 Gap open (HH/SS/other) | 18/18/6 
    6203 Gap extend | 1 
    6204 SS matrix |  |  | H | S | O 
    6205 ---|---|---|--- 
    6206 H | 6 | -9 | -6 
    6207 S |  | 6 | -6 
    6208 O |  |  | 4 
    6209 Iteration cutoff | 2 
    6210  
    6211 Matchmaker 2zn_2mg_model_0.cif, chain A (#2) with 412_26NT_1-coot-8.pdb, chain
    6212 A (#5), sequence alignment score = 3383.2 
    6213 RMSD between 418 pruned atom pairs is 1.088 angstroms; (across all 736 pairs:
    6214 4.016) 
    6215  
    6216 
    6217 > ui mousemode right select
    6218 
    6219 > select #5/A:596
    6220 
    6221 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6222 
    6223 > select #5/A:920
    6224 
    6225 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6226 
    6227 > show sel atoms
    6228 
    6229 > select #5/A:917
    6230 
    6231 10 atoms, 10 bonds, 1 residue, 1 model selected 
    6232 
    6233 > show sel atoms
    6234 
    6235 > select #5/A:734
    6236 
    6237 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6238 
    6239 > show sel atoms
    6240 
    6241 > select #5/A:733
    6242 
    6243 7 atoms, 7 bonds, 1 residue, 1 model selected 
    6244 
    6245 > show sel atoms
    6246 
    6247 > select #5/A:921
    6248 
    6249 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6250 
    6251 > show sel atoms
    6252 
    6253 > label @@display
    6254 
    6255 > select clear
    6256 
    6257 > hide #!2 models
    6258 
    6259 > ui mousemode right "move label"
    6260 
    6261 > show #!2 models
    6262 
    6263 > hide #!2 models
    6264 
    6265 > show #!2 models
    6266 
    6267 > hide #!2 models
    6268 
    6269 > show #!2 models
    6270 
    6271 > hide #!2 models
    6272 
    6273 > save /home/dell/Desktop/image5.png supersample 3
    6274 
    6275 > open
    6276 > /home/dell/shen_data/PIWI/PIWIL2/mismatch/fold_2024_05_09_efpiwi_emgtsf1_model_0.cif
    6277 
    6278 Chain information for fold_2024_05_09_efpiwi_emgtsf1_model_0.cif #7 
    6279 --- 
    6280 Chain | Description 
    6281 A | . 
    6282 B | . 
    6283 G | . 
    6284 H | . 
    6285  
    6286 
    6287 > ui tool show Matchmaker
    6288 
    6289 > matchmaker #7 to #1
    6290 
    6291 Parameters 
    6292 --- 
    6293 Chain pairing | bb 
    6294 Alignment algorithm | Needleman-Wunsch 
    6295 Similarity matrix | BLOSUM-62 
    6296 SS fraction | 0.3 
    6297 Gap open (HH/SS/other) | 18/18/6 
    6298 Gap extend | 1 
    6299 SS matrix |  |  | H | S | O 
    6300 ---|---|---|--- 
    6301 H | 6 | -9 | -6 
    6302 S |  | 6 | -6 
    6303 O |  |  | 4 
    6304 Iteration cutoff | 2 
    6305  
    6306 Matchmaker ranked_0.pdb, chain A (#1) with
    6307 fold_2024_05_09_efpiwi_emgtsf1_model_0.cif, chain A (#7), sequence alignment
    6308 score = 2301.1 
    6309 RMSD between 470 pruned atom pairs is 1.001 angstroms; (across all 757 pairs:
    6310 5.493) 
    6311  
    6312 
    6313 > matchmaker #7 to #1
    6314 
    6315 Parameters 
    6316 --- 
    6317 Chain pairing | bb 
    6318 Alignment algorithm | Needleman-Wunsch 
    6319 Similarity matrix | BLOSUM-62 
    6320 SS fraction | 0.3 
    6321 Gap open (HH/SS/other) | 18/18/6 
    6322 Gap extend | 1 
    6323 SS matrix |  |  | H | S | O 
    6324 ---|---|---|--- 
    6325 H | 6 | -9 | -6 
    6326 S |  | 6 | -6 
    6327 O |  |  | 4 
    6328 Iteration cutoff | 2 
    6329  
    6330 Matchmaker ranked_0.pdb, chain A (#1) with
    6331 fold_2024_05_09_efpiwi_emgtsf1_model_0.cif, chain A (#7), sequence alignment
    6332 score = 2301.1 
    6333 RMSD between 470 pruned atom pairs is 1.001 angstroms; (across all 757 pairs:
    6334 5.493) 
    6335  
    6336 
    6337 > show #!2 models
    6338 
    6339 > hide #!5 models
    6340 
    6341 > set bgColor white
    6342 
    6343 > ui mousemode right select
    6344 
    6345 > select #7/B:109
    6346 
    6347 14 atoms, 15 bonds, 1 residue, 1 model selected 
    6348 
    6349 > show sel atoms
    6350 
    6351 > select #7/A:531
    6352 
    6353 7 atoms, 7 bonds, 1 residue, 1 model selected 
    6354 
    6355 > select add #7/A:532
    6356 
    6357 15 atoms, 14 bonds, 2 residues, 1 model selected 
    6358 
    6359 > show sel atoms
    6360 
    6361 > select #7/A:714
    6362 
    6363 10 atoms, 10 bonds, 1 residue, 1 model selected 
    6364 
    6365 > select add #7/A:717
    6366 
    6367 21 atoms, 20 bonds, 2 residues, 1 model selected 
    6368 
    6369 > show sel atoms
    6370 
    6371 > select #7/A:718
    6372 
    6373 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6374 
    6375 > show sel atoms
    6376 
    6377 > select #7/A:530
    6378 
    6379 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6380 
    6381 > select add #2/A:524
    6382 
    6383 16 atoms, 14 bonds, 2 residues, 2 models selected 
    6384 
    6385 > show sel atoms
    6386 
    6387 > select clear
    6388 
    6389 > hide #!2 models
    6390 
    6391 > label @@display
    6392 
    6393 > open "/home/dell/shen_data/PIWI/PIWIL2/PIWI_structures_published/7yfq
    6394 > EfPIWI(N959K) 2024.pdb"
    6395 
    6396 7yfq EfPIWI(N959K) 2024.pdb title: 
    6397 Cryo-em structure of the efpiwi (N959K)-piRNA-target ternary complex [more
    6398 info...] 
    6399  
    6400 Chain information for 7yfq EfPIWI(N959K) 2024.pdb #8 
    6401 --- 
    6402 Chain | Description | UniProt 
    6403 A | PIWI | D5MRY8_9METZ 220-987 
    6404 B | PIRNA | 
    6405 C | RNA (5'-R(*up*CP*CP*ap*up*GP*up*up*GP*ap*up*GP*GP*up*ap*A)- 3')
    6406 | 
    6407  
    6408 Non-standard residues in 7yfq EfPIWI(N959K) 2024.pdb #8 
    6409 --- 
    6410 MG — magnesium ion 
    6411 OMU — O2'-methyluridine 5'-monophosphate 
    6412  
    6413 
    6414 > ui tool show Matchmaker
    6415 
    6416 > matchmaker #!8 to #7
    6417 
    6418 Parameters 
    6419 --- 
    6420 Chain pairing | bb 
    6421 Alignment algorithm | Needleman-Wunsch 
    6422 Similarity matrix | BLOSUM-62 
    6423 SS fraction | 0.3 
    6424 Gap open (HH/SS/other) | 18/18/6 
    6425 Gap extend | 1 
    6426 SS matrix |  |  | H | S | O 
    6427 ---|---|---|--- 
    6428 H | 6 | -9 | -6 
    6429 S |  | 6 | -6 
    6430 O |  |  | 4 
    6431 Iteration cutoff | 2 
    6432  
    6433 Matchmaker fold_2024_05_09_efpiwi_emgtsf1_model_0.cif, chain A (#7) with 7yfq
    6434 EfPIWI(N959K) 2024.pdb, chain A (#8), sequence alignment score = 3604.5 
    6435 RMSD between 469 pruned atom pairs is 0.891 angstroms; (across all 733 pairs:
    6436 3.573) 
    6437  
    6438 
    6439 > matchmaker #!8 to #7
    6440 
    6441 Parameters 
    6442 --- 
    6443 Chain pairing | bb 
    6444 Alignment algorithm | Needleman-Wunsch 
    6445 Similarity matrix | BLOSUM-62 
    6446 SS fraction | 0.3 
    6447 Gap open (HH/SS/other) | 18/18/6 
    6448 Gap extend | 1 
    6449 SS matrix |  |  | H | S | O 
    6450 ---|---|---|--- 
    6451 H | 6 | -9 | -6 
    6452 S |  | 6 | -6 
    6453 O |  |  | 4 
    6454 Iteration cutoff | 2 
    6455  
    6456 Matchmaker fold_2024_05_09_efpiwi_emgtsf1_model_0.cif, chain A (#7) with 7yfq
    6457 EfPIWI(N959K) 2024.pdb, chain A (#8), sequence alignment score = 3604.5 
    6458 RMSD between 469 pruned atom pairs is 0.891 angstroms; (across all 733 pairs:
    6459 3.573) 
    6460  
    6461 
    6462 > select #8/A:936
    6463 
    6464 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6465 
    6466 > select add #8/A:937
    6467 
    6468 19 atoms, 17 bonds, 2 residues, 1 model selected 
    6469 
    6470 > select add #8/A:749
    6471 
    6472 27 atoms, 24 bonds, 3 residues, 1 model selected 
    6473 
    6474 > select add #8/A:750
    6475 
    6476 34 atoms, 31 bonds, 4 residues, 1 model selected 
    6477 
    6478 > select add #8/A:751
    6479 
    6480 42 atoms, 38 bonds, 5 residues, 1 model selected 
    6481 
    6482 > select subtract #8/A:749
    6483 
    6484 34 atoms, 31 bonds, 4 residues, 1 model selected 
    6485 
    6486 > select add #8/A:933
    6487 
    6488 44 atoms, 41 bonds, 5 residues, 1 model selected 
    6489 
    6490 > show sel atoms
    6491 
    6492 > select add #8/A:749
    6493 
    6494 52 atoms, 48 bonds, 6 residues, 1 model selected 
    6495 
    6496 > show sel atoms
    6497 
    6498 > label @@display
    6499 
    6500 > hide #!7 models
    6501 
    6502 > select clear
    6503 
    6504 > show #!7 models
    6505 
    6506 > show #!2 models
    6507 
    6508 > save /home/dell/shen_data/Alpha.Pred./AF3/AF3.cxs
    6509 
    6510 > rename #7 efpiwi_emgtsf1_AF3_model_0.cif
    6511 
    6512 > select #8/A:615
    6513 
    6514 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6515 
    6516 > show sel atoms
    6517 
    6518 > select #8/A:591
    6519 
    6520 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6521 
    6522 > select #8/A:592
    6523 
    6524 11 atoms, 11 bonds, 1 residue, 1 model selected 
    6525 
    6526 > show sel atoms
    6527 
    6528 > select #8/A:591
    6529 
    6530 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6531 
    6532 > show sel atoms
    6533 
    6534 > select #7/A:526
    6535 
    6536 14 atoms, 15 bonds, 1 residue, 1 model selected 
    6537 
    6538 > show sel atoms
    6539 
    6540 > label @@display
    6541 
    6542 > hide #!7 models
    6543 
    6544 > hide #!8 models
    6545 
    6546 > show #!8 models
    6547 
    6548 > hide #!2 models
    6549 
    6550 > show #!7 models
    6551 
    6552 > select #7/A:372
    6553 
    6554 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6555 
    6556 > show #!2 models
    6557 
    6558 > color sel byhetero
    6559 
    6560 > select clear
    6561 
    6562 > select #8/A:593
    6563 
    6564 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6565 
    6566 > select #8/A:590
    6567 
    6568 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6569 
    6570 > select #2/A:363
    6571 
    6572 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6573 
    6574 > select clear
    6575 
    6576 > select #8/A:592
    6577 
    6578 11 atoms, 11 bonds, 1 residue, 1 model selected 
    6579 
    6580 > select #8/A:593
    6581 
    6582 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6583 
    6584 > rename #2 2zn_2mg_AF3_model_0.cif
    6585 
    6586 > rename #1 AF2_MILI_GTSF1
    6587 
    6588 > show #!3 models
    6589 
    6590 > hide #!2 models
    6591 
    6592 > show #!1 models
    6593 
    6594 > hide #!1 models
    6595 
    6596 > close #1
    6597 
    6598 > save /home/dell/shen_data/Alpha.Pred./AF3/AF3.cxs
    6599 
    6600 ——— End of log from Thu May 9 18:31:50 2024 ———
    6601 
    6602 opened ChimeraX session 
    6603 
    6604 > open
    6605 > /home/dell/shen_data/Alpha.Pred./AF3/fold_2024_05_09_26nt_2/fold_af3_hili_209_t718s_model_0.cif
    6606 
    6607 Chain information for fold_af3_hili_209_t718s_model_0.cif #1 
    6608 --- 
    6609 Chain | Description 
    6610 A | . 
    6611  
    6612 
    6613 > open /home/dell/shen_data/Alpha.Pred./AF3/fold_hili_210_l718t_model_0.cif
    6614 
    6615 Chain information for fold_hili_210_l718t_model_0.cif #9 
    6616 --- 
    6617 Chain | Description 
    6618 A | . 
    6619  
    6620 
    6621 > ui tool show Matchmaker
    6622 
    6623 > matchmaker #1,9 to #2
    6624 
    6625 Parameters 
    6626 --- 
    6627 Chain pairing | bb 
    6628 Alignment algorithm | Needleman-Wunsch 
    6629 Similarity matrix | BLOSUM-62 
    6630 SS fraction | 0.3 
    6631 Gap open (HH/SS/other) | 18/18/6 
    6632 Gap extend | 1 
    6633 SS matrix |  |  | H | S | O 
    6634 ---|---|---|--- 
    6635 H | 6 | -9 | -6 
    6636 S |  | 6 | -6 
    6637 O |  |  | 4 
    6638 Iteration cutoff | 2 
    6639  
    6640 Matchmaker 2zn_2mg_AF3_model_0.cif, chain A (#2) with
    6641 fold_af3_hili_209_t718s_model_0.cif, chain A (#1), sequence alignment score =
    6642 3854.7 
    6643 RMSD between 509 pruned atom pairs is 0.757 angstroms; (across all 763 pairs:
    6644 3.449) 
    6645  
    6646 Matchmaker 2zn_2mg_AF3_model_0.cif, chain A (#2) with
    6647 fold_hili_210_l718t_model_0.cif, chain A (#9), sequence alignment score = 3844 
    6648 RMSD between 552 pruned atom pairs is 0.811 angstroms; (across all 763 pairs:
    6649 3.187) 
    6650  
    6651 
    6652 > matchmaker #1,9 to #2
    6653 
    6654 Parameters 
    6655 --- 
    6656 Chain pairing | bb 
    6657 Alignment algorithm | Needleman-Wunsch 
    6658 Similarity matrix | BLOSUM-62 
    6659 SS fraction | 0.3 
    6660 Gap open (HH/SS/other) | 18/18/6 
    6661 Gap extend | 1 
    6662 SS matrix |  |  | H | S | O 
    6663 ---|---|---|--- 
    6664 H | 6 | -9 | -6 
    6665 S |  | 6 | -6 
    6666 O |  |  | 4 
    6667 Iteration cutoff | 2 
    6668  
    6669 Matchmaker 2zn_2mg_AF3_model_0.cif, chain A (#2) with
    6670 fold_af3_hili_209_t718s_model_0.cif, chain A (#1), sequence alignment score =
    6671 3854.7 
    6672 RMSD between 509 pruned atom pairs is 0.757 angstroms; (across all 763 pairs:
    6673 3.449) 
    6674  
    6675 Matchmaker 2zn_2mg_AF3_model_0.cif, chain A (#2) with
    6676 fold_hili_210_l718t_model_0.cif, chain A (#9), sequence alignment score = 3844 
    6677 RMSD between 552 pruned atom pairs is 0.811 angstroms; (across all 763 pairs:
    6678 3.187) 
    6679  
    6680 
    6681 > view clip false
    6682 
    6683 > show #!5 models
    6684 
    6685 > hide #!7 models
    6686 
    6687 > hide #!8 models
    6688 
    6689 > hide #9 models
    6690 
    6691 > hide #4.1 models
    6692 
    6693 > hide #!3 models
    6694 
    6695 > rename #1 fold_af3_hili_209_l718s_model_0.cif
    6696 
    6697 > rename #1 id #10
    6698 
    6699 > show #9 models
    6700 
    6701 > nucleotides #9-10#!5 ladder
    6702 
    6703 > close #6.1
    6704 
    6705 > close #7.1
    6706 
    6707 > close #2.1
    6708 
    6709 > close #3.1
    6710 
    6711 > close #5.2
    6712 
    6713 > select /a:718
    6714 
    6715 59 atoms, 51 bonds, 8 residues, 8 models selected 
    6716 
    6717 > select #5/a:718
    6718 
    6719 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6720 
    6721 > show sel atoms
    6722 
    6723 > view sel
    6724 
    6725 > hide #!4 models
    6726 
    6727 > select #5/a:716
    6728 
    6729 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6730 
    6731 > show sel atoms
    6732 
    6733 > view sel
    6734 
    6735 > ui mousemode right select
    6736 
    6737 > select #10/A:508
    6738 
    6739 6 atoms, 5 bonds, 1 residue, 1 model selected 
    6740 
    6741 > show sel atoms
    6742 
    6743 > select #9/A:508
    6744 
    6745 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6746 
    6747 > show sel atoms
    6748 
    6749 > select clear
    6750 
    6751 > ui mousemode right label
    6752 
    6753 > label delete residues
    6754 
    6755 > label #5/A:716
    6756 
    6757 > label #10/A:508
    6758 
    6759 > label #9/A:508
    6760 
    6761 > ui mousemode right "move label"
    6762 
    6763 > save /home/dell/Desktop/image1.png supersample 3
    6764 
    6765 > view clip false
    6766 
    6767 > save /home/dell/Desktop/image2.png supersample 3
    6768 
    6769 > show #!2 models
    6770 
    6771 > hide #!5 models
    6772 
    6773 > show #6 models
    6774 
    6775 > hide #6 models
    6776 
    6777 > show #6 models
    6778 
    6779 > hide #6 models
    6780 
    6781 > hide #!2 models
    6782 
    6783 > save /home/dell/Desktop/image3.png supersample 3
    6784 
    6785 > ui mousemode right select
    6786 
    6787 > select #9/A:418
    6788 
    6789 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6790 
    6791 > select #9/A:415
    6792 
    6793 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6794 
    6795 > show sel atoms
    6796 
    6797 > select #9/A:418
    6798 
    6799 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6800 
    6801 > show sel atoms
    6802 
    6803 > select #9/A:419
    6804 
    6805 5 atoms, 4 bonds, 1 residue, 1 model selected 
    6806 
    6807 > save /home/dell/Desktop/image4.png supersample 3
    6808 
    6809 > show sel atoms
    6810 
    6811 > save /home/dell/shen_data/Alpha.Pred./AF3/AF3.cxs
    6812 
    6813 ——— End of log from Fri May 10 12:32:23 2024 ———
    6814 
    6815 opened ChimeraX session 
    6816 
    6817 > open /home/dell/shen_data/Alpha.Pred./AF3/fold_mili_18nt_gtsf1_model_0.cif
