Changes between Initial Version and Version 1 of Ticket #17903


Ignore:
Timestamp:
Jun 4, 2025, 5:41:49 PM (5 months ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #17903

    • Property Component Unassigned → Sessions
    • Property Owner set to Tom Goddard
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → Session save: Similar Structures: 'NoneType' object has no attribute 'hits'

  • Ticket #17903 – Description

    initial v1  
    358735879 atoms, 8 bonds, 1 residue, 1 model selected 
    35883588
    3589 > select #2/I:169
    3590 
    3591 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3592 
    3593 > select #2/I:165
    3594 
    3595 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3596 
    3597 > select #2/I:165
    3598 
    3599 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3600 
    3601 > select #2/I:183
    3602 
    3603 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3604 
    3605 > select #2/I:183-184
    3606 
    3607 20 atoms, 20 bonds, 2 residues, 1 model selected 
    3608 
    3609 > select #2/I:190
    3610 
    3611 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3612 
    3613 > select #2/I:190
    3614 
    3615 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3616 
    3617 > select #2/I:122
    3618 
    3619 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3620 
    3621 > select #2/I:122
    3622 
    3623 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3624 
    3625 > ui mousemode right select
    3626 
    3627 > select #7/A:126
    3628 
    3629 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3630 
    3631 > select #2/I:147
    3632 
    3633 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3634 Drag select of 4 residues 
    3635 
    3636 > ui mousemode right rotate
    3637 
    3638 > select #7/A:190
    3639 
    3640 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3641 
    3642 > select #7/A:190
    3643 
    3644 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3645 
    3646 > select #7/A:190
    3647 
    3648 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3649 
    3650 > select #7/A:190
    3651 
    3652 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3653 
    3654 > select #7/A:183
    3655 
    3656 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3657 
    3658 > select #7/A:183-184
    3659 
    3660 21 atoms, 21 bonds, 2 residues, 1 model selected 
    3661 
    3662 > save
    3663 > /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
    3664 
    3665 > hide #!7 models
    3666 
    3667 > show #1 models
    3668 
    3669 > hide #1 models
    3670 
    3671 > show #9 models
    3672 
    3673 > ui tool show "Show Sequence Viewer"
    3674 
    3675 > sequence chain #9/A
    3676 
    3677 Alignment identifier is 9/A 
    3678 
    3679 > select #9/A:174
    3680 
    3681 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3682 
    3683 > select #9/A:174
    3684 
    3685 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3686 
    3687 > style sel stick
    3688 
    3689 Changed 9 atom styles 
    3690 
    3691 > show sel atoms
    3692 
    3693 > color sel blue
    3694 
    3695 > select #9/A:181
    3696 
    3697 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3698 
    3699 > select #9/A:181
    3700 
    3701 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3702 
    3703 > style sel stick
    3704 
    3705 Changed 9 atom styles 
    3706 
    3707 > show sel atoms
    3708 
    3709 > color sel red
    3710 
    3711 > select clear
    3712 
    3713 > save /Users/mauriciocomas/Desktop/image32.png supersample 3
    3714 
    3715 > ui mousemode right select
    3716 
    3717 > select #9/A:156
    3718 
    3719 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3720 
    3721 > select #9/A:181
    3722 
    3723 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3724 
    3725 > hide #9 models
    3726 
    3727 > show #1 models
    3728 
    3729 > select #9/A:174
    3730 
    3731 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3732 
    3733 > select #9/A:174
    3734 
    3735 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3736 
    3737 > ui tool show "Show Sequence Viewer"
    3738 
    3739 > sequence chain #1/C
    3740 
    3741 Alignment identifier is 1/C 
    3742 
    3743 > select #1/C:184
    3744 
    3745 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3746 
    3747 > select #1/C:184
    3748 
    3749 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3750 
    3751 > style sel stick
    3752 
    3753 Changed 9 atom styles 
    3754 
    3755 > show sel atoms
    3756 
    3757 > color sel blue
    3758 
    3759 > save /Users/mauriciocomas/Desktop/image33.png supersample 3
    3760 
    3761 > select #1/C:191
    3762 
    3763 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3764 
    3765 > select #1/C:191
    3766 
    3767 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3768 
    3769 > show sel atoms
    3770 
    3771 > show sel atoms
    3772 
    3773 > style sel stick
    3774 
    3775 Changed 9 atom styles 
    3776 
    3777 > color sel red
    3778 
    3779 > select #1/C:148
    3780 
    3781 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3782 
    3783 > color sel blue
    3784 
    3785 > select clear
    3786 
    3787 > save /Users/mauriciocomas/Desktop/image34.png supersample 3
    3788 
    3789 > save
    3790 > /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
    3791 
    3792 > hide #2 models
    3793 
    3794 > show #!8 models
    3795 
    3796 > ui tool show "Show Sequence Viewer"
    3797 
    3798 > sequence chain #8/A
    3799 
    3800 Alignment identifier is 8/A 
    3801 
    3802 > select #8/A:169
    3803 
    3804 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3805 
    3806 > select #8/A:169
    3807 
    3808 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3809 
    3810 > style sel stick
    3811 
    3812 Changed 9 atom styles 
    3813 
    3814 > show sel atoms
    3815 
    3816 > color sel blue
    3817 
    3818 > select #8/A:176
    3819 
    3820 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3821 
    3822 > select #8/A:176
    3823 
    3824 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3825 
    3826 > style sel stick
    3827 
    3828 Changed 9 atom styles 
    3829 
    3830 > show sel atoms
    3831 
    3832 > color sel red
    3833 
    3834 > select clear
    3835 
    3836 > save /Users/mauriciocomas/Desktop/image35.png supersample 3
    3837 
    3838 > select #8/A:133@CB
    3839 
    3840 1 atom, 1 residue, 1 model selected 
    3841 
    3842 > show #2 models
    3843 
    3844 > hide #1 models
    3845 
    3846 > hide sel atoms
    3847 
    3848 > undo
    3849 
    3850 > select #8/A:176
    3851 
    3852 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3853 
    3854 > select #8/A:176
    3855 
    3856 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3857 
    3858 > save /Users/mauriciocomas/Desktop/image36.png supersample 3
    3859 
    3860 > select #8/A:151
    3861 
    3862 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3863 
    3864 > hide #!8 models
    3865 
    3866 > show #3 models
    3867 
    3868 > ui tool show "Show Sequence Viewer"
    3869 
    3870 > sequence chain #3/A
    3871 
    3872 Alignment identifier is 3/A 
    3873 
    3874 > select #3/A:162
    3875 
    3876 12 atoms, 12 bonds, 1 residue, 1 model selected 
    3877 
    3878 > select #3/A:162
    3879 
    3880 12 atoms, 12 bonds, 1 residue, 1 model selected 
    3881 
    3882 > style sel stick
    3883 
    3884 Changed 12 atom styles 
    3885 
    3886 > style sel stick
    3887 
    3888 Changed 12 atom styles 
    3889 
    3890 > show sel atoms
    3891 
    3892 > color sel dark gray
    3893 
    3894 > select #3/A:168
    3895 
    3896 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3897 
    3898 > select #3/A:168
    3899 
    3900 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3901 
    3902 > style sel stick
    3903 
    3904 Changed 9 atom styles 
    3905 
    3906 > show sel atoms
    3907 
    3908 > hide sel atoms
    3909 
    3910 > select #3/A:161-162
    3911 
    3912 17 atoms, 17 bonds, 2 residues, 1 model selected 
    3913 
    3914 > select #3/A:161-162
    3915 
    3916 17 atoms, 17 bonds, 2 residues, 1 model selected 
    3917 
    3918 > select #3/A:162
    3919 
    3920 12 atoms, 12 bonds, 1 residue, 1 model selected 
    3921 
    3922 > select #3/A:162-163
    3923 
    3924 20 atoms, 20 bonds, 2 residues, 1 model selected 
    3925 
    3926 > select #3/A:162
    3927 
    3928 12 atoms, 12 bonds, 1 residue, 1 model selected 
    3929 
    3930 > select #3/A:162
    3931 
    3932 12 atoms, 12 bonds, 1 residue, 1 model selected 
    3933 
    3934 > hide sel atoms
    3935 
    3936 > select #3/A:179
    3937 
    3938 7 atoms, 6 bonds, 1 residue, 1 model selected 
    3939 
    3940 > select #3/A:178
    3941 
    3942 11 atoms, 11 bonds, 1 residue, 1 model selected 
    3943 
    3944 > select #3/A:178
    3945 
    3946 11 atoms, 11 bonds, 1 residue, 1 model selected 
    3947 
    3948 > select #3/A:179
    3949 
    3950 7 atoms, 6 bonds, 1 residue, 1 model selected 
    3951 
    3952 > select #3/A:179-180
    3953 
    3954 19 atoms, 19 bonds, 2 residues, 1 model selected 
    3955 
    3956 > select #3/A:179
    3957 
    3958 7 atoms, 6 bonds, 1 residue, 1 model selected 
    3959 
    3960 > select #3/A:179
    3961 
    3962 7 atoms, 6 bonds, 1 residue, 1 model selected 
    3963 
    3964 > style sel stick
    3965 
    3966 Changed 7 atom styles 
    3967 
    3968 > show sel atoms
    3969 
    3970 > color sel dim gray
    3971 
    3972 > select #3/A:186
    3973 
    3974 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3975 
    3976 > select #3/A:186
    3977 
    3978 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3979 
    3980 > style sel stick
    3981 
    3982 Changed 9 atom styles 
    3983 
    3984 > style sel stick
    3985 
    3986 Changed 9 atom styles 
    3987 
    3988 > show sel atoms
    3989 
    3990 > color sel red
    3991 
    3992 > select clear
    3993 
    3994 > select #3/A:186
    3995 
    3996 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3997 
    3998 > select #3/A:186
    3999 
    4000 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4001 
    4002 > save /Users/mauriciocomas/Desktop/image37.png supersample 3
    4003 
    4004 > select #3/A:121
    4005 
    4006 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4007 
    4008 > color sel red
    4009 
    4010 > select clear
    4011 
    4012 > save /Users/mauriciocomas/Desktop/image38.png supersample 3
    4013 
    4014 > save
    4015 > /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
    4016 
    4017 > hide #3 models
    4018 
    4019 > show #6 models
    4020 
    4021 > ui tool show "Show Sequence Viewer"
    4022 
    4023 > sequence chain #6/A
    4024 
    4025 Alignment identifier is 6/A 
    4026 
    4027 > select #6/A:181
    4028 
    4029 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4030 
    4031 > select #6/A:181
    4032 
    4033 11 atoms, 11 bonds, 1 residue, 1 model selected 
    4034 
    4035 > select #6/A:182
    4036 
    4037 4 atoms, 3 bonds, 1 residue, 1 model selected 
    4038 
    4039 > select #6/A:182
    4040 
    4041 4 atoms, 3 bonds, 1 residue, 1 model selected 
    4042 
    4043 > style sel stick
    4044 
    4045 Changed 4 atom styles 
    4046 
    4047 > show sel atoms
    4048 
    4049 > show sel atoms
    4050 
    4051 > show sel cartoons
    4052 
    4053 > select #6/A:131
    4054 
    4055 12 atoms, 12 bonds, 1 residue, 1 model selected 
    4056 
    4057 > select #6/A:131-267
    4058 
    4059 1036 atoms, 1064 bonds, 137 residues, 1 model selected 
    4060 
    4061 > select #6/A:182
    4062 
    4063 4 atoms, 3 bonds, 1 residue, 1 model selected 
    4064 
    4065 > select #6/A:182
    4066 
    4067 4 atoms, 3 bonds, 1 residue, 1 model selected 
    4068 
    4069 > style sel stick
    4070 
    4071 Changed 4 atom styles 
    4072 
    4073 > style sel sphere
    4074 
    4075 Changed 4 atom styles 
    4076 
    4077 > style sel stick
    4078 
    4079 Changed 4 atom styles 
    4080 
    4081 > show sel atoms
    4082 
    4083 > style sel sphere
    4084 
    4085 Changed 4 atom styles 
    4086 
    4087 > color sel dim gray
    4088 
    4089 > select #6/A:182
    4090 
    4091 4 atoms, 3 bonds, 1 residue, 1 model selected 
    4092 
    4093 > select #6/A:182
    4094 
    4095 4 atoms, 3 bonds, 1 residue, 1 model selected 
    4096 
    4097 > select #6/A:189
    4098 
    4099 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4100 
    4101 > select #6/A:189
    4102 
    4103 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4104 
    4105 > style sel stick
    4106 
    4107 Changed 9 atom styles 
    4108 
    4109 > show sel atoms
    4110 
    4111 > color sel red
    4112 
    4113 > select clear
    4114 
    4115 > save /Users/mauriciocomas/Desktop/image39.png supersample 3
    4116 
    4117 > save
    4118 > /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
    4119 
    4120 > hide #6 models
    4121 
    4122 > show #4 models
    4123 
    4124 > ui tool show "Show Sequence Viewer"
    4125 
    4126 > sequence chain #4/L
    4127 
    4128 Alignment identifier is 4/L 
    4129 
    4130 > select #4/L:133
    4131 
    4132 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4133 
    4134 > color sel red
    4135 
    4136 > select clear
    4137 
    4138 > select #4/L:154
    4139 
    4140 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4141 
    4142 > select #4/L:203
    4143 
    4144 10 atoms, 10 bonds, 1 residue, 1 model selected 
    4145 
    4146 > select #4/L:172
    4147 
    4148 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4149 
    4150 > select #4/L:190
    4151 
    4152 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4153 
    4154 > style sel stick
    4155 
    4156 Changed 9 atom styles 
    4157 
    4158 > show sel atoms
    4159 
    4160 > color sel blue
    4161 
    4162 > select #2/I:183
    4163 
    4164 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4165 
    4166 > select #4/L:190
    4167 
    4168 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4169 
    4170 > select #4/L:197
    4171 
    4172 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4173 
    4174 > select #4/L:197
    4175 
    4176 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4177 
    4178 > select #4/L:198
    4179 
    4180 4 atoms, 3 bonds, 1 residue, 1 model selected 
    4181 
    4182 > select #4/L:198
    4183 
    4184 4 atoms, 3 bonds, 1 residue, 1 model selected 
    4185 
    4186 > select #4/L:197
    4187 
    4188 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4189 
    4190 > select #4/L:197
    4191 
    4192 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4193 
    4194 > style sel stick
    4195 
    4196 Changed 9 atom styles 
    4197 
    4198 > show sel atoms
    4199 
    4200 > color sel red
    4201 
    4202 > select #4/L:133
    4203 
    4204 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4205 
    4206 > select #4/L:133
    4207 
    4208 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4209 
    4210 > select #4/L:196-197
    4211 
    4212 16 atoms, 16 bonds, 2 residues, 1 model selected 
    4213 
    4214 > select #4/L:196-197
    4215 
    4216 16 atoms, 16 bonds, 2 residues, 1 model selected 
    4217 
    4218 > select #4/L:197
    4219 
    4220 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4221 
    4222 > select #4/L:197
    4223 
    4224 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4225 
    4226 > select #4/L:198
    4227 
    4228 4 atoms, 3 bonds, 1 residue, 1 model selected 
    4229 
    4230 > select #4/L:198
    4231 
    4232 4 atoms, 3 bonds, 1 residue, 1 model selected 
    4233 
    4234 > select #4/L:197
    4235 
    4236 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4237 
    4238 > select #4/L:197
    4239 
    4240 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4241 
    4242 > color sel dim gray
    4243 
    4244 > select clear
    4245 
    4246 > save /Users/mauriciocomas/Desktop/image40.png supersample 3
    4247 
    4248 > save
    4249 > /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
    4250 
    4251 > show #!5 models
    4252 
    4253 > hide #!5 models
    4254 
    4255 > hide #4 models
    4256 
    4257 > show #!5 models
    4258 
    4259 > ui tool show "Show Sequence Viewer"
    4260 
    4261 > sequence chain #5/C
    4262 
    4263 Alignment identifier is 5/C 
    4264 
    4265 > select #5/C:176
    4266 
    4267 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4268 
    4269 > select #5/C:175
    4270 
    4271 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4272 
    4273 > color sel dark gray
    4274 
    4275 > style sel stick
    4276 
    4277 Changed 8 atom styles 
    4278 
    4279 > show sel atoms
    4280 
    4281 > color sel dim gray
    4282 
    4283 > ui mousemode right select
    4284 
    4285 > select #5/C:183
    4286 
    4287 7 atoms, 7 bonds, 1 residue, 1 model selected 
    4288 
    4289 > select #5/C:183
    4290 
    4291 7 atoms, 7 bonds, 1 residue, 1 model selected 
    4292 
    4293 > select #5/C:183-184
    4294 
    4295 11 atoms, 11 bonds, 2 residues, 1 model selected 
    4296 
    4297 > select #5/C:184
    4298 
    4299 4 atoms, 3 bonds, 1 residue, 1 model selected 
    4300 
    4301 > select #5/C:184
    4302 
    4303 4 atoms, 3 bonds, 1 residue, 1 model selected 
    4304 
    4305 > select #5/C:183
    4306 
    4307 7 atoms, 7 bonds, 1 residue, 1 model selected 
    4308 
    4309 > select #5/C:183
    4310 
    4311 7 atoms, 7 bonds, 1 residue, 1 model selected 
    4312 
    4313 > style sel stick
    4314 
    4315 Changed 7 atom styles 
    4316 
    4317 > show sel atoms
    4318 
    4319 > color sel dim gray
    4320 
    4321 > select clear
    4322 
    4323 > save /Users/mauriciocomas/Desktop/image41.png supersample 3
    4324 
    4325 > save
    4326 > /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
    4327 
    4328 > hide #!5 models
    4329 
    4330 > select clear
    4331 
    4332 > save /Users/mauriciocomas/Desktop/image42.png supersample 3
    4333 
    4334 > save
    4335 > /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
    4336 
    4337 ——— End of log from Wed Mar 15 16:42:48 2023 ———
    4338 
    4339 opened ChimeraX session 
    4340 
    4341 > select #2/I:126
    4342 
    4343 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4344 
    4345 > select #2/I:126
    4346 
    4347 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4348 
    4349 > select #2/I:126-127
    4350 
    4351 13 atoms, 12 bonds, 2 residues, 1 model selected 
    4352 
    4353 > select #2/I:126-184
    4354 
    4355 448 atoms, 455 bonds, 59 residues, 1 model selected 
    4356 
    4357 > select #2/I:126
    4358 
    4359 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4360 
    4361 > select #2/I:126
    4362 
    4363 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4364 
    4365 > style sel stick
    4366 
    4367 Changed 9 atom styles 
    4368 
    4369 > show sel atoms
    4370 
    4371 > color sel red
    4372 
    4373 > ui tool show "Show Sequence Viewer"
    4374 
    4375 > sequence chain #2/I
    4376 
    4377 Alignment identifier is 2/I 
    4378 
    4379 > select #2/I:126
    4380 
    4381 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4382 
    4383 > select #2/I:126-133
    4384 
    4385 58 atoms, 58 bonds, 8 residues, 1 model selected 
    4386 
    4387 > select #2/I:126
    4388 
    4389 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4390 
    4391 > select #2/I:126-127
    4392 
    4393 13 atoms, 12 bonds, 2 residues, 1 model selected 
    4394 
    4395 > select #2/I:126
    4396 
    4397 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4398 
    4399 > select #2/I:126
    4400 
    4401 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4402 
    4403 > select #2/I:128
    4404 
    4405 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4406 
    4407 > select #2/I:128
    4408 
    4409 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4410 
    4411 > style sel stick
    4412 
    4413 Changed 9 atom styles 
    4414 
    4415 > show sel atoms
    4416 
    4417 > color sel blue
    4418 
    4419 > select #2/I:154
    4420 
    4421 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4422 
    4423 > select #2/I:154
    4424 
    4425 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4426 
    4427 > color sel red
    4428 
    4429 > style sel stick
    4430 
    4431 Changed 8 atom styles 
    4432 
    4433 > show sel atoms
    4434 
    4435 > save /Users/mauriciocomas/Desktop/image9.png supersample 3
    4436 
    4437 > show #3 models
    4438 
    4439 > hide #3 models
    4440 
    4441 > show #!7 models
    4442 
    4443 > ui tool show "Show Sequence Viewer"
    4444 
    4445 > sequence chain #7/A
    4446 
    4447 Alignment identifier is 7/A 
    4448 
    4449 > select #7/A:128
    4450 
    4451 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4452 
    4453 > select #7/A:128
    4454 
    4455 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4456 
    4457 > style sel stick
    4458 
    4459 Changed 9 atom styles 
    4460 
    4461 > show sel atoms
    4462 
    4463 > color sel blue
    4464 
    4465 > select #7/A:154
    4466 
    4467 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4468 
    4469 > select #7/A:154
    4470 
    4471 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4472 
    4473 > style sel stick
    4474 
    4475 Changed 8 atom styles 
    4476 
    4477 > show sel atoms
    4478 
    4479 > color sel red
    4480 
    4481 > save /Users/mauriciocomas/Desktop/image10.png supersample 3
    4482 
    4483 > hide #!7 models
    4484 
    4485 > show #9 models
    4486 
    4487 > ui tool show "Show Sequence Viewer"
    4488 
    4489 > sequence chain #9/A
    4490 
    4491 Alignment identifier is 9/A 
    4492 
    4493 > select #9/A:119
    4494 
    4495 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4496 
    4497 > select #9/A:119
    4498 
    4499 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4500 
    4501 > style sel stick
    4502 
    4503 Changed 9 atom styles 
    4504 
    4505 > show sel atoms
    4506 
    4507 > color sel blue
    4508 
    4509 > select #9/A:145
    4510 
    4511 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4512 
    4513 > select #9/A:145
    4514 
    4515 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4516 
    4517 > style sel stick
    4518 
    4519 Changed 8 atom styles 
    4520 
    4521 > show sel atoms
    4522 
    4523 > color sel red
    4524 
    4525 > select clear
    4526 
    4527 > save /Users/mauriciocomas/Desktop/image11.png supersample 3
    4528 
    4529 > save
    4530 > /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
    4531 
    4532 > ui mousemode right select
    4533 
    4534 > select #2/I:154@CG
    4535 
    4536 1 atom, 1 residue, 1 model selected 
    4537 
    4538 > hide #9 models
    4539 
    4540 > show #1 models
    4541 
    4542 > ui tool show "Show Sequence Viewer"
    4543 
    4544 > sequence chain #1/C
    4545 
    4546 Alignment identifier is 1/C 
    4547 
    4548 > select #1/C:123
    4549 
    4550 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4551 
    4552 > select #1/C:123
    4553 
    4554 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4555 
    4556 > select #1/C:123
    4557 
    4558 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4559 
    4560 > select #1/C:123-128
    4561 
    4562 45 atoms, 44 bonds, 6 residues, 1 model selected 
    4563 
    4564 > select #1/C:123
    4565 
    4566 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4567 
    4568 > select #1/C:123
    4569 
    4570 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4571 
    4572 > select #1/C:127
    4573 
    4574 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4575 
    4576 > select #1/C:127
    4577 
    4578 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4579 
    4580 > select #1/C:129
    4581 
    4582 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4583 
    4584 > select #1/C:129
    4585 
    4586 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4587 
    4588 > style sel stick
    4589 
    4590 Changed 9 atom styles 
    4591 