    6818 > /home/dell/shen_data/Alpha.Pred./AF3/fold_mili_20nt_gtsf1_model_0.cif
    6819 
    6820 Chain information for fold_mili_18nt_gtsf1_model_0.cif #1 
    6821 --- 
    6822 Chain | Description 
    6823 A | . 
    6824 B | . 
    6825 G | . 
    6826 H | . 
    6827  
    6828 Chain information for fold_mili_20nt_gtsf1_model_0.cif #11 
    6829 --- 
    6830 Chain | Description 
    6831 A | . 
    6832 B | . 
    6833 G | . 
    6834 H | . 
    6835  
    6836 
    6837 > ui tool show Matchmaker
    6838 
    6839 > matchmaker #1,11 to #2
    6840 
    6841 Parameters 
    6842 --- 
    6843 Chain pairing | bb 
    6844 Alignment algorithm | Needleman-Wunsch 
    6845 Similarity matrix | BLOSUM-62 
    6846 SS fraction | 0.3 
    6847 Gap open (HH/SS/other) | 18/18/6 
    6848 Gap extend | 1 
    6849 SS matrix |  |  | H | S | O 
    6850 ---|---|---|--- 
    6851 H | 6 | -9 | -6 
    6852 S |  | 6 | -6 
    6853 O |  |  | 4 
    6854 Iteration cutoff | 2 
    6855  
    6856 Matchmaker 2zn_2mg_AF3_model_0.cif, chain A (#2) with
    6857 fold_mili_18nt_gtsf1_model_0.cif, chain A (#1), sequence alignment score =
    6858 3996.7 
    6859 RMSD between 752 pruned atom pairs is 0.550 angstroms; (across all 763 pairs:
    6860 0.658) 
    6861  
    6862 Matchmaker 2zn_2mg_AF3_model_0.cif, chain A (#2) with
    6863 fold_mili_20nt_gtsf1_model_0.cif, chain A (#11), sequence alignment score =
    6864 4006.9 
    6865 RMSD between 701 pruned atom pairs is 0.626 angstroms; (across all 763 pairs:
    6866 1.257) 
    6867  
    6868 
    6869 > matchmaker #1,11 to #2
    6870 
    6871 Parameters 
    6872 --- 
    6873 Chain pairing | bb 
    6874 Alignment algorithm | Needleman-Wunsch 
    6875 Similarity matrix | BLOSUM-62 
    6876 SS fraction | 0.3 
    6877 Gap open (HH/SS/other) | 18/18/6 
    6878 Gap extend | 1 
    6879 SS matrix |  |  | H | S | O 
    6880 ---|---|---|--- 
    6881 H | 6 | -9 | -6 
    6882 S |  | 6 | -6 
    6883 O |  |  | 4 
    6884 Iteration cutoff | 2 
    6885  
    6886 Matchmaker 2zn_2mg_AF3_model_0.cif, chain A (#2) with
    6887 fold_mili_18nt_gtsf1_model_0.cif, chain A (#1), sequence alignment score =
    6888 3996.7 
    6889 RMSD between 752 pruned atom pairs is 0.550 angstroms; (across all 763 pairs:
    6890 0.658) 
    6891  
    6892 Matchmaker 2zn_2mg_AF3_model_0.cif, chain A (#2) with
    6893 fold_mili_20nt_gtsf1_model_0.cif, chain A (#11), sequence alignment score =
    6894 4006.9 
    6895 RMSD between 701 pruned atom pairs is 0.626 angstroms; (across all 763 pairs:
    6896 1.257) 
    6897  
    6898 
    6899 > select /a:1-209
    6900 
    6901 14846 atoms, 15119 bonds, 1672 residues, 8 models selected 
    6902 
    6903 > hide #!9 models
    6904 
    6905 > hide #!10 models
    6906 
    6907 > hide sel & #1,11 cartoons
    6908 
    6909 > delete atoms (#1,11 & sel)
    6910 
    6911 > delete bonds (#1,11 & sel)
    6912 
    6913 > show #!2 models
    6914 
    6915 > ui mousemode right select
    6916 
    6917 > select clear
    6918 
    6919 > show #!5 models
    6920 
    6921 > save /home/dell/shen_data/Alpha.Pred./AF3/AF3.cxs
    6922 
    6923 ——— End of log from Wed May 15 11:25:55 2024 ———
    6924 
    6925 opened ChimeraX session 
    6926 
    6927 > close #1
    6928 
    6929 > close #11
    6930 
    6931 > show #3 models
    6932 
    6933 > hide #3 models
    6934 
    6935 > show #3 models
    6936 
    6937 > show #7 models
    6938 
    6939 > hide #!5 models
    6940 
    6941 > hide #3 models
    6942 
    6943 > hide #!2 models
    6944 
    6945 > show #!2 models
    6946 
    6947 > ui mousemode right select
    6948 
    6949 > select #7/B:79
    6950 
    6951 6 atoms, 5 bonds, 1 residue, 1 model selected 
    6952 
    6953 > select up
    6954 
    6955 87 atoms, 86 bonds, 11 residues, 1 model selected 
    6956 
    6957 > select up
    6958 
    6959 2263 atoms, 2310 bonds, 282 residues, 1 model selected 
    6960 
    6961 > color sel lime
    6962 
    6963 > color sel byhetero
    6964 
    6965 > select clear
    6966 
    6967 > hide #7 models
    6968 
    6969 > show #3 models
    6970 
    6971 > show #!4 models
    6972 
    6973 > cartoon style #2-3#!4 xsection oval modeHelix default
    6974 
    6975 > select clear
    6976 
    6977 > select add #2
    6978 
    6979 8578 atoms, 8878 bonds, 3 pseudobonds, 986 residues, 2 models selected 
    6980 
    6981 > select clear
    6982 
    6983 > select #2/A:738
    6984 
    6985 10 atoms, 10 bonds, 1 residue, 1 model selected 
    6986 
    6987 > select #3/B:86
    6988 
    6989 24 atoms, 23 bonds, 1 residue, 1 model selected 
    6990 
    6991 > select #3/B:87
    6992 
    6993 14 atoms, 13 bonds, 1 residue, 1 model selected 
    6994 
    6995 > view sel
    6996 
    6997 > hide #!2 models
    6998 
    6999 > show #!2 models
    7000 
    7001 > hide #!2 models
    7002 
    7003 > show #!2 models
    7004 
    7005 > ui mousemode right distance
    7006 
    7007 > distance #2/A:755@NE2 #2/B:83@ND2
    7008 
    7009 Distance between 2zn_2mg_AF3_model_0.cif #2/A GLN 755 NE2 and /B ASN 83 ND2:
    7010 4.220Å 
    7011 
    7012 > show #4.1 models
    7013 
    7014 > distance #2/A:755@NE2 #2/B:83@OD1
    7015 
    7016 Distance between 2zn_2mg_AF3_model_0.cif #2/A GLN 755 NE2 and /B ASN 83 OD1:
    7017 4.282Å 
    7018 
    7019 > ~distance #2/A:755@NE2 #2/B:83@ND2
    7020 
    7021 > ~distance #2/A:755@NE2 #2/B:83@OD1
    7022 
    7023 > ui mousemode right select
    7024 
    7025 > select #2/B:87
    7026 
    7027 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7028 
    7029 > hide sel atoms
    7030 
    7031 > select clear
    7032 
    7033 > select #2/A:588
    7034 
    7035 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7036 
    7037 > hide sel atoms
    7038 
    7039 > select #3/B:81
    7040 
    7041 16 atoms, 15 bonds, 1 residue, 1 model selected 
    7042 
    7043 > select #3/B:78
    7044 
    7045 15 atoms, 14 bonds, 1 residue, 1 model selected 
    7046 
    7047 > show sel atoms
    7048 
    7049 > hide sel atoms
    7050 
    7051 > select #3/B:77
    7052 
    7053 19 atoms, 18 bonds, 1 residue, 1 model selected 
    7054 
    7055 > select #3/B:81
    7056 
    7057 16 atoms, 15 bonds, 1 residue, 1 model selected 
    7058 
    7059 > select #2/A:587
    7060 
    7061 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7062 
    7063 > hide sel atoms
    7064 
    7065 > select #3/B:77
    7066 
    7067 19 atoms, 18 bonds, 1 residue, 1 model selected 
    7068 
    7069 > select #2/A:566
    7070 
    7071 7 atoms, 6 bonds, 1 residue, 1 model selected 
    7072 
    7073 > select #2/A:567
    7074 
    7075 11 atoms, 11 bonds, 1 residue, 1 model selected 
    7076 
    7077 > select #2/A:565
    7078 
    7079 7 atoms, 6 bonds, 1 residue, 1 model selected 
    7080 
    7081 > select clear
    7082 
    7083 > ui tool show Distances
    7084 
    7085 > distance style color black
    7086 
    7087 > distance style radius 0.06
    7088 
    7089 > select clear
    7090 
    7091 > hide #!2 models
    7092 
    7093 > show #!2 models
    7094 
    7095 > ui mousemode right distance
    7096 
    7097 > hide #3 models
    7098 
    7099 > show #3 models
    7100 
    7101 > distance #2/A:577@OG #2/B:73@OD1
    7102 
    7103 Distance between 2zn_2mg_AF3_model_0.cif #2/A SER 577 OG and /B ASP 73 OD1:
    7104 6.068Å 
    7105 
    7106 > ui mousemode right swapaa
    7107 
    7108 > swapaa mousemode #2/B:73 ASN
    7109 
    7110 > swapaa mousemode #2/B:73 GLN
    7111 
    7112 > swapaa mousemode #2/B:73 CYS
    7113 
    7114 > swapaa mousemode #2/B:73 GLN
    7115 
    7116 > ui mousemode right "bond rotation"
    7117 
    7118 > ui mousemode right swapaa
    7119 
    7120 > swapaa mousemode #2/B:73 GLU
    7121 
    7122 > ui mousemode right "bond rotation"
    7123 
    7124 > undo
    7125 
    7126 > show #3 models
    7127 
    7128 > ui mousemode right select
    7129 
    7130 > select #2/A:577@OG
    7131 
    7132 1 atom, 1 residue, 1 model selected 
    7133 
    7134 > ui mousemode right distance
    7135 
    7136 > distance #2/B:73@OE1 #2/A:577@OG
    7137 
    7138 Distance between 2zn_2mg_AF3_model_0.cif #2/B GLU 73 OE1 and /A SER 577 OG:
    7139 4.457Å 
    7140 
    7141 > distance #2/A:577@OG #3/B:54@ND2
    7142 
    7143 Distance between 2zn_2mg_AF3_model_0.cif #2/A SER 577 OG and copy of
    7144 ranked_0.pdb #3/B ASN 54 ND2: 4.930Å 
    7145 
    7146 > ui mousemode right select
    7147 
    7148 > select clear
    7149 
    7150 > select #3/B:94
    7151 
    7152 10 atoms, 9 bonds, 1 residue, 1 model selected 
    7153 
    7154 > select #3/B:93
    7155 
    7156 19 atoms, 18 bonds, 1 residue, 1 model selected 
    7157 
    7158 > select #2/B:94
    7159 
    7160 5 atoms, 4 bonds, 1 residue, 1 model selected 
    7161 
    7162 > select #2/B:93
    7163 
    7164 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7165 
    7166 > select #2/A:365
    7167 
    7168 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7169 
    7170 > show sel atoms
    7171 
    7172 > select clear
    7173 
    7174 > select #3/A:557
    7175 
    7176 14 atoms, 13 bonds, 1 residue, 1 model selected 
    7177 Drag select of 10 residues 
    7178 
    7179 > show sel atoms
    7180 
    7181 > hide H
    7182 
    7183 > select clear
    7184 
    7185 > select #2/A:523
    7186 
    7187 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7188 
    7189 > show sel atoms
    7190 
    7191 > ui mousemode right distance
    7192 
    7193 > distance #2/A:523@OD1 #2/B:100@SG
    7194 
    7195 Distance between 2zn_2mg_AF3_model_0.cif #2/A ASP 523 OD1 and /B CYS 100 SG:
    7196 3.987Å 
    7197 
    7198 > ui mousemode right select
    7199 
    7200 > select clear
    7201 
    7202 > select #2/A:365
    7203 
    7204 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7205 Drag select of 69 atoms, 52 residues, 61 bonds, 3 pseudobonds 
    7206 
    7207 > mlp sel
    7208 
    7209 Map values for surface "copy of ranked_0.pdb_A SES surface": minimum -28.98,
    7210 mean -3.606, maximum 24.24 
    7211 Map values for surface "copy of ranked_0.pdb_B SES surface": minimum -28.26,
    7212 mean -3.591, maximum 22.8 
    7213 Map values for surface "2zn_2mg_model_0.cif_A SES surface": minimum -30.51,
    7214 mean -4.508, maximum 23.12 
    7215 Map values for surface "2zn_2mg_AF3_model_0.cif_B SES surface": minimum
    7216 -28.54, mean -4.617, maximum 23.24 
    7217 To also show corresponding color key, enter the above mlp command and add key
    7218 true 
    7219 
    7220 > transparency (#!2-3 & sel) 50
    7221 
    7222 > hide sel surfaces
    7223 
    7224 > select clear
    7225 
    7226 Drag select of 2 atoms, 2 residues 
    7227 
    7228 > select up
    7229 
    7230 324 atoms, 328 bonds, 28 residues, 4 models selected 
    7231 Drag select of 2 residues, 1 atoms 
    7232 
    7233 > hide sel atoms
    7234 
    7235 > select clear
    7236 
    7237 Drag select of 2 residues, 1 atoms 
    7238 
    7239 > hide sel atoms
    7240 
    7241 > select clear
    7242 
    7243 Drag select of 18 atoms, 10 residues, 15 bonds 
    7244 
    7245 > hide sel atoms
    7246 
    7247 > select clear
    7248 
    7249 > select #3/A:557
    7250 
    7251 14 atoms, 13 bonds, 1 residue, 1 model selected 
    7252 
    7253 > select #2/A:559
    7254 
    7255 7 atoms, 6 bonds, 1 residue, 1 model selected 
    7256 
    7257 > select clear
    7258 
    7259 Drag select of 2 residues, 1 atoms 
    7260 
    7261 > hide sel atoms
    7262 
    7263 > select clear
    7264 
    7265 Drag select of 1 atoms, 6 residues 
    7266 
    7267 > hide sel atoms
    7268 
    7269 > select clear
    7270 
    7271 > select #3/B:94
    7272 
    7273 10 atoms, 9 bonds, 1 residue, 1 model selected 
    7274 
    7275 > select clear
    7276 
    7277 > select #2/B:110
    7278 
    7279 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7280 
    7281 > show sel atoms
    7282 
    7283 > select clear
    7284 
    7285 > hide #!3 models
    7286 
    7287 > ui mousemode right distance
    7288 
    7289 > distance #2/A:709@NE2 #2/B:110@OD2
    7290 
    7291 Distance between 2zn_2mg_AF3_model_0.cif #2/A HIS 709 NE2 and /B ASP 110 OD2:
    7292 3.315Å 
    7293 
    7294 > distance #2/B:105@OE2 #2/B:107@NE1
    7295 
    7296 Distance between 2zn_2mg_AF3_model_0.cif #2/B GLU 105 OE2 and TRP 107 NE1:
    7297 2.993Å 
    7298 
    7299 > distance #2/A:712@NH1 #2/B:105@OE2
    7300 
    7301 Distance between 2zn_2mg_AF3_model_0.cif #2/A ARG 712 NH1 and /B GLU 105 OE2:
    7302 2.807Å 
    7303 
    7304 > ui mousemode right select
    7305 
    7306 > select #2/B:111
    7307 
    7308 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7309 
    7310 > hide sel atoms
    7311 
    7312 > view clip false
    7313 
    7314 > nucleotides sel ladder
    7315 
    7316 > select clear
    7317 
    7318 > nucleotides #!2 ladder
    7319 
    7320 > show #!3 models
    7321 
    7322 > select #2/B:26
    7323 
    7324 11 atoms, 10 bonds, 1 residue, 1 model selected 
    7325 
    7326 > show sel atoms
    7327 
    7328 > view sel
    7329 
    7330 > select #2/B:29
    7331 
    7332 11 atoms, 10 bonds, 1 residue, 1 model selected 
    7333 
    7334 > show sel atoms
    7335 
    7336 > select #2/B:36
    7337 
    7338 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7339 
    7340 > show sel atoms
    7341 
    7342 > select #2/B:32
    7343 
    7344 12 atoms, 12 bonds, 1 residue, 1 model selected 
    7345 
    7346 > show sel atoms
    7347 
    7348 > select clear
    7349 
    7350 > select #3/B:33
    7351 
    7352 17 atoms, 17 bonds, 1 residue, 1 model selected 
    7353 
    7354 > show sel atoms
    7355 
    7356 > select #3/B:23
    7357 
    7358 17 atoms, 17 bonds, 1 residue, 1 model selected 
    7359 
    7360 > show sel atoms
    7361 
    7362 > hide H
    7363 
    7364 > select clear
    7365 
    7366 > show #!5 models
    7367 
    7368 > hide #!5 models
    7369 
    7370 > select #2/H:7
    7371 
    7372 22 atoms, 24 bonds, 1 residue, 1 model selected 
    7373 
    7374 > select up
    7375 
    7376 556 atoms, 621 bonds, 26 residues, 1 model selected 
    7377 
    7378 > color sel blue
    7379 
    7380 > select #2/G:22
    7381 
    7382 23 atoms, 25 bonds, 1 residue, 1 model selected 
    7383 
    7384 > select up
    7385 
    7386 549 atoms, 612 bonds, 26 residues, 1 model selected 
    7387 
    7388 > color sel red
    7389 
    7390 > select clear
    7391 
    7392 > select #3/B:39
    7393 
    7394 22 atoms, 21 bonds, 1 residue, 1 model selected 
    7395 
    7396 > show sel atoms
    7397 
    7398 > hide H
    7399 
    7400 > select #2/B:40
    7401 
    7402 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7403 
    7404 > select #2/B:39
    7405 
    7406 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7407 
    7408 > show sel atoms
    7409 
    7410 > select clear
    7411 
    7412 > hide #!3 models
    7413 
    7414 > select clear
    7415 
    7416 > select #2/G:15
    7417 
    7418 23 atoms, 25 bonds, 1 residue, 1 model selected 
    7419 
    7420 > hide sel cartoons
    7421 
    7422 > select #2/G:14
    7423 
    7424 23 atoms, 25 bonds, 1 residue, 1 model selected 
    7425 
    7426 > hide sel cartoons
    7427 
    7428 > select #2/G:16
    7429 
    7430 22 atoms, 24 bonds, 1 residue, 1 model selected 
    7431 
    7432 > hide sel cartoons
    7433 
    7434 > select #2/H:6
    7435 
    7436 22 atoms, 24 bonds, 1 residue, 1 model selected 
    7437 
    7438 > hide sel cartoons
    7439 
    7440 > select #2/H:7
    7441 
    7442 22 atoms, 24 bonds, 1 residue, 1 model selected 
    7443 
    7444 > hide sel cartoons
    7445 
    7446 > select up
    7447 
    7448 2 atoms, 1 bond, 1 residue, 1 model selected 
    7449 
    7450 > select up
    7451 
    7452 22 atoms, 24 bonds, 1 residue, 1 model selected 
    7453 
    7454 > show sel cartoons
    7455 
    7456 > select clear
    7457 
    7458 > ui mousemode right distance
    7459 
    7460 > distance #2/B:26@NH1 #2/H:7@OP1
    7461 
    7462 Distance between 2zn_2mg_AF3_model_0.cif #2/B ARG 26 NH1 and /H A 7 OP1:
    7463 2.881Å 
    7464 
    7465 > ui mousemode right select
    7466 
    7467 > select clear
    7468 
    7469 > select #2/H:6
    7470 
    7471 22 atoms, 24 bonds, 1 residue, 1 model selected 
    7472 
    7473 > hide sel cartoons
    7474 
    7475 > ui mousemode right distance
    7476 
    7477 > distance #2/B:26@NH2 #2/H:6@O3'
    7478 
    7479 Distance between 2zn_2mg_AF3_model_0.cif #2/B ARG 26 NH2 and /H A 6 O3':
    7480 2.455Å 
    7481 
    7482 > ui mousemode right select
    7483 
    7484 > select clear
    7485 
    7486 > ui mousemode right label
    7487 
    7488 > ui mousemode right distance
    7489 
    7490 > distance #2/B:29@NH2 #2/G:16@OP2
    7491 
    7492 Distance between 2zn_2mg_AF3_model_0.cif #2/B ARG 29 NH2 and /G A 16 OP2:
    7493 2.795Å 
    7494 
    7495 > ui mousemode right select
    7496 
    7497 > select #2/B:32
    7498 
    7499 12 atoms, 12 bonds, 1 residue, 1 model selected 
    7500 
    7501 > hide sel atoms
    7502 
    7503 > show #!3 models
    7504 
    7505 > hide #!3 models
    7506 
    7507 > show sel atoms
    7508 
    7509 > select #2/A:611
    7510 
    7511 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7512 
    7513 > show sel atoms
    7514 
    7515 > ui mousemode right distance
    7516 
    7517 > ~distance #3/A:611@NE2 #3/B:32@OH
    7518 
    7519 > distance #2/B:32@OH #2/A:611@NE2
    7520 
    7521 Distance between 2zn_2mg_AF3_model_0.cif #2/B TYR 32 OH and /A GLN 611 NE2:
    7522 3.160Å 
    7523 
    7524 > ui mousemode right select
    7525 
    7526 > show #!3 models
    7527 
    7528 > hide #!3 models
    7529 
    7530 > select #2/H:5
    7531 
    7532 20 atoms, 21 bonds, 1 residue, 1 model selected 
    7533 
    7534 > hide sel cartoons
    7535 
    7536 > select #2/H:4
    7537 
    7538 20 atoms, 21 bonds, 1 residue, 1 model selected 
    7539 
    7540 > hide sel cartoons
    7541 
    7542 > ui mousemode right distance
    7543 
    7544 > ui mousemode right select
    7545 
    7546 > select #2/D:1@ZN
    7547 
    7548 1 atom, 1 residue, 1 model selected 
    7549 
    7550 > ui mousemode right distance
    7551 
    7552 > distance #2/B:36@NZ #2/H:4@OP1
    7553 
    7554 Distance between 2zn_2mg_AF3_model_0.cif #2/B LYS 36 NZ and /H C 4 OP1: 2.535Å 
    7555 
    7556 > distance #2/H:5@OP1 #2/B:33@ND1
    7557 
    7558 Distance between 2zn_2mg_AF3_model_0.cif #2/H C 5 OP1 and /B HIS 33 ND1:
    7559 2.754Å 
    7560 
    7561 > distance style radius 0.06
    7562 
    7563 > view #3 clip false
    7564 
    7565 > close #9-10
    7566 
    7567 > show #7 models
    7568 
    7569 > show #!8 models
    7570 
    7571 > hide #!8 models
    7572 
    7573 > show #!8 models
    7574 
    7575 > hide #!8 models
    7576 
    7577 > show #!8 models
    7578 
    7579 > hide #!8 models
    7580 
    7581 > close #8
    7582 
    7583 > close #6
    7584 
    7585 > hide #7 models
    7586 
    7587 > show #!3 models
    7588 
    7589 > select /a
    7590 
    7591 30602 atoms, 31146 bonds, 3030 residues, 4 models selected 
    7592 
    7593 > transparency sel 80 cartoons
    7594 
    7595 > lighting full
    7596 
    7597 > ui mousemode right select
    7598 
    7599 > select clear
    7600 
    7601 > graphics silhouettes false
    7602 
    7603 > select clear
    7604 
    7605 > save /home/dell/shen_data/PIWI/PIWIL2/Figures/Fig4_overall.cxs
    7606 
    7607 > select /b,c
    7608 
    7609 7289 atoms, 7533 bonds, 1 pseudobond, 669 residues, 5 models selected 
    7610 
    7611 > cartoon style sel width 0.8 thickness 0.8
    7612 
    7613 > select #2/G:4
    7614 
    7615 20 atoms, 21 bonds, 1 residue, 1 model selected 
    7616 
    7617 > select add #2/H:25
    7618 
    7619 42 atoms, 45 bonds, 2 residues, 1 model selected 
    7620 
    7621 > select up
    7622 
    7623 1105 atoms, 1233 bonds, 52 residues, 1 model selected 
    7624 
    7625 > select up
    7626 
    7627 8579 atoms, 8879 bonds, 986 residues, 1 model selected 
    7628 
    7629 > select down
    7630 
    7631 1105 atoms, 1233 bonds, 52 residues, 3 models selected 
    7632 
    7633 > cartoon style sel width 0.8 thickness 0.8
    7634 
    7635 > select clear
    7636 
    7637 > select #3/B:121
    7638 
    7639 24 atoms, 25 bonds, 1 residue, 1 model selected 
    7640 
    7641 > hide sel atoms
    7642 
    7643 > select #3/A:676
    7644 
    7645 24 atoms, 25 bonds, 1 residue, 1 model selected 
    7646 
    7647 > undo
    7648 
    7649 > show sel atoms
    7650 
    7651 > select clear
    7652 
    7653 > hide H
    7654 
    7655 > select clear
    7656 
    7657 > lighting shadows false
    7658 
    7659 > select clear
    7660 
    7661 > hide #!3 models
    7662 
    7663 > hide #!2 atoms
    7664 
    7665 > show #!2 cartoons
    7666 
    7667 Drag select of 61 residues 
    7668 
    7669 > select up
    7670 
    7671 805 atoms, 819 bonds, 98 residues, 2 models selected 
    7672 
    7673 > select up
    7674 
    7675 6132 atoms, 6271 bonds, 763 residues, 2 models selected 
    7676 
    7677 > rename #2 id #1
    7678 
    7679 > rename #3 id #2
    7680 
    7681 > color #1 #3584e4ff
    7682 
    7683 > select clear
    7684 
    7685 Drag select of 8 residues 
    7686 
    7687 > select up
    7688 
    7689 104 atoms, 106 bonds, 13 residues, 2 models selected 
    7690 
    7691 > select up
    7692 
    7693 1338 atoms, 1375 bonds, 167 residues, 2 models selected 
    7694 
    7695 > color (#!1 & sel) lime
    7696 
    7697 > select clear
    7698 
    7699 Drag select of 46 residues 
    7700 
    7701 > select #1/H:19
    7702 
    7703 23 atoms, 25 bonds, 1 residue, 1 model selected 
    7704 
    7705 > select up
    7706 
    7707 556 atoms, 621 bonds, 26 residues, 1 model selected 
    7708 
    7709 > color sel blue
    7710 
    7711 > select #1/G:11
    7712 
    7713 20 atoms, 21 bonds, 1 residue, 1 model selected 
    7714 
    7715 > select up
    7716 
    7717 549 atoms, 612 bonds, 26 residues, 1 model selected 
    7718 
    7719 > color sel red
    7720 
    7721 > select clear
    7722 
    7723 Drag select of 133 residues 
    7724 
    7725 > select /a
    7726 
    7727 30602 atoms, 31146 bonds, 3030 residues, 4 models selected 
    7728 
    7729 > color (#!1 & sel) orange
    7730 
    7731 > select clear
    7732 
    7733 > select /a
    7734 
    7735 30602 atoms, 31146 bonds, 3030 residues, 4 models selected 
    7736 
    7737 > color (#!1 & sel) dark gray
    7738 
    7739 > color (#!1 & sel) yellow
    7740 
    7741 > select clear
    7742 
    7743 > select /a
    7744 
    7745 30602 atoms, 31146 bonds, 3030 residues, 4 models selected 
    7746 
    7747 > color (#!1 & sel) byhetero
    7748 
    7749 > ui tool show "Color Actions"
    7750 
    7751 > color sel hot pink
    7752 
    7753 > select clear
    7754 
    7755 Drag select of 83 residues 
    7756 
    7757 > select up
    7758 
    7759 937 atoms, 954 bonds, 113 residues, 2 models selected 
    7760 
    7761 > select up
    7762 
    7763 6132 atoms, 6271 bonds, 763 residues, 2 models selected 
    7764 
    7765 > ui tool show "Color Actions"
    7766 
    7767 > color sel light salmon
    7768 
    7769 > select clear
    7770 
    7771 Drag select of 97 residues 
    7772 
    7773 > select /a
    7774 
    7775 30602 atoms, 31146 bonds, 3030 residues, 4 models selected 