    4592 > show sel atoms
    4593 
    4594 > color sel blue
    4595 
    4596 > select #1/C:155
    4597 
    4598 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4599 
    4600 > select #1/C:155
    4601 
    4602 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4603 
    4604 > style sel stick
    4605 
    4606 Changed 8 atom styles 
    4607 
    4608 > show sel atoms
    4609 
    4610 > color sel red
    4611 
    4612 > save /Users/mauriciocomas/Desktop/image12.png supersample 3
    4613 
    4614 > hide #1 models
    4615 
    4616 > show #!8 models
    4617 
    4618 > hide #!8 models
    4619 
    4620 > ui mousemode right rotate
    4621 
    4622 > ui mousemode right translate
    4623 
    4624 > ui mousemode right rotate
    4625 
    4626 > ui mousemode right zoom
    4627 
    4628 > ui mousemode right translate
    4629 
    4630 > show #!8 models
    4631 
    4632 > ui tool show "Show Sequence Viewer"
    4633 
    4634 > sequence chain #8/A
    4635 
    4636 Alignment identifier is 8/A 
    4637 
    4638 > select #8/A:112
    4639 
    4640 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4641 
    4642 > select #8/A:112-113
    4643 
    4644 12 atoms, 11 bonds, 2 residues, 1 model selected 
    4645 
    4646 > select #8/A:112
    4647 
    4648 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4649 
    4650 > select #8/A:112
    4651 
    4652 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4653 
    4654 > select #8/A:114
    4655 
    4656 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4657 
    4658 > select #8/A:114
    4659 
    4660 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4661 
    4662 > style sel stick
    4663 
    4664 Changed 9 atom styles 
    4665 
    4666 > show sel atoms
    4667 
    4668 > color sel blue
    4669 
    4670 > select #8/A:153
    4671 
    4672 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4673 
    4674 > select #8/A:153
    4675 
    4676 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4677 
    4678 > select #8/A:155
    4679 
    4680 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4681 
    4682 > select #8/A:155
    4683 
    4684 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4685 
    4686 > select #8/A:153
    4687 
    4688 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4689 
    4690 > select #8/A:153
    4691 
    4692 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4693 
    4694 > style sel stick
    4695 
    4696 Changed 8 atom styles 
    4697 
    4698 > show sel atoms
    4699 
    4700 > hide sel cartoons
    4701 
    4702 > hide sel cartoons
    4703 
    4704 > show sel cartoons
    4705 
    4706 > style sel stick
    4707 
    4708 Changed 8 atom styles 
    4709 
    4710 > style sel stick
    4711 
    4712 Changed 8 atom styles 
    4713 
    4714 > select #8/A:153
    4715 
    4716 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4717 
    4718 > select #8/A:153
    4719 
    4720 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4721 
    4722 > hide sel atoms
    4723 
    4724 > ui mousemode right select
    4725 
    4726 > select #8/A:140
    4727 
    4728 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4729 
    4730 > select #8/A:140
    4731 
    4732 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4733 
    4734 > select #8/A:140
    4735 
    4736 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4737 
    4738 > style sel stick
    4739 
    4740 Changed 9 atom styles 
    4741 
    4742 > style sel stick
    4743 
    4744 Changed 9 atom styles 
    4745 
    4746 > show sel atoms
    4747 
    4748 > color sel red
    4749 
    4750 > select clear
    4751 
    4752 > save /Users/mauriciocomas/Desktop/image13.png supersample 3
    4753 
    4754 > hide #!8 models
    4755 
    4756 > show #!7 models
    4757 
    4758 > hide #!7 models
    4759 
    4760 > show #6 models
    4761 
    4762 > hide #6 models
    4763 
    4764 > show #3 models
    4765 
    4766 > ui tool show "Show Sequence Viewer"
    4767 
    4768 > sequence chain #6/A
    4769 
    4770 Alignment identifier is 6/A 
    4771 
    4772 > select #6/A:136
    4773 
    4774 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4775 
    4776 > select #6/A:136
    4777 
    4778 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4779 
    4780 > select #6/A:137
    4781 
    4782 4 atoms, 3 bonds, 1 residue, 1 model selected 
    4783 
    4784 > select #6/A:137-186
    4785 
    4786 390 atoms, 399 bonds, 50 residues, 1 model selected 
    4787 
    4788 > show #6 models
    4789 
    4790 > hide #6 models
    4791 
    4792 > select #6
    4793 
    4794 1279 atoms, 1181 bonds, 279 residues, 1 model selected 
    4795 
    4796 > ~select #6
    4797 
    4798 Nothing selected 
    4799 
    4800 > select #6
    4801 
    4802 1279 atoms, 1181 bonds, 279 residues, 1 model selected 
    4803 
    4804 > ~select #6
    4805 
    4806 Nothing selected 
    4807 
    4808 > select #3
    4809 
    4810 1240 atoms, 1252 bonds, 175 residues, 1 model selected 
    4811 
    4812 > ~select #3
    4813 
    4814 Nothing selected 
    4815 
    4816 > ui tool show "Show Sequence Viewer"
    4817 
    4818 > sequence chain #3/A
    4819 
    4820 Alignment identifier is 3/A 
    4821 
    4822 > select #3/A:135
    4823 
    4824 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4825 
    4826 > select #3/A:135
    4827 
    4828 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4829 
    4830 > style sel stick
    4831 
    4832 Changed 9 atom styles 
    4833 
    4834 > style sel stick
    4835 
    4836 Changed 9 atom styles 
    4837 
    4838 > show sel atoms
    4839 
    4840 > hide sel atoms
    4841 
    4842 > select #3/A:121
    4843 
    4844 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4845 
    4846 > select #3/A:123
    4847 
    4848 4 atoms, 3 bonds, 1 residue, 1 model selected 
    4849 
    4850 > select #3/A:123
    4851 
    4852 4 atoms, 3 bonds, 1 residue, 1 model selected 
    4853 
    4854 > style sel stick
    4855 
    4856 Changed 4 atom styles 
    4857 
    4858 > show sel atoms
    4859 
    4860 > show sel atoms
    4861 
    4862 > style sel stick
    4863 
    4864 Changed 4 atom styles 
    4865 
    4866 > show sel atoms
    4867 
    4868 > hide sel atoms
    4869 
    4870 > select #3/A:123
    4871 
    4872 4 atoms, 3 bonds, 1 residue, 1 model selected 
    4873 
    4874 > select #3/A:123
    4875 
    4876 4 atoms, 3 bonds, 1 residue, 1 model selected 
    4877 
    4878 > select #3/A:123
    4879 
    4880 4 atoms, 3 bonds, 1 residue, 1 model selected 
    4881 
    4882 > select #3/A:123-129
    4883 
    4884 46 atoms, 46 bonds, 7 residues, 1 model selected 
    4885 
    4886 > select #3/A:123
    4887 
    4888 4 atoms, 3 bonds, 1 residue, 1 model selected 
    4889 
    4890 > select #3/A:123
    4891 
    4892 4 atoms, 3 bonds, 1 residue, 1 model selected 
    4893 
    4894 > select #3/A:123-124
    4895 
    4896 12 atoms, 11 bonds, 2 residues, 1 model selected 
    4897 
    4898 > select #3/A:123-124
    4899 
    4900 12 atoms, 11 bonds, 2 residues, 1 model selected 
    4901 
    4902 > select #3/A:124-125
    4903 
    4904 15 atoms, 14 bonds, 2 residues, 1 model selected 
    4905 
    4906 > select #3/A:124-125
    4907 
    4908 15 atoms, 14 bonds, 2 residues, 1 model selected 
    4909 
    4910 > select #3/A:124
    4911 
    4912 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4913 
    4914 > select #3/A:124
    4915 
    4916 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4917 
    4918 > style sel stick
    4919 
    4920 Changed 8 atom styles 
    4921 
    4922 > show sel atoms
    4923 
    4924 > color sel red
    4925 
    4926 > select #3/A:163
    4927 
    4928 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4929 
    4930 > select #3/A:163
    4931 
    4932 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4933 
    4934 > style sel stick
    4935 
    4936 Changed 8 atom styles 
    4937 
    4938 > show sel atoms
    4939 
    4940 > hide sel atoms
    4941 
    4942 > select #3/A:150
    4943 
    4944 7 atoms, 6 bonds, 1 residue, 1 model selected 
    4945 
    4946 > style sel stick
    4947 
    4948 Changed 7 atom styles 
    4949 
    4950 > show sel atoms
    4951 
    4952 > color sel gray
    4953 
    4954 > select clear
    4955 
    4956 > save /Users/mauriciocomas/Desktop/image14.png supersample 3
    4957 
    4958 > hide #3 models
    4959 
    4960 > show #9 models
    4961 
    4962 > hide #9 models
    4963 
    4964 > show #6 models
    4965 
    4966 > ui tool show "Show Sequence Viewer"
    4967 
    4968 > sequence chain #6/A
    4969 
    4970 Alignment identifier is 6/A 
    4971 
    4972 > select #6/A:138
    4973 
    4974 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4975 
    4976 > select #6/A:138
    4977 
    4978 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4979 
    4980 > style sel stick
    4981 
    4982 Changed 9 atom styles 
    4983 
    4984 > show sel atoms
    4985 
    4986 > hide sel atoms
    4987 
    4988 > select #6/A:125
    4989 
    4990 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4991 
    4992 > select #6/A:125
    4993 
    4994 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4995 
    4996 > select #6/A:127
    4997 
    4998 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4999 
    5000 > select #6/A:127
    5001 
    5002 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5003 
    5004 > show sel cartoons
    5005 
    5006 > show sel atoms
    5007 
    5008 > color sel blue
    5009 
    5010 > select #2/I:154
    5011 
    5012 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5013 
    5014 > select #6/A:157
    5015 
    5016 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5017 
    5018 > select #6/A:156
    5019 
    5020 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5021 
    5022 > select #6/A:156
    5023 
    5024 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5025 
    5026 > style sel stick
    5027 
    5028 Changed 9 atom styles 
    5029 
    5030 > show sel atoms
    5031 
    5032 > color sel blue
    5033 
    5034 > save /Users/mauriciocomas/Desktop/image15.png supersample 3
    5035 
    5036 > hide #6 models
    5037 
    5038 > show #!5 models
    5039 
    5040 > ui tool show "Show Sequence Viewer"
    5041 
    5042 > sequence chain #5/C
    5043 
    5044 Alignment identifier is 5/C 
    5045 
    5046 > select clear
    5047 
    5048 > select #5/C:121
    5049 
    5050 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5051 
    5052 > select #5/C:120
    5053 
    5054 4 atoms, 3 bonds, 1 residue, 1 model selected 
    5055 
    5056 > select #5/C:120
    5057 
    5058 4 atoms, 3 bonds, 1 residue, 1 model selected 
    5059 
    5060 > select #5/C:121
    5061 
    5062 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5063 
    5064 > select #5/C:121
    5065 
    5066 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5067 
    5068 > select #5/C:118
    5069 
    5070 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5071 
    5072 > select #5/C:118
    5073 
    5074 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5075 
    5076 > select #5/C:119
    5077 
    5078 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5079 
    5080 > select #5/C:119
    5081 
    5082 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5083 
    5084 > select #5/C:121
    5085 
    5086 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5087 
    5088 > select #5/C:121
    5089 
    5090 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5091 
    5092 > style sel stick
    5093 
    5094 Changed 9 atom styles 
    5095 
    5096 > show sel atoms
    5097 
    5098 > color sel red
    5099 
    5100 > color sel dim gray
    5101 
    5102 > select #5/C:150
    5103 
    5104 5 atoms, 4 bonds, 1 residue, 1 model selected 
    5105 
    5106 > select #5/C:119-120
    5107 
    5108 12 atoms, 11 bonds, 2 residues, 1 model selected 
    5109 
    5110 > select #5/C:119-120
    5111 
    5112 12 atoms, 11 bonds, 2 residues, 1 model selected 
    5113 
    5114 > select #5/C:120
    5115 
    5116 4 atoms, 3 bonds, 1 residue, 1 model selected 
    5117 
    5118 > select #5/C:120
    5119 
    5120 4 atoms, 3 bonds, 1 residue, 1 model selected 
    5121 
    5122 > style sel stick
    5123 
    5124 Changed 4 atom styles 
    5125 
    5126 > show sel atoms
    5127 
    5128 > hide sel atoms
    5129 
    5130 > select #5/C:117
    5131 
    5132 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5133 
    5134 > select #5/C:117-123
    5135 
    5136 52 atoms, 51 bonds, 7 residues, 1 model selected 
    5137 
    5138 > select #5/C:115
    5139 
    5140 7 atoms, 7 bonds, 1 residue, 1 model selected 
    5141 
    5142 > select #5/C:115-118
    5143 
    5144 31 atoms, 31 bonds, 4 residues, 1 model selected 
    5145 
    5146 > select #5/C:150
    5147 
    5148 5 atoms, 4 bonds, 1 residue, 1 model selected 
    5149 
    5150 > select #5/C:148
    5151 
    5152 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5153 
    5154 > select #5/C:148-149
    5155 
    5156 13 atoms, 12 bonds, 2 residues, 1 model selected 
    5157 
    5158 > select #5/C:147
    5159 
    5160 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5161 
    5162 > select #5/C:147
    5163 
    5164 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5165 
    5166 > select #5/C:145
    5167 
    5168 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5169 
    5170 > select #5/C:145-146
    5171 
    5172 17 atoms, 16 bonds, 2 residues, 1 model selected 
    5173 
    5174 > select #5/C:146
    5175 
    5176 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5177 
    5178 > select #5/C:146
    5179 
    5180 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5181 
    5182 > style sel stick
    5183 
    5184 Changed 9 atom styles 
    5185 
    5186 > show sel atoms
    5187 
    5188 > hide sel atoms
    5189 
    5190 > select #5/C:146-147
    5191 
    5192 18 atoms, 17 bonds, 2 residues, 1 model selected 
    5193 
    5194 > select #5/C:146-147
    5195 
    5196 18 atoms, 17 bonds, 2 residues, 1 model selected 
    5197 
    5198 > select #5/C:147-148
    5199 
    5200 17 atoms, 16 bonds, 2 residues, 1 model selected 
    5201 
    5202 > select #5/C:147-148
    5203 
    5204 17 atoms, 16 bonds, 2 residues, 1 model selected 
    5205 
    5206 > select #5/C:147
    5207 
    5208 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5209 
    5210 > select #5/C:147
    5211 
    5212 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5213 
    5214 > show sel cartoons
    5215 
    5216 > style sel stick
    5217 
    5218 Changed 9 atom styles 
    5219 
    5220 > show sel atoms
    5221 
    5222 > color sel dim gray
    5223 
    5224 > save /Users/mauriciocomas/Desktop/image16.png supersample 3
    5225 
    5226 > hide #!5 models
    5227 
    5228 > show #4 models
    5229 
    5230 > select clear
    5231 
    5232 > ui mousemode right zoom
    5233 
    5234 > ui mousemode right translate
    5235 
    5236 > ui mousemode right select
    5237 
    5238 > ui tool show "Show Sequence Viewer"
    5239 
    5240 > sequence chain #4/L
    5241 
    5242 Alignment identifier is 4/L 
    5243 
    5244 > select #4/L:135
    5245 
    5246 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5247 
    5248 > select #4/L:135-136
    5249 
    5250 17 atoms, 16 bonds, 2 residues, 1 model selected 
    5251 
    5252 > select #4/L:135
    5253 
    5254 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5255 
    5256 > select #4/L:135
    5257 
    5258 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5259 
    5260 > style sel stick
    5261 
    5262 Changed 9 atom styles 
    5263 
    5264 > show sel atoms
    5265 
    5266 > color sel blue
    5267 
    5268 > select #4/L:164
    5269 
    5270 5 atoms, 4 bonds, 1 residue, 1 model selected 
    5271 
    5272 > select #4/L:165
    5273 
    5274 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5275 
    5276 > select #4/L:165-166
    5277 
    5278 17 atoms, 16 bonds, 2 residues, 1 model selected 
    5279 
    5280 > select #4/L:162
    5281 
    5282 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5283 
    5284 > select #4/L:162
    5285 
    5286 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5287 
    5288 > select #4/L:161
    5289 
    5290 7 atoms, 6 bonds, 1 residue, 1 model selected 
    5291 
    5292 > select #4/L:161
    5293 
    5294 7 atoms, 6 bonds, 1 residue, 1 model selected 
    5295 
    5296 > style sel stick
    5297 
    5298 Changed 7 atom styles 
    5299 
    5300 > show sel atoms
    5301 
    5302 > color sel dim gray
    5303 
    5304 > save
    5305 > /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
    5306 
    5307 ——— End of log from Fri Mar 17 10:55:50 2023 ———
    5308 
    5309 opened ChimeraX session 
    5310 
    5311 > show #1 models
    5312 
    5313 > hide #4 models
    5314 
    5315 > ui mousemode right select
    5316 
    5317 > select #1/C:127
    5318 
    5319 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5320 
    5321 > color sel red
    5322 
    5323 > select clear
    5324 
    5325 > select clear
    5326 
    5327 > save /Users/mauriciocomas/Desktop/image1.png supersample 3
    5328 
    5329 > save
    5330 > /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
    5331 
    5332 ——— End of log from Thu Mar 23 12:13:26 2023 ———
    5333 
    5334 opened ChimeraX session 
    5335 
    5336 > hide #1 models
    5337 
    5338 > ui mousemode right select
    5339 
    5340 > select #2/I:126
    5341 
    5342 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5343 
    5344 > select #2/I:120
    5345 
    5346 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5347 
    5348 > select #2/I:120
    5349 
    5350 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5351 
    5352 > select #2/I:126
    5353 
    5354 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5355 
    5356 > select #2/I:126
    5357 
    5358 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5359 
    5360 > save "/Users/mauriciocomas/Desktop/3j2w monomer" format fasta alignment 2/I
    5361 
    5362 > select #2/I:128
    5363 
    5364 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5365 
    5366 > select #2/I:128
    5367 
    5368 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5369 
    5370 > ui mousemode right "move label"
    5371 
    5372 > ui mousemode right label
    5373 
    5374 > label #2/I:128
    5375 
    5376 > ui mousemode right "move label"
    5377 
    5378 > ui mousemode right label
    5379 
    5380 > label delete residues
    5381 
    5382 > select #2/I:126
    5383 
    5384 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5385 
    5386 > select #2/I:126-127
    5387 
    5388 13 atoms, 12 bonds, 2 residues, 1 model selected 
    5389 
    5390 > select #2/I:126
    5391 
    5392 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5393 
    5394 > select #2/I:126
    5395 
    5396 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5397 
    5398 > select #2/I:128
    5399 
    5400 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5401 
    5402 > select #2/I:128
    5403 
    5404 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5405 
    5406 > select #2/I:154
    5407 
    5408 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5409 
    5410 > select #2/I:154
    5411 
    5412 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5413 
    5414 > select #2/I:147
    5415 
    5416 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5417 
    5418 > select #2/I:147
    5419 
    5420 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5421 
    5422 > select #2/I:147
    5423 
    5424 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5425 
    5426 > select #2/I:147
    5427 
    5428 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5429 
    5430 > select #2/I:154
    5431 
    5432 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5433 
    5434 > select #2/I:154
    5435 
    5436 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5437 
    5438 > select #2/I:147
    5439 
    5440 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5441 
    5442 > select #2/I:147
    5443 
    5444 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5445 
    5446 > select #2/I:122
    5447 
    5448 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5449 
    5450 > select #2/I:122
    5451 
    5452 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5453 
    5454 > select #2/I:126
    5455 
    5456 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5457 
    5458 > select #2/I:126
    5459 
    5460 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5461 
    5462 > select #2/I:128
    5463 
    5464 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5465 
    5466 > select #2/I:128
    5467 
    5468 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5469 
    5470 > select #2/I:154
    5471 
    5472 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5473 
    5474 > select #2/I:154
    5475 
    5476 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5477 
    5478 > select #2/I:157
    5479 
    5480 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5481 
    5482 > select #2/I:157
    5483 
    5484 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5485 
    5486 > style sel stick
    5487 
    5488 Changed 9 atom styles 
    5489 
    5490 > show sel atoms
    5491 
    5492 > color sel blue
    5493 
    5494 > ui mousemode right select
    5495 
    5496 > select #2/I:147
    5497 
    5498 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5499 
    5500 > hide sel atoms
    5501 
    5502 > ui tool show "Color Actions"
    5503 
    5504 > color sel bychain
    5505 
    5506 > color sel cyan
    5507 
    5508 > select clear
    5509 
    5510 > select #2/I:180
    5511 
    5512 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5513 
    5514 > select #2/I:180
    5515 
    5516 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5517 
    5518 > select #2/I:190
    5519 
    5520 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5521 
    5522 > select #2/I:190
    5523 
    5524 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5525 
    5526 > select #2/I:190
    5527 
    5528 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5529 
    5530 > select #2/I:190
    5531 
    5532 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5533 
    5534 > select #2/I:183
    5535 
    5536 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5537 
    5538 > select #2/I:183
    5539 
    5540 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5541 
    5542 > select #2/I:139
    5543 
    5544 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5545 
    5546 > select #2/I:139
    5547 
    5548 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5549 
    5550 > select #2/I:183
    5551 
    5552 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5553 
    5554 > select #2/I:183
    5555 
    5556 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5557 
    5558 > select #2/I:178
    5559 
    5560 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5561 
    5562 > select #2/I:178
    5563 
    5564 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5565 
    5566 > style sel stick
    5567 
    5568 Changed 9 atom styles 
    5569 
    5570 > show sel atoms
    5571 
    5572 > color sel blue
    5573 
    5574 > select #2/I:240
    5575 
    5576 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5577 
    5578 > select #2/I:240
    5579 
    5580 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5581 
    5582 > select #2/I:126
    5583 
    5584 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5585 
    5586 > select #2/I:128
    5587 
    5588 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5589 
    5590 > select #2/I:157
    5591 
    5592 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5593 
    5594 > select #2/I:154
    5595 
    5596 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5597 
    5598 > select #2/I:178
    5599 
    5600 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5601 
    5602 > select #2/I:183
    5603 
    5604 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5605 
    5606 > select clear
    5607 
    5608 > select #2/I:165
    5609 
    5610 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5611 
    5612 > hide sel atoms
    5613 
    5614 > color sel cyan
    5615 
    5616 > select #2/I:190@CB
    5617 
    5618 1 atom, 1 residue, 1 model selected 
    5619 
    5620 > select clear
    5621 
    5622 > select #2/I:126
    5623 
    5624 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5625 
    5626 > select #2/I:128
    5627 
    5628 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5629 
    5630 > select #2/I:154
    5631 
    5632 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5633 
    5634 > select #2/I:154
    5635 
    5636 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5637 
    5638 > select #2/I:157
    5639 
    5640 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5641 
    5642 > select #2/I:157
    5643 
    5644 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5645 
    5646 > select #2/I:178
    5647 
    5648 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5649 
    5650 > select #2/I:183
    5651 
    5652 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5653 
    5654 > select #2/I:190
    5655 
    5656 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5657 
    5658 > select #2/I:240
    5659 
    5660 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5661 
    5662 > select clear
    5663 
    5664 > save /Users/mauriciocomas/Desktop/image2.png supersample 3
    5665 
    5666 > select #2/I:157
    5667 
    5668 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5669 
    5670 > select #2/I:178
    5671 
    5672 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5673 
    5674 > select clear
    5675 
    5676 > select #2/I:183
    5677 
    5678 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5679 
    5680 > select #2/I:183
    5681 
    5682 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5683 
    5684 > select #2/I:183
    5685 
    5686 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5687 
    5688 > select #2/I:183
    5689 
    5690 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5691 
    5692 > select #2/I:190
    5693 
    5694 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5695 
    5696 > select #2/I:190
    5697 
    5698 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5699 
    5700 > select #2/I:190
    5701 
    5702 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5703 
    5704 > show #!7 models
    5705 
    5706 > select #7/A:147
    5707 
    5708 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5709 
    5710 > hide sel atoms
    5711 
    5712 > color sel hot pink
    5713 
    5714 > ui tool show "Color Actions"
    5715 
    5716 > select #7/A:126
    5717 
    5718 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5719 
    5720 > color sel red
    5721 
    5722 > select #7/A:128
    5723 
    5724 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5725 
    5726 > select #7/A:126
    5727 
    5728 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5729 
    5730 > select #2/I:128
    5731 
    5732 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5733 
    5734 > select #7/A:128
    5735 
    5736 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5737 
    5738 > select #7/A:128
    5739 
    5740 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5741 
    5742 > select clear
    5743 
    5744 > select #7/A:128
    5745 
    5746 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5747 
    5748 > ui mousemode right label
    5749 
    5750 > label #7/A:128
    5751 
    5752 > ui mousemode right "move label"
    5753 
    5754 > ui mousemode right label
    5755 
    5756 > label delete residues
    5757 
    5758 > color sel blue
    5759 
    5760 > ui tool show "Show Sequence Viewer"
    5761 
    5762 > sequence chain #7/A
    5763 
    5764 Alignment identifier is 7/A 
    5765 
    5766 > ui mousemode right select
    5767 
    5768 > select #7/A:154@CB
    5769 
    5770 1 atom, 1 residue, 1 model selected 
    5771 
    5772 > select #7/A:154
    5773 
    5774 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5775 
    5776 > select #7/A:154
    5777 
    5778 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5779 
    5780 > color sel red
    5781 
    5782 > select #2/I:157
    5783 
    5784 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5785 
    5786 > select #7/A:157
    5787 
    5788 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5789 
    5790 > select #7/A:157
    5791 
    5792 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5793 
    5794 > style sel stick
    5795 
    5796 Changed 9 atom styles 
    5797 
    5798 > show sel atoms
    5799 
    5800 > color sel blue
    5801 
    5802 > select #7/A:157
    5803 
    5804 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5805 
    5806 > select #7/A:157
    5807 
    5808 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5809 
    5810 > select #7/A:178
    5811 
    5812 11 atoms, 10 bonds, 1 residue, 1 model selected 
    5813 
    5814 > select #7/A:126
    5815 
    5816 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5817 
    5818 > select #7/A:128
    5819 
    5820 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5821 
    5822 > select #7/A:157
    5823 
    5824 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5825 
    5826 > select #2/I:154
    5827 
    5828 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5829 
    5830 > select #7/A:154@CB
    5831 
    5832 1 atom, 1 residue, 1 model selected 
    5833 
    5834 > select #2/I:178
    5835 
    5836 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5837 
    5838 > select #7/A:178
    5839 
    5840 11 atoms, 10 bonds, 1 residue, 1 model selected 
    5841 
    5842 > style sel stick
    5843 
    5844 Changed 11 atom styles 
    5845 
    5846 > show sel atoms
    5847 
    5848 > color sel blue
    5849 
    5850 > select #7/A:183@CB
    5851 
    5852 1 atom, 1 residue, 1 model selected 
    5853 
    5854 > color sel blue
    5855 
    5856 > select #7/A:190@CB
    5857 
    5858 1 atom, 1 residue, 1 model selected 
    5859 
    5860 > color sel red
    5861 
    5862 > select #7/A:240
    5863 
    5864 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5865 
    5866 > color sel red
    5867 
    5868 > select clear
    5869 
    5870 > save /Users/mauriciocomas/Desktop/image2.png supersample 3
    5871 
    5872 > select clear
    5873 
    5874 > select #7/A:190
    5875 
    5876 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5877 
    5878 > color sel red
    5879 
    5880 > select clear
    5881 
    5882 > save /Users/mauriciocomas/Desktop/image2.png supersample 3
    5883 
    5884 > select #7/A:183@CA
    5885 
    5886 1 atom, 1 residue, 1 model selected 
    5887 
    5888 > select #7/A:183
    5889 
    5890 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5891 
    5892 > color sel blue
    5893 
    5894 > select clear
    5895 
    5896 > save /Users/mauriciocomas/Desktop/image2.png supersample 3
    5897 
    5898 > save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
    5899 > structures correct.cxs"
    5900 
    5901 > hide #!7 models
    5902 
    5903 > hide #2 models
    5904 
    5905 > show #2 models
    5906 
    5907 > show #9 models
    5908 
    5909 > select #9/A:138
    5910 
    5911 7 atoms, 7 bonds, 1 residue, 1 model selected 
    5912 
    5913 > style sel stick
    5914 
    5915 Changed 7 atom styles 
    5916 
    5917 > style sel stick
    5918 
    5919 Changed 7 atom styles 
    5920 
    5921 > hide sel atoms
    5922 
    5923 > select #9/A:117
    5924 
    5925 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5926 
    5927 > color sel red
    5928 
    5929 > select #9/A:119
    5930 
    5931 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5932 
    5933 > color sel blue
    5934 
    5935 > select #9/A:145@CB
    5936 
    5937 1 atom, 1 residue, 1 model selected 
    5938 
    5939 > select #9/A:148
    5940 
    5941 11 atoms, 10 bonds, 1 residue, 1 model selected 
    5942 
    5943 > select #9/A:145
    5944 
    5945 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5946 
    5947 > color sel red
    5948 
    5949 > ui tool show "Show Sequence Viewer"
    5950 
    5951 > sequence chain #9/A
    5952 
    5953 Alignment identifier is 9/A 
    5954 
    5955 > select #9/A:148
    5956 
    5957 11 atoms, 10 bonds, 1 residue, 1 model selected 
    5958 
    5959 > style sel stick
    5960 
    5961 Changed 11 atom styles 
    5962 
    5963 > show sel atoms
    5964 
    5965 > color sel blue
    5966 
    5967 > select #2/I:178
    5968 
    5969 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5970 
    5971 > select #2/I:179
    5972 
    5973 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5974 
    5975 > select #9/A:170
    5976 
    5977 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5978 
    5979 > select #9/A:169
    5980 
    5981 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5982 
    5983 > select #9/A:169
    5984 
    5985 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5986 
    5987 > select #9/A:169
    5988 
    5989 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5990 
    5991 > style sel stick
    5992 
    5993 Changed 9 atom styles 
    5994 
    5995 > show sel atoms
    5996 
    5997 > color sel blue
    5998 
    5999 > select #9/A:174@CD
    6000 
    6001 1 atom, 1 residue, 1 model selected 
    6002 
    6003 > select #9/A:174
    6004 
    6005 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6006 
    6007 > select #9/A:174
    6008 
    6009 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6010 
    6011 > color sel blue
    6012 
    6013 > select #9/A:169
    6014 
    6015 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6016 
    6017 > select #9/A:169
    6018 
    6019 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6020 
    6021 > select #9/A:181
    6022 
    6023 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6024 
    6025 > color sel red
    6026 
    6027 > select #9/A:231@CA
    6028 
    6029 1 atom, 1 residue, 1 model selected 
    6030 
    6031 > select #9/A:231
    6032 
    6033 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6034 
    6035 > select #9/A:231
    6036 
    6037 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6038 
    6039 > color sel red
    6040 
    6041 > select clear
    6042 
    6043 > save /Users/mauriciocomas/Desktop/image2.png supersample 3
    6044 
    6045 > save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
    6046 > structures correct.cxs"
    6047 
    6048 > hide #9 models
    6049 
    6050 > show #1 models
    6051 
    6052 > ui tool show "Show Sequence Viewer"
    6053 
    6054 > sequence chain #1/C
    6055 
    6056 Alignment identifier is 1/C 
    6057 
    6058 > hide #1-2 atoms
    6059 
    6060 > undo
    6061 
    6062 > select #1/C:148
    6063 
    6064 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6065 
    6066 > hide sel atoms
    6067 
    6068 > select #1/C:127
    6069 
    6070 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6071 
    6072 > color sel red
    6073 
    6074 > select #1/C:129
    6075 
    6076 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6077 
    6078 > color sel blue
    6079 
    6080 > select #1/C:129
    6081 
    6082 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6083 
    6084 > select #1/C:129
    6085 
    6086 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6087 
    6088 > select #1/C:155
    6089 
    6090 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6091 
    6092 > select #2/I:157
    6093 
    6094 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6095 
    6096 > select #1/C:157-158
    6097 
    6098 14 atoms, 13 bonds, 2 residues, 1 model selected 
    6099 
    6100 > select #1/C:157-158
    6101 
    6102 14 atoms, 13 bonds, 2 residues, 1 model selected 
    6103 
    6104 > select #1/C:158
    6105 
    6106 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6107 
    6108 > select #1/C:158
    6109 
    6110 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6111 
    6112 > style sel stick
    6113 
    6114 Changed 9 atom styles 
    6115 
    6116 > show sel atoms
    6117 
    6118 > color sel blue
    6119 
    6120 > ui mousemode right select
    6121 
    6122 > select #1/C:155
    6123 
    6124 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6125 
    6126 > color sel red
    6127 
    6128 > select #2/I:178
    6129 
    6130 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6131 
    6132 > select #1/C:179
    6133 
    6134 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6135 
    6136 > select #1/C:179
    6137 
    6138 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6139 
    6140 > style sel stick
    6141 
    6142 Changed 9 atom styles 
    6143 
    6144 > show sel atoms
    6145 
    6146 > color sel blue
    6147 
    6148 > select #1/C:179
    6149 
    6150 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6151 
    6152 > select #1/C:179
    6153 
    6154 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6155 
    6156 > select #1/C:184
    6157 
    6158 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6159 
    6160 > color sel blue
    6161 
    6162 > select #1/C:191
    6163 
    6164 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6165 
    6166 > color sel red
    6167 
    6168 > select #1/C:241
    6169 
    6170 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6171 
    6172 > select #1/C:241
    6173 
    6174 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6175 
    6176 > color sel red
    6177 
    6178 > select #1/C:191
    6179 
    6180 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6181 
    6182 > select clear
    6183 
    6184 > save /Users/mauriciocomas/Desktop/image2.png supersample 3
    6185 
    6186 > save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
    6187 > structures correct.cxs"
    6188 
    6189 > hide #1 models
    6190 
    6191 > show #!8 models
    6192 
    6193 > select #8/A:133
    6194 
    6195 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6196 
    6197 > hide sel cartoons
    6198 
    6199 > select #8/A:112
    6200 
    6201 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6202 
    6203 > ui tool show "Show Sequence Viewer"
    6204 
    6205 > sequence chain #8/A
    6206 
    6207 Alignment identifier is 8/A 
    6208 
    6209 > color sel red
    6210 
    6211 > select #2/I:128
    6212 
    6213 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6214 
    6215 > select #8/A:114
    6216 
    6217 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6218 
    6219 > color sel blue
    6220 
    6221 > select #8/A:133@N
    6222 
    6223 1 atom, 1 residue, 1 model selected 
    6224 
    6225 > select #8/A:133@CA
    6226 
    6227 1 atom, 1 residue, 1 model selected 
    6228 
    6229 > select #8/A:133
    6230 
    6231 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6232 
    6233 > select #8/A:133
    6234 
    6235 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6236 
    6237 > hide sel atoms
    6238 
    6239 > select #8/A:143
    6240 
    6241 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6242 
    6243 > select #8/A:143
    6244 
    6245 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6246 
    6247 > select #8/A:143
    6248 
    6249 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6250 
    6251 > select #8/A:143
    6252 
    6253 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6254 
    6255 > style sel stick
    6256 
    6257 Changed 9 atom styles 
    6258 
    6259 > show sel atoms
    6260 
    6261 > color sel blue
    6262 
    6263 > select #8/A:140
    6264 
    6265 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6266 
    6267 > select #8/A:140
    6268 
    6269 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6270 
    6271 > color sel red
    6272 
    6273 > select #2/I:178
    6274 
    6275 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6276 
    6277 > select #8/A:164
    6278 
    6279 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6280 
    6281 > select #8/A:164
    6282 
    6283 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6284 
    6285 > style sel stick
    6286 
    6287 Changed 9 atom styles 
    6288 
    6289 > show sel atoms
    6290 
    6291 > color sel blue
    6292 
    6293 > select #8/A:164
    6294 
    6295 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6296 
    6297 > select #8/A:164
    6298 
    6299 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6300 
    6301 > select #8/A:169
    6302 
    6303 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6304 
    6305 > select #8/A:169
    6306 
    6307 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6308 
    6309 > color sel blue
    6310 
    6311 > select clear
    6312 
    6313 > select #8/A:242
    6314 
    6315 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6316 
    6317 > select #2/I:190
    6318 
    6319 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6320 
    6321 > select #2/I:178
    6322 
    6323 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6324 
    6325 > select #2/I:178-179
    6326 
    6327 15 atoms, 14 bonds, 2 residues, 1 model selected 
    6328 
    6329 > select #8/A:176
    6330 
    6331 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6332 
    6333 > select #8/A:176
    6334 
    6335 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6336 
    6337 > color sel red
    6338 
    6339 > select #8/A:226
    6340 
    6341 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6342 
    6343 > select #8/A:226
    6344 
    6345 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6346 
    6347 > color sel red
    6348 
    6349 > select clear
    6350 
    6351 > save /Users/mauriciocomas/Desktop/image2.png supersample 3
    6352 
    6353 > save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
    6354 > structures correct.cxs"
    6355 
    6356 > show #3 models
    6357 
    6358 > hide #!8 models
    6359 
    6360 > ui tool show "Show Sequence Viewer"
    6361 
    6362 > sequence chain #3/A
    6363 
    6364 Alignment identifier is 3/A 
    6365 
    6366 > select #3/A:143
    6367 
    6368 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6369 
    6370 > hide sel atoms
    6371 
    6372 > select #3/A:161
    6373 
    6374 5 atoms, 4 bonds, 1 residue, 1 model selected 
    6375 
    6376 > hide sel atoms
    6377 
    6378 > select #3/A:121
    6379 
    6380 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6381 
    6382 > color sel red
    6383 
    6384 > select #3/A:124
    6385 
    6386 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6387 
    6388 > color sel red
    6389 
    6390 > select #3/A:150@CB
    6391 
    6392 1 atom, 1 residue, 1 model selected 
    6393 
    6394 > select #3/A:150@CB
    6395 
    6396 1 atom, 1 residue, 1 model selected 
    6397 
    6398 > select #3/A:150
    6399 
    6400 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6401 
    6402 > select #3/A:150
    6403 
    6404 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6405 
    6406 > select #2/I:154
    6407 
    6408 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6409 
    6410 > select #3/A:150
    6411 
    6412 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6413 
    6414 > select #3/A:150
    6415 
    6416 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6417 
    6418 > color sel dim gray
    6419 
    6420 > select #2/I:154@CB
    6421 
    6422 1 atom, 1 residue, 1 model selected 
    6423 
    6424 > select #3/A:153
    6425 
    6426 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6427 
    6428 > select #3/A:153-154
    6429 
    6430 17 atoms, 16 bonds, 2 residues, 1 model selected 
    6431 
    6432 > select #3/A:153
    6433 
    6434 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6435 
    6436 > select #3/A:153
    6437 
    6438 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6439 
    6440 > style sel stick
    6441 
    6442 Changed 9 atom styles 
    6443 
    6444 > style sel stick
    6445 
    6446 Changed 9 atom styles 
    6447 
    6448 > show sel atoms
    6449 
    6450 > color sel blue
    6451 
    6452 > select #2/I:178
    6453 
    6454 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6455 
    6456 > select #3/A:174
    6457 
    6458 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6459 
    6460 > select #3/A:174
    6461 
    6462 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6463 
    6464 > select #3/A:174
    6465 
    6466 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6467 
    6468 > style sel stick
    6469 
    6470 Changed 11 atom styles 
    6471 
    6472 > style sel stick
    6473 
    6474 Changed 11 atom styles 
    6475 
    6476 > show sel atoms
    6477 
    6478 > color sel blue
    6479 
    6480 > select #3/A:174
    6481 
    6482 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6483 
    6484 > select #3/A:174
    6485 
    6486 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6487 
    6488 > select #3/A:174
    6489 
    6490 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6491 
    6492 > select #3/A:174
    6493 
    6494 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6495 
    6496 > select #3/A:176
    6497 
    6498 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6499 
    6500 > select #3/A:176-177
    6501 
    6502 14 atoms, 13 bonds, 2 residues, 1 model selected 
    6503 
    6504 > select #3/A:174
    6505 
    6506 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6507 
    6508 > select #3/A:174
    6509 
    6510 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6511 
    6512 > select #3/A:179@CA
    6513 
    6514 1 atom, 1 residue, 1 model selected 
    6515 
    6516 > select #3/A:179
    6517 
    6518 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6519 
    6520 > select #3/A:179
    6521 
    6522 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6523 
    6524 > select #3/A:179
    6525 
    6526 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6527 
    6528 > color sel dim gray
    6529 
    6530 > select #2/I:183
    6531 
    6532 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6533 
    6534 > select #3/A:174
    6535 
    6536 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6537 
    6538 > select #3/A:174
    6539 
    6540 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6541 
    6542 > select #3/A:180
    6543 
    6544 12 atoms, 12 bonds, 1 residue, 1 model selected 
    6545 
    6546 > select #3/A:180
    6547 
    6548 12 atoms, 12 bonds, 1 residue, 1 model selected 
    6549 
    6550 > select #3/A:186
    6551 
    6552 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6553 
    6554 > color sel red
    6555 
    6556 > select #3/A:236
    6557 
    6558 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6559 
    6560 > color sel red
    6561 
    6562 > select clear
    6563 
    6564 > save /Users/mauriciocomas/Desktop/image2.png supersample 3
    6565 
    6566 > select #3/A:186
    6567 
    6568 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6569 
    6570 > select #3/A:236
    6571 
    6572 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6573 
    6574 > select #3/A:236
    6575 
    6576 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6577 
    6578 > select #2/I:240@OE2
    6579 
    6580 1 atom, 1 residue, 1 model selected 
    6581 
    6582 > select #2/I:240@CB
    6583 
    6584 1 atom, 1 residue, 1 model selected 
    6585 
    6586 > select #3/A:236
    6587 
    6588 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6589 
    6590 > save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
    6591 > structures correct.cxs"
    6592 
    6593 > show #6 models
    6594 
    6595 > hide #3 models
    6596 
    6597 > ui tool show "Show Sequence Viewer"
    6598 
    6599 > sequence chain #6/A
    6600 
    6601 Alignment identifier is 6/A 
    6602 
    6603 > select #6/A:146@CA
    6604 
    6605 1 atom, 1 residue, 1 model selected 
    6606 
    6607 > select #6/A:146
    6608 
    6609 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6610 
    6611 > hide sel atoms
    6612 
    6613 > select #6/A:164
    6614 
    6615 6 atoms, 5 bonds, 1 residue, 1 model selected 
    6616 
    6617 > hide sel atoms
    6618 
    6619 > select #6/A:125
    6620 
    6621 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6622 
    6623 > color sel red
    6624 
    6625 > select #6/A:127
    6626 
    6627 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6628 
    6629 > color sel red
    6630 
    6631 > select #2/I:154