    7776 
    7777 > ui tool show "Color Actions"
    7778 
    7779 > color sel gold
    7780 
    7781 > select clear
    7782 
    7783 > select /a
    7784 
    7785 30602 atoms, 31146 bonds, 3030 residues, 4 models selected 
    7786 
    7787 > ui tool show "Color Actions"
    7788 
    7789 > color sel sandy brown
    7790 
    7791 > select clear
    7792 
    7793 Drag select of 3 residues 
    7794 
    7795 > select up
    7796 
    7797 1105 atoms, 1233 bonds, 52 residues, 1 model selected 
    7798 
    7799 > select clear
    7800 
    7801 Drag select of 2 residues 
    7802 
    7803 > select up
    7804 
    7805 1105 atoms, 1233 bonds, 52 residues, 1 model selected 
    7806 
    7807 > show sel atoms
    7808 
    7809 > nucleotides sel ladder
    7810 
    7811 > select clear
    7812 
    7813 > view name p1
    7814 
    7815 > graphics silhouettes true
    7816 
    7817 > graphics silhouettes false
    7818 
    7819 > graphics silhouettes true
    7820 
    7821 > lighting simple
    7822 
    7823 > lighting soft
    7824 
    7825 > graphics silhouettes false
    7826 
    7827 > graphics silhouettes true
    7828 
    7829 > save /home/dell/Desktop/2.png width 1872 height 1872 supersample 3
    7830 
    7831 > turn y 90
    7832 
    7833 > turn y 10
    7834 
    7835 > view name p2
    7836 
    7837 > save /home/dell/Desktop/3.png width 1872 height 1872 supersample 3
    7838 
    7839 > view p2
    7840 
    7841 > view p1
    7842 
    7843 > select add #1/H:7
    7844 
    7845 45 atoms, 24 bonds, 2 residues, 1 model selected 
    7846 
    7847 > select up
    7848 
    7849 1105 atoms, 1233 bonds, 52 residues, 1 model selected 
    7850 
    7851 > cartoon style sel width 0.7 thickness 0.7
    7852 
    7853 > select clear
    7854 
    7855 > nucleotides sel ladder radius 0.3
    7856 
    7857 > select #1/G:24
    7858 
    7859 20 atoms, 21 bonds, 1 residue, 1 model selected 
    7860 
    7861 > select add #1/H:6
    7862 
    7863 42 atoms, 45 bonds, 2 residues, 1 model selected 
    7864 
    7865 > select up
    7866 
    7867 1105 atoms, 1233 bonds, 52 residues, 1 model selected 
    7868 
    7869 > nucleotides sel ladder radius 0.3
    7870 
    7871 > select clear
    7872 
    7873 > undo
    7874 
    7875 > cartoon style sel width 0.6 thickness 0.6
    7876 
    7877 > select clear
    7878 
    7879 > save /home/dell/shen_data/PIWI/PIWIL2/Figures/Fig4_overall.cxs
    7880 
    7881 > lighting flat
    7882 
    7883 > lighting soft
    7884 
    7885 > lighting full
    7886 
    7887 > lighting shadows false
    7888 
    7889 > lighting soft
    7890 
    7891 > graphics silhouettes false
    7892 
    7893 > lighting soft
    7894 
    7895 > graphics silhouettes true
    7896 
    7897 > preset cartoons/nucleotides cylinders/stubs
    7898 
    7899 Using preset: Cartoons/Nucleotides / Cylinders/Stubs 
    7900 Changed 0 atom styles 
    7901 Preset expands to these ChimeraX commands:
    7902 
    7903    
    7904    
    7905     show nucleic
    7906     hide protein|solvent|H
    7907     surf hide
    7908     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    7909     cartoon
    7910     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    7911     cartoon style ~(nucleic|strand) x round
    7912     cartoon style (nucleic|strand) x rect
    7913     cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    7914     cartoon style nucleic x round width 1.6 thick 1.6
    7915     nucleotides stubs
    7916 
    7917  
    7918 
    7919 > select #1/H:7
    7920 
    7921 22 atoms, 24 bonds, 1 residue, 1 model selected 
    7922 
    7923 > select add #1/G:22
    7924 
    7925 45 atoms, 49 bonds, 2 residues, 1 model selected 
    7926 
    7927 > select up
    7928 
    7929 1105 atoms, 1233 bonds, 52 residues, 1 model selected 
    7930 
    7931 > cartoon style sel width 0.6 thickness 0.6
    7932 
    7933 > select clear
    7934 
    7935 > view p2
    7936 
    7937 > open /home/dell/shen_data/PIWI/PIWIL2/Figures/Fig4_overall.cxs
    7938 
    7939 opened ChimeraX session 
    7940 Drag select of 61 residues 
    7941 
    7942 > select up
    7943 
    7944 1225 atoms, 1244 bonds, 150 residues, 2 models selected 
    7945 
    7946 > select up
    7947 
    7948 6132 atoms, 6271 bonds, 763 residues, 2 models selected 
    7949 
    7950 > coulombic sel
    7951 
    7952 Using Amber 20 recommended default charges and atom types for standard
    7953 residues 
    7954 Coulombic values for 2zn_2mg_model_0.cif_A SES surface #1.2: minimum, -24.08,
    7955 mean 1.18, maximum 16.69 
    7956 To also show corresponding color key, enter the above coulombic command and
    7957 add key true 
    7958 
    7959 > select clear
    7960 
    7961 > transparency #1,4 50
    7962 
    7963 > view p2
    7964 
    7965 > view name p2
    7966 
    7967 > select /a
    7968 
    7969 30602 atoms, 31146 bonds, 3030 residues, 4 models selected 
    7970 
    7971 > hide sel & #!1 cartoons
    7972 
    7973 > select clear
    7974 
    7975 > transparency #1,4 0
    7976 
    7977 > select clear
    7978 
    7979 > select /a
    7980 
    7981 30602 atoms, 31146 bonds, 3030 residues, 4 models selected 
    7982 
    7983 > mlp sel & #!1
    7984 
    7985 Map values for surface "2zn_2mg_model_0.cif_A SES surface": minimum -30.51,
    7986 mean -4.508, maximum 23.12 
    7987 To also show corresponding color key, enter the above mlp command and add key
    7988 true 
    7989 
    7990 > coulombic sel & #!1
    7991 
    7992 Coulombic values for 2zn_2mg_model_0.cif_A SES surface #1.2: minimum, -24.08,
    7993 mean 1.18, maximum 16.69 
    7994 To also show corresponding color key, enter the above coulombic command and
    7995 add key true 
    7996 
    7997 > select clear
    7998 
    7999 > view p1
    8000 
    8001 > turn y 90
    8002 
    8003 > turn y 10
    8004 
    8005 > turn y 20
    8006 
    8007 > ui mousemode right "color key"
    8008 
    8009 > key blue-white-red :min : :1
    8010 
    8011 > key blue-white-red :min : :10
    8012 
    8013 > key blue-white-red :- : :10
    8014 
    8015 > key blue-white-red :-1 : :10
    8016 
    8017 > key blue-white-red :-10 : :10
    8018 
    8019 > ui mousemode right "move label"
    8020 
    8021 > ui mousemode right label
    8022 
    8023 > label delete residues
    8024 
    8025 > key size 0.2000,0.05000
    8026 
    8027 > key red-white-blue :10 : :-10
    8028 
    8029 > key blue-white-red :-10 : :10
    8030 
    8031 > key red-white-blue :10 : :-10
    8032 
    8033 > key blue-white-red :-10 : :10
    8034 
    8035 > key size 0.20000,0.0000
    8036 
    8037 > key size 0.20000,0.00000
    8038 
    8039 > key size 0.20000,0.30000
    8040 
    8041 > key size 0.20000,0.03000
    8042 
    8043 > key labelColor #bfbfbf
    8044 
    8045 > key labelColor default
    8046 
    8047 > key fontSize 23
    8048 
    8049 > key fontSize 22
    8050 
    8051 > key fontSize 21
    8052 
    8053 > key fontSize 20
    8054 
    8055 > key fontSize 19
    8056 
    8057 > key fontSize 20
    8058 
    8059 > view name p3
    8060 
    8061 > save /home/dell/shen_data/PIWI/PIWIL2/Figures/Fig4_overall.cxs
    8062 
    8063 > select /a
    8064 
    8065 30602 atoms, 31146 bonds, 3030 residues, 4 models selected 
    8066 
    8067 > mlp sel & #!1
    8068 
    8069 Map values for surface "2zn_2mg_model_0.cif_A SES surface": minimum -30.51,
    8070 mean -4.508, maximum 23.12 
    8071 To also show corresponding color key, enter the above mlp command and add key
    8072 true 
    8073 
    8074 > coulombic sel & #!1
    8075 
    8076 Coulombic values for 2zn_2mg_model_0.cif_A SES surface #1.2: minimum, -24.08,
    8077 mean 1.18, maximum 16.69 
    8078 To also show corresponding color key, enter the above coulombic command and
    8079 add key true 
    8080 
    8081 > transparency (#!1 & sel) 10
    8082 
    8083 > transparency (#!1 & sel) 0
    8084 
    8085 > label delete residues
    8086 
    8087 > ui mousemode right select
    8088 
    8089 > select clear
    8090 
    8091 > save /home/dell/Desktop/4.png width 1872 height 1872 supersample 3
    8092 
    8093 > select #1/A:392@CG
    8094 
    8095 1 atom, 1 residue, 1 model selected 
    8096 
    8097 > select up
    8098 
    8099 7 atoms, 7 bonds, 1 residue, 2 models selected 
    8100 
    8101 > select up
    8102 
    8103 86 atoms, 88 bonds, 11 residues, 2 models selected 
    8104 
    8105 > select up
    8106 
    8107 6132 atoms, 6271 bonds, 763 residues, 2 models selected 
    8108 
    8109 > select /a
    8110 
    8111 30602 atoms, 31146 bonds, 3030 residues, 4 models selected 
    8112 
    8113 > show sel & #!1 cartoons
    8114 
    8115 > hide sel & #!1 surfaces
    8116 
    8117 > select clear
    8118 
    8119 > select #1/B:81
    8120 
    8121 7 atoms, 6 bonds, 1 residue, 1 model selected 
    8122 
    8123 > select up
    8124 
    8125 95 atoms, 94 bonds, 12 residues, 2 models selected 
    8126 
    8127 > select up
    8128 
    8129 1338 atoms, 1375 bonds, 167 residues, 2 models selected 
    8130 
    8131 > coulombic sel
    8132 
    8133 Using Amber 20 recommended default charges and atom types for standard
    8134 residues 
    8135 Coulombic values for 2zn_2mg_AF3_model_0.cif_B SES surface #1.1: minimum,
    8136 -16.15, mean -1.20, maximum 10.61 
    8137 To also show corresponding color key, enter the above coulombic command and
    8138 add key true 
    8139 
    8140 > select /a
    8141 
    8142 30602 atoms, 31146 bonds, 3030 residues, 4 models selected 
    8143 
    8144 > coulombic sel & #!1
    8145 
    8146 Coulombic values for 2zn_2mg_model_0.cif_A SES surface #1.2: minimum, -24.08,
    8147 mean 1.18, maximum 16.69 
    8148 To also show corresponding color key, enter the above coulombic command and
    8149 add key true 
    8150 
    8151 > select clear
    8152 
    8153 > select #1/B:89@O
    8154 
    8155 1 atom, 1 residue, 1 model selected 
    8156 
    8157 > select up
    8158 
    8159 4 atoms, 3 bonds, 1 residue, 2 models selected 
    8160 
    8161 > select up
    8162 
    8163 20 atoms, 19 bonds, 3 residues, 2 models selected 
    8164 
    8165 > select up
    8166 
    8167 1338 atoms, 1375 bonds, 167 residues, 2 models selected 
    8168 
    8169 > transparency (#!1 & sel) 40
    8170 
    8171 > select clear
    8172 
    8173 > graphics silhouettes false
    8174 
    8175 > select #1/B:99@CG
    8176 
    8177 1 atom, 1 residue, 1 model selected 
    8178 
    8179 > hide sel surfaces
    8180 
    8181 > select clear
    8182 
    8183 > hide #!1 surfaces
    8184 
    8185 > graphics silhouettes true
    8186 
    8187 > select #1/B:85
    8188 
    8189 7 atoms, 6 bonds, 1 residue, 1 model selected 
    8190 
    8191 > select up
    8192 
    8193 95 atoms, 94 bonds, 12 residues, 2 models selected 
    8194 
    8195 > select up
    8196 
    8197 1338 atoms, 1375 bonds, 167 residues, 2 models selected 
    8198 
    8199 > mlp sel
    8200 
    8201 Map values for surface "2zn_2mg_AF3_model_0.cif_B SES surface": minimum
    8202 -28.54, mean -4.617, maximum 23.24 
    8203 To also show corresponding color key, enter the above mlp command and add key
    8204 true 
    8205 
    8206 > hide sel surfaces
    8207 
    8208 > select clear
    8209 
    8210 > hide #3 models
    8211 
    8212 > coulombic #!1
    8213 
    8214 Using Amber 20 recommended default charges and atom types for standard
    8215 residues 
    8216 Coulombic values for 2zn_2mg_model_0.cif_A SES surface #1.2: minimum, -24.08,
    8217 mean 1.18, maximum 16.69 
    8218 Coulombic values for 2zn_2mg_AF3_model_0.cif_B SES surface #1.1: minimum,
    8219 -16.15, mean -1.20, maximum 10.61 
    8220 Coulombic values for 2zn_2mg_AF3_model_0.cif_G SES surface #1.3: minimum,
    8221 -24.18, mean -11.72, maximum -2.49 
    8222 Coulombic values for 2zn_2mg_AF3_model_0.cif_H SES surface #1.4: minimum,
    8223 -23.26, mean -11.61, maximum -2.20 
    8224 To also show corresponding color key, enter the above coulombic command and
    8225 add key true 
    8226 
    8227 > coulombic #!1 key true
    8228 
    8229 Coulombic values for 2zn_2mg_model_0.cif_A SES surface #1.2: minimum, -24.08,
    8230 mean 1.18, maximum 16.69 
    8231 Coulombic values for 2zn_2mg_AF3_model_0.cif_B SES surface #1.1: minimum,
    8232 -16.15, mean -1.20, maximum 10.61 
    8233 Coulombic values for 2zn_2mg_AF3_model_0.cif_G SES surface #1.3: minimum,
    8234 -24.18, mean -11.72, maximum -2.49 
    8235 Coulombic values for 2zn_2mg_AF3_model_0.cif_H SES surface #1.4: minimum,
    8236 -23.26, mean -11.61, maximum -2.20 
    8237 
    8238 > key red-white-blue :-10 :0 :10 showTool true
    8239 
    8240 > ui mousemode right "color key"
    8241 
    8242 > show #3 models
    8243 
    8244 > ui mousemode right select
    8245 
    8246 > select #1/B:95@CA
    8247 
    8248 1 atom, 1 residue, 1 model selected 
    8249 
    8250 > select #1/B:93@O
    8251 
    8252 1 atom, 1 residue, 1 model selected 
    8253 
    8254 > open /home/dell/shen_data/PIWI/PIWIL2/Figures/Fig4_overall.cxs
    8255 
    8256 
    8257 ===== Log before crash end =====
    8258 
    8259 Log:
    8260 UCSF ChimeraX version: 1.7 (2023-12-19) 
    8261 © 2016-2023 Regents of the University of California. All rights reserved. 
    8262 
    8263 > open /home/dell/shen_data/PIWI/PIWIL2/Figures/Fig4_overall.cxs
    8264 
    8265 Log from Thu May 16 14:53:45 2024UCSF ChimeraX version: 1.7 (2023-12-19) 
    8266 © 2016-2023 Regents of the University of California. All rights reserved. 
    8267 
    8268 > open /home/dell/shen_data/PIWI/PIWIL2/Figures/Fig4_overall.cxs
    8269 
    8270 Log from Thu May 16 14:46:31 2024UCSF ChimeraX version: 1.7 (2023-12-19) 
    8271 © 2016-2023 Regents of the University of California. All rights reserved. 
    8272 
    8273 > open /home/dell/shen_data/Alpha.Pred./AF3/AF3.cxs
    8274 
    8275 Log from Wed May 15 11:25:55 2024UCSF ChimeraX version: 1.7 (2023-12-19) 
    8276 © 2016-2023 Regents of the University of California. All rights reserved. 
    8277 
    8278 > open /home/dell/shen_data/Alpha.Pred./AF3/AF3.cxs
    8279 
    8280 Log from Fri May 10 12:32:23 2024UCSF ChimeraX version: 1.7 (2023-12-19) 
    8281 © 2016-2023 Regents of the University of California. All rights reserved. 
    8282 
    8283 > open /home/dell/shen_data/Alpha.Pred./AF3/AF3.cxs
    8284 
    8285 Log from Thu May 9 18:31:50 2024UCSF ChimeraX version: 1.7 (2023-12-19) 
    8286 © 2016-2023 Regents of the University of California. All rights reserved. 
    8287 
    8288 > open
    8289 > /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/AF_GTSF1_complex_inter.cxs
    8290 
    8291 Log from Fri Apr 12 21:01:49 2024UCSF ChimeraX version: 1.7 (2023-12-19) 
    8292 © 2016-2023 Regents of the University of California. All rights reserved. 
    8293 
    8294 > open
    8295 > /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/AF_MILI_GTSF1_FL.cxs
    8296 
    8297 Log from Fri Apr 12 10:48:13 2024UCSF ChimeraX version: 1.7 (2023-12-19) 
    8298 © 2016-2023 Regents of the University of California. All rights reserved. 
    8299 
    8300 > open
    8301 > /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/AF_MILI_GTSF1_FL.cxs
    8302 > format session
    8303 
    8304 Log from Fri Apr 12 09:21:22 2024 Startup Messages 
    8305 --- 
    8306 warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
    8307 bundle with that from NMRSTAR bundle 
    8308  
    8309 UCSF ChimeraX version: 1.7 (2023-12-19) 
    8310 © 2016-2023 Regents of the University of California. All rights reserved. 
    8311 How to cite UCSF ChimeraX 
    8312 
    8313 > open
    8314 > /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/Galaxy38-[MILI_GTSF1_pdb]/ranked_0.pdb
    8315 
    8316 Chain information for ranked_0.pdb #1 
    8317 --- 
    8318 Chain | Description 
    8319 A | No description available 
    8320 B | No description available 
    8321  
    8322 
    8323 > set bgColor white
    8324 
    8325 > color bychain
    8326 
    8327 > open
    8328 > /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/Galaxy38-[MILI_GTSF1_pdb]/ranked_1.pdb
    8329 > /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/Galaxy38-[MILI_GTSF1_pdb]/ranked_2.pdb
    8330 > /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/Galaxy38-[MILI_GTSF1_pdb]/ranked_3.pdb
    8331 > /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/Galaxy38-[MILI_GTSF1_pdb]/ranked_4.pdb
    8332 > /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/Galaxy38-[MILI_GTSF1_pdb]/ranked_5.pdb
    8333 > /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/Galaxy38-[MILI_GTSF1_pdb]/ranked_6.pdb
    8334 > /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/Galaxy38-[MILI_GTSF1_pdb]/ranked_7.pdb
    8335 > /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/Galaxy38-[MILI_GTSF1_pdb]/ranked_8.pdb
    8336 > /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/Galaxy38-[MILI_GTSF1_pdb]/ranked_9.pdb
    8337 > /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/Galaxy38-[MILI_GTSF1_pdb]/ranked_10.pdb
    8338 
    8339 Chain information for ranked_1.pdb #2 
    8340 --- 
    8341 Chain | Description 
    8342 A | No description available 
    8343 B | No description available 
    8344  
    8345 Chain information for ranked_2.pdb #3 
    8346 --- 
    8347 Chain | Description 
    8348 A | No description available 
    8349 B | No description available 
    8350  
    8351 Chain information for ranked_3.pdb #4 
    8352 --- 
    8353 Chain | Description 
    8354 A | No description available 
    8355 B | No description available 
    8356  
    8357 Chain information for ranked_4.pdb #5 
    8358 --- 
    8359 Chain | Description 
    8360 A | No description available 
    8361 B | No description available 
    8362  
    8363 Chain information for ranked_5.pdb #6 
    8364 --- 
    8365 Chain | Description 
    8366 A | No description available 
    8367 B | No description available 
    8368  
    8369 Chain information for ranked_6.pdb #7 
    8370 --- 
    8371 Chain | Description 
    8372 A | No description available 
    8373 B | No description available 
    8374  
    8375 Chain information for ranked_7.pdb #8 
    8376 --- 
    8377 Chain | Description 
    8378 A | No description available 
    8379 B | No description available 
    8380  
    8381 Chain information for ranked_8.pdb #9 
    8382 --- 
    8383 Chain | Description 
    8384 A | No description available 
    8385 B | No description available 
    8386  
    8387 Chain information for ranked_9.pdb #10 
    8388 --- 
    8389 Chain | Description 
    8390 A | No description available 
    8391 B | No description available 
    8392  
    8393 Chain information for ranked_10.pdb #11 
    8394 --- 
    8395 Chain | Description 
    8396 A | No description available 
    8397 B | No description available 
    8398  
    8399 
    8400 > ui tool show Matchmaker
    8401 
    8402 > matchmaker #2-11 to #1
    8403 
    8404 Parameters 
    8405 --- 
    8406 Chain pairing | bb 
    8407 Alignment algorithm | Needleman-Wunsch 
    8408 Similarity matrix | BLOSUM-62 
    8409 SS fraction | 0.3 
    8410 Gap open (HH/SS/other) | 18/18/6 
    8411 Gap extend | 1 
    8412 SS matrix |  |  | H | S | O 
    8413 ---|---|---|--- 
    8414 H | 6 | -9 | -6 
    8415 S |  | 6 | -6 
    8416 O |  |  | 4 
    8417 Iteration cutoff | 2 
    8418  
    8419 Matchmaker ranked_0.pdb, chain A (#1) with ranked_1.pdb, chain A (#2),
    8420 sequence alignment score = 3986.5 
    8421 RMSD between 746 pruned atom pairs is 0.827 angstroms; (across all 763 pairs:
    8422 0.928) 
    8423  
    8424 Matchmaker ranked_0.pdb, chain A (#1) with ranked_2.pdb, chain A (#3),
    8425 sequence alignment score = 3999.7 
    8426 RMSD between 761 pruned atom pairs is 0.324 angstroms; (across all 763 pairs:
    8427 0.359) 
    8428  
    8429 Matchmaker ranked_0.pdb, chain A (#1) with ranked_3.pdb, chain A (#4),
    8430 sequence alignment score = 3933.7 
    8431 RMSD between 718 pruned atom pairs is 0.806 angstroms; (across all 763 pairs:
    8432 1.041) 
    8433  
    8434 Matchmaker ranked_0.pdb, chain A (#1) with ranked_4.pdb, chain A (#5),
    8435 sequence alignment score = 3955.3 
    8436 RMSD between 708 pruned atom pairs is 0.837 angstroms; (across all 763 pairs:
    8437 1.111) 
    8438  
    8439 Matchmaker ranked_0.pdb, chain A (#1) with ranked_5.pdb, chain A (#6),
    8440 sequence alignment score = 3985.9 
    8441 RMSD between 752 pruned atom pairs is 0.761 angstroms; (across all 763 pairs:
    8442 0.858) 
    8443  
    8444 Matchmaker ranked_0.pdb, chain A (#1) with ranked_6.pdb, chain A (#7),
    8445 sequence alignment score = 3989.5 
    8446 RMSD between 709 pruned atom pairs is 0.882 angstroms; (across all 763 pairs:
    8447 1.139) 
    8448  
    8449 Matchmaker ranked_0.pdb, chain A (#1) with ranked_7.pdb, chain A (#8),
    8450 sequence alignment score = 3993.1 
    8451 RMSD between 761 pruned atom pairs is 0.437 angstroms; (across all 763 pairs:
    8452 0.455) 
    8453  
    8454 Matchmaker ranked_0.pdb, chain A (#1) with ranked_8.pdb, chain A (#9),
    8455 sequence alignment score = 3992.5 
    8456 RMSD between 756 pruned atom pairs is 0.279 angstroms; (across all 763 pairs:
    8457 0.449) 
    8458  
    8459 Matchmaker ranked_0.pdb, chain A (#1) with ranked_9.pdb, chain A (#10),
    8460 sequence alignment score = 3999.7 
    8461 RMSD between 762 pruned atom pairs is 0.329 angstroms; (across all 763 pairs:
    8462 0.345) 
    8463  
    8464 Matchmaker ranked_0.pdb, chain A (#1) with ranked_10.pdb, chain A (#11),
    8465 sequence alignment score = 3947.5 
    8466 RMSD between 745 pruned atom pairs is 0.640 angstroms; (across all 763 pairs:
    8467 0.737) 
    8468  
    8469 
    8470 > matchmaker #2-11 to #1
    8471 
    8472 Parameters 
    8473 --- 
    8474 Chain pairing | bb 
    8475 Alignment algorithm | Needleman-Wunsch 
    8476 Similarity matrix | BLOSUM-62 
    8477 SS fraction | 0.3 
    8478 Gap open (HH/SS/other) | 18/18/6 
    8479 Gap extend | 1 
    8480 SS matrix |  |  | H | S | O 
    8481 ---|---|---|--- 
    8482 H | 6 | -9 | -6 
    8483 S |  | 6 | -6 
    8484 O |  |  | 4 
    8485 Iteration cutoff | 2 
    8486  
    8487 Matchmaker ranked_0.pdb, chain A (#1) with ranked_1.pdb, chain A (#2),
    8488 sequence alignment score = 3986.5 
    8489 RMSD between 746 pruned atom pairs is 0.827 angstroms; (across all 763 pairs:
    8490 0.928) 
    8491  
    8492 Matchmaker ranked_0.pdb, chain A (#1) with ranked_2.pdb, chain A (#3),
    8493 sequence alignment score = 3999.7 
    8494 RMSD between 761 pruned atom pairs is 0.324 angstroms; (across all 763 pairs:
    8495 0.359) 
    8496  
    8497 Matchmaker ranked_0.pdb, chain A (#1) with ranked_3.pdb, chain A (#4),
    8498 sequence alignment score = 3933.7 
    8499 RMSD between 718 pruned atom pairs is 0.806 angstroms; (across all 763 pairs:
    8500 1.041) 
    8501  
    8502 Matchmaker ranked_0.pdb, chain A (#1) with ranked_4.pdb, chain A (#5),
    8503 sequence alignment score = 3955.3 
    8504 RMSD between 708 pruned atom pairs is 0.837 angstroms; (across all 763 pairs:
    8505 1.111) 
    8506  
    8507 Matchmaker ranked_0.pdb, chain A (#1) with ranked_5.pdb, chain A (#6),
    8508 sequence alignment score = 3985.9 
    8509 RMSD between 752 pruned atom pairs is 0.761 angstroms; (across all 763 pairs:
    8510 0.858) 
    8511  