    6632 
    6633 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6634 
    6635 > select #6/A:156@CA
    6636 
    6637 1 atom, 1 residue, 1 model selected 
    6638 
    6639 > select #6/A:156
    6640 
    6641 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6642 
    6643 > select #6/A:156
    6644 
    6645 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6646 
    6647 > select #6/A:156
    6648 
    6649 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6650 
    6651 > select #6/A:127
    6652 
    6653 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6654 
    6655 > color sel blue
    6656 
    6657 > select #2/I:153
    6658 
    6659 5 atoms, 4 bonds, 1 residue, 1 model selected 
    6660 
    6661 > select #6/A:156
    6662 
    6663 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6664 
    6665 > color sel blue
    6666 
    6667 > select #2/I:154
    6668 
    6669 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6670 
    6671 > select #6/A:168
    6672 
    6673 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6674 
    6675 > select #6/A:168
    6676 
    6677 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6678 
    6679 > select #6/A:153
    6680 
    6681 5 atoms, 4 bonds, 1 residue, 1 model selected 
    6682 
    6683 > select #6/A:156
    6684 
    6685 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6686 
    6687 > select #6/A:156
    6688 
    6689 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6690 
    6691 > select #2/I:154
    6692 
    6693 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6694 
    6695 > select #2/I:152
    6696 
    6697 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6698 
    6699 > select #2/I:152-156
    6700 
    6701 34 atoms, 33 bonds, 5 residues, 1 model selected 
    6702 
    6703 > select #6/A:160
    6704 
    6705 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6706 
    6707 > select #6/A:160-162
    6708 
    6709 22 atoms, 21 bonds, 3 residues, 1 model selected 
    6710 
    6711 > select #6/A:148
    6712 
    6713 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6714 
    6715 > select #6/A:148-157
    6716 
    6717 75 atoms, 76 bonds, 10 residues, 1 model selected 
    6718 
    6719 > select #6/A:156
    6720 
    6721 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6722 
    6723 > select #6/A:156
    6724 
    6725 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6726 
    6727 > select #6/A:154
    6728 
    6729 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6730 
    6731 > select #6/A:154
    6732 
    6733 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6734 
    6735 > select #6/A:153
    6736 
    6737 5 atoms, 4 bonds, 1 residue, 1 model selected 
    6738 
    6739 > select #6/A:153
    6740 
    6741 5 atoms, 4 bonds, 1 residue, 1 model selected 
    6742 
    6743 > select #6/A:152
    6744 
    6745 7 atoms, 7 bonds, 1 residue, 1 model selected 
    6746 
    6747 > select #6/A:152
    6748 
    6749 7 atoms, 7 bonds, 1 residue, 1 model selected 
    6750 
    6751 > select #6/A:153
    6752 
    6753 5 atoms, 4 bonds, 1 residue, 1 model selected 
    6754 
    6755 > select #6/A:153
    6756 
    6757 5 atoms, 4 bonds, 1 residue, 1 model selected 
    6758 
    6759 > hide sel cartoons
    6760 
    6761 > show sel atoms
    6762 
    6763 > color sel dim gray
    6764 
    6765 > select #2/I:178
    6766 
    6767 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6768 
    6769 > select #6/A:177
    6770 
    6771 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6772 
    6773 > select #6/A:153
    6774 
    6775 5 atoms, 4 bonds, 1 residue, 1 model selected 
    6776 
    6777 > select #6/A:153
    6778 
    6779 5 atoms, 4 bonds, 1 residue, 1 model selected 
    6780 
    6781 > select #6/A:156-157
    6782 
    6783 17 atoms, 16 bonds, 2 residues, 1 model selected 
    6784 
    6785 > select #6/A:156-157
    6786 
    6787 17 atoms, 16 bonds, 2 residues, 1 model selected 
    6788 
    6789 > select #6/A:177
    6790 
    6791 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6792 
    6793 > select #6/A:177
    6794 
    6795 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6796 
    6797 > select #6/A:177
    6798 
    6799 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6800 
    6801 > style sel stick
    6802 
    6803 Changed 9 atom styles 
    6804 
    6805 > show sel atoms
    6806 
    6807 > color sel blue
    6808 
    6809 > select #6/A:182
    6810 
    6811 4 atoms, 3 bonds, 1 residue, 1 model selected 
    6812 
    6813 > select clear
    6814 
    6815 > select #6/A:183
    6816 
    6817 12 atoms, 12 bonds, 1 residue, 1 model selected 
    6818 
    6819 > select clear
    6820 
    6821 > select #6/A:182
    6822 
    6823 4 atoms, 3 bonds, 1 residue, 1 model selected 
    6824 
    6825 > select #6/A:183
    6826 
    6827 12 atoms, 12 bonds, 1 residue, 1 model selected 
    6828 
    6829 > select #6/A:183
    6830 
    6831 12 atoms, 12 bonds, 1 residue, 1 model selected 
    6832 
    6833 > select #6/A:182
    6834 
    6835 4 atoms, 3 bonds, 1 residue, 1 model selected 
    6836 
    6837 > select #6/A:182
    6838 
    6839 4 atoms, 3 bonds, 1 residue, 1 model selected 
    6840 
    6841 > style sel stick
    6842 
    6843 Changed 4 atom styles 
    6844 
    6845 > show sel atoms
    6846 
    6847 > color sel dim gray
    6848 
    6849 > select clear
    6850 
    6851 > select #6/A:189
    6852 
    6853 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6854 
    6855 > color sel red
    6856 
    6857 > select #6/A:239
    6858 
    6859 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6860 
    6861 > color sel red
    6862 
    6863 > select clear
    6864 
    6865 > save /Users/mauriciocomas/Desktop/image2.png supersample 3
    6866 
    6867 > save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
    6868 > structures correct.cxs"
    6869 
    6870 > hide #6 models
    6871 
    6872 > show #!5 models
    6873 
    6874 > ui tool show "Show Sequence Viewer"
    6875 
    6876 > sequence chain #5/C
    6877 
    6878 Alignment identifier is 5/C 
    6879 
    6880 > select #5/C:119
    6881 
    6882 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6883 
    6884 > select #5/C:119
    6885 
    6886 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6887 
    6888 > color sel dim gray
    6889 
    6890 > select #2/I:128
    6891 
    6892 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6893 
    6894 > select #5/C:121@CA
    6895 
    6896 1 atom, 1 residue, 1 model selected 
    6897 
    6898 > select #5/C:121
    6899 
    6900 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6901 
    6902 > select #5/C:121
    6903 
    6904 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6905 
    6906 > color sel dim gray
    6907 
    6908 > select #5/C:140
    6909 
    6910 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6911 
    6912 > hide sel atoms
    6913 
    6914 > select #5/C:147
    6915 
    6916 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6917 
    6918 > select #5/C:147
    6919 
    6920 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6921 
    6922 > color sel dim gray
    6923 
    6924 > select #5/C:150
    6925 
    6926 5 atoms, 4 bonds, 1 residue, 1 model selected 
    6927 
    6928 > select clear
    6929 
    6930 > select #2/I:157@CB
    6931 
    6932 1 atom, 1 residue, 1 model selected 
    6933 
    6934 > select #5/C:150
    6935 
    6936 5 atoms, 4 bonds, 1 residue, 1 model selected 
    6937 
    6938 > select #5/C:150
    6939 
    6940 5 atoms, 4 bonds, 1 residue, 1 model selected 
    6941 
    6942 > select #5/C:152
    6943 
    6944 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6945 
    6946 > select #5/C:152
    6947 
    6948 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6949 
    6950 > select #5/C:150
    6951 
    6952 5 atoms, 4 bonds, 1 residue, 1 model selected 
    6953 
    6954 > select #5/C:150-151
    6955 
    6956 13 atoms, 12 bonds, 2 residues, 1 model selected 
    6957 
    6958 > select #5/C:150
    6959 
    6960 5 atoms, 4 bonds, 1 residue, 1 model selected 
    6961 
    6962 > select #5/C:150
    6963 
    6964 5 atoms, 4 bonds, 1 residue, 1 model selected 
    6965 
    6966 > style sel stick
    6967 
    6968 Changed 5 atom styles 
    6969 
    6970 > show sel atoms
    6971 
    6972 > select #5/C:147
    6973 
    6974 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6975 
    6976 > select #5/C:147
    6977 
    6978 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6979 
    6980 > select #5/C:150
    6981 
    6982 5 atoms, 4 bonds, 1 residue, 1 model selected 
    6983 
    6984 > select #5/C:150
    6985 
    6986 5 atoms, 4 bonds, 1 residue, 1 model selected 
    6987 
    6988 > select #2/I:157
    6989 
    6990 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6991 
    6992 > select #2/I:157
    6993 
    6994 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6995 
    6996 > select #5/C:155-156
    6997 
    6998 14 atoms, 13 bonds, 2 residues, 1 model selected 
    6999 
    7000 > select #5/C:154-156
    7001 
    7002 23 atoms, 22 bonds, 3 residues, 1 model selected 
    7003 
    7004 > select #5/C:152
    7005 
    7006 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7007 
    7008 > select #5/C:152-153
    7009 
    7010 17 atoms, 16 bonds, 2 residues, 1 model selected 
    7011 
    7012 > select #5/C:152
    7013 
    7014 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7015 
    7016 > select #5/C:152
    7017 
    7018 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7019 
    7020 > select #2/I:161
    7021 
    7022 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7023 
    7024 > select #2/I:161
    7025 
    7026 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7027 
    7028 > select #5/C:154
    7029 
    7030 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7031 
    7032 > select #5/C:154
    7033 
    7034 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7035 
    7036 > select #5/C:153
    7037 
    7038 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7039 
    7040 > select #5/C:153
    7041 
    7042 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7043 
    7044 > select #2/I:159-160
    7045 
    7046 16 atoms, 16 bonds, 2 residues, 1 model selected 
    7047 
    7048 > select #2/I:159-160
    7049 
    7050 16 atoms, 16 bonds, 2 residues, 1 model selected 
    7051 
    7052 > select #2/I:160
    7053 
    7054 11 atoms, 11 bonds, 1 residue, 1 model selected 
    7055 
    7056 > select #2/I:160
    7057 
    7058 11 atoms, 11 bonds, 1 residue, 1 model selected 
    7059 
    7060 > select #5/C:152
    7061 
    7062 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7063 
    7064 > select #5/C:152
    7065 
    7066 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7067 
    7068 > select #2/I:159
    7069 
    7070 5 atoms, 4 bonds, 1 residue, 1 model selected 
    7071 
    7072 > select #2/I:159
    7073 
    7074 5 atoms, 4 bonds, 1 residue, 1 model selected 
    7075 
    7076 > select #5/C:152
    7077 
    7078 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7079 
    7080 > select #5/C:152
    7081 
    7082 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7083 
    7084 > select #5/C:149
    7085 
    7086 5 atoms, 4 bonds, 1 residue, 1 model selected 
    7087 
    7088 > select #5/C:149
    7089 
    7090 5 atoms, 4 bonds, 1 residue, 1 model selected 
    7091 
    7092 > select #5/C:150
    7093 
    7094 5 atoms, 4 bonds, 1 residue, 1 model selected 
    7095 
    7096 > select #5/C:150
    7097 
    7098 5 atoms, 4 bonds, 1 residue, 1 model selected 
    7099 
    7100 > color sel dim gray
    7101 
    7102 > select #2/I:178
    7103 
    7104 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7105 
    7106 > select #5/C:171
    7107 
    7108 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7109 
    7110 > select #5/C:171
    7111 
    7112 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7113 
    7114 > select #5/C:171
    7115 
    7116 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7117 
    7118 > style sel stick
    7119 
    7120 Changed 9 atom styles 
    7121 
    7122 > show sel cartoons
    7123 
    7124 > show sel atoms
    7125 
    7126 > color sel blue
    7127 
    7128 > select #5/C:171
    7129 
    7130 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7131 
    7132 > select #5/C:171
    7133 
    7134 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7135 
    7136 > select #5/C:158
    7137 
    7138 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7139 
    7140 > select #5/C:158
    7141 
    7142 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7143 
    7144 > hide sel atoms
    7145 
    7146 > select #5/C:175
    7147 
    7148 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7149 
    7150 > color sel dim gray
    7151 
    7152 > select #2/I:190@CG
    7153 
    7154 1 atom, 1 residue, 1 model selected 
    7155 
    7156 > select #5/C:183
    7157 
    7158 7 atoms, 7 bonds, 1 residue, 1 model selected 
    7159 
    7160 > color sel dim gray
    7161 
    7162 > select #5/C:233-234
    7163 
    7164 13 atoms, 12 bonds, 2 residues, 1 model selected 
    7165 
    7166 > select #5/C:233-234
    7167 
    7168 13 atoms, 12 bonds, 2 residues, 1 model selected 
    7169 
    7170 > select #5/C:233
    7171 
    7172 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7173 
    7174 > select #5/C:233
    7175 
    7176 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7177 
    7178 > color sel dim gray
    7179 
    7180 > select clear
    7181 
    7182 > save /Users/mauriciocomas/Desktop/image2.png supersample 3
    7183 
    7184 > save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
    7185 > structures correct.cxs"
    7186 
    7187 > hide #!5 models
    7188 
    7189 > show #4 models
    7190 
    7191 > ui tool show "Show Sequence Viewer"
    7192 
    7193 > sequence chain #4/L
    7194 
    7195 Alignment identifier is 4/L 
    7196 
    7197 > select #4/L:154
    7198 
    7199 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7200 
    7201 > hide sel atoms
    7202 
    7203 > select #4/L:172
    7204 
    7205 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7206 
    7207 > hide sel atoms
    7208 
    7209 > select #4/L:133
    7210 
    7211 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7212 
    7213 > color sel red
    7214 
    7215 > select #4/L:135
    7216 
    7217 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7218 
    7219 > color sel blue
    7220 
    7221 > select #4/L:161
    7222 
    7223 7 atoms, 6 bonds, 1 residue, 1 model selected 
    7224 
    7225 > select #4/L:161
    7226 
    7227 7 atoms, 6 bonds, 1 residue, 1 model selected 
    7228 
    7229 > color sel dim gray
    7230 
    7231 > select #4/L:164
    7232 
    7233 5 atoms, 4 bonds, 1 residue, 1 model selected 
    7234 
    7235 > style sel stick
    7236 
    7237 Changed 5 atom styles 
    7238 
    7239 > show sel atoms
    7240 
    7241 > color sel dim gray
    7242 
    7243 > select #4/L:185
    7244 
    7245 11 atoms, 10 bonds, 1 residue, 1 model selected 
    7246 
    7247 > select #4/L:164
    7248 
    7249 5 atoms, 4 bonds, 1 residue, 1 model selected 
    7250 
    7251 > select #2/I:178
    7252 
    7253 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7254 
    7255 > select clear
    7256 
    7257 > select #2/I:178
    7258 
    7259 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7260 
    7261 > select #2/I:178
    7262 
    7263 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7264 
    7265 > select #2/I:178
    7266 
    7267 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7268 
    7269 > select #2/I:178
    7270 
    7271 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7272 
    7273 > select #2/I:178
    7274 
    7275 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7276 
    7277 > select #4/L:185
    7278 
    7279 11 atoms, 10 bonds, 1 residue, 1 model selected 
    7280 
    7281 > style sel stick
    7282 
    7283 Changed 11 atom styles 
    7284 
    7285 > show sel atoms
    7286 
    7287 > color sel blue
    7288 
    7289 > select clear
    7290 
    7291 > select #4/L:190
    7292 
    7293 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7294 
    7295 > color sel blue
    7296 
    7297 > select #4/L:197
    7298 
    7299 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7300 
    7301 > color sel dim gray
    7302 
    7303 > select #4/L:247
    7304 
    7305 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7306 
    7307 > color sel red
    7308 
    7309 > select clear
    7310 
    7311 > save /Users/mauriciocomas/Desktop/image2.png supersample 3
    7312 
    7313 > save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
    7314 > structures correct.cxs"
    7315 
    7316 > save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
    7317 > structures correct.cxs"
    7318 
    7319 ——— End of log from Wed Mar 29 11:43:44 2023 ———
    7320 
    7321 opened ChimeraX session 
    7322 
    7323 > hide #4 models
    7324 
    7325 > open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/AlphFold
    7326 > Colaboratory Ross River.pdb"
    7327 
    7328 Chain information for AlphFold Colaboratory Ross River.pdb #10 
    7329 --- 
    7330 Chain | Description 
    7331 A | No description available 
    7332  
    7333 
    7334 > ui tool show Matchmaker
    7335 
    7336 > matchmaker #10 to #2
    7337 
    7338 Parameters 
    7339 --- 
    7340 Chain pairing | bb 
    7341 Alignment algorithm | Needleman-Wunsch 
    7342 Similarity matrix | BLOSUM-62 
    7343 SS fraction | 0.3 
    7344 Gap open (HH/SS/other) | 18/18/6 
    7345 Gap extend | 1 
    7346 SS matrix |  |  | H | S | O 
    7347 ---|---|---|--- 
    7348 H | 6 | -9 | -6 
    7349 S |  | 6 | -6 
    7350 O |  |  | 4 
    7351 Iteration cutoff | 2 
    7352  
    7353 Matchmaker 3j2w.pdb, chain I (#2) with AlphFold Colaboratory Ross River.pdb,
    7354 chain A (#10), sequence alignment score = 670.2 
    7355 RMSD between 146 pruned atom pairs is 0.751 angstroms; (across all 149 pairs:
    7356 0.841) 
    7357  
    7358 
    7359 > ui tool show "Show Sequence Viewer"
    7360 
    7361 > sequence chain #10/A
    7362 
    7363 Alignment identifier is 10/A 
    7364 
    7365 > ui mousemode right select
    7366 
    7367 > select #10/A:129
    7368 
    7369 12 atoms, 11 bonds, 1 residue, 1 model selected 
    7370 
    7371 > style sel stick
    7372 
    7373 Changed 12 atom styles 
    7374 
    7375 > style sel stick
    7376 
    7377 Changed 12 atom styles 
    7378 
    7379 > show sel atoms
    7380 
    7381 > color sel red
    7382 
    7383 > select #10/A:131
    7384 
    7385 22 atoms, 21 bonds, 1 residue, 1 model selected 
    7386 
    7387 > style sel stick
    7388 
    7389 Changed 22 atom styles 
    7390 
    7391 > show sel atoms
    7392 
    7393 > color sel blue
    7394 
    7395 > select #10/A:160
    7396 
    7397 22 atoms, 21 bonds, 1 residue, 1 model selected 
    7398 
    7399 > style sel stick
    7400 
    7401 Changed 22 atom styles 
    7402 
    7403 > show sel atoms
    7404 
    7405 > color sel blue
    7406 
    7407 > select #10/A:157
    7408 
    7409 12 atoms, 11 bonds, 1 residue, 1 model selected 
    7410 
    7411 > style sel stick
    7412 
    7413 Changed 12 atom styles 
    7414 
    7415 > show sel atoms
    7416 
    7417 > color sel blue
    7418 
    7419 > select #10/A:181
    7420 
    7421 22 atoms, 21 bonds, 1 residue, 1 model selected 
    7422 
    7423 > style sel stick
    7424 
    7425 Changed 22 atom styles 
    7426 
    7427 > show sel atoms
    7428 
    7429 > color sel blue
    7430 
    7431 > select #10/A:186
    7432 
    7433 22 atoms, 21 bonds, 1 residue, 1 model selected 
    7434 
    7435 > style sel stick
    7436 
    7437 Changed 22 atom styles 
    7438 
    7439 > show sel atoms
    7440 
    7441 > color sel blue
    7442 
    7443 > select #10/A:193
    7444 
    7445 15 atoms, 14 bonds, 1 residue, 1 model selected 
    7446 
    7447 > style sel stick
    7448 
    7449 Changed 15 atom styles 
    7450 
    7451 > show sel atoms
    7452 
    7453 > color sel red
    7454 
    7455 > select #10/A:243
    7456 
    7457 15 atoms, 14 bonds, 1 residue, 1 model selected 
    7458 
    7459 > style sel stick
    7460 
    7461 Changed 15 atom styles 
    7462 
    7463 > show sel atoms
    7464 
    7465 > color sel red
    7466 
    7467 > select clear
    7468 
    7469 > save /Users/mauriciocomas/Desktop/image3.png supersample 3
    7470 
    7471 > select #10/A:157
    7472 
    7473 12 atoms, 11 bonds, 1 residue, 1 model selected 
    7474 
    7475 > color sel red
    7476 
    7477 > select clear
    7478 
    7479 > save /Users/mauriciocomas/Desktop/image4.png supersample 3
    7480 
    7481 > save
    7482 > /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
    7483 
    7484 > open "/Users/mauriciocomas/Downloads/YP_009020571.1 and 20 other
    7485 > sequences.aln"
    7486 
    7487 Traceback (most recent call last): 
    7488 File
    7489 "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    7490 packages/chimerax/seqalign/parse.py", line 31, in open_file 
    7491 seqs, file_attrs, file_markups = ns['read'](session, stream) 
    7492 File
    7493 "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    7494 packages/chimerax/seqalign/io/readALN.py", line 33, in read 
    7495 raise FormatSyntaxError("First non-blank line does not start with 'CLUSTAL'") 
    7496 chimerax.seqalign.parse.FormatSyntaxError: First non-blank line does not start
    7497 with 'CLUSTAL' 
    7498  
    7499 During handling of the above exception, another exception occurred: 
    7500  
    7501 Traceback (most recent call last): 
    7502 File
    7503 "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    7504 packages/chimerax/ui/gui.py", line 261, in event 
    7505 _open_dropped_file(self.session, event.file()) 
    7506 File
    7507 "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    7508 packages/chimerax/ui/gui.py", line 1812, in _open_dropped_file 
    7509 run(session, 'open %s' % FileNameArg.unparse(path)) 
    7510 File
    7511 "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    7512 packages/chimerax/core/commands/run.py", line 36, in run 
    7513 results = command.run(text, log=log, return_json=return_json) 
    7514 File
    7515 "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    7516 packages/chimerax/core/commands/cli.py", line 2852, in run 
    7517 result = ci.function(session, **kw_args) 
    7518 File
    7519 "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    7520 packages/chimerax/open_command/cmd.py", line 118, in cmd_open 
    7521 models = Command(session, registry=registry).run(provider_cmd_text,
    7522 log=log)[0] 
    7523 File
    7524 "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    7525 packages/chimerax/core/commands/cli.py", line 2852, in run 
    7526 result = ci.function(session, **kw_args) 
    7527 File
    7528 "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    7529 packages/chimerax/open_command/cmd.py", line 179, in provider_open 
    7530 models, status = collated_open(session, None, [data], data_format,
    7531 _add_models, 
    7532 File
    7533 "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    7534 packages/chimerax/open_command/cmd.py", line 421, in collated_open 
    7535 return func(*func_args, **func_kw) 
    7536 File
    7537 "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    7538 packages/chimerax/seqalign/__init__.py", line 61, in open 
    7539 return open_file(session, data, file_name, 
    7540 File
    7541 "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    7542 packages/chimerax/seqalign/parse.py", line 33, in open_file 
    7543 raise IOError("Syntax error in %s file '%s': %s" % (format_name, fname, err)) 
    7544 OSError: Syntax error in ALN file 'YP_009020571.1 and 20 other sequences.aln':
    7545 First non-blank line does not start with 'CLUSTAL' 
    7546  
    7547 OSError: Syntax error in ALN file 'YP_009020571.1 and 20 other sequences.aln':
    7548 First non-blank line does not start with 'CLUSTAL' 
    7549  
    7550 File
    7551 "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    7552 packages/chimerax/seqalign/parse.py", line 33, in open_file 
    7553 raise IOError("Syntax error in %s file '%s': %s" % (format_name, fname, err)) 