    8512 Matchmaker ranked_0.pdb, chain A (#1) with ranked_6.pdb, chain A (#7),
    8513 sequence alignment score = 3989.5 
    8514 RMSD between 709 pruned atom pairs is 0.882 angstroms; (across all 763 pairs:
    8515 1.139) 
    8516  
    8517 Matchmaker ranked_0.pdb, chain A (#1) with ranked_7.pdb, chain A (#8),
    8518 sequence alignment score = 3993.1 
    8519 RMSD between 761 pruned atom pairs is 0.437 angstroms; (across all 763 pairs:
    8520 0.455) 
    8521  
    8522 Matchmaker ranked_0.pdb, chain A (#1) with ranked_8.pdb, chain A (#9),
    8523 sequence alignment score = 3992.5 
    8524 RMSD between 756 pruned atom pairs is 0.279 angstroms; (across all 763 pairs:
    8525 0.449) 
    8526  
    8527 Matchmaker ranked_0.pdb, chain A (#1) with ranked_9.pdb, chain A (#10),
    8528 sequence alignment score = 3999.7 
    8529 RMSD between 762 pruned atom pairs is 0.329 angstroms; (across all 763 pairs:
    8530 0.345) 
    8531  
    8532 Matchmaker ranked_0.pdb, chain A (#1) with ranked_10.pdb, chain A (#11),
    8533 sequence alignment score = 3947.5 
    8534 RMSD between 745 pruned atom pairs is 0.640 angstroms; (across all 763 pairs:
    8535 0.737) 
    8536  
    8537 
    8538 > color bychain
    8539 
    8540 > select /a:26,29,36,39
    8541 
    8542 605 atoms, 583 bonds, 44 residues, 11 models selected 
    8543 
    8544 > ui mousemode right select
    8545 
    8546 > select clear
    8547 
    8548 > open
    8549 > /home/dell/shen_data/PIWI/PIWIL2/RT_structures/RT_MILI_26nt_2-coot-0.pdb
    8550 
    8551 Chain information for RT_MILI_26nt_2-coot-0.pdb #12 
    8552 --- 
    8553 Chain | Description 
    8554 A | No description available 
    8555 B | No description available 
    8556 C | No description available 
    8557  
    8558 
    8559 > ui tool show Matchmaker
    8560 
    8561 > matchmaker #!12 to #1
    8562 
    8563 Parameters 
    8564 --- 
    8565 Chain pairing | bb 
    8566 Alignment algorithm | Needleman-Wunsch 
    8567 Similarity matrix | BLOSUM-62 
    8568 SS fraction | 0.3 
    8569 Gap open (HH/SS/other) | 18/18/6 
    8570 Gap extend | 1 
    8571 SS matrix |  |  | H | S | O 
    8572 ---|---|---|--- 
    8573 H | 6 | -9 | -6 
    8574 S |  | 6 | -6 
    8575 O |  |  | 4 
    8576 Iteration cutoff | 2 
    8577  
    8578 Matchmaker ranked_0.pdb, chain A (#1) with RT_MILI_26nt_2-coot-0.pdb, chain A
    8579 (#12), sequence alignment score = 3243.4 
    8580 RMSD between 324 pruned atom pairs is 1.118 angstroms; (across all 751 pairs:
    8581 5.211) 
    8582  
    8583 
    8584 > matchmaker #!12 to #1
    8585 
    8586 Parameters 
    8587 --- 
    8588 Chain pairing | bb 
    8589 Alignment algorithm | Needleman-Wunsch 
    8590 Similarity matrix | BLOSUM-62 
    8591 SS fraction | 0.3 
    8592 Gap open (HH/SS/other) | 18/18/6 
    8593 Gap extend | 1 
    8594 SS matrix |  |  | H | S | O 
    8595 ---|---|---|--- 
    8596 H | 6 | -9 | -6 
    8597 S |  | 6 | -6 
    8598 O |  |  | 4 
    8599 Iteration cutoff | 2 
    8600  
    8601 Matchmaker ranked_0.pdb, chain A (#1) with RT_MILI_26nt_2-coot-0.pdb, chain A
    8602 (#12), sequence alignment score = 3243.4 
    8603 RMSD between 324 pruned atom pairs is 1.118 angstroms; (across all 751 pairs:
    8604 5.211) 
    8605  
    8606 
    8607 > show cartoons
    8608 
    8609 > nucleotides ladder
    8610 
    8611 > select clear
    8612 
    8613 > color bychain
    8614 
    8615 > select clear
    8616 
    8617 > select /B:26,29,36,39
    8618 
    8619 1033 atoms, 990 bonds, 45 residues, 12 models selected 
    8620 
    8621 > show sel atoms
    8622 
    8623 > select clear
    8624 
    8625 > hide #2-11 target m
    8626 
    8627 > select #1/B:75
    8628 
    8629 11 atoms, 10 bonds, 1 residue, 1 model selected 
    8630 
    8631 > select up
    8632 
    8633 246 atoms, 245 bonds, 16 residues, 1 model selected 
    8634 
    8635 > select up
    8636 
    8637 2603 atoms, 2640 bonds, 167 residues, 1 model selected 
    8638 
    8639 > color sel magenta
    8640 
    8641 > select clear
    8642 
    8643 > select /B:98,112,107
    8644 
    8645 792 atoms, 825 bonds, 33 residues, 11 models selected 
    8646 
    8647 > show sel & #1 atoms
    8648 
    8649 > hide H
    8650 
    8651 > select clear
    8652 
    8653 [Repeated 1 time(s)]
    8654 
    8655 > save
    8656 > /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/AF_MILI_GTSF1_FL.cxs
    8657 
    8658 ——— End of log from Fri Apr 12 09:21:22 2024 ———
    8659 
    8660 opened ChimeraX session 
    8661 
    8662 > show #7 models
    8663 
    8664 > hide #7 models
    8665 
    8666 > show #7 models
    8667 
    8668 > show #11 models
    8669 
    8670 > hide #11 models
    8671 
    8672 > close #2-11
    8673 
    8674 > combine #1
    8675 
    8676 > hide #2 models
    8677 
    8678 > hide #!12 models
    8679 
    8680 > coulombic #1
    8681 
    8682 Using Amber 20 recommended default charges and atom types for standard
    8683 residues 
    8684 Coulombic values for ranked_0.pdb_A SES surface #1.1: minimum, -23.31, mean
    8685 2.59, maximum 28.26 
    8686 Coulombic values for ranked_0.pdb_B SES surface #1.2: minimum, -15.32, mean
    8687 -0.57, maximum 12.26 
    8688 To also show corresponding color key, enter the above coulombic command and
    8689 add key true 
    8690 
    8691 > ui mousemode right select
    8692 
    8693 > select #1/B:13@HE3
    8694 
    8695 1 atom, 1 residue, 1 model selected 
    8696 
    8697 > select up
    8698 
    8699 22 atoms, 21 bonds, 1 residue, 2 models selected 
    8700 
    8701 > select up
    8702 
    8703 93 atoms, 93 bonds, 6 residues, 2 models selected 
    8704 
    8705 > select up
    8706 
    8707 2603 atoms, 2640 bonds, 167 residues, 2 models selected 
    8708 
    8709 > hide sel surfaces
    8710 
    8711 > select clear
    8712 
    8713 > select #1/B:82
    8714 
    8715 16 atoms, 15 bonds, 1 residue, 1 model selected 
    8716 
    8717 > select up
    8718 
    8719 246 atoms, 245 bonds, 16 residues, 2 models selected 
    8720 
    8721 > select up
    8722 
    8723 2603 atoms, 2640 bonds, 167 residues, 2 models selected 
    8724 
    8725 > color sel byhetero
    8726 
    8727 > select clear
    8728 
    8729 > show #2 models
    8730 
    8731 > hide #!1 models
    8732 
    8733 > select clear
    8734 
    8735 > mlp #2
    8736 
    8737 Map values for surface "copy of ranked_0.pdb_A SES surface": minimum -28.98,
    8738 mean -3.606, maximum 24.24 
    8739 Map values for surface "copy of ranked_0.pdb_B SES surface": minimum -28.26,
    8740 mean -3.591, maximum 22.8 
    8741 To also show corresponding color key, enter the above mlp command and add key
    8742 true 
    8743 
    8744 > select #2/B:75@OG
    8745 
    8746 1 atom, 1 residue, 1 model selected 
    8747 
    8748 > select up
    8749 
    8750 11 atoms, 10 bonds, 1 residue, 2 models selected 
    8751 
    8752 > select up
    8753 
    8754 246 atoms, 245 bonds, 16 residues, 2 models selected 
    8755 
    8756 > select up
    8757 
    8758 2603 atoms, 2640 bonds, 167 residues, 2 models selected 
    8759 
    8760 > hide sel surfaces
    8761 
    8762 > select clear
    8763 
    8764 > select #2/B:75
    8765 
    8766 11 atoms, 10 bonds, 1 residue, 1 model selected 
    8767 
    8768 > select up
    8769 
    8770 246 atoms, 245 bonds, 16 residues, 2 models selected 
    8771 
    8772 > select up
    8773 
    8774 2603 atoms, 2640 bonds, 167 residues, 2 models selected 
    8775 
    8776 > color sel byhetero
    8777 
    8778 > select clear
    8779 
    8780 > open https://www.rbvi.ucsf.edu/chimerax/tutorials.html
    8781 
    8782 Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html 
    8783 
    8784 > select #2/B:94
    8785 
    8786 10 atoms, 9 bonds, 1 residue, 1 model selected 
    8787 
    8788 > show sel atoms
    8789 
    8790 > select #2/B:92
    8791 
    8792 14 atoms, 13 bonds, 1 residue, 1 model selected 
    8793 
    8794 > show sel atoms
    8795 
    8796 > select #2/A:388@CG2
    8797 
    8798 1 atom, 1 residue, 1 model selected 
    8799 
    8800 > select #2/A:388@HD12
    8801 
    8802 1 atom, 1 residue, 1 model selected 
    8803 
    8804 > select #2/B:95
    8805 
    8806 15 atoms, 14 bonds, 1 residue, 1 model selected 
    8807 
    8808 > show sel atoms
    8809 
    8810 > show #!12 models
    8811 
    8812 > select #12/a
    8813 
    8814 6035 atoms, 6171 bonds, 751 residues, 1 model selected 
    8815 
    8816 > hide sel cartoons
    8817 
    8818 > select clear
    8819 
    8820 > select #12/b
    8821 
    8822 550 atoms, 613 bonds, 26 residues, 1 model selected 
    8823 
    8824 > select clear
    8825 
    8826 > show #!1 models
    8827 
    8828 > hide #!1 models
    8829 
    8830 > show #!1 models
    8831 
    8832 > hide #!1 models
    8833 
    8834 > show #!1 models
    8835 
    8836 > hide #!1 models
    8837 
    8838 > show #!1 models
    8839 
    8840 > hide #!1 models
    8841 
    8842 > show #!1 models
    8843 
    8844 > hide #!1 models
    8845 
    8846 > show #!1 models
    8847 
    8848 > hide H
    8849 
    8850 > select clear
    8851 
    8852 > select #1/B:91
    8853 
    8854 15 atoms, 14 bonds, 1 residue, 1 model selected 
    8855 
    8856 > show sel atoms
    8857 
    8858 > hide H
    8859 
    8860 > select clear
    8861 
    8862 > select #1/B:96
    8863 
    8864 11 atoms, 10 bonds, 1 residue, 1 model selected 
    8865 
    8866 > show sel atoms
    8867 
    8868 > hide H
    8869 
    8870 > select #1/A:587@CB
    8871 
    8872 1 atom, 1 residue, 1 model selected 
    8873 
    8874 > select clear
    8875 
    8876 > select #1/B:118
    8877 
    8878 14 atoms, 14 bonds, 1 residue, 1 model selected 
    8879 
    8880 > select add #1/B:119
    8881 
    8882 34 atoms, 34 bonds, 2 residues, 2 models selected 
    8883 
    8884 > select add #1/B:120
    8885 
    8886 50 atoms, 49 bonds, 3 residues, 2 models selected 
    8887 
    8888 > select add #1/A:698@O
    8889 
    8890 51 atoms, 49 bonds, 4 residues, 2 models selected 
    8891 
    8892 > select subtract #1/A:698@O
    8893 
    8894 50 atoms, 49 bonds, 3 residues, 3 models selected 
    8895 
    8896 > select add #1/B:121
    8897 
    8898 74 atoms, 74 bonds, 4 residues, 2 models selected 
    8899 
    8900 > select add #1/B:122
    8901 
    8902 81 atoms, 80 bonds, 5 residues, 2 models selected 
    8903 
    8904 > select add #1/B:123
    8905 
    8906 95 atoms, 93 bonds, 6 residues, 2 models selected 
    8907 
    8908 > show sel atoms
    8909 
    8910 > hide H
    8911 
    8912 > select clear
    8913 
    8914 > hide #!1 models
    8915 
    8916 > show #!1 models
    8917 
    8918 > hide #!1 models
    8919 
    8920 > select #2/B:119
    8921 
    8922 20 atoms, 20 bonds, 1 residue, 1 model selected 
    8923 
    8924 > select add #2/B:121
    8925 
    8926 44 atoms, 45 bonds, 2 residues, 2 models selected 
    8927 
    8928 > show sel atoms
    8929 
    8930 > hide H
    8931 
    8932 > select clear
    8933 
    8934 > show #!1 models
    8935 
    8936 > hide #!2 models
    8937 
    8938 > show #!2 models
    8939 
    8940 > hide #!1 models
    8941 
    8942 > show #!1 models
    8943 
    8944 > graphics silhouettes true
    8945 
    8946 > graphics silhouettes false
    8947 
    8948 > label @@display
    8949 
    8950 > label height 1.2
    8951 
    8952 > hide #12.2 models
    8953 
    8954 > label @@display
    8955 
    8956 > label height 1.5
    8957 
    8958 > select clear
    8959 
    8960 > hide #2.3 models
    8961 
    8962 > select #1/A:523@HB2
    8963 
    8964 1 atom, 1 residue, 1 model selected 
    8965 
    8966 > select #1/B:106
    8967 
    8968 12 atoms, 11 bonds, 1 residue, 1 model selected 
    8969 
    8970 > show sel atoms
    8971 
    8972 > select #1/B:105
    8973 
    8974 15 atoms, 14 bonds, 1 residue, 1 model selected 
    8975 
    8976 > show sel atoms
    8977 
    8978 > hide H
    8979 
    8980 > select clear
    8981 
    8982 > hide #!2 models
    8983 
    8984 > show #!2 models
    8985 
    8986 > hide #!1 models
    8987 
    8988 > show #!1 models
    8989 
    8990 > hide #!1 models
    8991 
    8992 > show #!1 models
    8993 
    8994 > save /home/dell/Desktop/image5.png supersample 3
    8995 
    8996 > lighting soft
    8997 
    8998 > hide #!2 models
    8999 
    9000 > save /home/dell/Desktop/image6.png supersample 3
    9001 
    9002 > save
    9003 > /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/AF_MILI_GTSF1_FL.cxs
    9004 
    9005 ——— End of log from Fri Apr 12 10:48:13 2024 ———
    9006 
    9007 opened ChimeraX session 
    9008 
    9009 > combine #1
    9010 
    9011 > hide #3 models
    9012 
    9013 > hide #!12 models
    9014 
    9015 > show #!2 models
    9016 
    9017 > hide #!2 models
    9018 
    9019 > hide #!1 models
    9020 
    9021 > show #3 models
    9022 
    9023 > ui mousemode right select
    9024 
    9025 > select #3/B:79
    9026 
    9027 17 atoms, 16 bonds, 1 residue, 1 model selected 
    9028 
    9029 > select up
    9030 
    9031 246 atoms, 245 bonds, 16 residues, 1 model selected 
    9032 
    9033 > select up
    9034 
    9035 2603 atoms, 2640 bonds, 167 residues, 1 model selected 
    9036 
    9037 > select sel @< 4 & ~sel
    9038 
    9039 7105 atoms, 6819 bonds, 610 residues, 4 models selected 
    9040 
    9041 > show sel & #3 atoms
    9042 
    9043 > show (#3 & sel-residues & sidechain) target ab
    9044 
    9045 > select #3/B:86
    9046 
    9047 24 atoms, 23 bonds, 1 residue, 1 model selected 
    9048 
    9049 > select up
    9050 
    9051 246 atoms, 245 bonds, 16 residues, 1 model selected 
    9052 
    9053 > select up
    9054 
    9055 2603 atoms, 2640 bonds, 167 residues, 1 model selected 
    9056 
    9057 > hide H
    9058 
    9059 > select clear
    9060 
    9061 > show #!1 models
    9062 
    9063 > hide #!1 models
    9064 
    9065 > select #3/B:86
    9066 
    9067 24 atoms, 23 bonds, 1 residue, 1 model selected 
    9068 
    9069 > select add #3/B:108
    9070 
    9071 36 atoms, 34 bonds, 2 residues, 1 model selected 
    9072 
    9073 > select add #3/B:73
    9074 
    9075 48 atoms, 45 bonds, 3 residues, 1 model selected 
    9076 
    9077 > select add #3/B:75
    9078 
    9079 59 atoms, 55 bonds, 4 residues, 1 model selected 
    9080 
    9081 > select up
    9082 
    9083 359 atoms, 361 bonds, 22 residues, 1 model selected 
    9084 
    9085 > show sel atoms
    9086 
    9087 > select #3/B:70
    9088 
    9089 11 atoms, 10 bonds, 1 residue, 1 model selected 
    9090 
    9091 > select up
    9092 
    9093 41 atoms, 40 bonds, 3 residues, 1 model selected 
    9094 
    9095 > select up
    9096 
    9097 2603 atoms, 2640 bonds, 167 residues, 1 model selected 
    9098 
    9099 > color sel lime
    9100 
    9101 > hide H
    9102 
    9103 > show #!12 models
    9104 
    9105 > hide #3 models
    9106 
    9107 > select #12/a:716
    9108 
    9109 8 atoms, 7 bonds, 1 residue, 1 model selected 
    9110 
    9111 > show sel cartoons
    9112 
    9113 > select clear
    9114 
    9115 > show #!12 cartoons
    9116 
    9117 > select #12/a:716
    9118 
    9119 8 atoms, 7 bonds, 1 residue, 1 model selected 
    9120 
    9121 > color sel yellow
    9122 
    9123 > show #3 models
    9124 
    9125 > hide #!12 models
    9126 
    9127 > color #3 byhetero
    9128 
    9129 > select clear
    9130 
    9131 [Repeated 1 time(s)]
    9132 
    9133 > undo
    9134 
    9135 [Repeated 9 time(s)]
    9136 
    9137 > select clear
    9138 
    9139 > undo
    9140 
    9141 [Repeated 1 time(s)]
    9142 
    9143 > show #3 models
    9144 
    9145 > hide #!12 models
    9146 
    9147 > select #3/B:99
    9148 
    9149 17 atoms, 16 bonds, 1 residue, 1 model selected 
    9150 
    9151 > select up
    9152 
    9153 271 atoms, 274 bonds, 19 residues, 1 model selected 
    9154 
    9155 > show sel atoms
    9156 
    9157 > hide H
    9158 
    9159 > select clear
    9160 
    9161 > color #3 byhetero
    9162 
    9163 > select clear
    9164 
    9165 Drag select of 6 atoms, 5 bonds, 5 residues 
    9166 Drag select of 1 atoms, 1 bonds, 2 residues 
    9167 
    9168 > select clear
    9169 
    9170 Drag select of 9 atoms, 7 bonds, 7 residues 
    9171 
    9172 > hide sel atoms
    9173 
    9174 > select clear
    9175 
    9176 > color #3 byhetero
    9177 
    9178 > select clear
    9179 
    9180 > select #3/B:35
    9181 
    9182 19 atoms, 18 bonds, 1 residue, 1 model selected 
    9183 
    9184 > show sel atoms
    9185 
    9186 > select #3/B:32
    9187 
    9188 21 atoms, 21 bonds, 1 residue, 1 model selected 
    9189 
    9190 > show sel atoms
    9191 
    9192 > select #3/B:39
    9193 
    9194 22 atoms, 21 bonds, 1 residue, 1 model selected 
    9195 
    9196 > select clear
    9197 
    9198 > hide H
    9199 
    9200 > select clear
    9201 
    9202 > select #3/B:78
    9203 
    9204 15 atoms, 14 bonds, 1 residue, 1 model selected 
    9205 
    9206 > hide sel atoms
    9207 
    9208 > select #3/B:74
    9209 
    9210 22 atoms, 21 bonds, 1 residue, 1 model selected 
    9211 
    9212 > hide sel atoms
    9213 
    9214 > select #3/B:82
    9215 
    9216 16 atoms, 15 bonds, 1 residue, 1 model selected 
    9217 
    9218 > hide sel atoms
    9219 
    9220 > select #3/B:86@CB
    9221 
    9222 1 atom, 1 residue, 1 model selected 
    9223 
    9224 > hide sel atoms
    9225 
    9226 > select #3/B:86
    9227 
    9228 24 atoms, 23 bonds, 1 residue, 1 model selected 
    9229 
    9230 > hide sel atoms
    9231 
    9232 > select clear
    9233 
    9234 > select #3/A:593
    9235 
    9236 14 atoms, 13 bonds, 1 residue, 1 model selected 
    9237 
    9238 > show sel atoms
    9239 
    9240 > hide sel atoms
    9241 
    9242 > select clear
    9243 
    9244 > select #3/B:28
    9245 
    9246 11 atoms, 10 bonds, 1 residue, 1 model selected 
    9247 
    9248 > select #3/B:1
    9249 
    9250 19 atoms, 18 bonds, 1 residue, 1 model selected 
    9251 
    9252 > view sel
    9253 
    9254 > select #3/B:28
    9255 
    9256 11 atoms, 10 bonds, 1 residue, 1 model selected 
    9257 
    9258 > show sel atoms
    9259 
    9260 > select #3/B:10
    9261 
    9262 12 atoms, 11 bonds, 1 residue, 1 model selected 
    9263 
    9264 > show sel atoms
    9265 
    9266 > select #3/B:9
    9267 
    9268 19 atoms, 18 bonds, 1 residue, 1 model selected 
    9269 
    9270 > show sel atoms
    9271 
    9272 > select clear
    9273 
    9274 > select #3/B:11
    9275 
    9276 14 atoms, 14 bonds, 1 residue, 1 model selected 
    9277 
    9278 > show sel atoms
    9279 
    9280 > hide H
    9281 
    9282 > select #3/B:28
    9283 
    9284 11 atoms, 10 bonds, 1 residue, 1 model selected 
    9285 
    9286 > show sel atoms
    9287 
    9288 > undo
    9289 
    9290 > view sel
    9291 
    9292 > select #3/B:30
    9293 
    9294 20 atoms, 20 bonds, 1 residue, 1 model selected 
    9295 
    9296 > show sel atoms
    9297 
    9298 > select #3/B:33
    9299 
    9300 17 atoms, 17 bonds, 1 residue, 1 model selected 
    9301 
    9302 > select #3/B:33
    9303 
    9304 17 atoms, 17 bonds, 1 residue, 1 model selected 
    9305 
    9306 > select #3/B:33
    9307 
    9308 17 atoms, 17 bonds, 1 residue, 1 model selected 
    9309 
    9310 > select up
    9311 
    9312 183 atoms, 185 bonds, 10 residues, 1 model selected 
    9313 
    9314 > select up
    9315 
    9316 2603 atoms, 2640 bonds, 167 residues, 1 model selected 
    9317 
    9318 > show sel atoms
    9319 
    9320 > hide H
    9321 
    9322 > select clear
    9323 
    9324 > ui tool show Distances
    9325 
    9326 > select #3/A:611@NE2
    9327 
    9328 1 atom, 1 residue, 1 model selected 
    9329 
    9330 > select add #3/B:32@OH
    9331 
    9332 2 atoms, 2 residues, 1 model selected 
    9333 
    9334 > distance #3/A:611@NE2 #3/B:32@OH
    9335 
    9336 Distance between copy of ranked_0.pdb #3/A GLN 611 NE2 and /B TYR 32 OH:
    9337 2.843Å 
    9338 
    9339 > distance style color black
    9340 
    9341 [Repeated 2 time(s)]
    9342 
    9343 > select #3/A:617@OD1
    9344 
    9345 1 atom, 1 residue, 1 model selected 
    9346 
    9347 > select add #3/B:38@NH2
    9348 
    9349 2 atoms, 2 residues, 1 model selected 
    9350 
    9351 > distance #3/A:617@OD1 #3/B:38@NH2
    9352 
    9353 Distance between copy of ranked_0.pdb #3/A ASN 617 OD1 and /B ARG 38 NH2:
    9354 4.159Å 
    9355 
    9356 > select #3/A:614
    9357 
    9358 14 atoms, 13 bonds, 1 residue, 1 model selected 
    9359 
    9360 > select #3/B:80@OD2
    9361 
    9362 1 atom, 1 residue, 1 model selected 
    9363 
    9364 > select add #3/A:564@NH2
    9365 
    9366 2 atoms, 2 residues, 1 model selected 
    9367 
    9368 > distance #3/B:80@OD2 #3/A:564@NH2
    9369 
    9370 Distance between copy of ranked_0.pdb #3/B ASP 80 OD2 and /A ARG 564 NH2:
    9371 2.667Å 
    9372 
    9373 > select clear
    9374 
    9375 > select #3/B:84@NE2
    9376 
    9377 1 atom, 1 residue, 1 model selected 
    9378 
    9379 > select #3/B:84@NE2
    9380 
    9381 1 atom, 1 residue, 1 model selected 
    9382 
    9383 > select add #3/A:562@OH
    9384 
    9385 2 atoms, 2 residues, 1 model selected 
    9386 
    9387 > distance #3/B:84@NE2 #3/A:562@OH
    9388 
    9389 Distance between copy of ranked_0.pdb #3/B GLN 84 NE2 and /A TYR 562 OH:
    9390 3.130Å 
    9391 
    9392 > select #3/B:84
    9393 
    9394 17 atoms, 16 bonds, 1 residue, 1 model selected 
    9395 
    9396 > select #3/A:755@NE2
    9397 
    9398 1 atom, 1 residue, 1 model selected 
    9399 
    9400 > select add #3/B:87@OD1
    9401 
    9402 2 atoms, 2 residues, 1 model selected 
    9403 
    9404 > distance #3/A:755@NE2 #3/B:87@OD1
    9405 
    9406 Distance between copy of ranked_0.pdb #3/A GLN 755 NE2 and /B ASN 87 OD1:
    9407 3.235Å 
    9408 
    9409 > select #3/B:86
    9410 
    9411 24 atoms, 23 bonds, 1 residue, 1 model selected 
    9412 
    9413 > hide sel atoms
    9414 
    9415 > select #3/B:82
    9416 
    9417 16 atoms, 15 bonds, 1 residue, 1 model selected 
    9418 
    9419 > hide sel atoms
    9420 
    9421 > select #3/B:81
    9422 
    9423 16 atoms, 15 bonds, 1 residue, 1 model selected 
    9424 
    9425 > hide sel atoms
    9426 
    9427 > select #3/A:577@OG
    9428 
    9429 1 atom, 1 residue, 1 model selected 
    9430 
    9431 > lighting simple
    9432 
    9433 > select clear
    9434 
    9435 > select #3/A:577@OG
    9436 
    9437 1 atom, 1 residue, 1 model selected 
    9438 
    9439 > select add #3/B:73@OD1
    9440 
    9441 2 atoms, 2 residues, 1 model selected 
    9442 
    9443 > distance #3/A:577@OG #3/B:73@OD1
    9444 
    9445 Distance between copy of ranked_0.pdb #3/A SER 577 OG and /B ASP 73 OD1:
    9446 3.929Å 
    9447 
    9448 > select #3/B:56@NH1
    9449 
    9450 1 atom, 1 residue, 1 model selected 
    9451 
    9452 > select add #3/A:576@OD2
    9453 
    9454 2 atoms, 2 residues, 1 model selected 
    9455 
    9456 > distance #3/B:56@NH1 #3/A:576@OD2
    9457 
    9458 Distance between copy of ranked_0.pdb #3/B ARG 56 NH1 and /A ASP 576 OD2:
    9459 3.224Å 
    9460 
    9461 > select #3/B:88
    9462 
    9463 19 atoms, 18 bonds, 1 residue, 1 model selected 
    9464 
    9465 > select #3/B:81
    9466 
    9467 16 atoms, 15 bonds, 1 residue, 1 model selected 
    9468 
    9469 > show sel atoms
    9470 
    9471 > hide H
    9472 
    9473 > select clear
    9474 
    9475 [Repeated 1 time(s)]