    7554  
    7555 See log for complete Python traceback. 
    7556  
    7557 
    7558 > open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/Alphavirus
    7559 > sequences/Madaragia YP_009020571.1 and 20 other sequences.aln"
    7560 
    7561 Traceback (most recent call last): 
    7562 File
    7563 "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    7564 packages/chimerax/seqalign/parse.py", line 31, in open_file 
    7565 seqs, file_attrs, file_markups = ns['read'](session, stream) 
    7566 File
    7567 "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    7568 packages/chimerax/seqalign/io/readALN.py", line 33, in read 
    7569 raise FormatSyntaxError("First non-blank line does not start with 'CLUSTAL'") 
    7570 chimerax.seqalign.parse.FormatSyntaxError: First non-blank line does not start
    7571 with 'CLUSTAL' 
    7572  
    7573 During handling of the above exception, another exception occurred: 
    7574  
    7575 Traceback (most recent call last): 
    7576 File
    7577 "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    7578 packages/chimerax/ui/gui.py", line 261, in event 
    7579 _open_dropped_file(self.session, event.file()) 
    7580 File
    7581 "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    7582 packages/chimerax/ui/gui.py", line 1812, in _open_dropped_file 
    7583 run(session, 'open %s' % FileNameArg.unparse(path)) 
    7584 File
    7585 "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    7586 packages/chimerax/core/commands/run.py", line 36, in run 
    7587 results = command.run(text, log=log, return_json=return_json) 
    7588 File
    7589 "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    7590 packages/chimerax/core/commands/cli.py", line 2852, in run 
    7591 result = ci.function(session, **kw_args) 
    7592 File
    7593 "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    7594 packages/chimerax/open_command/cmd.py", line 118, in cmd_open 
    7595 models = Command(session, registry=registry).run(provider_cmd_text,
    7596 log=log)[0] 
    7597 File
    7598 "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    7599 packages/chimerax/core/commands/cli.py", line 2852, in run 
    7600 result = ci.function(session, **kw_args) 
    7601 File
    7602 "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    7603 packages/chimerax/open_command/cmd.py", line 179, in provider_open 
    7604 models, status = collated_open(session, None, [data], data_format,
    7605 _add_models, 
    7606 File
    7607 "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    7608 packages/chimerax/open_command/cmd.py", line 421, in collated_open 
    7609 return func(*func_args, **func_kw) 
    7610 File
    7611 "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    7612 packages/chimerax/seqalign/__init__.py", line 61, in open 
    7613 return open_file(session, data, file_name, 
    7614 File
    7615 "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    7616 packages/chimerax/seqalign/parse.py", line 33, in open_file 
    7617 raise IOError("Syntax error in %s file '%s': %s" % (format_name, fname, err)) 
    7618 OSError: Syntax error in ALN file 'Madaragia YP_009020571.1 and 20 other
    7619 sequences.aln': First non-blank line does not start with 'CLUSTAL' 
    7620  
    7621 OSError: Syntax error in ALN file 'Madaragia YP_009020571.1 and 20 other
    7622 sequences.aln': First non-blank line does not start with 'CLUSTAL' 
    7623  
    7624 File
    7625 "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
    7626 packages/chimerax/seqalign/parse.py", line 33, in open_file 
    7627 raise IOError("Syntax error in %s file '%s': %s" % (format_name, fname, err)) 
    7628  
    7629 See log for complete Python traceback. 
    7630  
    7631 
    7632 > hide #10 models
    7633 
    7634 > open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/AlphaFold
    7635 > 2/AlphaFold Colaboratory Middelburg virus.pdb"
    7636 
    7637 Chain information for AlphaFold Colaboratory Middelburg virus.pdb #11 
    7638 --- 
    7639 Chain | Description 
    7640 A | No description available 
    7641  
    7642 
    7643 > ui tool show Matchmaker
    7644 
    7645 > matchmaker #11 to #1
    7646 
    7647 Parameters 
    7648 --- 
    7649 Chain pairing | bb 
    7650 Alignment algorithm | Needleman-Wunsch 
    7651 Similarity matrix | BLOSUM-62 
    7652 SS fraction | 0.3 
    7653 Gap open (HH/SS/other) | 18/18/6 
    7654 Gap extend | 1 
    7655 SS matrix |  |  | H | S | O 
    7656 ---|---|---|--- 
    7657 H | 6 | -9 | -6 
    7658 S |  | 6 | -6 
    7659 O |  |  | 4 
    7660 Iteration cutoff | 2 
    7661  
    7662 Matchmaker 7vga.pdb, chain C (#1) with AlphaFold Colaboratory Middelburg
    7663 virus.pdb, chain A (#11), sequence alignment score = 810.9 
    7664 RMSD between 151 pruned atom pairs is 0.862 angstroms; (across all 158 pairs:
    7665 1.359) 
    7666  
    7667 
    7668 > show #10 models
    7669 
    7670 > hide #10 models
    7671 
    7672 > ui tool show "Show Sequence Viewer"
    7673 
    7674 > sequence chain #11/A
    7675 
    7676 Alignment identifier is 11/A 
    7677 
    7678 > select #11/A:130
    7679 
    7680 15 atoms, 14 bonds, 1 residue, 1 model selected 
    7681 
    7682 > style sel stick
    7683 
    7684 Changed 15 atom styles 
    7685 
    7686 > show sel atoms
    7687 
    7688 > color sel red
    7689 
    7690 > select #11/A:132
    7691 
    7692 22 atoms, 21 bonds, 1 residue, 1 model selected 
    7693 
    7694 > style sel stick
    7695 
    7696 Changed 22 atom styles 
    7697 
    7698 > show sel atoms
    7699 
    7700 > color sel blue
    7701 
    7702 > ui mousemode right select
    7703 
    7704 > select #11/A:158
    7705 
    7706 12 atoms, 11 bonds, 1 residue, 1 model selected 
    7707 
    7708 > style sel stick
    7709 
    7710 Changed 12 atom styles 
    7711 
    7712 > show sel atoms
    7713 
    7714 > color sel red
    7715 
    7716 > select #11/A:161
    7717 
    7718 22 atoms, 21 bonds, 1 residue, 1 model selected 
    7719 
    7720 > style sel stick
    7721 
    7722 Changed 22 atom styles 
    7723 
    7724 > style sel stick
    7725 
    7726 Changed 22 atom styles 
    7727 
    7728 > show sel atoms
    7729 
    7730 > color sel blue
    7731 
    7732 > select #11/A:182
    7733 
    7734 22 atoms, 21 bonds, 1 residue, 1 model selected 
    7735 
    7736 > style sel stick
    7737 
    7738 Changed 22 atom styles 
    7739 
    7740 > show sel atoms
    7741 
    7742 > color sel blue
    7743 
    7744 > select #11/A:187
    7745 
    7746 17 atoms, 16 bonds, 1 residue, 1 model selected 
    7747 
    7748 > style sel stick
    7749 
    7750 Changed 17 atom styles 
    7751 
    7752 > show sel atoms
    7753 
    7754 > color sel dim gray
    7755 
    7756 > select #11/A:184
    7757 
    7758 12 atoms, 11 bonds, 1 residue, 1 model selected 
    7759 
    7760 > select #11/A:184
    7761 
    7762 12 atoms, 11 bonds, 1 residue, 1 model selected 
    7763 
    7764 > select #11/A:184
    7765 
    7766 12 atoms, 11 bonds, 1 residue, 1 model selected 
    7767 
    7768 > select #11/A:184-185
    7769 
    7770 22 atoms, 21 bonds, 2 residues, 1 model selected 
    7771 
    7772 > select #11/A:184
    7773 
    7774 12 atoms, 11 bonds, 1 residue, 1 model selected 
    7775 
    7776 > select #11/A:184
    7777 
    7778 12 atoms, 11 bonds, 1 residue, 1 model selected 
    7779 
    7780 > select #11/A:194
    7781 
    7782 15 atoms, 14 bonds, 1 residue, 1 model selected 
    7783 
    7784 > style sel stick
    7785 
    7786 Changed 15 atom styles 
    7787 
    7788 > show sel atoms
    7789 
    7790 > color sel red
    7791 
    7792 > select #11/A:244
    7793 
    7794 15 atoms, 14 bonds, 1 residue, 1 model selected 
    7795 
    7796 > style sel stick
    7797 
    7798 Changed 15 atom styles 
    7799 
    7800 > show sel atoms
    7801 
    7802 > color sel red
    7803 
    7804 > select clear
    7805 
    7806 > save /Users/mauriciocomas/Desktop/image1.png supersample 3
    7807 
    7808 > show #10 models
    7809 
    7810 > hide #10 models
    7811 
    7812 > show #10 models
    7813 
    7814 > hide #10 models
    7815 
    7816 > show #10 models
    7817 
    7818 > hide #10 models
    7819 
    7820 > show #10 models
    7821 
    7822 > hide #10 models
    7823 
    7824 > show #10 models
    7825 
    7826 > hide #10 models
    7827 
    7828 > show #10 models
    7829 
    7830 > hide #10 models
    7831 
    7832 > save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/Chimera X
    7833 > sessions/structures.cxs"
    7834 
    7835 ——— End of log from Wed May 24 12:56:46 2023 ———
    7836 
    7837 opened ChimeraX session 
    7838 
    7839 > hide #11 models
    7840 
    7841 > open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/AlphaFold
    7842 > 2/AlphaFold Colaboratory Everglades virus.pdb"
    7843 
    7844 Chain information for AlphaFold Colaboratory Everglades virus.pdb #12 
    7845 --- 
    7846 Chain | Description 
    7847 A | No description available 
    7848  
    7849 
    7850 > ui tool show Matchmaker
    7851 
    7852 > matchmaker #12 to #1
    7853 
    7854 Parameters 
    7855 --- 
    7856 Chain pairing | bb 
    7857 Alignment algorithm | Needleman-Wunsch 
    7858 Similarity matrix | BLOSUM-62 
    7859 SS fraction | 0.3 
    7860 Gap open (HH/SS/other) | 18/18/6 
    7861 Gap extend | 1 
    7862 SS matrix |  |  | H | S | O 
    7863 ---|---|---|--- 
    7864 H | 6 | -9 | -6 
    7865 S |  | 6 | -6 
    7866 O |  |  | 4 
    7867 Iteration cutoff | 2 
    7868  
    7869 Matchmaker 7vga.pdb, chain C (#1) with AlphaFold Colaboratory Everglades
    7870 virus.pdb, chain A (#12), sequence alignment score = 512.4 
    7871 RMSD between 151 pruned atom pairs is 0.937 angstroms; (across all 158 pairs:
    7872 1.296) 
    7873  
    7874 
    7875 > ui tool show "Show Sequence Viewer"
    7876 
    7877 > sequence chain #12/A
    7878 
    7879 Alignment identifier is 12/A 
    7880 
    7881 > ui mousemode right select
    7882 
    7883 > select #12/A:132
    7884 
    7885 15 atoms, 14 bonds, 1 residue, 1 model selected 
    7886 
    7887 > style sel stick
    7888 
    7889 Changed 15 atom styles 
    7890 
    7891 > show sel atoms
    7892 
    7893 > color sel red
    7894 
    7895 > select #12/A:134
    7896 
    7897 22 atoms, 21 bonds, 1 residue, 1 model selected 
    7898 
    7899 > style sel stick
    7900 
    7901 Changed 22 atom styles 
    7902 
    7903 > show sel atoms
    7904 
    7905 > color sel blue
    7906 
    7907 > select #12/A:163
    7908 
    7909 10 atoms, 9 bonds, 1 residue, 1 model selected 
    7910 
    7911 > select #12/A:159
    7912 
    7913 12 atoms, 11 bonds, 1 residue, 1 model selected 
    7914 
    7915 > select #12/A:160
    7916 
    7917 16 atoms, 15 bonds, 1 residue, 1 model selected 
    7918 
    7919 > select #12/A:163
    7920 
    7921 10 atoms, 9 bonds, 1 residue, 1 model selected 
    7922 
    7923 > style sel stick
    7924 
    7925 Changed 10 atom styles 
    7926 
    7927 > show sel atoms
    7928 
    7929 > color sel dim gray
    7930 
    7931 > select #12/A:160
    7932 
    7933 16 atoms, 15 bonds, 1 residue, 1 model selected 
    7934 
    7935 > style sel stick
    7936 
    7937 Changed 16 atom styles 
    7938 
    7939 > style sel stick
    7940 
    7941 Changed 16 atom styles 
    7942 
    7943 > show sel atoms
    7944 
    7945 > color sel dim gray
    7946 
    7947 > select #12/A:159-160
    7948 
    7949 28 atoms, 27 bonds, 2 residues, 1 model selected 
    7950 
    7951 > select #12/A:159-160
    7952 
    7953 28 atoms, 27 bonds, 2 residues, 1 model selected 
    7954 
    7955 > style sel stick
    7956 
    7957 Changed 28 atom styles 
    7958 
    7959 > show sel atoms
    7960 
    7961 > select #12/A:160
    7962 
    7963 16 atoms, 15 bonds, 1 residue, 1 model selected 
    7964 
    7965 > select #12/A:160
    7966 
    7967 16 atoms, 15 bonds, 1 residue, 1 model selected 
    7968 
    7969 > hide sel atoms
    7970 
    7971 > ui tool show "Color Actions"
    7972 
    7973 > color sel bychain
    7974 
    7975 > select #12/A:159
    7976 
    7977 12 atoms, 11 bonds, 1 residue, 1 model selected 
    7978 
    7979 > select #12/A:159
    7980 
    7981 12 atoms, 11 bonds, 1 residue, 1 model selected 
    7982 
    7983 > show sel atoms
    7984 
    7985 > color sel red
    7986 
    7987 > select #2/I:152
    7988 
    7989 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7990 
    7991 > select #12/A:163
    7992 
    7993 10 atoms, 9 bonds, 1 residue, 1 model selected 
    7994 
    7995 > select #12/A:165
    7996 
    7997 22 atoms, 21 bonds, 1 residue, 1 model selected 
    7998 
    7999 > select #12/A:165
    8000 
    8001 22 atoms, 21 bonds, 1 residue, 1 model selected 
    8002 
    8003 > select #12/A:184
    8004 
    8005 24 atoms, 23 bonds, 1 residue, 1 model selected 
    8006 
    8007 > style sel stick
    8008 
    8009 Changed 24 atom styles 
    8010 
    8011 > show sel atoms
    8012 
    8013 > color sel blue
    8014 
    8015 > select #12/A:189
    8016 
    8017 22 atoms, 21 bonds, 1 residue, 1 model selected 
    8018 
    8019 > style sel stick
    8020 
    8021 Changed 22 atom styles 
    8022 
    8023 > show sel atoms
    8024 
    8025 > color sel medium blue
    8026 
    8027 > select #12/A:196
    8028 
    8029 17 atoms, 16 bonds, 1 residue, 1 model selected 
    8030 
    8031 > style sel stick
    8032 
    8033 Changed 17 atom styles 
    8034 
    8035 > show sel atoms
    8036 
    8037 > color sel dim gray
    8038 
    8039 > select #12/A:247
    8040 
    8041 7 atoms, 6 bonds, 1 residue, 1 model selected 
    8042 
    8043 > select #12/A:246
    8044 
    8045 15 atoms, 14 bonds, 1 residue, 1 model selected 
    8046 
    8047 > select #12/A:246
    8048 
    8049 15 atoms, 14 bonds, 1 residue, 1 model selected 
    8050 
    8051 > style sel stick
    8052 
    8053 Changed 15 atom styles 
    8054 
    8055 > show sel atoms
    8056 
    8057 > color sel red
    8058 
    8059 > select clear
    8060 
    8061 > save /Users/mauriciocomas/Desktop/image2.png supersample 3
    8062 
    8063 > save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/Chimera X
    8064 > sessions/structures.cxs"
    8065 
    8066 > select #2/I:128
    8067 
    8068 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8069 
    8070 > select #2/I:126
    8071 
    8072 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8073 
    8074 > select #12/A:163
    8075 
    8076 10 atoms, 9 bonds, 1 residue, 1 model selected 
    8077 
    8078 > save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/Chimera X
    8079 > sessions/overlap of CP structures.cxs"
    8080 
    8081 ——— End of log from Thu May 25 12:52:10 2023 ———
    8082 
    8083 opened ChimeraX session 
    8084 
    8085 > hide #12 models
    8086 
    8087 > open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/AlphaFold
    8088 > 2/Alpha Fold Collaboratory Salmon Pancrease Disease.pdb"
    8089 
    8090 Chain information for Alpha Fold Collaboratory Salmon Pancrease Disease.pdb
    8091 #13 
    8092 --- 
    8093 Chain | Description 
    8094 A | No description available 
    8095  
    8096 
    8097 > ui tool show Matchmaker
    8098 
    8099 > matchmaker #13 to #1
    8100 
    8101 Parameters 
    8102 --- 
    8103 Chain pairing | bb 
    8104 Alignment algorithm | Needleman-Wunsch 
    8105 Similarity matrix | BLOSUM-62 
    8106 SS fraction | 0.3 
    8107 Gap open (HH/SS/other) | 18/18/6 
    8108 Gap extend | 1 
    8109 SS matrix |  |  | H | S | O 
    8110 ---|---|---|--- 
    8111 H | 6 | -9 | -6 
    8112 S |  | 6 | -6 
    8113 O |  |  | 4 
    8114 Iteration cutoff | 2 
    8115  
    8116 Matchmaker 7vga.pdb, chain C (#1) with Alpha Fold Collaboratory Salmon
    8117 Pancrease Disease.pdb, chain A (#13), sequence alignment score = 305.8 
    8118 RMSD between 123 pruned atom pairs is 1.087 angstroms; (across all 157 pairs:
    8119 2.548) 
    8120  
    8121 
    8122 > ui mousemode right rotate
    8123 
    8124 > ui tool show "Show Sequence Viewer"
    8125 
    8126 > sequence chain #13/A
    8127 
    8128 Alignment identifier is 13/A 
    8129 
    8130 > ui mousemode right select
    8131 
    8132 > select #13/A:141
    8133 
    8134 12 atoms, 11 bonds, 1 residue, 1 model selected 
    8135 
    8136 > style sel stick
    8137 
    8138 Changed 12 atom styles 
    8139 
    8140 > show sel atoms
    8141 
    8142 > color sel red
    8143 
    8144 > select #13/A:143
    8145 
    8146 10 atoms, 9 bonds, 1 residue, 1 model selected 
    8147 
    8148 > select #13/A:144
    8149 
    8150 19 atoms, 18 bonds, 1 residue, 1 model selected 
    8151 
    8152 > select #13/A:143
    8153 
    8154 10 atoms, 9 bonds, 1 residue, 1 model selected 
    8155 
    8156 > style sel stick
    8157 
    8158 Changed 10 atom styles 
    8159 
    8160 > show sel atoms
    8161 
    8162 > color sel dim gray
    8163 
    8164 > select #13/A:142
    8165 
    8166 7 atoms, 6 bonds, 1 residue, 1 model selected 
    8167 
    8168 > select #13/A:142
    8169 
    8170 7 atoms, 6 bonds, 1 residue, 1 model selected 
    8171 
    8172 > select #13/A:143
    8173 
    8174 10 atoms, 9 bonds, 1 residue, 1 model selected 
    8175 
    8176 > select #13/A:143
    8177 
    8178 10 atoms, 9 bonds, 1 residue, 1 model selected 
    8179 
    8180 > select #13/A:172
    8181 
    8182 12 atoms, 11 bonds, 1 residue, 1 model selected 
    8183 
    8184 > select #13/A:169
    8185 
    8186 15 atoms, 14 bonds, 1 residue, 1 model selected 
    8187 
    8188 > select #13/A:172
    8189 
    8190 12 atoms, 11 bonds, 1 residue, 1 model selected 
    8191 
    8192 > style sel stick
    8193 
    8194 Changed 12 atom styles 
    8195 
    8196 > show sel atoms
    8197 
    8198 > color sel red
    8199 
    8200 > select #13/A:174
    8201 
    8202 22 atoms, 21 bonds, 1 residue, 1 model selected 
    8203 
    8204 > select #13/A:174-175
    8205 
    8206 42 atoms, 42 bonds, 2 residues, 1 model selected 
    8207 
    8208 > select #13/A:174
    8209 
    8210 22 atoms, 21 bonds, 1 residue, 1 model selected 
    8211 
    8212 > select #13/A:174
    8213 
    8214 22 atoms, 21 bonds, 1 residue, 1 model selected 
    8215 Drag select of 5 residues 
    8216 
    8217 > select #13/A:174
    8218 
    8219 22 atoms, 21 bonds, 1 residue, 1 model selected 
    8220 
    8221 > select #13/A:174
    8222 
    8223 22 atoms, 21 bonds, 1 residue, 1 model selected 
    8224 
    8225 > select #13/A:169
    8226 
    8227 15 atoms, 14 bonds, 1 residue, 1 model selected 
    8228 
    8229 > color sel red
    8230 
    8231 > style sel stick
    8232 
    8233 Changed 15 atom styles 
    8234 
    8235 > show sel atoms
    8236 
    8237 > select #13/A:192
    8238 
    8239 17 atoms, 16 bonds, 1 residue, 1 model selected 
    8240 
    8241 > select #13/A:193
    8242 
    8243 24 atoms, 23 bonds, 1 residue, 1 model selected 
    8244 
    8245 > select #13/A:193
    8246 
    8247 24 atoms, 23 bonds, 1 residue, 1 model selected 
    8248 
    8249 > color sel blue
    8250 
    8251 > style sel stick
    8252 
    8253 Changed 24 atom styles 
    8254 
    8255 > show sel atoms
    8256 
    8257 > select #13/A:129
    8258 
    8259 22 atoms, 21 bonds, 1 residue, 1 model selected 
    8260 
    8261 > select #13/A:198
    8262 
    8263 15 atoms, 14 bonds, 1 residue, 1 model selected 
    8264 
    8265 > color sel red
    8266 
    8267 > style sel stick
    8268 
    8269 Changed 15 atom styles 
    8270 
    8271 > show sel atoms
    8272 