    9476 
    9477 > select add #3/A:518@OE1
    9478 
    9479 1 atom, 1 residue, 1 model selected 
    9480 Exactly two atoms must be selected! 
    9481 
    9482 > select add #3/B:96@OG
    9483 
    9484 2 atoms, 2 residues, 1 model selected 
    9485 
    9486 > distance #3/A:518@OE1 #3/B:96@OG
    9487 
    9488 Distance between copy of ranked_0.pdb #3/A GLU 518 OE1 and /B SER 96 OG:
    9489 4.209Å 
    9490 
    9491 > select #3/B:100@SG
    9492 
    9493 1 atom, 1 residue, 1 model selected 
    9494 
    9495 > select add #3/A:364@ND2
    9496 
    9497 2 atoms, 2 residues, 1 model selected 
    9498 
    9499 > distance #3/B:100@SG #3/A:364@ND2
    9500 
    9501 Distance between copy of ranked_0.pdb #3/B CYS 100 SG and /A ASN 364 ND2:
    9502 3.782Å 
    9503 
    9504 > select #3/B:103@SG
    9505 
    9506 1 atom, 1 residue, 1 model selected 
    9507 
    9508 > select add #3/A:523@OD2
    9509 
    9510 2 atoms, 2 residues, 1 model selected 
    9511 
    9512 > distance #3/B:103@SG #3/A:523@OD2
    9513 
    9514 Distance between copy of ranked_0.pdb #3/B CYS 103 SG and /A ASP 523 OD2:
    9515 4.693Å 
    9516 
    9517 > select clear
    9518 
    9519 > select #3/B:106@OD2
    9520 
    9521 1 atom, 1 residue, 1 model selected 
    9522 
    9523 > select add #3/A:527@NZ
    9524 
    9525 2 atoms, 2 residues, 1 model selected 
    9526 
    9527 > distance #3/B:106@OD2 #3/A:527@NZ
    9528 
    9529 Distance between copy of ranked_0.pdb #3/B ASP 106 OD2 and /A LYS 527 NZ:
    9530 2.753Å 
    9531 
    9532 > select clear
    9533 
    9534 > select #3/B:110@OD2
    9535 
    9536 1 atom, 1 residue, 1 model selected 
    9537 
    9538 > select add #3/A:709@NE2
    9539 
    9540 2 atoms, 2 residues, 1 model selected 
    9541 
    9542 > distance #3/B:110@OD2 #3/A:709@NE2
    9543 
    9544 Distance between copy of ranked_0.pdb #3/B ASP 110 OD2 and /A HIS 709 NE2:
    9545 3.429Å 
    9546 
    9547 > select #3/A:704@ND2
    9548 
    9549 1 atom, 1 residue, 1 model selected 
    9550 
    9551 > select add #3/B:114@OE1
    9552 
    9553 2 atoms, 2 residues, 1 model selected 
    9554 
    9555 > distance #3/A:704@ND2 #3/B:114@OE1
    9556 
    9557 Distance between copy of ranked_0.pdb #3/A ASN 704 ND2 and /B GLN 114 OE1:
    9558 3.437Å 
    9559 
    9560 > select #3/B:116@OG
    9561 
    9562 1 atom, 1 residue, 1 model selected 
    9563 
    9564 > select add #3/A:704@ND2
    9565 
    9566 2 atoms, 2 residues, 1 model selected 
    9567 
    9568 > distance #3/B:116@OG #3/A:704@ND2
    9569 
    9570 Distance between copy of ranked_0.pdb #3/B SER 116 OG and /A ASN 704 ND2:
    9571 2.930Å 
    9572 
    9573 > select #3/B:118
    9574 
    9575 14 atoms, 14 bonds, 1 residue, 1 model selected 
    9576 
    9577 > select #3/B:118@N
    9578 
    9579 1 atom, 1 residue, 1 model selected 
    9580 
    9581 > select add #3/A:704@OD1
    9582 
    9583 2 atoms, 2 residues, 1 model selected 
    9584 
    9585 > distance #3/B:118@N #3/A:704@OD1
    9586 
    9587 Distance between copy of ranked_0.pdb #3/B PRO 118 N and /A ASN 704 OD1:
    9588 3.907Å 
    9589 
    9590 > select clear
    9591 
    9592 > select #3/B:119
    9593 
    9594 20 atoms, 20 bonds, 1 residue, 1 model selected 
    9595 
    9596 > select add #3/B:121
    9597 
    9598 44 atoms, 45 bonds, 2 residues, 1 model selected 
    9599 
    9600 > color sel orange
    9601 
    9602 > select clear
    9603 
    9604 > select #3/A:675
    9605 
    9606 15 atoms, 14 bonds, 1 residue, 1 model selected 
    9607 
    9608 > color sel byhetero
    9609 
    9610 > select clear
    9611 
    9612 [Repeated 1 time(s)]
    9613 
    9614 > color #3-4 byhetero
    9615 
    9616 > select #3/A:620
    9617 
    9618 19 atoms, 18 bonds, 1 residue, 1 model selected 
    9619 
    9620 > select #3/A:675
    9621 
    9622 15 atoms, 14 bonds, 1 residue, 1 model selected 
    9623 
    9624 > hide sel atoms
    9625 
    9626 > select #3/A:617
    9627 
    9628 14 atoms, 13 bonds, 1 residue, 1 model selected 
    9629 
    9630 > select #3/B:120
    9631 
    9632 16 atoms, 15 bonds, 1 residue, 1 model selected 
    9633 
    9634 > hide sel atoms
    9635 
    9636 > select clear
    9637 
    9638 > select #3/A:702
    9639 
    9640 14 atoms, 13 bonds, 1 residue, 1 model selected 
    9641 
    9642 > hide sel atoms
    9643 
    9644 Drag select of 33 atoms, 27 bonds, 10 residues 
    9645 
    9646 > hide sel atoms
    9647 
    9648 > select clear
    9649 
    9650 > select #3/B:111
    9651 
    9652 19 atoms, 18 bonds, 1 residue, 1 model selected 
    9653 
    9654 > color sel orange
    9655 
    9656 > select clear
    9657 
    9658 > select #3/B:108@OD1
    9659 
    9660 1 atom, 1 residue, 1 model selected 
    9661 
    9662 > undo
    9663 
    9664 [Repeated 9 time(s)]
    9665 
    9666 > select clear
    9667 
    9668 > undo
    9669 
    9670 [Repeated 1 time(s)]
    9671 
    9672 > select #3/A:599@NZ
    9673 
    9674 1 atom, 1 residue, 1 model selected 
    9675 
    9676 > undo
    9677 
    9678 [Repeated 1 time(s)]
    9679 
    9680 > select clear
    9681 
    9682 > select #3/A:599@NZ
    9683 
    9684 1 atom, 1 residue, 1 model selected 
    9685 
    9686 > undo
    9687 
    9688 [Repeated 3 time(s)]
    9689 
    9690 > select #3/B:108@OD1
    9691 
    9692 1 atom, 1 residue, 1 model selected 
    9693 
    9694 > undo
    9695 
    9696 [Repeated 1 time(s)]
    9697 
    9698 > select #3/B:111
    9699 
    9700 19 atoms, 18 bonds, 1 residue, 1 model selected 
    9701 
    9702 > color sel orange
    9703 
    9704 > select clear
    9705 
    9706 > select #3/A:599@NZ
    9707 
    9708 1 atom, 1 residue, 1 model selected 
    9709 
    9710 > select add #3/B:108@OD1
    9711 
    9712 2 atoms, 2 residues, 1 model selected 
    9713 
    9714 > distance #3/A:599@NZ #3/B:108@OD1
    9715 
    9716 Distance between copy of ranked_0.pdb #3/A LYS 599 NZ and /B ASP 108 OD1:
    9717 2.599Å 
    9718 
    9719 > select #3/A:700
    9720 
    9721 19 atoms, 18 bonds, 1 residue, 1 model selected 
    9722 
    9723 > hide sel atoms
    9724 
    9725 Drag select of 30 atoms, 25 bonds, 10 residues 
    9726 
    9727 > hide sel atoms
    9728 
    9729 > select clear
    9730 
    9731 > select #3/B:123
    9732 
    9733 14 atoms, 13 bonds, 1 residue, 1 model selected 
    9734 
    9735 > hide sel atoms
    9736 
    9737 > select clear
    9738 
    9739 > select #3/B:117
    9740 
    9741 14 atoms, 13 bonds, 1 residue, 1 model selected 
    9742 
    9743 > hide sel atoms
    9744 
    9745 > select clear
    9746 
    9747 > select #3/B:115
    9748 
    9749 14 atoms, 13 bonds, 1 residue, 1 model selected 
    9750 
    9751 > hide sel atoms
    9752 
    9753 > select #3/B:107
    9754 
    9755 24 atoms, 25 bonds, 1 residue, 1 model selected 
    9756 
    9757 > color sel orange
    9758 
    9759 > select clear
    9760 
    9761 > select #3/A:712@NH1
    9762 
    9763 1 atom, 1 residue, 1 model selected 
    9764 
    9765 > select add #3/B:105@OE2
    9766 
    9767 2 atoms, 2 residues, 1 model selected 
    9768 
    9769 > distance #3/A:712@NH1 #3/B:105@OE2
    9770 
    9771 Distance between copy of ranked_0.pdb #3/A ARG 712 NH1 and /B GLU 105 OE2:
    9772 2.704Å 
    9773 
    9774 > select #3/A:712@NH2
    9775 
    9776 1 atom, 1 residue, 1 model selected 
    9777 
    9778 > select add #3/B:105@OE1
    9779 
    9780 2 atoms, 2 residues, 1 model selected 
    9781 
    9782 > distance #3/A:712@NH2 #3/B:105@OE1
    9783 
    9784 Distance between copy of ranked_0.pdb #3/A ARG 712 NH2 and /B GLU 105 OE1:
    9785 2.703Å 
    9786 
    9787 > select clear
    9788 
    9789 [Repeated 1 time(s)]
    9790 
    9791 > select #3/B:102
    9792 
    9793 14 atoms, 14 bonds, 1 residue, 1 model selected 
    9794 
    9795 > select #3/A:362
    9796 
    9797 24 atoms, 23 bonds, 1 residue, 1 model selected 
    9798 
    9799 > hide sel atoms
    9800 
    9801 > select #3/B:102
    9802 
    9803 14 atoms, 14 bonds, 1 residue, 1 model selected 
    9804 
    9805 > hide sel atoms
    9806 
    9807 > select #3/B:101
    9808 
    9809 14 atoms, 14 bonds, 1 residue, 1 model selected 
    9810 
    9811 > hide sel atoms
    9812 
    9813 > select clear
    9814 
    9815 > select #3/B:104
    9816 
    9817 12 atoms, 11 bonds, 1 residue, 1 model selected 
    9818 
    9819 > hide sel atoms
    9820 
    9821 > select clear
    9822 
    9823 > select #3/B:98@CA
    9824 
    9825 1 atom, 1 residue, 1 model selected 
    9826 
    9827 > select #3/B:85
    9828 
    9829 14 atoms, 13 bonds, 1 residue, 1 model selected 
    9830 
    9831 > hide sel atoms
    9832 
    9833 > select clear
    9834 
    9835 > select #3/B:88
    9836 
    9837 19 atoms, 18 bonds, 1 residue, 1 model selected 
    9838 
    9839 > hide sel atoms
    9840 
    9841 > select #3/B:90
    9842 
    9843 17 atoms, 16 bonds, 1 residue, 1 model selected 
    9844 
    9845 > hide sel atoms
    9846 
    9847 > select #3/B:91
    9848 
    9849 15 atoms, 14 bonds, 1 residue, 1 model selected 
    9850 
    9851 > hide sel atoms
    9852 
    9853 > select #3/B:92
    9854 
    9855 14 atoms, 13 bonds, 1 residue, 1 model selected 
    9856 
    9857 > select #3/B:92
    9858 
    9859 14 atoms, 13 bonds, 1 residue, 1 model selected 
    9860 
    9861 > hide sel atoms
    9862 
    9863 > show #!2 models
    9864 
    9865 > hide #!2 models
    9866 
    9867 > select #3/B:93
    9868 
    9869 19 atoms, 18 bonds, 1 residue, 1 model selected 
    9870 
    9871 > color sel orange
    9872 
    9873 > select clear
    9874 
    9875 > show #!2 models
    9876 
    9877 > select #2/b
    9878 
    9879 2603 atoms, 2640 bonds, 167 residues, 1 model selected 
    9880 
    9881 > hide sel cartoons
    9882 
    9883 > select #2/A:527@CD
    9884 
    9885 1 atom, 1 residue, 1 model selected 
    9886 
    9887 > select #3/B:94
    9888 
    9889 10 atoms, 9 bonds, 1 residue, 1 model selected 
    9890 
    9891 > color sel orange
    9892 
    9893 > select clear
    9894 
    9895 > hide #!2 models
    9896 
    9897 > select #3/B:98
    9898 
    9899 24 atoms, 25 bonds, 1 residue, 1 model selected 
    9900 
    9901 > color sel orange
    9902 
    9903 > select clear
    9904 
    9905 > select #3/A:369
    9906 
    9907 11 atoms, 10 bonds, 1 residue, 1 model selected 
    9908 
    9909 > hide sel atoms
    9910 
    9911 > select clear
    9912 
    9913 > show #!2 models
    9914 
    9915 > select #3/B:96
    9916 
    9917 11 atoms, 10 bonds, 1 residue, 1 model selected 
    9918 
    9919 > select #3/B:96
    9920 
    9921 11 atoms, 10 bonds, 1 residue, 1 model selected 
    9922 
    9923 > hide sel atoms
    9924 
    9925 > select clear
    9926 
    9927 > select #3/B:101
    9928 
    9929 14 atoms, 14 bonds, 1 residue, 1 model selected 
    9930 
    9931 > hide #!2 models
    9932 
    9933 > show #!2 models
    9934 
    9935 > hide #!2 models
    9936 
    9937 > select #3/B:112
    9938 
    9939 24 atoms, 25 bonds, 1 residue, 1 model selected 
    9940 
    9941 > hide sel atoms
    9942 
    9943 > select #3/A:701
    9944 
    9945 14 atoms, 13 bonds, 1 residue, 1 model selected 
    9946 
    9947 > hide sel atoms
    9948 
    9949 > select clear
    9950 
    9951 > select #3/A:698
    9952 
    9953 11 atoms, 10 bonds, 1 residue, 1 model selected 
    9954 
    9955 > hide sel atoms
    9956 
    9957 > select clear
    9958 
    9959 > select #3/A:613
    9960 
    9961 22 atoms, 21 bonds, 1 residue, 1 model selected 
    9962 
    9963 > hide sel atoms
    9964 
    9965 > select clear
    9966 
    9967 > select #3/A:614
    9968 
    9969 14 atoms, 13 bonds, 1 residue, 1 model selected 
    9970 
    9971 > hide sel atoms
    9972 
    9973 > select clear
    9974 
    9975 > show #!2 models
    9976 
    9977 > select #3/B:35
    9978 
    9979 19 atoms, 18 bonds, 1 residue, 1 model selected 
    9980 
    9981 > hide sel atoms
    9982 
    9983 > select clear
    9984 
    9985 > hide #!2 models
    9986 
    9987 > select #3/B:53
    9988 
    9989 20 atoms, 20 bonds, 1 residue, 1 model selected 
    9990 
    9991 > color sel orange
    9992 
    9993 > select clear
    9994 
    9995 > select #3/B:74
    9996 
    9997 22 atoms, 21 bonds, 1 residue, 1 model selected 
    9998 
    9999 > hide sel atoms
    10000 
    10001 > select #3/B:78
    10002 
    10003 15 atoms, 14 bonds, 1 residue, 1 model selected 
    10004 
    10005 > hide sel atoms
    10006 
    10007 > select #3/B:69
    10008 
    10009 11 atoms, 10 bonds, 1 residue, 1 model selected 
    10010 
    10011 > hide sel atoms
    10012 
    10013 > select clear
    10014 
    10015 > select #3/B:70
    10016 
    10017 11 atoms, 10 bonds, 1 residue, 1 model selected 
    10018 
    10019 > hide sel atoms
    10020 
    10021 > select #3/B:79
    10022 
    10023 17 atoms, 16 bonds, 1 residue, 1 model selected 
    10024 
    10025 > hide sel atoms
    10026 
    10027 > select #3/B:75
    10028 
    10029 11 atoms, 10 bonds, 1 residue, 1 model selected 
    10030 
    10031 > hide sel atoms
    10032 
    10033 > select #3/B:83
    10034 
    10035 14 atoms, 13 bonds, 1 residue, 1 model selected 
    10036 
    10037 > hide sel atoms
    10038 
    10039 > select clear
    10040 
    10041 > select #3/A:754
    10042 
    10043 19 atoms, 18 bonds, 1 residue, 1 model selected 
    10044 
    10045 > hide sel atoms
    10046 
    10047 > select #3/B:82
    10048 
    10049 16 atoms, 15 bonds, 1 residue, 1 model selected 
    10050 
    10051 > show #!2 models
    10052 
    10053 > select #3/B:78
    10054 
    10055 15 atoms, 14 bonds, 1 residue, 1 model selected 
    10056 
    10057 > select #3/B:81
    10058 
    10059 16 atoms, 15 bonds, 1 residue, 1 model selected 
    10060 
    10061 > hide sel atoms
    10062 
    10063 > select #3/B:53@CA
    10064 
    10065 1 atom, 1 residue, 1 model selected 
    10066 
    10067 > hide sel atoms
    10068 
    10069 > select #3/B:53
    10070 
    10071 20 atoms, 20 bonds, 1 residue, 1 model selected 
    10072 
    10073 > hide sel atoms
    10074 
    10075 > select #2/A:622@HA
    10076 
    10077 1 atom, 1 residue, 1 model selected 
    10078 
    10079 > select #3/B:52
    10080 
    10081 14 atoms, 14 bonds, 1 residue, 1 model selected 
    10082 
    10083 > hide sel atoms
    10084 
    10085 > select #3/B:68
    10086 
    10087 19 atoms, 18 bonds, 1 residue, 1 model selected 
    10088 
    10089 > hide sel atoms
    10090 
    10091 > select clear
    10092 
    10093 Drag select of 33 atoms, 27 bonds, 7 residues 
    10094 
    10095 > hide sel atoms
    10096 
    10097 > select clear
    10098 
    10099 > select #3/B:8
    10100 
    10101 11 atoms, 10 bonds, 1 residue, 1 model selected 
    10102 
    10103 > hide sel atoms
    10104 
    10105 > select clear
    10106 
    10107 > select #3/B:9
    10108 
    10109 19 atoms, 18 bonds, 1 residue, 1 model selected 
    10110 
    10111 > hide sel atoms
    10112 
    10113 > select #3/B:28
    10114 
    10115 11 atoms, 10 bonds, 1 residue, 1 model selected 
    10116 
    10117 > hide sel atoms
    10118 
    10119 > select clear
    10120 
    10121 > select #3/B:12
    10122 
    10123 15 atoms, 14 bonds, 1 residue, 1 model selected 
    10124 
    10125 > hide sel atoms
    10126 
    10127 > select clear
    10128 
    10129 > select #3/B:10
    10130 
    10131 12 atoms, 11 bonds, 1 residue, 1 model selected 
    10132 
    10133 > hide sel atoms
    10134 
    10135 > select #3/B:13
    10136 
    10137 22 atoms, 21 bonds, 1 residue, 1 model selected 
    10138 
    10139 > hide sel atoms
    10140 
    10141 > select #3/B:31
    10142 
    10143 14 atoms, 14 bonds, 1 residue, 1 model selected 
    10144 
    10145 > color sel orange
    10146 
    10147 > select #2/A:625@HE2
    10148 
    10149 1 atom, 1 residue, 1 model selected 
    10150 
    10151 > select #3/B:30
    10152 
    10153 20 atoms, 20 bonds, 1 residue, 1 model selected 
    10154 
    10155 > hide sel atoms
    10156 
    10157 > select #3/B:25
    10158 
    10159 19 atoms, 18 bonds, 1 residue, 1 model selected 
    10160 
    10161 > hide sel atoms
    10162 
    10163 > select #3/B:33
    10164 
    10165 17 atoms, 17 bonds, 1 residue, 1 model selected 
    10166 
    10167 > hide sel atoms
    10168 
    10169 > select #3/B:18
    10170 
    10171 14 atoms, 14 bonds, 1 residue, 1 model selected 
    10172 
    10173 > hide sel atoms
    10174 
    10175 > select clear
    10176 
    10177 Drag select of 34 atoms, 30 bonds, 6 residues 
    10178 
    10179 > hide sel atoms
    10180 
    10181 > select clear
    10182 
    10183 > select #3/B:14
    10184 
    10185 19 atoms, 18 bonds, 1 residue, 1 model selected 
    10186 
    10187 > hide sel atoms
    10188 
    10189 > select #3/B:15
    10190 
    10191 19 atoms, 18 bonds, 1 residue, 1 model selected 
    10192 
    10193 > hide sel atoms
    10194 
    10195 > select #3/B:57
    10196 
    10197 17 atoms, 17 bonds, 1 residue, 1 model selected 
    10198 
    10199 > hide sel atoms
    10200 
    10201 > select #3/B:67
    10202 
    10203 17 atoms, 17 bonds, 1 residue, 1 model selected 
    10204 
    10205 > hide sel atoms
    10206 
    10207 Drag select of 3 atoms, 2 bonds, 2 residues 
    10208 
    10209 > hide sel atoms
    10210 
    10211 Drag select of 5 atoms, 6 bonds 
    10212 
    10213 > select #3/B:66
    10214 
    10215 17 atoms, 17 bonds, 1 residue, 1 model selected 
    10216 
    10217 > hide sel atoms
    10218 
    10219 > select clear
    10220 
    10221 > select #3/B:71
    10222 
    10223 11 atoms, 10 bonds, 1 residue, 1 model selected 
    10224 
    10225 > hide sel atoms
    10226 
    10227 > select #3/B:51
    10228 
    10229 11 atoms, 10 bonds, 1 residue, 1 model selected 
    10230 
    10231 > hide sel atoms
    10232 
    10233 > select clear
    10234 
    10235 > select #3/B:59
    10236 
    10237 16 atoms, 15 bonds, 1 residue, 1 model selected 
    10238 
    10239 > hide sel atoms
    10240 
    10241 > select #3/B:65
    10242 
    10243 11 atoms, 10 bonds, 1 residue, 1 model selected 
    10244 
    10245 > hide sel atoms
    10246 
    10247 > select #3/B:61
    10248 
    10249 24 atoms, 23 bonds, 1 residue, 1 model selected 
    10250 
    10251 > hide sel atoms
    10252 
    10253 > select #3/B:59
    10254 
    10255 16 atoms, 15 bonds, 1 residue, 1 model selected 
    10256 
    10257 > select #3/B:59
    10258 
    10259 16 atoms, 15 bonds, 1 residue, 1 model selected 
    10260 
    10261 > select #3/B:60
    10262 
    10263 14 atoms, 14 bonds, 1 residue, 1 model selected 
    10264 
    10265 > hide sel atoms
    10266 
    10267 > select #3/B:11
    10268 
    10269 14 atoms, 14 bonds, 1 residue, 1 model selected 
    10270 
    10271 > hide sel atoms
    10272 
    10273 Drag select of 29 atoms, 23 bonds, 9 residues 
    10274 
    10275 > hide sel atoms
    10276 
    10277 > select clear
    10278 
    10279 > select #3/B:64
    10280 
    10281 19 atoms, 18 bonds, 1 residue, 1 model selected 
    10282 
    10283 > hide sel atoms
    10284 
    10285 > select clear
    10286 
    10287 > select #3/B:49
    10288 
    10289 10 atoms, 9 bonds, 1 residue, 1 model selected 
    10290 
    10291 > hide sel atoms
    10292 
    10293 > select clear
    10294 
    10295 Drag select of 9 atoms, 8 bonds, 7 residues 
    10296 
    10297 > hide sel atoms
    10298 
    10299 > select clear
    10300 
    10301 > select #3/B:55
    10302 
    10303 10 atoms, 9 bonds, 1 residue, 1 model selected 
    10304 
    10305 > hide sel atoms
    10306 
    10307 > hide #!2 models
    10308 
    10309 > select #3/A:577@OG
    10310 
    10311 1 atom, 1 residue, 1 model selected 
    10312 
    10313 > select add #3/B:54@ND2
    10314 
    10315 2 atoms, 2 residues, 1 model selected 
    10316 
    10317 > distance #3/A:577@OG #3/B:54@ND2
    10318 
    10319 Distance between copy of ranked_0.pdb #3/A SER 577 OG and /B ASN 54 ND2:
    10320 3.842Å 
    10321 
    10322 > select clear
    10323 
    10324 > distance style color #241f31
    10325 
    10326 [Repeated 2 time(s)]
    10327 
    10328 > distance style color black
    10329 
    10330 [Repeated 2 time(s)]
    10331 
    10332 > select clear
    10333 
    10334 > select #3/A:622
    10335 
    10336 17 atoms, 16 bonds, 1 residue, 1 model selected 
    10337 
    10338 > hide sel atoms
    10339 
    10340 > select clear
    10341 
    10342 > select #3/A:579
    10343 
    10344 22 atoms, 21 bonds, 1 residue, 1 model selected 
    10345 
    10346 > hide sel atoms
    10347 
    10348 > select #3/A:625
    10349 
    10350 22 atoms, 21 bonds, 1 residue, 1 model selected 
    10351 
    10352 > hide sel atoms
    10353 
    10354 > show #!2 models
    10355 
    10356 > hide #!2 models
    10357 
    10358 > select #3/B:26
    10359 
    10360 24 atoms, 23 bonds, 1 residue, 1 model selected 
    10361 
    10362 > hide sel atoms
    10363 
    10364 > select #3/B:28
    10365 
    10366 11 atoms, 10 bonds, 1 residue, 1 model selected 
    10367 
    10368 > select #3/B:29
    10369 
    10370 24 atoms, 23 bonds, 1 residue, 1 model selected 
    10371 
    10372 > hide sel atoms
    10373 
    10374 > select clear
    10375 
    10376 Drag select of 17 atoms, 14 bonds, 4 residues 
    10377 
    10378 > hide sel atoms
    10379 
    10380 > select clear
    10381 
    10382 > show #!2 models
    10383 
    10384 > hide #!2 models
    10385 
    10386 > show #!1 models
    10387 
    10388 > show #!2 models
    10389 
    10390 > hide #!1 models
    10391 
    10392 > select #1/b
    10393 
    10394 2603 atoms, 2640 bonds, 167 residues, 1 model selected 
    10395 
    10396 > show #!1 models
    10397 
    10398 > hide sel cartoons
    10399 
    10400 > select clear
    10401 
    10402 > select #1/b
    10403 
    10404 2603 atoms, 2640 bonds, 167 residues, 1 model selected 
    10405 
    10406 > hide sel atoms
    10407 
    10408 > select clear
    10409 
    10410 > hide #!2 models
    10411 
    10412 > select #3/B:112
    10413 
    10414 24 atoms, 25 bonds, 1 residue, 1 model selected 
    10415 
    10416 > show sel atoms
    10417 
    10418 > open
    10419 > /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/Galaxy38-[MILI_GTSF1_pdb]/ranked_1.pdb
    10420 > /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/Galaxy38-[MILI_GTSF1_pdb]/ranked_2.pdb
    10421 
    10422 Chain information for ranked_1.pdb #5 
    10423 --- 
    10424 Chain | Description 
    10425 A | No description available 
    10426 B | No description available 
    10427  
    10428 Chain information for ranked_2.pdb #6 
    10429 --- 
    10430 Chain | Description 
    10431 A | No description available 
    10432 B | No description available 
    10433  
    10434 
    10435 > ui tool show Matchmaker
    10436 
    10437 > matchmaker #5-6 to #1
    10438 
    10439 Parameters 
    10440 --- 
    10441 Chain pairing | bb 
    10442 Alignment algorithm | Needleman-Wunsch 
    10443 Similarity matrix | BLOSUM-62 
    10444 SS fraction | 0.3 
    10445 Gap open (HH/SS/other) | 18/18/6 
    10446 Gap extend | 1 
    10447 SS matrix |  |  | H | S | O 
    10448 ---|---|---|--- 
    10449 H | 6 | -9 | -6 
    10450 S |  | 6 | -6 
    10451 O |  |  | 4 
    10452 Iteration cutoff | 2 
    10453  
    10454 Matchmaker ranked_0.pdb, chain A (#1) with ranked_1.pdb, chain A (#5),
    10455 sequence alignment score = 3986.5 
    10456 RMSD between 746 pruned atom pairs is 0.827 angstroms; (across all 763 pairs:
    10457 0.928) 
    10458  
    10459 Matchmaker ranked_0.pdb, chain A (#1) with ranked_2.pdb, chain A (#6),
    10460 sequence alignment score = 3999.7 
    10461 RMSD between 761 pruned atom pairs is 0.324 angstroms; (across all 763 pairs:
    10462 0.359) 
    10463  
    10464 
    10465 > matchmaker #5-6 to #1
    10466 
    10467 Parameters 
    10468 --- 
    10469 Chain pairing | bb 
    10470 Alignment algorithm | Needleman-Wunsch 
    10471 Similarity matrix | BLOSUM-62 
    10472 SS fraction | 0.3 
    10473 Gap open (HH/SS/other) | 18/18/6 
    10474 Gap extend | 1 
    10475 SS matrix |  |  | H | S | O 
    10476 ---|---|---|--- 
    10477 H | 6 | -9 | -6 
    10478 S |  | 6 | -6 
    10479 O |  |  | 4 
    10480 Iteration cutoff | 2 
    10481  
    10482 Matchmaker ranked_0.pdb, chain A (#1) with ranked_1.pdb, chain A (#5),
    10483 sequence alignment score = 3986.5 
    10484 RMSD between 746 pruned atom pairs is 0.827 angstroms; (across all 763 pairs:
    10485 0.928) 
    10486  
    10487 Matchmaker ranked_0.pdb, chain A (#1) with ranked_2.pdb, chain A (#6),
    10488 sequence alignment score = 3999.7 
    10489 RMSD between 761 pruned atom pairs is 0.324 angstroms; (across all 763 pairs:
    10490 0.359) 