    8273 > select #13/A:204
    8274 
    8275 12 atoms, 11 bonds, 1 residue, 1 model selected 
    8276 
    8277 > style sel stick
    8278 
    8279 Changed 12 atom styles 
    8280 
    8281 > show sel atoms
    8282 
    8283 > color sel red
    8284 
    8285 > select #13/A:254
    8286 
    8287 12 atoms, 11 bonds, 1 residue, 1 model selected 
    8288 
    8289 > style sel stick
    8290 
    8291 Changed 12 atom styles 
    8292 
    8293 > show sel atoms
    8294 
    8295 > color sel red
    8296 
    8297 > select clear
    8298 
    8299 > select clear
    8300 
    8301 > ui mousemode right rotate
    8302 
    8303 > save /Users/mauriciocomas/Desktop/image9.png supersample 3
    8304 
    8305 > save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/Chimera X
    8306 > sessions/overlap of CP structures.cxs"
    8307 
    8308 ——— End of log from Thu May 25 17:54:54 2023 ———
    8309 
    8310 opened ChimeraX session 
    8311 
    8312 > hide #13 models
    8313 
    8314 > open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/AlphaFold
    8315 > 2/Alpha Fold Collaboratory Fort Morgan virus.pdb"
    8316 
    8317 Chain information for Alpha Fold Collaboratory Fort Morgan virus.pdb #14 
    8318 --- 
    8319 Chain | Description 
    8320 A | No description available 
    8321  
    8322 
    8323 > ui tool show Matchmaker
    8324 
    8325 > matchmaker #14 to #1
    8326 
    8327 Parameters 
    8328 --- 
    8329 Chain pairing | bb 
    8330 Alignment algorithm | Needleman-Wunsch 
    8331 Similarity matrix | BLOSUM-62 
    8332 SS fraction | 0.3 
    8333 Gap open (HH/SS/other) | 18/18/6 
    8334 Gap extend | 1 
    8335 SS matrix |  |  | H | S | O 
    8336 ---|---|---|--- 
    8337 H | 6 | -9 | -6 
    8338 S |  | 6 | -6 
    8339 O |  |  | 4 
    8340 Iteration cutoff | 2 
    8341  
    8342 Matchmaker 7vga.pdb, chain C (#1) with Alpha Fold Collaboratory Fort Morgan
    8343 virus.pdb, chain A (#14), sequence alignment score = 506.1 
    8344 RMSD between 152 pruned atom pairs is 0.926 angstroms; (across all 158 pairs:
    8345 1.271) 
    8346  
    8347 
    8348 > ui tool show "Show Sequence Viewer"
    8349 
    8350 > sequence chain #14/A
    8351 
    8352 Alignment identifier is 14/A 
    8353 
    8354 > ui mousemode right select
    8355 
    8356 > select #14/A:119
    8357 
    8358 14 atoms, 13 bonds, 1 residue, 1 model selected 
    8359 
    8360 > select #14/A:120
    8361 
    8362 7 atoms, 6 bonds, 1 residue, 1 model selected 
    8363 
    8364 > select #14/A:120
    8365 
    8366 7 atoms, 6 bonds, 1 residue, 1 model selected 
    8367 
    8368 > select #14/A:121
    8369 
    8370 17 atoms, 16 bonds, 1 residue, 1 model selected 
    8371 
    8372 > select #14/A:121
    8373 
    8374 17 atoms, 16 bonds, 1 residue, 1 model selected 
    8375 
    8376 > select #14/A:118
    8377 
    8378 19 atoms, 18 bonds, 1 residue, 1 model selected 
    8379 
    8380 > select #14/A:118
    8381 
    8382 19 atoms, 18 bonds, 1 residue, 1 model selected 
    8383 
    8384 > select #14/A:119
    8385 
    8386 14 atoms, 13 bonds, 1 residue, 1 model selected 
    8387 
    8388 > select #14/A:119
    8389 
    8390 14 atoms, 13 bonds, 1 residue, 1 model selected 
    8391 
    8392 > style sel stick
    8393 
    8394 Changed 14 atom styles 
    8395 
    8396 > show sel atoms
    8397 
    8398 > color sel dim gray
    8399 
    8400 > select #14/A:121
    8401 
    8402 17 atoms, 16 bonds, 1 residue, 1 model selected 
    8403 
    8404 > select #2/I:128
    8405 
    8406 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8407 
    8408 > select #14/A:121
    8409 
    8410 17 atoms, 16 bonds, 1 residue, 1 model selected 
    8411 
    8412 > style sel stick
    8413 
    8414 Changed 17 atom styles 
    8415 
    8416 > show sel atoms
    8417 
    8418 > color sel dim gray
    8419 
    8420 > select #14/A:150
    8421 
    8422 10 atoms, 9 bonds, 1 residue, 1 model selected 
    8423 
    8424 > select #14/A:147
    8425 
    8426 17 atoms, 16 bonds, 1 residue, 1 model selected 
    8427 
    8428 > select #14/A:146
    8429 
    8430 15 atoms, 14 bonds, 1 residue, 1 model selected 
    8431 
    8432 > select #14/A:146
    8433 
    8434 15 atoms, 14 bonds, 1 residue, 1 model selected 
    8435 
    8436 > style sel stick
    8437 
    8438 Changed 15 atom styles 
    8439 
    8440 > show sel atoms
    8441 
    8442 > color sel red
    8443 
    8444 > select #14/A:150
    8445 
    8446 10 atoms, 9 bonds, 1 residue, 1 model selected 
    8447 
    8448 > select #14/A:151-152
    8449 
    8450 38 atoms, 37 bonds, 2 residues, 1 model selected 
    8451 
    8452 > select #14/A:151-152
    8453 
    8454 38 atoms, 37 bonds, 2 residues, 1 model selected 
    8455 
    8456 > select #14/A:152
    8457 
    8458 22 atoms, 21 bonds, 1 residue, 1 model selected 
    8459 
    8460 > select #14/A:152
    8461 
    8462 22 atoms, 21 bonds, 1 residue, 1 model selected 
    8463 
    8464 > select #14/A:150
    8465 
    8466 10 atoms, 9 bonds, 1 residue, 1 model selected 
    8467 
    8468 > select #14/A:150
    8469 
    8470 10 atoms, 9 bonds, 1 residue, 1 model selected 
    8471 
    8472 > style sel stick
    8473 
    8474 Changed 10 atom styles 
    8475 
    8476 > show sel atoms
    8477 
    8478 > color sel dim gray
    8479 
    8480 > select #14/A:171
    8481 
    8482 22 atoms, 21 bonds, 1 residue, 1 model selected 
    8483 
    8484 > color sel medium blue
    8485 
    8486 > style sel stick
    8487 
    8488 Changed 22 atom styles 
    8489 
    8490 > show sel atoms
    8491 
    8492 > select #14/A:176
    8493 
    8494 17 atoms, 16 bonds, 1 residue, 1 model selected 
    8495 
    8496 > style sel stick
    8497 
    8498 Changed 17 atom styles 
    8499 
    8500 > show sel atoms
    8501 
    8502 > color sel dim gray
    8503 
    8504 > select #14/A:183
    8505 
    8506 14 atoms, 14 bonds, 1 residue, 1 model selected 
    8507 
    8508 > select #14/A:184
    8509 
    8510 7 atoms, 6 bonds, 1 residue, 1 model selected 
    8511 
    8512 > select #14/A:184
    8513 
    8514 7 atoms, 6 bonds, 1 residue, 1 model selected 
    8515 
    8516 > select #14/A:183
    8517 
    8518 14 atoms, 14 bonds, 1 residue, 1 model selected 
    8519 
    8520 > select #14/A:183
    8521 
    8522 14 atoms, 14 bonds, 1 residue, 1 model selected 
    8523 
    8524 > style sel stick
    8525 
    8526 Changed 14 atom styles 
    8527 
    8528 > show sel atoms
    8529 
    8530 > color sel dim gray
    8531 
    8532 > select #14/A:234
    8533 
    8534 7 atoms, 6 bonds, 1 residue, 1 model selected 
    8535 
    8536 > select #14/A:233
    8537 
    8538 15 atoms, 14 bonds, 1 residue, 1 model selected 
    8539 
    8540 > select #14/A:233
    8541 
    8542 15 atoms, 14 bonds, 1 residue, 1 model selected 
    8543 
    8544 > style sel stick
    8545 
    8546 Changed 15 atom styles 
    8547 
    8548 > show sel atoms
    8549 
    8550 > color sel red
    8551 
    8552 > select clear
    8553 
    8554 > save /Users/mauriciocomas/Desktop/image11.png supersample 3
    8555 
    8556 > save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/Chimera X
    8557 > sessions/overlap of CP structures.cxs"
    8558 
    8559 ——— End of log from Fri May 26 15:30:48 2023 ———
    8560 
    8561 opened ChimeraX session 
    8562 
    8563 > hide #14 models
    8564 
    8565 > open "C:/Users/Carolina/Downloads/Ndumu virus Alphafold.pdb"
    8566 
    8567 Chain information for Ndumu virus Alphafold.pdb #15 
    8568 --- 
    8569 Chain | Description 
    8570 A | No description available 
    8571  
    8572 
    8573 > ui tool show Matchmaker
    8574 
    8575 > matchmaker #15 to #2
    8576 
    8577 Parameters 
    8578 --- 
    8579 Chain pairing | bb 
    8580 Alignment algorithm | Needleman-Wunsch 
    8581 Similarity matrix | BLOSUM-62 
    8582 SS fraction | 0.3 
    8583 Gap open (HH/SS/other) | 18/18/6 
    8584 Gap extend | 1 
    8585 SS matrix |  |  | H | S | O 
    8586 ---|---|---|--- 
    8587 H | 6 | -9 | -6 
    8588 S |  | 6 | -6 
    8589 O |  |  | 4 
    8590 Iteration cutoff | 2 
    8591  
    8592 Matchmaker 3j2w.pdb, chain I (#2) with Ndumu virus Alphafold.pdb, chain A
    8593 (#15), sequence alignment score = 653.9 
    8594 RMSD between 144 pruned atom pairs is 0.776 angstroms; (across all 149 pairs:
    8595 1.015) 
    8596  
    8597 
    8598 > matchmaker #15 to #2
    8599 
    8600 Parameters 
    8601 --- 
    8602 Chain pairing | bb 
    8603 Alignment algorithm | Needleman-Wunsch 
    8604 Similarity matrix | BLOSUM-62 
    8605 SS fraction | 0.3 
    8606 Gap open (HH/SS/other) | 18/18/6 
    8607 Gap extend | 1 
    8608 SS matrix |  |  | H | S | O 
    8609 ---|---|---|--- 
    8610 H | 6 | -9 | -6 
    8611 S |  | 6 | -6 
    8612 O |  |  | 4 
    8613 Iteration cutoff | 2 
    8614  
    8615 Matchmaker 3j2w.pdb, chain I (#2) with Ndumu virus Alphafold.pdb, chain A
    8616 (#15), sequence alignment score = 653.9 
    8617 RMSD between 144 pruned atom pairs is 0.776 angstroms; (across all 149 pairs:
    8618 1.015) 
    8619  
    8620 
    8621 > save "C:/Users/Carolina/Downloads/overlap of CP structures.cxs"
    8622 
    8623 > ui mousemode right translate
    8624 
    8625 > show #10 models
    8626 
    8627 > hide #10 models
    8628 
    8629 > color #15 #ff5500ff
    8630 
    8631 > color #15 #ffaa00ff
    8632 
    8633 > color #15 #ffaa7fff
    8634 
    8635 > color #15 #ffa470ff
    8636 
    8637 > color #15 #ff9c6bff
    8638 
    8639 > color #15 #ff9a67ff
    8640 
    8641 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    8642 > UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
    8643 
    8644 ——— End of log from Tue Jun 6 14:16:52 2023 ———
    8645 
    8646 opened ChimeraX session 
    8647 
    8648 > ui tool show "Show Sequence Viewer"
    8649 
    8650 > sequence chain #15/A
    8651 
    8652 Alignment identifier is 15/A 
    8653 
    8654 > ui mousemode right select
    8655 
    8656 > ui mousemode right translate
    8657 
    8658 > ui mousemode right select
    8659 
    8660 > select #15/A:128
    8661 
    8662 12 atoms, 11 bonds, 1 residue, 1 model selected 
    8663 
    8664 > style sel stick
    8665 
    8666 Changed 12 atom styles 
    8667 
    8668 > show sel atoms
    8669 
    8670 > color sel red
    8671 
    8672 > select #15/A:130
    8673 
    8674 15 atoms, 14 bonds, 1 residue, 1 model selected 
    8675 
    8676 > select clear
    8677 
    8678 [Repeated 2 time(s)]
    8679 
    8680 > select #15/A:130
    8681 
    8682 15 atoms, 14 bonds, 1 residue, 1 model selected 
    8683 
    8684 > style sel stick
    8685 
    8686 Changed 15 atom styles 
    8687 
    8688 > show sel atoms
    8689 
    8690 > color sel red
    8691 
    8692 > ui mousemode right translate
    8693 
    8694 > show sel atoms
    8695 
    8696 > style sel stick
    8697 
    8698 Changed 15 atom styles 
    8699 
    8700 > style sel stick
    8701 
    8702 Changed 15 atom styles 
    8703 
    8704 > show sel cartoons
    8705 
    8706 > style sel stick
    8707 
    8708 Changed 15 atom styles 
    8709 
    8710 > show sel atoms
    8711 
    8712 > hide sel atoms
    8713 
    8714 > show sel atoms
    8715 
    8716 > color sel red
    8717 
    8718 > ui mousemode right select
    8719 
    8720 > select #15/A:242
    8721 
    8722 15 atoms, 14 bonds, 1 residue, 1 model selected 
    8723 
    8724 > ui mousemode right translate
    8725 
    8726 [Repeated 1 time(s)]
    8727 
    8728 > ui mousemode right rotate
    8729 
    8730 > ui mousemode right translate
    8731 
    8732 > ui mousemode right select
    8733 
    8734 > select #15/A:159
    8735 
    8736 22 atoms, 21 bonds, 1 residue, 1 model selected 
    8737 
    8738 > select #15/A:156
    8739 
    8740 15 atoms, 14 bonds, 1 residue, 1 model selected 
    8741 
    8742 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    8743 > UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
    8744 
    8745 ——— End of log from Tue Jun 6 14:34:43 2023 ———
    8746 
    8747 opened ChimeraX session 
    8748 
    8749 > ui mousemode right select
    8750 
    8751 > select #2/I:128
    8752 
    8753 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8754 
    8755 > select #15/A:130
    8756 
    8757 15 atoms, 14 bonds, 1 residue, 1 model selected 
    8758 
    8759 > select #2/I:128
    8760 
    8761 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8762 
    8763 > select #15/A:130
    8764 
    8765 15 atoms, 14 bonds, 1 residue, 1 model selected 
    8766 
    8767 > select #15/A:127
    8768 
    8769 19 atoms, 18 bonds, 1 residue, 1 model selected 
    8770 
    8771 > select #2/I:126
    8772 
    8773 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8774 
    8775 > select #15/A:128
    8776 
    8777 12 atoms, 11 bonds, 1 residue, 1 model selected 
    8778 
    8779 > ui mousemode right translate
    8780 
    8781 > ui mousemode right select
    8782 
    8783 > select #2/I:240
    8784 
    8785 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8786 
    8787 > select #15/A:242
    8788 
    8789 15 atoms, 14 bonds, 1 residue, 1 model selected 
    8790 
    8791 > style sel stick
    8792 
    8793 Changed 15 atom styles 
    8794 
    8795 > show sel atoms
    8796 
    8797 > color sel red
    8798 
    8799 > ui mousemode right translate
    8800 
    8801 [Repeated 1 time(s)]
    8802 
    8803 > ui mousemode right select
    8804 
    8805 > select #2/I:190
    8806 
    8807 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8808 
    8809 > select #15/A:192
    8810 
    8811 15 atoms, 14 bonds, 1 residue, 1 model selected 
    8812 
    8813 > select #15/A:193
    8814 
    8815 7 atoms, 6 bonds, 1 residue, 1 model selected 
    8816 
    8817 > select #15/A:192
    8818 
    8819 15 atoms, 14 bonds, 1 residue, 1 model selected 
    8820 
    8821 > style sel stick
    8822 
    8823 Changed 15 atom styles 
    8824 
    8825 > show sel atoms
    8826 
    8827 > color sel red
    8828 
    8829 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    8830 > UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
    8831 
    8832 Drag select of 1 residues 
    8833 
    8834 > ui mousemode right select
    8835 
    8836 > ui mousemode right translate
    8837 
    8838 > ui mousemode right select
    8839 
    8840 > select #2/I:183
    8841 
    8842 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8843 
    8844 > select clear
    8845 
    8846 > select #2/I:183
    8847 
    8848 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8849 
    8850 > select #15/A:185
    8851 
    8852 22 atoms, 21 bonds, 1 residue, 1 model selected 
    8853 
    8854 > style sel stick
    8855 
    8856 Changed 22 atom styles 
    8857 
    8858 > show sel atoms
    8859 
    8860 > color sel blue
    8861 
    8862 > ui mousemode right select
    8863 
    8864 > ui mousemode right translate
    8865 
    8866 > ui mousemode right select
    8867 
    8868 > select #2/I:178
    8869 
    8870 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8871 
    8872 > select #15/A:180
    8873 
    8874 24 atoms, 23 bonds, 1 residue, 1 model selected 
    8875 
    8876 > select #2/I:178
    8877 
    8878 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8879 
    8880 > select #15/A:180
    8881 
    8882 24 atoms, 23 bonds, 1 residue, 1 model selected 
    8883 
    8884 > ui mousemode right translate
    8885 
    8886 > style sel stick
    8887 
    8888 Changed 24 atom styles 
    8889 
    8890 > show sel atoms
    8891 
    8892 > color sel blue
    8893 
    8894 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    8895 > UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
    8896 
    8897 > ui mousemode right select
    8898 
    8899 > select #2/I:153
    8900 
    8901 5 atoms, 4 bonds, 1 residue, 1 model selected 
    8902 
    8903 > select #2/I:154
    8904 
    8905 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8906 
    8907 > select #15/A:156
    8908 
    8909 15 atoms, 14 bonds, 1 residue, 1 model selected 
    8910 
    8911 > style sel stick
    8912 
    8913 Changed 15 atom styles 
    8914 
    8915 > show sel atoms
    8916 
    8917 > color sel red
    8918 
    8919 > select #2/I:157
    8920 
    8921 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8922 
    8923 > select #15/A:159
    8924 
    8925 22 atoms, 21 bonds, 1 residue, 1 model selected 
    8926 
    8927 > style sel stick
    8928 
    8929 Changed 22 atom styles 
    8930 
    8931 > show sel atoms
    8932 
    8933 > color sel blue
    8934 
    8935 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    8936 > UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
    8937 
    8938 ——— End of log from Wed Jun 7 14:34:33 2023 ———
    8939 
    8940 opened ChimeraX session 
    8941 
    8942 > show target m
    8943 
    8944 > hide target m
    8945 
    8946 > show #15 models
    8947 
    8948 > show #2 models
    8949 
    8950 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    8951 > UASLP/Lab Virología/Alpha fold/Everglades virus Alphafold.pdb"
    8952 
    8953 Chain information for Everglades virus Alphafold.pdb #16 
    8954 --- 
    8955 Chain | Description 
    8956 A | No description available 
    8957  
    8958 
    8959 > ui tool show Matchmaker
    8960 
    8961 > matchmaker #2-4,6,9-15#!5,7-8 to #16
    8962 
    8963 Parameters 
    8964 --- 
    8965 Chain pairing | bb 
    8966 Alignment algorithm | Needleman-Wunsch 
    8967 Similarity matrix | BLOSUM-62 
    8968 SS fraction | 0.3 
    8969 Gap open (HH/SS/other) | 18/18/6 
    8970 Gap extend | 1 
    8971 SS matrix |  |  | H | S | O 
    8972 ---|---|---|--- 
    8973 H | 6 | -9 | -6 
    8974 S |  | 6 | -6 
    8975 O |  |  | 4 
    8976 Iteration cutoff | 2 
    8977  
    8978 Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with 3j2w.pdb, chain
    8979 I (#2), sequence alignment score = 536 
    8980 RMSD between 147 pruned atom pairs is 0.728 angstroms; (across all 149 pairs:
    8981 0.822) 
    8982  
    8983 Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with 1kxf.pdb, chain
    8984 A (#3), sequence alignment score = 570.4 
    8985 RMSD between 149 pruned atom pairs is 0.682 angstroms; (across all 158 pairs:
    8986 2.151) 
    8987  
    8988 Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with 7sfu.pdb, chain
    8989 F (#4), sequence alignment score = 808 
    8990 RMSD between 147 pruned atom pairs is 0.721 angstroms; (across all 162 pairs:
    8991 2.067) 
    8992  
    8993 Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with 4agk.pdb, chain
    8994 A (#6), sequence alignment score = 550.5 
    8995 RMSD between 149 pruned atom pairs is 0.715 angstroms; (across all 151 pairs:
    8996 0.781) 
    8997  
    8998 Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with 7ko8.pdb, chain
    8999 G (#9), sequence alignment score = 563 
    9000 RMSD between 134 pruned atom pairs is 1.120 angstroms; (across all 152 pairs:
    9001 1.600) 
    9002  
    9003 Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with AlphFold
    9004 Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 797 
    9005 RMSD between 150 pruned atom pairs is 0.554 angstroms; (across all 260 pairs:
    9006 18.148) 
    9007  
    9008 Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with AlphaFold
    9009 Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
    9010 788.3 
    9011 RMSD between 152 pruned atom pairs is 0.630 angstroms; (across all 262 pairs:
    9012 22.549) 
    9013  
    9014 Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with AlphaFold