    10491  
    10492 
    10493 > select #6/B:117
    10494 
    10495 14 atoms, 13 bonds, 1 residue, 1 model selected 
    10496 
    10497 > show sel atoms
    10498 
    10499 > hide sel atoms
    10500 
    10501 > select #5/B:116
    10502 
    10503 11 atoms, 10 bonds, 1 residue, 1 model selected 
    10504 
    10505 > show sel atoms
    10506 
    10507 > hide sel atoms
    10508 
    10509 > select #6/B:117
    10510 
    10511 14 atoms, 13 bonds, 1 residue, 1 model selected 
    10512 
    10513 > show sel atoms
    10514 
    10515 > hide sel atoms
    10516 
    10517 > hide #5 models
    10518 
    10519 > hide #6 models
    10520 
    10521 > view clip false
    10522 
    10523 Drag select of 90 atoms, 79 bonds, 19 residues 
    10524 
    10525 > hide sel atoms
    10526 
    10527 > select clear
    10528 
    10529 Drag select of 54 atoms, 44 bonds, 13 residues 
    10530 
    10531 > hide sel atoms
    10532 
    10533 > select clear
    10534 
    10535 > select #3/B:76
    10536 
    10537 11 atoms, 10 bonds, 1 residue, 1 model selected 
    10538 
    10539 > hide sel atoms
    10540 
    10541 > select #3/B:77
    10542 
    10543 19 atoms, 18 bonds, 1 residue, 1 model selected 
    10544 
    10545 > hide sel atoms
    10546 
    10547 > select clear
    10548 
    10549 > select #1/A:622@CB
    10550 
    10551 1 atom, 1 residue, 1 model selected 
    10552 
    10553 > show #!2 models
    10554 
    10555 > hide #!1 models
    10556 
    10557 > hide #!2 models
    10558 
    10559 > show #!2 models
    10560 
    10561 > hide #3 models
    10562 
    10563 > show #3 models
    10564 
    10565 > select #3/B:103
    10566 
    10567 11 atoms, 10 bonds, 1 residue, 1 model selected 
    10568 
    10569 > hide #!2 models
    10570 
    10571 > show #!2 models
    10572 
    10573 > select #2/A:635@CA
    10574 
    10575 1 atom, 1 residue, 1 model selected 
    10576 
    10577 > select #3/b:26,29,36,39,98,107,112
    10578 
    10579 164 atoms, 163 bonds, 7 residues, 1 model selected 
    10580 
    10581 > show sel atoms
    10582 
    10583 > color sel yellow
    10584 
    10585 > undo
    10586 
    10587 > hide H
    10588 
    10589 > select clear
    10590 
    10591 > hide #!2 models
    10592 
    10593 > select #3/b:26,29,36,39,98,107,112
    10594 
    10595 164 atoms, 163 bonds, 7 residues, 1 model selected 
    10596 
    10597 > select clear
    10598 
    10599 > show #!12 models
    10600 
    10601 > select /a:813
    10602 
    10603 8 atoms, 7 bonds, 1 residue, 1 model selected 
    10604 
    10605 > view sel
    10606 
    10607 No displayed objects specified. 
    10608 
    10609 > select /a:813
    10610 
    10611 8 atoms, 7 bonds, 1 residue, 1 model selected 
    10612 
    10613 > view sel
    10614 
    10615 No displayed objects specified. 
    10616 
    10617 > hide #!4 models
    10618 
    10619 > hide #3 models
    10620 
    10621 > show sel cartoons
    10622 
    10623 > select clear
    10624 
    10625 > show #!12 cartoons
    10626 
    10627 > select /a:813
    10628 
    10629 8 atoms, 7 bonds, 1 residue, 1 model selected 
    10630 
    10631 > view sel
    10632 
    10633 > show #3 models
    10634 
    10635 > hide #!12 models
    10636 
    10637 > show #!2 models
    10638 
    10639 > save
    10640 > /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/AF_GTSF1_complex_inter.cxs
    10641 
    10642 > color #1 white
    10643 
    10644 > hide #3 models
    10645 
    10646 > show #3 models
    10647 
    10648 > hide #!2 models
    10649 
    10650 > select #3/A:524
    10651 
    10652 19 atoms, 18 bonds, 1 residue, 1 model selected 
    10653 
    10654 > hide sel atoms
    10655 
    10656 > select #3/A:713
    10657 
    10658 19 atoms, 18 bonds, 1 residue, 1 model selected 
    10659 
    10660 > show #!4 models
    10661 
    10662 > select #3/A:716
    10663 
    10664 22 atoms, 21 bonds, 1 residue, 1 model selected 
    10665 
    10666 > show #!2 models
    10667 
    10668 > view clip false
    10669 
    10670 > select #3/b:26,29,36,39,98,107,112
    10671 
    10672 164 atoms, 163 bonds, 7 residues, 1 model selected 
    10673 
    10674 > hide #!2 models
    10675 
    10676 > show #!2 models
    10677 
    10678 > open
    10679 > /home/dell/shen_data/PIWI/GTSF1_Predictions/EFPIWI_EMGTSF1/Galaxy41-[EfPIWI_EmGTSF1_pdb]/ranked_0.pdb
    10680 
    10681 Chain information for ranked_0.pdb #7 
    10682 --- 
    10683 Chain | Description 
    10684 A | No description available 
    10685 B | No description available 
    10686  
    10687 
    10688 > close #7
    10689 
    10690 > open
    10691 > /home/dell/shen_data/PIWI/GTSF1_Predictions/EFPIWI_EMGTSF1/Galaxy41-[EfPIWI_EmGTSF1_pdb]/AF_EFPIWI_EMGTSF1_0.pdb
    10692 
    10693 Chain information for AF_EFPIWI_EMGTSF1_0.pdb #7 
    10694 --- 
    10695 Chain | Description 
    10696 A | No description available 
    10697 B | No description available 
    10698  
    10699 
    10700 > ui tool show Matchmaker
    10701 
    10702 > matchmaker #7 to #1
    10703 
    10704 Parameters 
    10705 --- 
    10706 Chain pairing | bb 
    10707 Alignment algorithm | Needleman-Wunsch 
    10708 Similarity matrix | BLOSUM-62 
    10709 SS fraction | 0.3 
    10710 Gap open (HH/SS/other) | 18/18/6 
    10711 Gap extend | 1 
    10712 SS matrix |  |  | H | S | O 
    10713 ---|---|---|--- 
    10714 H | 6 | -9 | -6 
    10715 S |  | 6 | -6 
    10716 O |  |  | 4 
    10717 Iteration cutoff | 2 
    10718  
    10719 Matchmaker ranked_0.pdb, chain A (#1) with AF_EFPIWI_EMGTSF1_0.pdb, chain A
    10720 (#7), sequence alignment score = 2323.4 
    10721 RMSD between 645 pruned atom pairs is 0.925 angstroms; (across all 757 pairs:
    10722 1.863) 
    10723  
    10724 
    10725 > matchmaker #7 to #1
    10726 
    10727 Parameters 
    10728 --- 
    10729 Chain pairing | bb 
    10730 Alignment algorithm | Needleman-Wunsch 
    10731 Similarity matrix | BLOSUM-62 
    10732 SS fraction | 0.3 
    10733 Gap open (HH/SS/other) | 18/18/6 
    10734 Gap extend | 1 
    10735 SS matrix |  |  | H | S | O 
    10736 ---|---|---|--- 
    10737 H | 6 | -9 | -6 
    10738 S |  | 6 | -6 
    10739 O |  |  | 4 
    10740 Iteration cutoff | 2 
    10741  
    10742 Matchmaker ranked_0.pdb, chain A (#1) with AF_EFPIWI_EMGTSF1_0.pdb, chain A
    10743 (#7), sequence alignment score = 2323.4 
    10744 RMSD between 645 pruned atom pairs is 0.925 angstroms; (across all 757 pairs:
    10745 1.863) 
    10746  
    10747 
    10748 > hide #!2 models
    10749 
    10750 > show #5 models
    10751 
    10752 > hide #5 models
    10753 
    10754 > show #6 models
    10755 
    10756 > hide #6 models
    10757 
    10758 > close #5-6
    10759 
    10760 > hide #3 models
    10761 
    10762 > show #3 models
    10763 
    10764 > hide #3 models
    10765 
    10766 > show #3 models
    10767 
    10768 > hide #3 models
    10769 
    10770 > show #!1 models
    10771 
    10772 > hide #!1 models
    10773 
    10774 > show #3 models
    10775 
    10776 > select #3/B:26
    10777 
    10778 24 atoms, 23 bonds, 1 residue, 1 model selected 
    10779 
    10780 > select #7/B:21
    10781 
    10782 16 atoms, 15 bonds, 1 residue, 1 model selected 
    10783 
    10784 > select #7/B:22
    10785 
    10786 17 atoms, 16 bonds, 1 residue, 1 model selected 
    10787 
    10788 > show sel atoms
    10789 
    10790 > delete #7/H
    10791 
    10792 > delete #7/HG
    10793 
    10794 > select #7/B:22@HG2
    10795 
    10796 1 atom, 1 residue, 1 model selected 
    10797 
    10798 > delete #7/B:HG
    10799 
    10800 > delete #7/B:@HG
    10801 
    10802 Missing or invalid "atoms" argument: only initial part "#7/B" of atom
    10803 specifier valid 
    10804 
    10805 > select clear
    10806 
    10807 > select #7/B:22
    10808 
    10809 17 atoms, 16 bonds, 1 residue, 1 model selected 
    10810 
    10811 > hide H
    10812 
    10813 > select #3/A:711
    10814 
    10815 17 atoms, 16 bonds, 1 residue, 1 model selected 
    10816 
    10817 > select #7/B:25
    10818 
    10819 24 atoms, 23 bonds, 1 residue, 1 model selected 
    10820 
    10821 > show sel atoms
    10822 
    10823 > select clear
    10824 
    10825 > view sel
    10826 
    10827 > select #7/B:28
    10828 
    10829 21 atoms, 21 bonds, 1 residue, 1 model selected 
    10830 
    10831 > select #7/B:29
    10832 
    10833 17 atoms, 17 bonds, 1 residue, 1 model selected 
    10834 
    10835 > select #7/B:28
    10836 
    10837 21 atoms, 21 bonds, 1 residue, 1 model selected 
    10838 
    10839 > select #7/B:27
    10840 
    10841 14 atoms, 14 bonds, 1 residue, 1 model selected 
    10842 
    10843 > select #7/B:28
    10844 
    10845 21 atoms, 21 bonds, 1 residue, 1 model selected 
    10846 
    10847 > show sel atoms
    10848 
    10849 > select #7/B:32
    10850 
    10851 22 atoms, 21 bonds, 1 residue, 1 model selected 
    10852 
    10853 > show sel atoms
    10854 
    10855 > select #7/B:35
    10856 
    10857 22 atoms, 21 bonds, 1 residue, 1 model selected 
    10858 
    10859 > show sel atoms
    10860 
    10861 > hide H
    10862 
    10863 > select clear
    10864 
    10865 > select #7/B:52
    10866 
    10867 24 atoms, 23 bonds, 1 residue, 1 model selected 
    10868 
    10869 > show sel atoms
    10870 
    10871 > select #7/A:582
    10872 
    10873 17 atoms, 17 bonds, 1 residue, 1 model selected 
    10874 
    10875 > show sel atoms
    10876 
    10877 > select #7/A:583
    10878 
    10879 15 atoms, 14 bonds, 1 residue, 1 model selected 
    10880 
    10881 > show sel atoms
    10882 
    10883 > hide H
    10884 
    10885 > select clear
    10886 
    10887 > select #7/A:617
    10888 
    10889 24 atoms, 23 bonds, 1 residue, 1 model selected 
    10890 
    10891 > show sel atoms
    10892 
    10893 > select #7/A:586
    10894 
    10895 19 atoms, 18 bonds, 1 residue, 1 model selected 
    10896 
    10897 > show sel atoms
    10898 
    10899 > select #7/A:570
    10900 
    10901 24 atoms, 23 bonds, 1 residue, 1 model selected 
    10902 
    10903 > show sel atoms
    10904 
    10905 > select #7/A:568
    10906 
    10907 21 atoms, 21 bonds, 1 residue, 1 model selected 
    10908 
    10909 > show sel atoms
    10910 
    10911 > select #7/B:79
    10912 
    10913 11 atoms, 10 bonds, 1 residue, 1 model selected 
    10914 
    10915 > show sel atoms
    10916 
    10917 > select #7/B:76
    10918 
    10919 17 atoms, 16 bonds, 1 residue, 1 model selected 
    10920 
    10921 > show sel atoms
    10922 
    10923 > select #3/B:77
    10924 
    10925 19 atoms, 18 bonds, 1 residue, 1 model selected 
    10926 
    10927 > select #7/B:72
    10928 
    10929 24 atoms, 23 bonds, 1 residue, 1 model selected 
    10930 
    10931 > show sel atoms
    10932 
    10933 > select #7/B:69
    10934 
    10935 11 atoms, 10 bonds, 1 residue, 1 model selected 
    10936 
    10937 > show sel atoms
    10938 
    10939 > hide H
    10940 
    10941 > hide #3 models
    10942 
    10943 > select #7/A:571
    10944 
    10945 14 atoms, 13 bonds, 1 residue, 1 model selected 
    10946 
    10947 > show sel atoms
    10948 
    10949 > select #7/A:572
    10950 
    10951 10 atoms, 9 bonds, 1 residue, 1 model selected 
    10952 
    10953 > show sel atoms
    10954 
    10955 > select #7/A:571
    10956 
    10957 14 atoms, 13 bonds, 1 residue, 1 model selected 
    10958 
    10959 > hide sel atoms
    10960 
    10961 > show #3 models
    10962 
    10963 > select #7/A:594
    10964 
    10965 22 atoms, 21 bonds, 1 residue, 1 model selected 
    10966 
    10967 > show sel atoms
    10968 
    10969 > select #7/A:760
    10970 
    10971 15 atoms, 14 bonds, 1 residue, 1 model selected 
    10972 
    10973 > show sel atoms
    10974 
    10975 > select #7/A:597
    10976 
    10977 15 atoms, 14 bonds, 1 residue, 1 model selected 
    10978 
    10979 > show sel atoms
    10980 
    10981 > select #7/A:598
    10982 
    10983 17 atoms, 16 bonds, 1 residue, 1 model selected 
    10984 
    10985 > show sel atoms
    10986 
    10987 > select #7/A:560
    10988 
    10989 14 atoms, 13 bonds, 1 residue, 1 model selected 
    10990 
    10991 > show sel atoms
    10992 
    10993 > hide #3 models
    10994 
    10995 > hide H
    10996 
    10997 > select clear
    10998 
    10999 > show #3 models
    11000 
    11001 > select #7/A:566
    11002 
    11003 24 atoms, 23 bonds, 1 residue, 1 model selected 
    11004 
    11005 > show sel atoms
    11006 
    11007 > select clear
    11008 
    11009 > select #7/A:565
    11010 
    11011 14 atoms, 13 bonds, 1 residue, 1 model selected 
    11012 
    11013 > show sel atoms
    11014 
    11015 > select #7/A:563
    11016 
    11017 11 atoms, 10 bonds, 1 residue, 1 model selected 
    11018 
    11019 > show sel atoms
    11020 
    11021 > select #7/B:102
    11022 
    11023 14 atoms, 14 bonds, 1 residue, 1 model selected 
    11024 
    11025 > show sel atoms
    11026 
    11027 > select #7/B:105
    11028 
    11029 11 atoms, 10 bonds, 1 residue, 1 model selected 
    11030 
    11031 > show sel atoms
    11032 
    11033 > select #7/A:529
    11034 
    11035 15 atoms, 14 bonds, 1 residue, 1 model selected 
    11036 
    11037 > show sel atoms
    11038 
    11039 > select #7/A:531
    11040 
    11041 14 atoms, 14 bonds, 1 residue, 1 model selected 
    11042 
    11043 > show sel atoms
    11044 
    11045 > select #7/A:721
    11046 
    11047 22 atoms, 21 bonds, 1 residue, 1 model selected 
    11048 
    11049 > show sel atoms
    11050 
    11051 > select #7/A:718
    11052 
    11053 19 atoms, 18 bonds, 1 residue, 1 model selected 
    11054 
    11055 > select #7/A:717
    11056 
    11057 24 atoms, 23 bonds, 1 residue, 1 model selected 
    11058 
    11059 > show sel atoms
    11060 
    11061 > select #7/A:718
    11062 
    11063 19 atoms, 18 bonds, 1 residue, 1 model selected 
    11064 
    11065 > show sel atoms
    11066 
    11067 > select #7/A:714
    11068 
    11069 17 atoms, 17 bonds, 1 residue, 1 model selected 
    11070 
    11071 > show sel atoms
    11072 
    11073 > select #7/A:712
    11074 
    11075 14 atoms, 14 bonds, 1 residue, 1 model selected 
    11076 
    11077 > select #7/A:711
    11078 
    11079 22 atoms, 21 bonds, 1 residue, 1 model selected 
    11080 
    11081 > show sel atoms
    11082 
    11083 > select #7/B:113
    11084 
    11085 21 atoms, 21 bonds, 1 residue, 1 model selected 
    11086 
    11087 > show sel atoms
    11088 
    11089 > select #7/B:113
    11090 
    11091 21 atoms, 21 bonds, 1 residue, 1 model selected 
    11092 
    11093 > select #7/B:109
    11094 
    11095 24 atoms, 25 bonds, 1 residue, 1 model selected 
    11096 
    11097 > show sel atoms
    11098 
    11099 > select #7/A:532
    11100 
    11101 19 atoms, 18 bonds, 1 residue, 1 model selected 
    11102 
    11103 > show sel atoms
    11104 
    11105 > select #7/B:110
    11106 
    11107 15 atoms, 14 bonds, 1 residue, 1 model selected 
    11108 
    11109 > show sel atoms
    11110 
    11111 > select #7/B:114
    11112 
    11113 10 atoms, 9 bonds, 1 residue, 1 model selected 
    11114 
    11115 > show sel atoms
    11116 
    11117 > select #7/B:115
    11118 
    11119 17 atoms, 16 bonds, 1 residue, 1 model selected 
    11120 
    11121 > show sel atoms
    11122 
    11123 > select clear
    11124 
    11125 [Repeated 1 time(s)]
    11126 
    11127 > select #7/B:114
    11128 
    11129 10 atoms, 9 bonds, 1 residue, 1 model selected 
    11130 
    11131 > hide sel atoms
    11132 
    11133 > select clear
    11134 
    11135 > hide H
    11136 
    11137 > select clear
    11138 
    11139 Drag select of 3 residues 
    11140 
    11141 > select up
    11142 
    11143 2300 atoms, 2326 bonds, 153 residues, 1 model selected 
    11144 
    11145 > select up
    11146 
    11147 4491 atoms, 4538 bonds, 282 residues, 1 model selected 
    11148 
    11149 > select up
    11150 
    11151 16932 atoms, 17114 bonds, 1050 residues, 1 model selected 
    11152 
    11153 > select down
    11154 
    11155 4491 atoms, 4538 bonds, 282 residues, 1 model selected 
    11156 
    11157 > color sel cyan
    11158 
    11159 > select clear
    11160 
    11161 > color #3-4,7 byhetero
    11162 
    11163 > select clear
    11164 
    11165 > select #7/A:605
    11166 
    11167 24 atoms, 23 bonds, 1 residue, 1 model selected 
    11168 
    11169 > show sel atoms
    11170 
    11171 > hide H
    11172 
    11173 > select #7/B:110@OE1
    11174 
    11175 1 atom, 1 residue, 1 model selected 
    11176 
    11177 > select add #7/A:605@NH1
    11178 
    11179 2 atoms, 2 residues, 1 model selected 
    11180 
    11181 > distance #7/B:110@OE1 #7/A:605@NH1
    11182 
    11183 Distance between AF_EFPIWI_EMGTSF1_0.pdb #7/B GLU 110 OE1 and /A ARG 605 NH1:
    11184 2.642Å 
    11185 
    11186 > select clear
    11187 
    11188 > select #3/B:109
    11189 
    11190 22 atoms, 21 bonds, 1 residue, 1 model selected 
    11191 
    11192 > hide sel atoms
    11193 
    11194 Drag select of 12 atoms, 10 bonds, 4 residues 
    11195 
    11196 > select clear
    11197 
    11198 Drag select of 12 atoms, 10 bonds, 2 residues 
    11199 
    11200 > hide sel atoms
    11201 
    11202 > select clear
    11203 
    11204 > hide #3 models
    11205 
    11206 > select #7/A:529@OE1
    11207 
    11208 1 atom, 1 residue, 1 model selected 
    11209 
    11210 > select add #7/B:105@OG
    11211 
    11212 2 atoms, 2 residues, 1 model selected 
    11213 
    11214 > distance #7/A:529@OE1 #7/B:105@OG
    11215 
    11216 Distance between AF_EFPIWI_EMGTSF1_0.pdb #7/A GLU 529 OE1 and /B SER 105 OG:
    11217 2.572Å 
    11218 
    11219 > select #7/B:109
    11220 
    11221 24 atoms, 25 bonds, 1 residue, 1 model selected 
    11222 
    11223 > color sel orange
    11224 
    11225 > select clear
    11226 
    11227 > show #3 models
    11228 
    11229 > select #7/B:100
    11230 
    11231 24 atoms, 25 bonds, 1 residue, 1 model selected 
    11232 
    11233 > show sel atoms
    11234 
    11235 > color sel orange
    11236 
    11237 > select clear
    11238 
    11239 > select #3/B:94
    11240 
    11241 10 atoms, 9 bonds, 1 residue, 1 model selected 
    11242 
    11243 > hide sel atoms
    11244 
    11245 > select #3/B:93
    11246 
    11247 19 atoms, 18 bonds, 1 residue, 1 model selected 
    11248 
    11249 > hide sel atoms
    11250 
    11251 Drag select of 14 atoms, 10 bonds, 12 residues 
    11252 
    11253 > hide sel atoms
    11254 
    11255 > select clear
    11256 
    11257 > hide #3 models
    11258 
    11259 > select #7/A:590
    11260 
    11261 10 atoms, 9 bonds, 1 residue, 1 model selected 
    11262 
    11263 > show sel atoms
    11264 
    11265 > hide sel atoms
    11266 
    11267 > select #7/A:586
    11268 
    11269 19 atoms, 18 bonds, 1 residue, 1 model selected 
    11270 
    11271 > select #7/B:73
    11272 
    11273 19 atoms, 18 bonds, 1 residue, 1 model selected 
    11274 
    11275 > show sel atoms
    11276 
    11277 > hide H
    11278 
    11279 > select #7/B:76
    11280 
    11281 17 atoms, 16 bonds, 1 residue, 1 model selected 
    11282 
    11283 > hide sel atoms
    11284 
    11285 > select #7/A:570
    11286 
    11287 24 atoms, 23 bonds, 1 residue, 1 model selected 
    11288 
    11289 > hide sel atoms
    11290 
    11291 > select #7/A:568
    11292 
    11293 21 atoms, 21 bonds, 1 residue, 1 model selected 
    11294 
    11295 > hide sel atoms
    11296 
    11297 > select #7/A:560
    11298 
    11299 14 atoms, 13 bonds, 1 residue, 1 model selected 
    11300 
    11301 > hide sel atoms
    11302 
    11303 > select clear
    11304 
    11305 > show #3 models
    11306 
    11307 > select #7/B:97
    11308 
    11309 16 atoms, 15 bonds, 1 residue, 1 model selected 
    11310 
    11311 > show sel atoms
    11312 
    11313 > hide sel atoms
    11314 
    11315 > select clear
    11316 
    11317 > select #7/B:98
    11318 
    11319 14 atoms, 13 bonds, 1 residue, 1 model selected 
    11320 
    11321 > show sel atoms
    11322 
    11323 > hide #3 models
    11324 
    11325 > select #7/B:97
    11326 
    11327 16 atoms, 15 bonds, 1 residue, 1 model selected 
    11328 
    11329 > select #7/B:97
    11330 
    11331 16 atoms, 15 bonds, 1 residue, 1 model selected 
    11332 
    11333 > show sel atoms
    11334 
    11335 > select #7/B:96
    11336 
    11337 14 atoms, 14 bonds, 1 residue, 1 model selected 
    11338 
    11339 > show sel atoms