    9015 Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
    9016 1435.7 
    9017 RMSD between 274 pruned atom pairs is 0.060 angstroms; (across all 274 pairs:
    9018 0.060) 
    9019  
    9020 Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with Alpha Fold
    9021 Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
    9022 score = 549.1 
    9023 RMSD between 134 pruned atom pairs is 0.953 angstroms; (across all 266 pairs:
    9024 27.039) 
    9025  
    9026 Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with Alpha Fold
    9027 Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
    9028 1003.7 
    9029 RMSD between 162 pruned atom pairs is 0.329 angstroms; (across all 254 pairs:
    9030 31.074) 
    9031  
    9032 Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with Ndumu virus
    9033 Alphafold.pdb, chain A (#15), sequence alignment score = 814.3 
    9034 RMSD between 142 pruned atom pairs is 0.555 angstroms; (across all 266 pairs:
    9035 35.306) 
    9036  
    9037 Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with 6xo4.pdb, chain
    9038 C (#5), sequence alignment score = 677.5 
    9039 RMSD between 106 pruned atom pairs is 1.220 angstroms; (across all 151 pairs:
    9040 2.045) 
    9041  
    9042 Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with 1vcp.pdb, chain
    9043 C (#7), sequence alignment score = 569.9 
    9044 RMSD between 147 pruned atom pairs is 0.619 angstroms; (across all 149 pairs:
    9045 0.761) 
    9046  
    9047 Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with 2yew.pdb, chain
    9048 G (#8), sequence alignment score = 512.3 
    9049 RMSD between 55 pruned atom pairs is 1.276 angstroms; (across all 171 pairs:
    9050 11.421) 
    9051  
    9052 
    9053 > hide #15 models
    9054 
    9055 > color #16 #0055ffff
    9056 
    9057 > color #16 #ff55ffff
    9058 
    9059 > color #16 magenta
    9060 
    9061 > hide #16 models
    9062 
    9063 > show #16 models
    9064 
    9065 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    9066 > UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
    9067 
    9068 ——— End of log from Wed Jun 7 16:42:56 2023 ———
    9069 
    9070 opened ChimeraX session 
    9071 
    9072 > ui mousemode right select
    9073 
    9074 > select #2/I:126
    9075 
    9076 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9077 
    9078 > select #16/A:132
    9079 
    9080 15 atoms, 14 bonds, 1 residue, 1 model selected 
    9081 
    9082 > style sel stick
    9083 
    9084 Changed 15 atom styles 
    9085 
    9086 > show sel atoms
    9087 
    9088 > color sel red
    9089 
    9090 > select #2/I:128
    9091 
    9092 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9093 
    9094 > select #16/A:134
    9095 
    9096 22 atoms, 21 bonds, 1 residue, 1 model selected 
    9097 
    9098 > style sel stick
    9099 
    9100 Changed 22 atom styles 
    9101 
    9102 > style sel stick
    9103 
    9104 Changed 22 atom styles 
    9105 
    9106 > show sel atoms
    9107 
    9108 > color sel blue
    9109 
    9110 > ui mousemode right rotate
    9111 
    9112 > ui mousemode right translate
    9113 
    9114 > ui mousemode right select
    9115 
    9116 > select #2/I:240
    9117 
    9118 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9119 
    9120 > select #16/A:246
    9121 
    9122 15 atoms, 14 bonds, 1 residue, 1 model selected 
    9123 
    9124 > style sel stick
    9125 
    9126 Changed 15 atom styles 
    9127 
    9128 > show sel atoms
    9129 
    9130 > color sel red
    9131 
    9132 > ui mousemode right translate
    9133 
    9134 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    9135 > UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
    9136 
    9137 > ui mousemode right select
    9138 
    9139 > select #2/I:190
    9140 
    9141 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9142 
    9143 > select #16/A:196
    9144 
    9145 17 atoms, 16 bonds, 1 residue, 1 model selected 
    9146 
    9147 > select #2/I:190
    9148 
    9149 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9150 
    9151 > select #16/A:196
    9152 
    9153 17 atoms, 16 bonds, 1 residue, 1 model selected 
    9154 
    9155 > select #16/A:197
    9156 
    9157 7 atoms, 6 bonds, 1 residue, 1 model selected 
    9158 
    9159 > select #16/A:196
    9160 
    9161 17 atoms, 16 bonds, 1 residue, 1 model selected 
    9162 
    9163 > select #2/I:190
    9164 
    9165 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9166 
    9167 > select #16/A:196
    9168 
    9169 17 atoms, 16 bonds, 1 residue, 1 model selected 
    9170 
    9171 > view clip false
    9172 
    9173 [Repeated 1 time(s)]Drag select of 4 atoms, 9 residues, 2 bonds 
    9174 
    9175 > ui mousemode right translate
    9176 
    9177 > ui mousemode right select
    9178 
    9179 > select #16/A:196
    9180 
    9181 17 atoms, 16 bonds, 1 residue, 1 model selected 
    9182 
    9183 > select clear
    9184 
    9185 [Repeated 1 time(s)]
    9186 
    9187 > ui mousemode right translate
    9188 
    9189 > ui mousemode right select
    9190 
    9191 > select #16/A:196
    9192 
    9193 17 atoms, 16 bonds, 1 residue, 1 model selected 
    9194 
    9195 > select #16/A:197
    9196 
    9197 7 atoms, 6 bonds, 1 residue, 1 model selected 
    9198 
    9199 > select #16/A:196
    9200 
    9201 17 atoms, 16 bonds, 1 residue, 1 model selected 
    9202 
    9203 > select #16/A:195
    9204 
    9205 14 atoms, 14 bonds, 1 residue, 1 model selected 
    9206 
    9207 > select #16/A:196
    9208 
    9209 17 atoms, 16 bonds, 1 residue, 1 model selected 
    9210 Alignment identifier is 16/A 
    9211 Drag select of 3 residues 
    9212 
    9213 > ui mousemode right translate
    9214 
    9215 > ui mousemode right select
    9216 
    9217 > select #2/I:183
    9218 
    9219 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9220 
    9221 > select #16/A:189
    9222 
    9223 22 atoms, 21 bonds, 1 residue, 1 model selected 
    9224 
    9225 > style sel stick
    9226 
    9227 Changed 22 atom styles 
    9228 
    9229 > show sel atoms
    9230 
    9231 > color sel blue
    9232 
    9233 > select #2/I:178
    9234 
    9235 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9236 
    9237 > select #16/A:184
    9238 
    9239 24 atoms, 23 bonds, 1 residue, 1 model selected 
    9240 
    9241 > select #16/A:183
    9242 
    9243 17 atoms, 16 bonds, 1 residue, 1 model selected 
    9244 
    9245 > select #16/A:184
    9246 
    9247 24 atoms, 23 bonds, 1 residue, 1 model selected 
    9248 
    9249 > style sel stick
    9250 
    9251 Changed 24 atom styles 
    9252 
    9253 > show sel atoms
    9254 
    9255 > color sel blue
    9256 
    9257 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    9258 > UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
    9259 
    9260 > ui mousemode right translate
    9261 
    9262 > ui mousemode right select
    9263 
    9264 > select #2/I:154
    9265 
    9266 8 atoms, 7 bonds, 1 residue, 1 model selected 
    9267 
    9268 > select #16/A:160
    9269 
    9270 16 atoms, 15 bonds, 1 residue, 1 model selected 
    9271 
    9272 > select #2/I:154
    9273 
    9274 8 atoms, 7 bonds, 1 residue, 1 model selected 
    9275 
    9276 > select #16/A:160
    9277 
    9278 16 atoms, 15 bonds, 1 residue, 1 model selected 
    9279 
    9280 > style sel stick
    9281 
    9282 Changed 16 atom styles 
    9283 
    9284 > show sel atoms
    9285 
    9286 > select #2/I:157
    9287 
    9288 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9289 
    9290 > select #16/A:163
    9291 
    9292 10 atoms, 9 bonds, 1 residue, 1 model selected 
    9293 
    9294 > style sel stick
    9295 
    9296 Changed 10 atom styles 
    9297 
    9298 > show sel atoms
    9299 
    9300 > select clear
    9301 
    9302 > ui mousemode right translate
    9303 
    9304 > ui mousemode right select
    9305 
    9306 Drag select of 1 residues 
    9307 
    9308 > select #16/A:197
    9309 
    9310 7 atoms, 6 bonds, 1 residue, 1 model selected 
    9311 
    9312 > select #16/A:196
    9313 
    9314 17 atoms, 16 bonds, 1 residue, 1 model selected 
    9315 
    9316 > style sel stick
    9317 
    9318 Changed 17 atom styles 
    9319 
    9320 > show sel atoms
    9321 
    9322 > select clear
    9323 
    9324 > ui mousemode right translate
    9325 
    9326 > ui mousemode right select
    9327 
    9328 > select #16/A:163
    9329 
    9330 10 atoms, 9 bonds, 1 residue, 1 model selected 
    9331 
    9332 > select #16/A:160
    9333 
    9334 16 atoms, 15 bonds, 1 residue, 1 model selected 
    9335 
    9336 > select #16/A:163
    9337 
    9338 10 atoms, 9 bonds, 1 residue, 1 model selected 
    9339 
    9340 > ui mousemode right translate
    9341 
    9342 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    9343 > UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
    9344 
    9345 ——— End of log from Thu Jun 8 09:54:20 2023 ———
    9346 
    9347 opened ChimeraX session 
    9348 
    9349 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    9350 > UASLP/Lab Virología/Alpha fold/Bebaru virus Alphafold.pdb"
    9351 
    9352 Chain information for Bebaru virus Alphafold.pdb #17 
    9353 --- 
    9354 Chain | Description 
    9355 A | No description available 
    9356  
    9357 
    9358 > color #17 #00aa7fff
    9359 
    9360 > ui tool show Matchmaker
    9361 
    9362 > matchmaker #2-4,6,9-16#!5,7-8 to #17
    9363 
    9364 Parameters 
    9365 --- 
    9366 Chain pairing | bb 
    9367 Alignment algorithm | Needleman-Wunsch 
    9368 Similarity matrix | BLOSUM-62 
    9369 SS fraction | 0.3 
    9370 Gap open (HH/SS/other) | 18/18/6 
    9371 Gap extend | 1 
    9372 SS matrix |  |  | H | S | O 
    9373 ---|---|---|--- 
    9374 H | 6 | -9 | -6 
    9375 S |  | 6 | -6 
    9376 O |  |  | 4 
    9377 Iteration cutoff | 2 
    9378  
    9379 Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with 3j2w.pdb, chain I
    9380 (#2), sequence alignment score = 675.4 
    9381 RMSD between 148 pruned atom pairs is 0.764 angstroms; (across all 149 pairs:
    9382 0.786) 
    9383  
    9384 Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with 1kxf.pdb, chain A
    9385 (#3), sequence alignment score = 566.3 
    9386 RMSD between 148 pruned atom pairs is 0.837 angstroms; (across all 157 pairs:
    9387 1.897) 
    9388  
    9389 Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with 7sfu.pdb, chain I
    9390 (#4), sequence alignment score = 593 
    9391 RMSD between 143 pruned atom pairs is 0.808 angstroms; (across all 161 pairs:
    9392 2.693) 
    9393  
    9394 Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with 4agk.pdb, chain A
    9395 (#6), sequence alignment score = 561 
    9396 RMSD between 148 pruned atom pairs is 0.729 angstroms; (across all 150 pairs:
    9397 0.808) 
    9398  
    9399 Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with 7ko8.pdb, chain D
    9400 (#9), sequence alignment score = 805.5 
    9401 RMSD between 138 pruned atom pairs is 1.056 angstroms; (across all 152 pairs:
    9402 1.688) 
    9403  
    9404 Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with AlphFold
    9405 Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 1142 
    9406 RMSD between 163 pruned atom pairs is 0.340 angstroms; (across all 262 pairs:
    9407 25.400) 
    9408  
    9409 Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with AlphaFold
    9410 Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
    9411 1126.9 
    9412 RMSD between 166 pruned atom pairs is 0.337 angstroms; (across all 260 pairs:
    9413 13.918) 
    9414  
    9415 Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with AlphaFold
    9416 Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
    9417 814.6 
    9418 RMSD between 147 pruned atom pairs is 0.553 angstroms; (across all 256 pairs:
    9419 26.037) 
    9420  
    9421 Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with Alpha Fold
    9422 Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
    9423 score = 509.8 
    9424 RMSD between 129 pruned atom pairs is 0.766 angstroms; (across all 258 pairs:
    9425 33.546) 
    9426  
    9427 Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with Alpha Fold
    9428 Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
    9429 810.1 
    9430 RMSD between 148 pruned atom pairs is 0.467 angstroms; (across all 255 pairs:
    9431 22.095) 
    9432  
    9433 Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with Ndumu virus
    9434 Alphafold.pdb, chain A (#15), sequence alignment score = 946.6 
    9435 RMSD between 150 pruned atom pairs is 0.331 angstroms; (across all 257 pairs:
    9436 26.554) 
    9437  
    9438 Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with Everglades virus
    9439 Alphafold.pdb, chain A (#16), sequence alignment score = 814.6 
    9440 RMSD between 147 pruned atom pairs is 0.553 angstroms; (across all 256 pairs:
    9441 26.039) 
    9442  
    9443 Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with 6xo4.pdb, chain C
    9444 (#5), sequence alignment score = 520.4 
    9445 RMSD between 100 pruned atom pairs is 1.207 angstroms; (across all 150 pairs:
    9446 2.057) 
    9447  
    9448 Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with 1vcp.pdb, chain C
    9449 (#7), sequence alignment score = 729.6 
    9450 RMSD between 149 pruned atom pairs is 0.572 angstroms; (across all 149 pairs:
    9451 0.572) 
    9452  
    9453 Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with 2yew.pdb, chain G
    9454 (#8), sequence alignment score = 724.2 
    9455 RMSD between 49 pruned atom pairs is 1.194 angstroms; (across all 171 pairs:
    9456 9.614) 
    9457  
    9458 
    9459 > hide #16 models
    9460 
    9461 > color #17 #007d5cff
    9462 
    9463 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    9464 > UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
    9465 
    9466 > ui mousemode right select
    9467 
    9468 > select #2/I:126
    9469 
    9470 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9471 
    9472 > select #17/A:122
    9473 
    9474 12 atoms, 11 bonds, 1 residue, 1 model selected 
    9475 Alignment identifier is 17/A 
    9476 
    9477 > select #17/A:122
    9478 
    9479 12 atoms, 11 bonds, 1 residue, 1 model selected 
    9480 
    9481 > style sel stick
    9482 
    9483 Changed 12 atom styles 
    9484 
    9485 > style sel stick
    9486 
    9487 Changed 12 atom styles 
    9488 
    9489 > show sel atoms
    9490 
    9491 > color sel red
    9492 
    9493 > select #2/I:128
    9494 
    9495 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9496 
    9497 > select #17/A:124
    9498 
    9499 22 atoms, 21 bonds, 1 residue, 1 model selected 
    9500 
    9501 > style sel stick
    9502 
    9503 Changed 22 atom styles 
    9504 
    9505 > show sel atoms
    9506 
    9507 > color sel blue
    9508 
    9509 > ui mousemode right select
    9510 
    9511 Drag select of 1 atoms, 1 bonds 
    9512 Drag select of 4 residues 
    9513 
    9514 > ui mousemode right translate
    9515 
    9516 > ui mousemode right select
    9517 
    9518 > select #2/I:128
    9519 
    9520 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9521 
    9522 > ui mousemode right translate
    9523 
    9524 > ui mousemode right rotate
    9525 
    9526 > ui mousemode right select
    9527 
    9528 > select #2/I:240
    9529 
    9530 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9531 
    9532 > select #17/A:236
    9533 
    9534 15 atoms, 14 bonds, 1 residue, 1 model selected 
    9535 
    9536 > style sel stick
    9537 
    9538 Changed 15 atom styles 
    9539 
    9540 > show sel atoms
    9541 
    9542 > color sel red
    9543 
    9544 > ui mousemode right translate
    9545 
    9546 > ui mousemode right select
    9547 
    9548 > select #2/I:190
    9549 
    9550 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9551 
    9552 > select #17/A:186
    9553 
    9554 15 atoms, 14 bonds, 1 residue, 1 model selected 
    9555 
    9556 > select #17/A:187
    9557 
    9558 7 atoms, 6 bonds, 1 residue, 1 model selected 
    9559 
    9560 > select #17/A:186
    9561 
    9562 15 atoms, 14 bonds, 1 residue, 1 model selected 
    9563 
    9564 > style sel stick
    9565 
    9566 Changed 15 atom styles 
    9567 
    9568 > show sel atoms
    9569 
    9570 > color sel red
    9571 
    9572 > select clear
    9573 
    9574 > ui mousemode right translate
    9575 
    9576 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    9577 > UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
    9578 
    9579 > ui mousemode right select
    9580 
    9581 > select #17/A:124
    9582 
    9583 22 atoms, 21 bonds, 1 residue, 1 model selected 
    9584 
    9585 > select #17/A:122
    9586 
    9587 12 atoms, 11 bonds, 1 residue, 1 model selected 
    9588 
    9589 > select #17/A:124
    9590 
    9591 22 atoms, 21 bonds, 1 residue, 1 model selected 
    9592 
    9593 > select #17/A:236
    9594 
    9595 15 atoms, 14 bonds, 1 residue, 1 model selected 
    9596 
    9597 > ui mousemode right translate
    9598 
    9599 > ui mousemode right select
    9600 
    9601 > select #17/A:186
    9602 
    9603 15 atoms, 14 bonds, 1 residue, 1 model selected 
    9604 
    9605 > select #2/I:190
    9606 
    9607 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9608 
    9609 > ui mousemode right translate
    9610 
    9611 > ui mousemode right select
    9612 
    9613 > select #2/I:183
    9614 
    9615 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9616 
    9617 > select #17/A:179
    9618 
    9619 22 atoms, 21 bonds, 1 residue, 1 model selected 
    9620 
    9621 > select #2/I:183
    9622 
    9623 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9624 
    9625 > select #17/A:179
    9626 
    9627 22 atoms, 21 bonds, 1 residue, 1 model selected 
    9628 
    9629 > style sel stick
    9630 
    9631 Changed 22 atom styles 
    9632 
    9633 > show sel atoms
    9634 
    9635 > color sel blue
    9636 
    9637 > select #2/I:178
    9638 
    9639 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9640 
    9641 > select #17/A:174
    9642 
    9643 24 atoms, 23 bonds, 1 residue, 1 model selected 
    9644 
    9645 > style sel stick
    9646 
    9647 Changed 24 atom styles 
    9648 
    9649 > show sel atoms
    9650 
    9651 > color sel blue
    9652 
    9653 > select clear
    9654 
    9655 > ui mousemode right translate
    9656 
    9657 > ui mousemode right select
    9658 
    9659 > select #2/I:178
    9660 
    9661 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9662 
    9663 > select #17/A:174
    9664 
    9665 24 atoms, 23 bonds, 1 residue, 1 model selected 
    9666 
    9667 > ui mousemode right translate
    9668 
    9669 > ui mousemode right select
    9670 
    9671 > select #2/I:157
    9672 
    9673 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9674 
    9675 > select #17/A:153
    9676 
    9677 22 atoms, 21 bonds, 1 residue, 1 model selected 
    9678 
    9679 > style sel stick
    9680 
    9681 Changed 22 atom styles 
    9682 
    9683 > show sel atoms
    9684 
    9685 > color sel blue
    9686 
    9687 > select #2/I:154
    9688 
    9689 8 atoms, 7 bonds, 1 residue, 1 model selected 
    9690 
    9691 > select #17/A:150
    9692 
    9693 12 atoms, 11 bonds, 1 residue, 1 model selected 
    9694 
    9695 > style sel stick
    9696 
    9697 Changed 12 atom styles 
    9698 
    9699 > show sel atoms