    11340 
    11341 > select #7/B:98
    11342 
    11343 14 atoms, 13 bonds, 1 residue, 1 model selected 
    11344 
    11345 > hide (sel-residues & (protein|nucleic)) target a
    11346 
    11347 > cartoon hide sel-residues
    11348 
    11349 > show (sel-residues & backbone) target ab
    11350 
    11351 > select #7/B:98@N
    11352 
    11353 1 atom, 1 residue, 1 model selected 
    11354 
    11355 > select add #7/A:566@NH2
    11356 
    11357 2 atoms, 2 residues, 1 model selected 
    11358 
    11359 > distance #7/B:98@N #7/A:566@NH2
    11360 
    11361 Distance between AF_EFPIWI_EMGTSF1_0.pdb #7/B THR 98 N and /A ARG 566 NH2:
    11362 3.813Å 
    11363 
    11364 > select clear
    11365 
    11366 > select #7/B:96
    11367 
    11368 14 atoms, 14 bonds, 1 residue, 1 model selected 
    11369 
    11370 > hide sel atoms
    11371 
    11372 > select #7/B:97
    11373 
    11374 16 atoms, 15 bonds, 1 residue, 1 model selected 
    11375 
    11376 > hide sel atoms
    11377 
    11378 > select clear
    11379 
    11380 > show #3 models
    11381 
    11382 > select #7/A:396
    11383 
    11384 19 atoms, 18 bonds, 1 residue, 1 model selected 
    11385 
    11386 > show sel atoms
    11387 
    11388 > select #7/A:372
    11389 
    11390 19 atoms, 18 bonds, 1 residue, 1 model selected 
    11391 
    11392 > select #7/A:372
    11393 
    11394 19 atoms, 18 bonds, 1 residue, 1 model selected 
    11395 
    11396 > show sel atoms
    11397 
    11398 > select #7/A:373
    11399 
    11400 20 atoms, 20 bonds, 1 residue, 1 model selected 
    11401 
    11402 > show sel atoms
    11403 
    11404 > select #3/B:97
    11405 
    11406 14 atoms, 13 bonds, 1 residue, 1 model selected 
    11407 
    11408 > hide sel atoms
    11409 
    11410 > select clear
    11411 
    11412 > select #3/B:99
    11413 
    11414 17 atoms, 16 bonds, 1 residue, 1 model selected 
    11415 
    11416 > hide sel atoms
    11417 
    11418 > select clear
    11419 
    11420 > hide H
    11421 
    11422 > hide #3 models
    11423 
    11424 > show #3 models
    11425 
    11426 > select #7/A:374
    11427 
    11428 22 atoms, 21 bonds, 1 residue, 1 model selected 
    11429 
    11430 > show sel atoms
    11431 
    11432 Drag select of 2 atoms, 2 bonds, 3 residues 
    11433 
    11434 > select #7/A:374
    11435 
    11436 22 atoms, 21 bonds, 1 residue, 1 model selected 
    11437 
    11438 > hide sel atoms
    11439 
    11440 > select #3/A:366
    11441 
    11442 24 atoms, 23 bonds, 1 residue, 1 model selected 
    11443 
    11444 > hide sel atoms
    11445 
    11446 > select clear
    11447 
    11448 > select #7/B:96
    11449 
    11450 14 atoms, 14 bonds, 1 residue, 1 model selected 
    11451 
    11452 > show sel atoms
    11453 
    11454 > hide H
    11455 
    11456 > select clear
    11457 
    11458 > select #3/B:95
    11459 
    11460 15 atoms, 14 bonds, 1 residue, 1 model selected 
    11461 
    11462 > hide sel atoms
    11463 
    11464 > select #7/B:79@CA
    11465 
    11466 1 atom, 1 residue, 1 model selected 
    11467 
    11468 > hide sel atoms
    11469 
    11470 > select clear
    11471 
    11472 > select #7/B:79
    11473 
    11474 11 atoms, 10 bonds, 1 residue, 1 model selected 
    11475 
    11476 > hide sel atoms
    11477 
    11478 > select clear
    11479 
    11480 > hide #3 models
    11481 
    11482 > select #7/A:571
    11483 
    11484 14 atoms, 13 bonds, 1 residue, 1 model selected 
    11485 
    11486 > select #7/B:72@NH2
    11487 
    11488 1 atom, 1 residue, 1 model selected 
    11489 
    11490 > select add #7/A:583@OE1
    11491 
    11492 2 atoms, 2 residues, 1 model selected 
    11493 
    11494 > distance #7/B:72@NH2 #7/A:583@OE1
    11495 
    11496 Distance between AF_EFPIWI_EMGTSF1_0.pdb #7/B ARG 72 NH2 and /A GLU 583 OE1:
    11497 2.750Å 
    11498 
    11499 > select clear
    11500 
    11501 > distance style color #241f31
    11502 
    11503 [Repeated 2 time(s)]
    11504 
    11505 > distance style color black
    11506 
    11507 [Repeated 2 time(s)]
    11508 
    11509 > select #7/B:69
    11510 
    11511 11 atoms, 10 bonds, 1 residue, 1 model selected 
    11512 
    11513 > hide sel atoms
    11514 
    11515 > select clear
    11516 
    11517 > select #7/B:49
    11518 
    11519 20 atoms, 20 bonds, 1 residue, 1 model selected 
    11520 
    11521 > show sel atoms
    11522 
    11523 > hide H
    11524 
    11525 > select clear
    11526 
    11527 > select #7/A:575
    11528 
    11529 15 atoms, 14 bonds, 1 residue, 1 model selected 
    11530 
    11531 > show sel atoms
    11532 
    11533 > hide H
    11534 
    11535 > select #7/A:575@OE1
    11536 
    11537 1 atom, 1 residue, 1 model selected 
    11538 
    11539 > select add #7/B:52@NH1
    11540 
    11541 2 atoms, 2 residues, 1 model selected 
    11542 
    11543 > distance #7/A:575@OE1 #7/B:52@NH1
    11544 
    11545 Distance between AF_EFPIWI_EMGTSF1_0.pdb #7/A GLU 575 OE1 and /B ARG 52 NH1:
    11546 2.707Å 
    11547 
    11548 > select #7/A:582
    11549 
    11550 17 atoms, 17 bonds, 1 residue, 1 model selected 
    11551 
    11552 > hide sel atoms
    11553 
    11554 > show #3 models
    11555 
    11556 > select #3/A:569@SD
    11557 
    11558 1 atom, 1 residue, 1 model selected 
    11559 
    11560 > select add #3/B:56@NH2
    11561 
    11562 2 atoms, 2 residues, 1 model selected 
    11563 
    11564 > select #3/A:569
    11565 
    11566 17 atoms, 16 bonds, 1 residue, 1 model selected 
    11567 
    11568 > hide sel atoms
    11569 
    11570 > select clear
    11571 
    11572 > select #7/A:582
    11573 
    11574 17 atoms, 17 bonds, 1 residue, 1 model selected 
    11575 
    11576 > hide sel atoms
    11577 
    11578 > show sel atoms
    11579 
    11580 > hide H
    11581 
    11582 > select #3/A:545
    11583 
    11584 24 atoms, 23 bonds, 1 residue, 1 model selected 
    11585 
    11586 > hide sel atoms
    11587 
    11588 > select clear
    11589 
    11590 > undo
    11591 
    11592 > show sel atoms
    11593 
    11594 > hide sel atoms
    11595 
    11596 > select clear
    11597 
    11598 Drag select of 7 atoms, 5 bonds, 7 residues 
    11599 
    11600 > select clear
    11601 
    11602 [Repeated 1 time(s)]Drag select of 2 atoms, 2 residues, 1 bonds 
    11603 
    11604 > select #7/A:563
    11605 
    11606 11 atoms, 10 bonds, 1 residue, 1 model selected 
    11607 
    11608 > hide sel atoms
    11609 
    11610 > select #3/A:557
    11611 
    11612 14 atoms, 13 bonds, 1 residue, 1 model selected 
    11613 
    11614 > hide sel atoms
    11615 
    11616 > select clear
    11617 
    11618 > select #3/A:518
    11619 
    11620 15 atoms, 14 bonds, 1 residue, 1 model selected 
    11621 
    11622 > select #7/A:524
    11623 
    11624 15 atoms, 14 bonds, 1 residue, 1 model selected 
    11625 
    11626 > show sel atoms
    11627 
    11628 > select clear
    11629 
    11630 Drag select of 12 atoms, 14 bonds, 4 residues 
    11631 
    11632 > hide sel atoms
    11633 
    11634 > select clear
    11635 
    11636 Drag select of 2 atoms, 2 residues 
    11637 
    11638 > hide sel atoms
    11639 
    11640 > select clear
    11641 
    11642 [Repeated 1 time(s)]Drag select of 5 atoms, 4 bonds, 10 residues 
    11643 
    11644 > hide sel atoms
    11645 
    11646 > select clear
    11647 
    11648 Drag select of 3 atoms, 2 bonds, 2 residues 
    11649 
    11650 > select #7/A:721
    11651 
    11652 22 atoms, 21 bonds, 1 residue, 1 model selected 
    11653 
    11654 > hide sel atoms
    11655 
    11656 > select #7/A:721
    11657 
    11658 22 atoms, 21 bonds, 1 residue, 1 model selected 
    11659 
    11660 > select #3/A:716
    11661 
    11662 22 atoms, 21 bonds, 1 residue, 1 model selected 
    11663 
    11664 > hide sel atoms
    11665 
    11666 > select clear
    11667 
    11668 > select #3/A:706
    11669 
    11670 11 atoms, 10 bonds, 1 residue, 1 model selected 
    11671 
    11672 > hide sel atoms
    11673 
    11674 > select clear
    11675 
    11676 > hide #3 models
    11677 
    11678 > select #7/B:112
    11679 
    11680 15 atoms, 14 bonds, 1 residue, 1 model selected 
    11681 
    11682 > show sel atoms
    11683 
    11684 > select #7/B:112@OE2
    11685 
    11686 1 atom, 1 residue, 1 model selected 
    11687 
    11688 > select add #7/A:711@NZ
    11689 
    11690 2 atoms, 2 residues, 1 model selected 
    11691 
    11692 > distance #7/B:112@OE2 #7/A:711@NZ
    11693 
    11694 Distance between AF_EFPIWI_EMGTSF1_0.pdb #7/B GLU 112 OE2 and /A LYS 711 NZ:
    11695 2.846Å 
    11696 
    11697 > select clear
    11698 
    11699 > select #7/A:710
    11700 
    11701 19 atoms, 18 bonds, 1 residue, 1 model selected 
    11702 
    11703 > select #7/A:710
    11704 
    11705 19 atoms, 18 bonds, 1 residue, 1 model selected 
    11706 
    11707 > show #!2 models
    11708 
    11709 > hide #!2 models
    11710 
    11711 > combine #7
    11712 
    11713 > hide #7 models
    11714 
    11715 > view clip false
    11716 
    11717 > coulombic #5
    11718 
    11719 Using Amber 20 recommended default charges and atom types for standard
    11720 residues 
    11721 Coulombic values for copy of AF_EFPIWI_EMGTSF1_0.pdb_A SES surface #5.1:
    11722 minimum, -14.15, mean 2.15, maximum 20.16 
    11723 Coulombic values for copy of AF_EFPIWI_EMGTSF1_0.pdb_B SES surface #5.2:
    11724 minimum, -15.77, mean 0.23, maximum 14.05 
    11725 To also show corresponding color key, enter the above coulombic command and
    11726 add key true 
    11727 Drag select of copy of AF_EFPIWI_EMGTSF1_0.pdb_B SES surface, 9709 of 545966
    11728 triangles, 5 residues 
    11729 
    11730 > select up
    11731 
    11732 2300 atoms, 2326 bonds, 153 residues, 2 models selected 
    11733 
    11734 > hide sel surfaces
    11735 
    11736 > select up
    11737 
    11738 4491 atoms, 4538 bonds, 282 residues, 2 models selected 
    11739 
    11740 > hide sel surfaces
    11741 
    11742 Drag select of copy of AF_EFPIWI_EMGTSF1_0.pdb_A SES surface, 629 of 858262
    11743 triangles, 3 residues 
    11744 
    11745 > select #5/B:76
    11746 
    11747 17 atoms, 16 bonds, 1 residue, 1 model selected 
    11748 
    11749 > show sel atoms
    11750 
    11751 > show #7 models
    11752 
    11753 > hide #!5 models
    11754 
    11755 > show #!5 models
    11756 
    11757 > hide #!5 models
    11758 
    11759 > select #7/A:760
    11760 
    11761 15 atoms, 14 bonds, 1 residue, 1 model selected 
    11762 
    11763 > hide sel atoms
    11764 
    11765 > show #!5 models
    11766 
    11767 > hide #!5 models
    11768 
    11769 > show #!5 models
    11770 
    11771 > hide #!5 models
    11772 
    11773 > select #7/B:76
    11774 
    11775 17 atoms, 16 bonds, 1 residue, 1 model selected 
    11776 
    11777 > show sel atoms
    11778 
    11779 > select #7/A:587
    11780 
    11781 11 atoms, 10 bonds, 1 residue, 1 model selected 
    11782 
    11783 > show sel atoms
    11784 
    11785 [Repeated 1 time(s)]
    11786 
    11787 > hide sel atoms
    11788 
    11789 > select #7/A:589
    11790 
    11791 17 atoms, 16 bonds, 1 residue, 1 model selected 
    11792 
    11793 > show sel atoms
    11794 
    11795 > hide sel atoms
    11796 
    11797 > select clear
    11798 
    11799 > hide H
    11800 
    11801 > select clear
    11802 
    11803 > select #7/B:75
    11804 
    11805 16 atoms, 15 bonds, 1 residue, 1 model selected 
    11806 
    11807 > select clear
    11808 
    11809 > select #7/B:76
    11810 
    11811 17 atoms, 16 bonds, 1 residue, 1 model selected 
    11812 
    11813 > hide sel atoms
    11814 
    11815 > select clear
    11816 
    11817 > color #4,7 byhetero
    11818 
    11819 > select clear
    11820 
    11821 > select #7/B:23
    11822 
    11823 24 atoms, 23 bonds, 1 residue, 1 model selected 
    11824 
    11825 > show sel atoms
    11826 
    11827 > select #7/B:6
    11828 
    11829 12 atoms, 11 bonds, 1 residue, 1 model selected 
    11830 
    11831 > show sel atoms
    11832 
    11833 > hide sel atoms
    11834 
    11835 > select #7/B:7
    11836 
    11837 14 atoms, 14 bonds, 1 residue, 1 model selected 
    11838 
    11839 > show sel atoms
    11840 
    11841 > hide sel atoms
    11842 
    11843 > select #7/B:9
    11844 
    11845 15 atoms, 14 bonds, 1 residue, 1 model selected 
    11846 
    11847 > show sel atoms
    11848 
    11849 > hide H
    11850 
    11851 Drag select of 2 atoms, 2 residues, 1 bonds 
    11852 
    11853 > select clear
    11854 
    11855 > select #7/B:23@NH1
    11856 
    11857 1 atom, 1 residue, 1 model selected 
    11858 
    11859 > select add #7/A:575@OE1
    11860 
    11861 2 atoms, 2 residues, 1 model selected 
    11862 
    11863 > distance #7/B:23@NH1 #7/A:575@OE1
    11864 
    11865 Distance between AF_EFPIWI_EMGTSF1_0.pdb #7/B ARG 23 NH1 and /A GLU 575 OE1:
    11866 3.717Å 
    11867 
    11868 > select clear
    11869 
    11870 > select #7/B:9
    11871 
    11872 15 atoms, 14 bonds, 1 residue, 1 model selected 
    11873 
    11874 > hide sel atoms
    11875 
    11876 > show #!2 models
    11877 
    11878 > hide #!2 models
    11879 
    11880 > select #7/B:22
    11881 
    11882 17 atoms, 16 bonds, 1 residue, 1 model selected 
    11883 
    11884 > hide sel atoms
    11885 
    11886 > select #7/A:516
    11887 
    11888 17 atoms, 16 bonds, 1 residue, 1 model selected 
    11889 
    11890 > select #7/A:617@NE
    11891 
    11892 1 atom, 1 residue, 1 model selected 
    11893 
    11894 > select add #7/B:28@OH
    11895 
    11896 2 atoms, 2 residues, 1 model selected 
    11897 
    11898 > distance #7/A:617@NE #7/B:28@OH
    11899 
    11900 Distance between AF_EFPIWI_EMGTSF1_0.pdb #7/A ARG 617 NE and /B TYR 28 OH:
    11901 3.019Å 
    11902 
    11903 > select #7/B:25
    11904 
    11905 24 atoms, 23 bonds, 1 residue, 1 model selected 
    11906 
    11907 > hide sel atoms
    11908 
    11909 > select clear
    11910 
    11911 Drag select of 1 pseudobonds, 8 atoms, 28 residues, 7 bonds 
    11912 
    11913 > select clear
    11914 
    11915 > select #7/A:619
    11916 
    11917 15 atoms, 14 bonds, 1 residue, 1 model selected 
    11918 
    11919 > show sel atoms
    11920 
    11921 > select #7/A:619@OE1
    11922 
    11923 1 atom, 1 residue, 1 model selected 
    11924 
    11925 > view #2 clip false
    11926 
    11927 Drag select of 2 residues 
    11928 
    11929 > select #7/A:619@OE1
    11930 
    11931 1 atom, 1 residue, 1 model selected 
    11932 
    11933 > select add #7/B:35@NZ
    11934 
    11935 2 atoms, 2 residues, 1 model selected 
    11936 
    11937 > distance #7/A:619@OE1 #7/B:35@NZ
    11938 
    11939 Distance between AF_EFPIWI_EMGTSF1_0.pdb #7/A GLU 619 OE1 and /B LYS 35 NZ:
    11940 3.414Å 
    11941 
    11942 > select clear
    11943 
    11944 > select #7/A:619
    11945 
    11946 15 atoms, 14 bonds, 1 residue, 1 model selected 
    11947 
    11948 > select clear
    11949 
    11950 > hide H
    11951 
    11952 > select clear
    11953 
    11954 > distance style color #241f31
    11955 
    11956 [Repeated 2 time(s)]
    11957 
    11958 > distance style color black
    11959 
    11960 [Repeated 2 time(s)]
    11961 
    11962 > ui windowfill toggle
    11963 
    11964 [Repeated 2 time(s)]
    11965 
    11966 > ui tool show Log
    11967 
    11968 > select #7/B:32
    11969 
    11970 22 atoms, 21 bonds, 1 residue, 1 model selected 
    11971 
    11972 > hide sel atoms
    11973 
    11974 > show #3 models
    11975 
    11976 > hide #3 models
    11977 
    11978 > show #3 models
    11979 
    11980 > hide #!4 models
    11981 
    11982 > label @@display
    11983 
    11984 [Repeated 1 time(s)]
    11985 
    11986 > label height 1.5
    11987 
    11988 > save
    11989 > /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/AF_GTSF1_complex_inter.cxs
    11990 
    11991 > hide #!7 models
    11992 
    11993 Drag select of 8 residues 
    11994 
    11995 > hide sel atoms
    11996 
    11997 > select clear
    11998 
    11999 > ui tool show "Model Panel"
    12000 
    12001 > show #!4 models
    12002 
    12003 > select clear
    12004 
    12005 > select #3/B:38
    12006 
    12007 24 atoms, 23 bonds, 1 residue, 1 model selected 
    12008 
    12009 > hide sel atoms
    12010 
    12011 > select #3/A:617
    12012 
    12013 14 atoms, 13 bonds, 1 residue, 1 model selected 
    12014 
    12015 > hide sel atoms
    12016 
    12017 > select clear
    12018 
    12019 > select #3/A:618
    12020 
    12021 21 atoms, 21 bonds, 1 residue, 1 model selected 
    12022 
    12023 > hide sel atoms
    12024 
    12025 > select clear
    12026 
    12027 [Repeated 2 time(s)]
    12028 
    12029 > select #3/B:72
    12030 
    12031 12 atoms, 11 bonds, 1 residue, 1 model selected 
    12032 
    12033 > hide sel atoms
    12034 
    12035 > select clear
    12036 
    12037 > select #3/A:560
    12038 
    12039 22 atoms, 21 bonds, 1 residue, 1 model selected 
    12040 
    12041 > hide sel atoms
    12042 
    12043 > select #3/A:594
    12044 
    12045 17 atoms, 17 bonds, 1 residue, 1 model selected 
    12046 
    12047 > select #3/A:389
    12048 
    12049 19 atoms, 18 bonds, 1 residue, 1 model selected 
    12050 
    12051 > hide sel atoms
    12052 
    12053 > select #3/A:559
    12054 
    12055 14 atoms, 13 bonds, 1 residue, 1 model selected 
    12056 
    12057 > hide sel atoms
    12058 
    12059 > select clear
    12060 
    12061 > select #3/B:112
    12062 
    12063 24 atoms, 25 bonds, 1 residue, 1 model selected 
    12064 
    12065 > hide sel atoms
    12066 
    12067 > select clear
    12068 
    12069 [Repeated 2 time(s)]
    12070 
    12071 > select #3/A:630
    12072 
    12073 20 atoms, 20 bonds, 1 residue, 1 model selected 
    12074 
    12075 > ui tool show "Model Panel"
    12076 
    12077 Drag select of 23 residues 
    12078 
    12079 > hide sel atoms
    12080 
    12081 > select clear
    12082 
    12083 > close #3.1
    12084 
    12085 > label @@display
    12086 
    12087 > label height 1.5
    12088 
    12089 > hide #!3 models
    12090 
    12091 > hide #!4 models
    12092 
    12093 > show #!5 models
    12094 
    12095 > ui tool show "Model Panel"
    12096 
    12097 > show #!3 models
    12098 
    12099 > hide #!3 models
    12100 
    12101 > select #5/B:27
    12102 
    12103 14 atoms, 14 bonds, 1 residue, 1 model selected 
    12104 
    12105 > show sel atoms
    12106 
    12107 > show #!3 models
    12108 
    12109 > hide #!3 models
    12110 
    12111 > hide H
    12112 
    12113 > select clear
    12114 
    12115 > show #!7 models
    12116 
    12117 > hide #!5 models
    12118 
    12119 > show #!5 models
    12120 
    12121 > hide #!5 models
    12122 
    12123 > show #!5 models
    12124 
    12125 > hide #!5 models
    12126 
    12127 > hide #!7 models
    12128 
    12129 > show #!5 models
    12130 
    12131 > ui tool show "Model Panel"
    12132 
    12133 > show #!7 models
    12134 
    12135 > hide #!7 models
    12136 
    12137 > hide #!5 surfaces
    12138 
    12139 > show #!3 models
    12140 
    12141 > hide #5.3 models
    12142 
    12143 > hide #!5 models
    12144 
    12145 > hide #!3 models
    12146 
    12147 > show #!7 models
    12148 
    12149 > show #!5 models
    12150 
    12151 > hide #!5 models
    12152 
    12153 > show #!5 models
    12154 
    12155 > hide #!7 models
    12156 
    12157 > ui tool show Distances
    12158 
    12159 > select #5/B:110@OE1
    12160 
    12161 1 atom, 1 residue, 1 model selected 
    12162 
    12163 > select add #5/A:605@NH1
    12164 
    12165 2 atoms, 2 residues, 2 models selected 
    12166 
    12167 > distance #5/B:110@OE1 #5/A:605@NH1
    12168 
    12169 Distance between copy of AF_EFPIWI_EMGTSF1_0.pdb #5/B GLU 110 OE1 and /A ARG
    12170 605 NH1: 2.642Å 
    12171 
    12172 > show #!4 models
    12173 
    12174 > select clear
    12175 
    12176 > select #5/B:112@OE2
    12177 
    12178 1 atom, 1 residue, 1 model selected 
    12179 
    12180 > select add #5/A:711@NZ
    12181 
    12182 2 atoms, 2 residues, 2 models selected 
    12183 
    12184 > distance #5/B:112@OE2 #5/A:711@NZ
    12185 
    12186 Distance between copy of AF_EFPIWI_EMGTSF1_0.pdb #5/B GLU 112 OE2 and /A LYS
    12187 711 NZ: 2.846Å 
    12188 
    12189 > select #5/A:714@NE2
    12190 
    12191 1 atom, 1 residue, 1 model selected 
    12192 
    12193 > select add #5/B:112@OE2
    12194 
    12195 2 atoms, 2 residues, 2 models selected 
    12196 
    12197 > distance #5/A:714@NE2 #5/B:112@OE2
    12198 
    12199 Distance between copy of AF_EFPIWI_EMGTSF1_0.pdb #5/A HIS 714 NE2 and /B GLU
    12200 112 OE2: 3.377Å 
    12201 
    12202 > select clear
    12203 
    12204 > color #4#5.1-2#!5 byhetero
    12205 
    12206 > select clear
    12207 
    12208 > select #5/A:717@NH1
    12209 
    12210 1 atom, 1 residue, 1 model selected 
    12211 
    12212 > select clear
    12213 
    12214 > select #5/A:717@NH1
    12215 
    12216 1 atom, 1 residue, 1 model selected 
    12217 
    12218 > select add #5/B:109@NE1
    12219 
    12220 2 atoms, 2 residues, 2 models selected 
    12221 
    12222 > distance #5/A:717@NH1 #5/B:109@NE1
    12223 
    12224 Distance between copy of AF_EFPIWI_EMGTSF1_0.pdb #5/A ARG 717 NH1 and /B TRP
    12225 109 NE1: 3.454Å 
    12226 
    12227 > select clear
    12228 
    12229 > select #5/A:529@OE1
    12230 
    12231 1 atom, 1 residue, 1 model selected 
    12232 
    12233 > select add #5/B:105@OG
    12234 
    12235 2 atoms, 2 residues, 2 models selected 
    12236 
    12237 > distance #5/A:529@OE1 #5/B:105@OG
    12238 
    12239 Distance between copy of AF_EFPIWI_EMGTSF1_0.pdb #5/A GLU 529 OE1 and /B SER
    12240 105 OG: 2.572Å 
    12241 
    12242 > select clear
    12243 
    12244 > distance style color #241f31
    12245 
    12246 [Repeated 2 time(s)]
    12247 
    12248 > distance style color black
    12249 
    12250 [Repeated 2 time(s)]
    12251 
    12252 > select clear
    12253 
    12254 > select #5/B:113
    12255 
    12256 21 atoms, 21 bonds, 1 residue, 1 model selected 
    12257 
    12258 > hide sel atoms
    12259 
    12260 > select clear
    12261 
    12262 > select #5/A:566@NH2
    12263 
    12264 1 atom, 1 residue, 1 model selected 
    12265 
    12266 > select add #5/B:98@N
    12267 
    12268 2 atoms, 2 residues, 2 models selected 
    12269 
    12270 > distance #5/A:566@NH2 #5/B:98@N
    12271 
    12272 Distance between copy of AF_EFPIWI_EMGTSF1_0.pdb #5/A ARG 566 NH2 and /B THR
    12273 98 N: 3.813Å 
    12274 
    12275 > select clear
    12276 
    12277 > show #!3 models
    12278 
    12279 > hide #2.2 models
    12280 
    12281 > show #2.2 models
    12282 
    12283 > hide #!2 models
    12284 
    12285 > hide #!3 models
    12286 
    12287 > show #!3 models
    12288 
    12289 > hide #3.1 target m
    12290 
    12291 > select #5/A:372
    12292 
    12293 19 atoms, 18 bonds, 1 residue, 1 model selected 
    12294 
    12295 > hide sel atoms
    12296 
    12297 > select up
    12298 
    12299 2 atoms, 1 bond, 1 residue, 1 model selected 
    12300 
    12301 > select up
    12302 
    12303 14 atoms, 14 bonds, 1 residue, 2 models selected 
    12304 
    12305 > hide sel atoms
    12306 
    12307 > select clear
    12308 
    12309 > select #5/A:565
    12310 
    12311 14 atoms, 13 bonds, 1 residue, 1 model selected 
    12312 
    12313 > hide sel atoms
    12314 
    12315 > select up
    12316 
    12317 2 atoms, 1 bond, 1 residue, 1 model selected 
    12318 
    12319 > select up
    12320 
    12321 14 atoms, 14 bonds, 1 residue, 2 models selected 
    12322 
    12323 > hide sel atoms
    12324 
    12325 > select clear
    12326 
    12327 > select #5/A:586
    12328 
    12329 19 atoms, 18 bonds, 1 residue, 1 model selected 
    12330 
    12331 > select #5/B:76
    12332 
    12333 17 atoms, 16 bonds, 1 residue, 1 model selected 
    12334 
    12335 > hide sel atoms
    12336 
    12337 > select #5/B:72@NH2
    12338 
    12339 1 atom, 1 residue, 1 model selected 
    12340 
    12341 > select add #5/A:583@OE2
    12342 
    12343 2 atoms, 2 residues, 2 models selected 
    12344 
    12345 > distance #5/B:72@NH2 #5/A:583@OE2
    12346 
    12347 Distance between copy of AF_EFPIWI_EMGTSF1_0.pdb #5/B ARG 72 NH2 and /A GLU
    12348 583 OE2: 2.628Å 
    12349 
    12350 > select #5/A:583@OE1
    12351 
    12352 1 atom, 1 residue, 1 model selected 
    12353 
    12354 > select add #5/B:72@NH2
    12355 
    12356 2 atoms, 2 residues, 2 models selected 
    12357 
    12358 > distance #5/A:583@OE1 #5/B:72@NH2
    12359 
    12360 Distance between copy of AF_EFPIWI_EMGTSF1_0.pdb #5/A GLU 583 OE1 and /B ARG
    12361 72 NH2: 2.750Å 
    12362 
    12363 > select clear
    12364 
    12365 > hide #!3 models
    12366 
    12367 > select clear
    12368 
    12369 > select #5/B:52@NH1
    12370 
    12371 1 atom, 1 residue, 1 model selected 
    12372 
    12373 > select add #5/A:575@OE1
    12374 
    12375 2 atoms, 2 residues, 2 models selected 
    12376 
    12377 > distance #5/B:52@NH1 #5/A:575@OE1
    12378 
    12379 Distance between copy of AF_EFPIWI_EMGTSF1_0.pdb #5/B ARG 52 NH1 and /A GLU
    12380 575 OE1: 2.707Å 
    12381 
    12382 > select #5/B:52@NH2
    12383 
    12384 1 atom, 1 residue, 1 model selected 
    12385 
    12386 > select add #5/A:575@OE1
    12387 
    12388 2 atoms, 2 residues, 2 models selected 
    12389 
    12390 > distance #5/B:52@NH2 #5/A:575@OE1
    12391 
    12392 Distance between copy of AF_EFPIWI_EMGTSF1_0.pdb #5/B ARG 52 NH2 and /A GLU
    12393 575 OE1: 2.831Å 
    12394 
    12395 > select clear
    12396 
    12397 > distance style color #241f31
    12398 
    12399 [Repeated 2 time(s)]
    12400 
    12401 > distance style color black
    12402 
    12403 [Repeated 2 time(s)]
    12404 
    12405 > select #5/B:28@OH
    12406 
    12407 1 atom, 1 residue, 1 model selected 
    12408 
    12409 > select add #5/A:617@NE
    12410 
    12411 2 atoms, 2 residues, 2 models selected 
    12412 
    12413 > distance #5/B:28@OH #5/A:617@NE
    12414 
    12415 Distance between copy of AF_EFPIWI_EMGTSF1_0.pdb #5/B TYR 28 OH and /A ARG 617
    12416 NE: 3.019Å 
    12417 
    12418 > select clear
    12419 
    12420 > select #5/B:24
    12421 
    12422 22 atoms, 21 bonds, 1 residue, 1 model selected 
    12423 
    12424 > select #5/B:22
    12425 
    12426 17 atoms, 16 bonds, 1 residue, 1 model selected 
    12427 
    12428 > hide sel atoms
    12429 
    12430 > select #5/B:24
    12431 
    12432 22 atoms, 21 bonds, 1 residue, 1 model selected 
    12433 
    12434 > show sel atoms
    12435 
    12436 > hide H
    12437 
    12438 > select clear
    12439 
    12440 > select #5/A:586
    12441 
    12442 19 atoms, 18 bonds, 1 residue, 1 model selected 
    12443 
    12444 > hide sel atoms
    12445 
    12446 > select #5/B:73
    12447 
    12448 19 atoms, 18 bonds, 1 residue, 1 model selected 
    12449 
    12450 > hide sel atoms
    12451 
    12452 > select #5/B:49
    12453 
    12454 20 atoms, 20 bonds, 1 residue, 1 model selected 
    12455 
    12456 > hide sel atoms
    12457 
    12458 > select clear
    12459 
    12460 > show #!3 models
    12461 
    12462 > select #5/A:760
    12463 
    12464 15 atoms, 14 bonds, 1 residue, 1 model selected 
    12465 
    12466 > hide sel atoms
    12467 
    12468 > select clear
    12469 
    12470 > hide #!3 models
    12471 
    12472 > select #5/B:91
    12473 
    12474 7 atoms, 6 bonds, 1 residue, 1 model selected 
    12475 
    12476 > show sel atoms
    12477 
    12478 > select #5/B:92
    12479 
    12480 14 atoms, 13 bonds, 1 residue, 1 model selected 
    12481 
    12482 > show sel atoms
    12483 
    12484 > select #5/A:462
    12485 
    12486 19 atoms, 18 bonds, 1 residue, 1 model selected 
    12487 
    12488 > show sel atoms
    12489 
    12490 > select #5/A:461
    12491 
    12492 24 atoms, 23 bonds, 1 residue, 1 model selected 
    12493 
    12494 > show sel atoms
    12495 
    12496 > select #5/A:460
    12497 
    12498 14 atoms, 14 bonds, 1 residue, 1 model selected 
    12499 
    12500 > show sel atoms
    12501 
    12502 Drag select of 18 atoms, 18 bonds, 12 residues 
    12503 
    12504 > select up
    12505 
    12506 294 atoms, 295 bonds, 17 residues, 2 models selected 
    12507 
    12508 > hide sel atoms
    12509 
    12510 > select clear
    12511 
    12512 > select #5/B:91
    12513 
    12514 7 atoms, 6 bonds, 1 residue, 1 model selected 
    12515 
    12516 > show sel atoms
    12517 
    12518 > select #5/B:92
    12519 
    12520 14 atoms, 13 bonds, 1 residue, 1 model selected 
    12521 
    12522 > hide sel atoms
    12523 
    12524 > show #!3 models
    12525 
    12526 > select #5/B:76
    12527 
    12528 17 atoms, 16 bonds, 1 residue, 1 model selected 
    12529 
    12530 > show sel atoms
    12531 
    12532 > hide #!3 models
    12533 
    12534 > select #5/A:571
    12535 
    12536 14 atoms, 13 bonds, 1 residue, 1 model selected 
    12537 
    12538 > show sel atoms
    12539 
    12540 > select #5/A:570
    12541 
    12542 24 atoms, 23 bonds, 1 residue, 1 model selected 
    12543 
    12544 > show sel atoms
    12545 
    12546 > select #5/A:571
    12547 
    12548 14 atoms, 13 bonds, 1 residue, 1 model selected 
    12549 
    12550 > hide sel atoms
    12551 
    12552 > select clear
    12553 
    12554 > hide H
    12555 
    12556 > select #5/B:76@NE2
    12557 
    12558 1 atom, 1 residue, 1 model selected 
    12559 
    12560 > select add #5/A:570@NE
    12561 
    12562 2 atoms, 2 residues, 2 models selected 
    12563 
    12564 > distance #5/B:76@NE2 #5/A:570@NE
    12565 
    12566 Distance between copy of AF_EFPIWI_EMGTSF1_0.pdb #5/B GLN 76 NE2 and /A ARG
    12567 570 NE: 4.166Å 
    12568 
    12569 > select #5/A:587
    12570 
    12571 11 atoms, 10 bonds, 1 residue, 1 model selected 
    12572 
    12573 > show sel atoms
    12574 
    12575 > hide sel atoms
    12576 
    12577 > select clear
    12578 
    12579 > distance style color #241f31
    12580 
    12581 [Repeated 2 time(s)]
    12582 
    12583 > distance style color black
    12584 
    12585 [Repeated 2 time(s)]
    12586 
    12587 > select clear
    12588 
    12589 > select #5/A:574
    12590 
    12591 17 atoms, 16 bonds, 1 residue, 1 model selected 
    12592 
    12593 > show sel atoms
    12594 
    12595 > hide H
    12596 
    12597 > select #5/A:574@OE1
    12598 
    12599 1 atom, 1 residue, 1 model selected 
    12600 
    12601 > select add #5/A:582@ND1
    12602 
    12603 2 atoms, 2 residues, 1 model selected 
    12604 
    12605 > distance #5/A:574@OE1 #5/A:582@ND1
    12606 
    12607 Distance between copy of AF_EFPIWI_EMGTSF1_0.pdb #5/A GLN 574 OE1 and HIS 582
    12608 ND1: 3.433Å 
    12609 
    12610 > select clear
    12611 
    12612 > show #!3 models
    12613 
    12614 > select #3/A:568
    12615 
    12616 17 atoms, 16 bonds, 1 residue, 1 model selected 
    12617 
    12618 > show sel atoms
    12619 
    12620 > hide H
    12621 
    12622 > select #5/A:582
    12623 
    12624 17 atoms, 17 bonds, 1 residue, 1 model selected 
    12625 
    12626 > select #5/A:574
    12627 
    12628 17 atoms, 16 bonds, 1 residue, 1 model selected 
    12629 
    12630 > select #3/A:568
    12631 
    12632 17 atoms, 16 bonds, 1 residue, 1 model selected 
    12633 
    12634 > hide sel atoms
    12635 
    12636 > select clear
    12637 
    12638 > delete label
    12639 
    12640 Missing or invalid "atoms" argument: invalid atoms specifier 
    12641 
    12642 > delete labels
    12643 
    12644 Missing or invalid "atoms" argument: invalid atoms specifier 
    12645 
    12646 > close #2.3
    12647 
    12648 > close #3.1
    12649 
    12650 > close #5.3
    12651 
    12652 > close #7.1
    12653 
    12654 > close #12.2
    12655 
    12656 > close #1.3
    12657 
    12658 > hide #4.1 models
    12659 
    12660 > hide #!5 models
    12661 
    12662 > label @@display
    12663 
    12664 > label height 1.5
    12665 
    12666 > select #3/B:34
    12667 
    12668 19 atoms, 18 bonds, 1 residue, 1 model selected 
    12669 
    12670 > hide sel atoms
    12671 
    12672 > select #3/A:574
    12673 
    12674 19 atoms, 18 bonds, 1 residue, 1 model selected 
    12675 
    12676 > hide sel atoms
    12677 
    12678 > select #3/B:31
    12679 
    12680 14 atoms, 14 bonds, 1 residue, 1 model selected 
    12681 
    12682 > hide sel atoms
    12683 
    12684 > select clear
    12685 
    12686 > ui tool show "Side View"
    12687 
    12688 > ui tool show "Model Panel"
    12689 
    12690 > close #3.1
    12691 
    12692 > label @@display
    12693 
    12694 > label height 1.5
    12695 
    12696 > select #3/B:17
    12697 
    12698 11 atoms, 10 bonds, 1 residue, 1 model selected 
    12699 
    12700 > hide sel atoms
    12701 
    12702 Drag select of 30 residues 
    12703 
    12704 > select up
    12705 
    12706 1085 atoms, 1090 bonds, 66 residues, 1 model selected 
    12707 
    12708 > hide sel atoms
    12709 
    12710 > select clear
    12711 
    12712 > select #3/B:16
    12713 
    12714 17 atoms, 16 bonds, 1 residue, 1 model selected 
    12715 
    12716 > show sel atoms
    12717 
    12718 > select clear
    12719 
    12720 > hide H
    12721 
    12722 > select clear
    12723 
    12724 > select #3/B:37
    12725 
    12726 11 atoms, 10 bonds, 1 residue, 1 model selected 
    12727 
    12728 > hide sel atoms
    12729 
    12730 > select clear
    12731 
    12732 > select #3/B:26
    12733 
    12734 24 atoms, 23 bonds, 1 residue, 1 model selected 
    12735 
    12736 > select #3/B:26
    12737 
    12738 24 atoms, 23 bonds, 1 residue, 1 model selected 
    12739 
    12740 > show sel atoms
    12741 
    12742 > hide H
    12743 
    12744 > select clear
    12745 
    12746 > select #3/B:27
    12747 
    12748 10 atoms, 9 bonds, 1 residue, 1 model selected 
    12749 
    12750 > hide sel atoms
    12751 
    12752 Drag select of 4 atoms, 3 bonds, 19 residues 
    12753 
    12754 > hide sel atoms
    12755 
    12756 > select #3/B:11
    12757 
    12758 14 atoms, 14 bonds, 1 residue, 1 model selected 
    12759 
    12760 > select #3/B:111
    12761 
    12762 19 atoms, 18 bonds, 1 residue, 1 model selected 
    12763 
    12764 > hide sel atoms
    12765 
    12766 > select #3/A:705
    12767 
    12768 19 atoms, 18 bonds, 1 residue, 1 model selected 
    12769 
    12770 > hide sel atoms
    12771 
    12772 > select clear
    12773 
    12774 > select #3/A:703@CA
    12775 
    12776 1 atom, 1 residue, 1 model selected 
    12777 
    12778 > hide sel atoms
    12779 
    12780 > close #2.3
    12781 
    12782 > close #3.1
    12783 
    12784 > select #3/A:703
    12785 
    12786 10 atoms, 9 bonds, 1 residue, 1 model selected 
    12787 
    12788 > hide sel atoms
    12789 
    12790 > select clear
    12791 
    12792 > select #3/A:699
    12793 
    12794 16 atoms, 15 bonds, 1 residue, 1 model selected 
    12795 
    12796 > hide sel atoms
    12797 
    12798 > select clear
    12799 
    12800 > select #3/A:617
    12801 
    12802 14 atoms, 13 bonds, 1 residue, 1 model selected 
    12803 
    12804 > select #3/A:616
    12805 
    12806 10 atoms, 9 bonds, 1 residue, 1 model selected 
    12807 
    12808 > hide sel atoms
    12809 
    12810 > select clear
    12811 
    12812 > label @@display
    12813 
    12814 > label height 1.2
    12815 
    12816 > select #3/B:16
    12817 
    12818 17 atoms, 16 bonds, 1 residue, 1 model selected 
    12819 
    12820 > hide sel atoms
    12821 
    12822 > select clear
    12823 
    12824 > save
    12825 > /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/AF_GTSF1_complex_inter.cxs
    12826 
    12827 > hide #!3 models
    12828 
    12829 > show #!5 models
    12830 
    12831 > close #5.3
    12832 
    12833 > label @@display
    12834 
    12835 > label height 1.2
    12836 
    12837 > select #5/A:723
    12838 
    12839 14 atoms, 13 bonds, 1 residue, 1 model selected 
    12840 
    12841 > select #5/B:24
    12842 
    12843 22 atoms, 21 bonds, 1 residue, 1 model selected 
    12844 
    12845 > select #5/B:25
    12846 
    12847 24 atoms, 23 bonds, 1 residue, 1 model selected 
    12848 
    12849 > show #!3 models
    12850 
    12851 > hide #!3 models
    12852 
    12853 > select #5/B:21
    12854 
    12855 16 atoms, 15 bonds, 1 residue, 1 model selected 
    12856 
    12857 > show sel atoms
    12858 
    12859 > hide sel atoms
    12860 
    12861 > select #5/B:22
    12862 
    12863 17 atoms, 16 bonds, 1 residue, 1 model selected 
    12864 
    12865 > show sel atoms
    12866 
    12867 > hide H
    12868 
    12869 > select clear
    12870 
    12871 > select #5/B:24
    12872 
    12873 22 atoms, 21 bonds, 1 residue, 1 model selected 
    12874 
    12875 > hide sel atoms
    12876 
    12877 > select clear
    12878 
    12879 [Repeated 1 time(s)]
    12880 
    12881 > select #5/A:574
    12882 
    12883 17 atoms, 16 bonds, 1 residue, 1 model selected 
    12884 
    12885 > hide sel atoms
    12886 
    12887 > select #5/B:50
    12888 
    12889 14 atoms, 13 bonds, 1 residue, 1 model selected 
    12890 
    12891 > show sel atoms
    12892 
    12893 > hide H
    12894 
    12895 > select #5/A:582@NE2
    12896 
    12897 1 atom, 1 residue, 1 model selected 
    12898 
    12899 > select add #5/B:50@ND2
    12900 
    12901 2 atoms, 2 residues, 2 models selected 
    12902 
    12903 > ui tool show Distances
    12904 
    12905 > distance #5/A:582@NE2 #5/B:50@ND2
    12906 
    12907 Distance between copy of AF_EFPIWI_EMGTSF1_0.pdb #5/A HIS 582 NE2 and /B ASN
    12908 50 ND2: 4.009Å 
    12909 
    12910 > show #4.1 models
    12911 
    12912 > hide #4.1 models
    12913 
    12914 > distance style color #241f31
    12915 
    12916 [Repeated 2 time(s)]
    12917 
    12918 > distance style color black
    12919 
    12920 [Repeated 2 time(s)]
    12921 
    12922 > select clear
    12923 
    12924 > close #5.3
    12925 
    12926 > label @@display
    12927 
    12928 > label height 1.2
    12929 
    12930 > select #5/B:92
    12931 
    12932 14 atoms, 13 bonds, 1 residue, 1 model selected 
    12933 
    12934 > show sel atoms
    12935 
    12936 > select #5/B:93
    12937 
    12938 14 atoms, 13 bonds, 1 residue, 1 model selected 
    12939 
    12940 > show sel atoms
    12941 
    12942 > select #5/A:760
    12943 
    12944 15 atoms, 14 bonds, 1 residue, 1 model selected 
    12945 
    12946 > show sel atoms
    12947 
    12948 > select #5/A:761
    12949 
    12950 19 atoms, 18 bonds, 1 residue, 1 model selected 
    12951 Drag select of 18 atoms, 16 bonds, 28 residues 
    12952 
    12953 > hide sel atoms
    12954 
    12955 > select clear
    12956 
    12957 > select #5/B:92
    12958 
    12959 14 atoms, 13 bonds, 1 residue, 1 model selected 
    12960 
    12961 > hide sel atoms
    12962 
    12963 > select clear
    12964 
    12965 > select #5/A:527
    12966 
    12967 10 atoms, 9 bonds, 1 residue, 1 model selected 
    12968 
    12969 > show sel atoms
    12970 
    12971 > select #5/A:373
    12972 
    12973 20 atoms, 20 bonds, 1 residue, 1 model selected 
    12974 
    12975 > show sel atoms
    12976 
    12977 > select #5/A:374
    12978 
    12979 22 atoms, 21 bonds, 1 residue, 1 model selected 
    12980 
    12981 > show sel atoms
    12982 
    12983 > hide sel atoms
    12984 
    12985 > select #5/A:372
    12986 
    12987 19 atoms, 18 bonds, 1 residue, 1 model selected 
    12988 
    12989 > show sel atoms
    12990 
    12991 > select #5/A:376
    12992 
    12993 11 atoms, 10 bonds, 1 residue, 1 model selected 
    12994 
    12995 > select #5/A:373
    12996 
    12997 20 atoms, 20 bonds, 1 residue, 1 model selected 
    12998 
    12999 > hide sel atoms
    13000 
    13001 > hide H
    13002 
    13003 > select #5/B:80
    13004 
    13005 14 atoms, 13 bonds, 1 residue, 1 model selected 
    13006 
    13007 > show sel atoms
    13008 
    13009 > select #5/A:759
    13010 
    13011 17 atoms, 17 bonds, 1 residue, 1 model selected 
    13012 
    13013 > show sel atoms
    13014 
    13015 > hide sel atoms
    13016 
    13017 > select #5/B:80
    13018 
    13019 14 atoms, 13 bonds, 1 residue, 1 model selected 
    13020 
    13021 > hide sel atoms
    13022 
    13023 > select clear
    13024 
    13025 > save
    13026 > /home/dell/shen_data/PIWI/GTSF1_Predictions/MILI26NT_gtsf1/AF_GTSF1_complex_inter.cxs
    13027 
    13028 > ui tool show "Model Panel"
    13029 
    13030 > show #!3 models
    13031 
    13032 > hide #5.3 models
    13033 
    13034 > hide #7.1 models
    13035 
    13036 > hide #3.1 models
    13037 
    13038 > select #3/B:77
    13039 
    13040 19 atoms, 18 bonds, 1 residue, 1 model selected 
     3491[deleted to fit within ticket limits]
    130413492
    130423493> show #3.1 models