    9700 
    9701 > color sel red
    9702 
    9703 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    9704 > UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
    9705 
    9706 > select clear
    9707 
    9708 > ui mousemode right translate
    9709 
    9710 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    9711 > UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
    9712 
    9713 ——— End of log from Thu Jun 8 12:29:59 2023 ———
    9714 
    9715 opened ChimeraX session 
    9716 
    9717 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    9718 > UASLP/Lab Virología/Alpha fold/Caaingua virus AlphaFold.pdb"
    9719 
    9720 Chain information for Caaingua virus AlphaFold.pdb #18 
    9721 --- 
    9722 Chain | Description 
    9723 A | No description available 
    9724  
    9725 
    9726 > ui tool show Matchmaker
    9727 
    9728 > matchmaker #2-4,6,9-17#!5,7-8 to #18
    9729 
    9730 Parameters 
    9731 --- 
    9732 Chain pairing | bb 
    9733 Alignment algorithm | Needleman-Wunsch 
    9734 Similarity matrix | BLOSUM-62 
    9735 SS fraction | 0.3 
    9736 Gap open (HH/SS/other) | 18/18/6 
    9737 Gap extend | 1 
    9738 SS matrix |  |  | H | S | O 
    9739 ---|---|---|--- 
    9740 H | 6 | -9 | -6 
    9741 S |  | 6 | -6 
    9742 O |  |  | 4 
    9743 Iteration cutoff | 2 
    9744  
    9745 Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with 3j2w.pdb, chain I
    9746 (#2), sequence alignment score = 458.4 
    9747 RMSD between 130 pruned atom pairs is 0.780 angstroms; (across all 149 pairs:
    9748 2.000) 
    9749  
    9750 Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with 1kxf.pdb, chain A
    9751 (#3), sequence alignment score = 475.4 
    9752 RMSD between 137 pruned atom pairs is 0.844 angstroms; (across all 158 pairs:
    9753 2.636) 
    9754  
    9755 Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with 7sfu.pdb, chain I
    9756 (#4), sequence alignment score = 487.6 
    9757 RMSD between 132 pruned atom pairs is 0.852 angstroms; (across all 162 pairs:
    9758 2.515) 
    9759  
    9760 Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with 4agk.pdb, chain A
    9761 (#6), sequence alignment score = 508.1 
    9762 RMSD between 138 pruned atom pairs is 0.816 angstroms; (across all 151 pairs:
    9763 1.682) 
    9764  
    9765 Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with 7ko8.pdb, chain D
    9766 (#9), sequence alignment score = 485.3 
    9767 RMSD between 124 pruned atom pairs is 1.036 angstroms; (across all 152 pairs:
    9768 2.096) 
    9769  
    9770 Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with AlphFold
    9771 Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 707.3 
    9772 RMSD between 138 pruned atom pairs is 0.591 angstroms; (across all 252 pairs:
    9773 19.368) 
    9774  
    9775 Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with AlphaFold
    9776 Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
    9777 732 
    9778 RMSD between 133 pruned atom pairs is 0.547 angstroms; (across all 249 pairs:
    9779 27.925) 
    9780  
    9781 Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with AlphaFold
    9782 Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
    9783 681.8 
    9784 RMSD between 151 pruned atom pairs is 0.608 angstroms; (across all 265 pairs:
    9785 18.650) 
    9786  
    9787 Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with Alpha Fold
    9788 Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
    9789 score = 529 
    9790 RMSD between 121 pruned atom pairs is 0.853 angstroms; (across all 258 pairs:
    9791 27.133) 
    9792  
    9793 Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with Alpha Fold
    9794 Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
    9795 675.6 
    9796 RMSD between 139 pruned atom pairs is 0.598 angstroms; (across all 247 pairs:
    9797 34.105) 
    9798  
    9799 Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with Ndumu virus
    9800 Alphafold.pdb, chain A (#15), sequence alignment score = 669.2 
    9801 RMSD between 135 pruned atom pairs is 0.619 angstroms; (across all 259 pairs:
    9802 38.678) 
    9803  
    9804 Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with Everglades virus
    9805 Alphafold.pdb, chain A (#16), sequence alignment score = 681.8 
    9806 RMSD between 151 pruned atom pairs is 0.608 angstroms; (across all 265 pairs:
    9807 18.649) 
    9808  
    9809 Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with Bebaru virus
    9810 Alphafold.pdb, chain A (#17), sequence alignment score = 705 
    9811 RMSD between 117 pruned atom pairs is 0.563 angstroms; (across all 250 pairs:
    9812 34.618) 
    9813  
    9814 Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with 6xo4.pdb, chain C
    9815 (#5), sequence alignment score = 413.1 
    9816 RMSD between 95 pruned atom pairs is 1.212 angstroms; (across all 151 pairs:
    9817 2.833) 
    9818  
    9819 Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with 1vcp.pdb, chain C
    9820 (#7), sequence alignment score = 489.6 
    9821 RMSD between 136 pruned atom pairs is 0.711 angstroms; (across all 149 pairs:
    9822 1.711) 
    9823  
    9824 Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with 2yew.pdb, chain G
    9825 (#8), sequence alignment score = 446.9 
    9826 RMSD between 52 pruned atom pairs is 1.300 angstroms; (across all 171 pairs:
    9827 9.079) 
    9828  
    9829 
    9830 > hide #17 models
    9831 
    9832 > color #18 #ff5500ff
    9833 
    9834 > color #18 #c54200ff
    9835 
    9836 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    9837 > UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
    9838 
    9839 ——— End of log from Thu Jun 8 14:55:45 2023 ———
    9840 
    9841 opened ChimeraX session 
    9842 
    9843 > ui mousemode right select
    9844 
    9845 > select #2/I:126
    9846 
    9847 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9848 
    9849 > select #18/A:123
    9850 
    9851 12 atoms, 11 bonds, 1 residue, 1 model selected 
    9852 Alignment identifier is 18/A 
    9853 
    9854 > style sel stick
    9855 
    9856 Changed 12 atom styles 
    9857 
    9858 > show sel atoms
    9859 
    9860 > color sel red
    9861 
    9862 > select #18/A:125
    9863 
    9864 22 atoms, 21 bonds, 1 residue, 1 model selected 
    9865 
    9866 > select #2/I:128
    9867 
    9868 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9869 
    9870 > select #18/A:125
    9871 
    9872 22 atoms, 21 bonds, 1 residue, 1 model selected 
    9873 
    9874 > style sel stick
    9875 
    9876 Changed 22 atom styles 
    9877 
    9878 > show sel atoms
    9879 
    9880 > color sel blue
    9881 
    9882 > ui mousemode right translate
    9883 
    9884 [Repeated 1 time(s)]
    9885 
    9886 > ui mousemode right select
    9887 
    9888 > select #2/I:240
    9889 
    9890 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9891 
    9892 > select #18/A:242
    9893 
    9894 7 atoms, 6 bonds, 1 residue, 1 model selected 
    9895 
    9896 > select #18/A:242
    9897 
    9898 7 atoms, 6 bonds, 1 residue, 1 model selected 
    9899 
    9900 > select #18/A:241
    9901 
    9902 15 atoms, 14 bonds, 1 residue, 1 model selected 
    9903 
    9904 > ui mousemode right translate
    9905 
    9906 > style sel stick
    9907 
    9908 Changed 15 atom styles 
    9909 
    9910 > show sel atoms
    9911 
    9912 > color sel red
    9913 
    9914 > color #18 #f35100ff
    9915 
    9916 > color #18 #eb4e00ff
    9917 
    9918 > color sel red
    9919 
    9920 > color #18 #ffaa00ff
    9921 
    9922 > color #18 #ff9b0eff
    9923 
    9924 > color #18 #ff790cff
    9925 
    9926 > color #18 #ff850aff
    9927 
    9928 > show #15 models
    9929 
    9930 > hide #15 models
    9931 
    9932 > color #18 #ee7c09ff
    9933 
    9934 > color sel red
    9935 
    9936 > ui mousemode right select
    9937 
    9938 Drag select of 2 residues 
    9939 
    9940 > ui mousemode right translate
    9941 
    9942 > ui mousemode right select
    9943 
    9944 > select #18/A:123
    9945 
    9946 12 atoms, 11 bonds, 1 residue, 1 model selected 
    9947 
    9948 > color sel red
    9949 
    9950 > select #18/A:125
    9951 
    9952 22 atoms, 21 bonds, 1 residue, 1 model selected 
    9953 
    9954 > color sel blue
    9955 
    9956 > select clear
    9957 
    9958 > ui mousemode right translate
    9959 
    9960 > ui mousemode right select
    9961 
    9962 > select #2/I:240@CA
    9963 
    9964 1 atom, 1 residue, 1 model selected 
    9965 
    9966 > select #18/A:241
    9967 
    9968 15 atoms, 14 bonds, 1 residue, 1 model selected 
    9969 
    9970 > ui mousemode right translate
    9971 
    9972 > ui mousemode right select
    9973 
    9974 > select #18/A:189
    9975 
    9976 7 atoms, 6 bonds, 1 residue, 1 model selected 
    9977 
    9978 > select #18/A:190
    9979 
    9980 17 atoms, 16 bonds, 1 residue, 1 model selected 
    9981 
    9982 > select #18/A:189
    9983 
    9984 7 atoms, 6 bonds, 1 residue, 1 model selected 
    9985 
    9986 > select #2/I:190
    9987 
    9988 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9989 
    9990 > select #18/A:189
    9991 
    9992 7 atoms, 6 bonds, 1 residue, 1 model selected 
    9993 
    9994 > select #18/A:189
    9995 
    9996 7 atoms, 6 bonds, 1 residue, 1 model selected 
    9997 
    9998 > select #18/A:190
    9999 
    10000 17 atoms, 16 bonds, 1 residue, 1 model selected 
    10001 
    10002 > select #18/A:189
    10003 
    10004 7 atoms, 6 bonds, 1 residue, 1 model selected 
    10005 
    10006 > select #18/A:190
    10007 
    10008 17 atoms, 16 bonds, 1 residue, 1 model selected 
    10009 
    10010 > style sel stick
    10011 
    10012 Changed 17 atom styles 
    10013 
    10014 > show sel atoms
    10015 
    10016 > color sel gray
    10017 
    10018 > select #2/I:190
    10019 
    10020 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10021 
    10022 > select #18/A:190
    10023 
    10024 17 atoms, 16 bonds, 1 residue, 1 model selected 
    10025 
    10026 > ui mousemode right translate
    10027 
    10028 > ui mousemode right select
    10029 
    10030 > select #2/I:183
    10031 
    10032 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10033 
    10034 > select #18/A:182
    10035 
    10036 14 atoms, 13 bonds, 1 residue, 1 model selected 
    10037 
    10038 > select #18/A:181
    10039 
    10040 17 atoms, 17 bonds, 1 residue, 1 model selected 
    10041 
    10042 > select #18/A:182
    10043 
    10044 14 atoms, 13 bonds, 1 residue, 1 model selected 
    10045 
    10046 > style sel stick
    10047 
    10048 Changed 14 atom styles 
    10049 
    10050 > show sel atoms
    10051 
    10052 > color sel orange
    10053 
    10054 > ui mousemode right translate
    10055 
    10056 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    10057 > UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
    10058 
    10059 > ui mousemode right select
    10060 
    10061 > select #2/I:178
    10062 
    10063 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10064 
    10065 > select #18/A:175
    10066 
    10067 19 atoms, 18 bonds, 1 residue, 1 model selected 
    10068 
    10069 > select #18/A:174
    10070 
    10071 20 atoms, 20 bonds, 1 residue, 1 model selected 
    10072 
    10073 > select #2/I:178
    10074 
    10075 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10076 
    10077 > select #18/A:175
    10078 
    10079 19 atoms, 18 bonds, 1 residue, 1 model selected 
    10080 
    10081 > select #2/I:178
    10082 
    10083 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10084 
    10085 > select #18/A:175
    10086 
    10087 19 atoms, 18 bonds, 1 residue, 1 model selected 
    10088 
    10089 > style sel stick
    10090 
    10091 Changed 19 atom styles 
    10092 
    10093 > show sel atoms
    10094 
    10095 > color sel gray
    10096 
    10097 > select #2/I:183
    10098 
    10099 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10100 
    10101 > select #2/I:178
    10102 
    10103 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10104 
    10105 > select #18/A:175
    10106 
    10107 19 atoms, 18 bonds, 1 residue, 1 model selected 
    10108 
    10109 > ui mousemode right translate
    10110 
    10111 > ui mousemode right select
    10112 
    10113 > select #2/I:154
    10114 
    10115 8 atoms, 7 bonds, 1 residue, 1 model selected 
    10116 
    10117 > select #18/A:151
    10118 
    10119 15 atoms, 14 bonds, 1 residue, 1 model selected 
    10120 
    10121 > show sel atoms
    10122 
    10123 > style sel stick
    10124 
    10125 Changed 15 atom styles 
    10126 
    10127 > show sel atoms
    10128 
    10129 > color sel red
    10130 
    10131 Drag select of 3 residues 
    10132 
    10133 > ui mousemode right translate
    10134 
    10135 > ui mousemode right select
    10136 
    10137 > select #2/I:157
    10138 
    10139 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10140 
    10141 > select #18/A:154
    10142 
    10143 14 atoms, 13 bonds, 1 residue, 1 model selected 
    10144 
    10145 > style sel stick
    10146 
    10147 Changed 14 atom styles 
    10148 
    10149 > show sel atoms
    10150 
    10151 > color sel orange
    10152 
    10153 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    10154 > UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
    10155 
    10156 > ui mousemode right translate
    10157 
    10158 > ui mousemode right select
    10159 
    10160 > select #18/A:182
    10161 
    10162 14 atoms, 13 bonds, 1 residue, 1 model selected 
    10163 Drag select of 11 residues 
    10164 
    10165 > ui mousemode right translate
    10166 
    10167 > ui mousemode right select
    10168 
    10169 > select #2/I:154
    10170 
    10171 8 atoms, 7 bonds, 1 residue, 1 model selected 
    10172 
    10173 > ui mousemode right translate
    10174 
    10175 > hide #18 models
    10176 
    10177 > show #16 models
    10178 
    10179 > ui mousemode right rotate
    10180 
    10181 > ui mousemode right select
    10182 
    10183 > select #2/I:190
    10184 
    10185 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10186 
    10187 > select #16/A:196@CA
    10188 
    10189 1 atom, 1 residue, 1 model selected 
    10190 Alignment identifier is 16/A 
    10191 
    10192 > color sel orange
    10193 
    10194 > style sel stick
    10195 
    10196 Changed 1 atom style 
    10197 
    10198 > show sel atoms
    10199 
    10200 > select #16/A:196
    10201 
    10202 17 atoms, 16 bonds, 1 residue, 1 model selected 
    10203 
    10204 > ui mousemode right select
    10205 
    10206 > select #16/A:196
    10207 
    10208 17 atoms, 16 bonds, 1 residue, 1 model selected 
    10209 
    10210 > select #16/A:196
    10211 
    10212 17 atoms, 16 bonds, 1 residue, 1 model selected 
    10213 
    10214 > style sel stick
    10215 
    10216 Changed 17 atom styles 
    10217 
    10218 > show sel atoms
    10219 
    10220 > hide sel atoms
    10221 
    10222 > show sel atoms
    10223 
    10224 > color sel red
    10225 
    10226 > color sel orange
    10227 
    10228 > ui mousemode right translate
    10229 
    10230 > ui mousemode right rotate
    10231 
    10232 > ui mousemode right select
    10233 
    10234 > select #2/I:157
    10235 
    10236 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10237 
    10238 > select #16/A:163
    10239 
    10240 10 atoms, 9 bonds, 1 residue, 1 model selected 
    10241 
    10242 > color sel gray
    10243 
    10244 > select #2/I:154
    10245 
    10246 8 atoms, 7 bonds, 1 residue, 1 model selected 
    10247 
    10248 > select #16/A:160
    10249 
    10250 16 atoms, 15 bonds, 1 residue, 1 model selected 
    10251 
    10252 > color sel gray
    10253 
    10254 > ui mousemode right translate
    10255 
    10256 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    10257 > UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
    10258 
    10259 ——— End of log from Thu Jun 8 16:20:57 2023 ———
    10260 
    10261 opened ChimeraX session 
    10262 
    10263 > hide #16 models
    10264 
    10265 > show #18 models
    10266 
    10267 > ui mousemode right select
    10268 
    10269 Drag select of 1 residues 
    10270 
    10271 > select clear
    10272 
    10273 > select #2/I:157
    10274 
    10275 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10276 
    10277 > select #18/A:154
    10278 
    10279 14 atoms, 13 bonds, 1 residue, 1 model selected 
    10280 
    10281 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    10282 > UASLP/Lab Virología/Alpha fold/Cabassou virus Alphafold.pdb"
    10283 
    10284 Chain information for Cabassou virus Alphafold.pdb #19 
    10285 --- 
    10286 Chain | Description 
    10287 A | No description available 
    10288  
    10289 
    10290 > hide #18 models
    10291 
    10292 > select add #18
    10293 
    10294 4336 atoms, 4396 bonds, 269 residues, 1 model selected 
    10295 
    10296 > select subtract #18
    10297 
    10298 Nothing selected 
    10299 
    10300 > ui tool show Matchmaker
    10301 
    10302 > matchmaker #2-4,6,9-18#!5,7-8 to #19
    10303 
    10304 Parameters 
    10305 --- 
    10306 Chain pairing | bb 
    10307 Alignment algorithm | Needleman-Wunsch 
    10308 Similarity matrix | BLOSUM-62 
    10309 SS fraction | 0.3 
    10310 Gap open (HH/SS/other) | 18/18/6 
    10311 Gap extend | 1 
    10312 SS matrix |  |  | H | S | O 
    10313 ---|---|---|--- 
    10314 H | 6 | -9 | -6 
    10315 S |  | 6 | -6 
    10316 O |  |  | 4 
    10317 Iteration cutoff | 2 
    10318  
    10319 Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with 3j2w.pdb, chain I
    10320 (#2), sequence alignment score = 523.2 
    10321 RMSD between 146 pruned atom pairs is 0.713 angstroms; (across all 149 pairs:
    10322 0.884) 
    10323  
    10324 Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with 1kxf.pdb, chain A
    10325 (#3), sequence alignment score = 557.2 
    10326 RMSD between 150 pruned atom pairs is 0.659 angstroms; (across all 158 pairs:
    10327 2.145) 
    10328  
    10329 Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with 7sfu.pdb, chain F
    10330 (#4), sequence alignment score = 796.5 
    10331 RMSD between 148 pruned atom pairs is 0.761 angstroms; (across all 162 pairs:
    10332 2.057) 
    10333  
    10334 Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with 4agk.pdb, chain A
    10335 (#6), sequence alignment score = 555.1 
    10336 RMSD between 150 pruned atom pairs is 0.694 angstroms; (across all 151 pairs:
    10337 0.721) 
    10338  
    10339 Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with 7ko8.pdb, chain G
    10340 (#9), sequence alignment score = 565 
    10341 RMSD between 133 pruned atom pairs is 1.092 angstroms; (across all 152 pairs:
    10342 1.625) 
    10343  
    10344 Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with AlphFold
    10345 Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 820.3 
    10346 RMSD between 151 pruned atom pairs is 0.605 angstroms; (across all 258 pairs:
    10347 27.418) 
    10348  
    10349 Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with AlphaFold
    10350 Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
    10351 783.7 
    10352 RMSD between 8 pruned atom pairs is 1.343 angstroms; (across all 261 pairs:
    10353 33.012) 
    10354  
    10355 Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with AlphaFold
    10356 Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
    10357 1238.2 
    10358 RMSD between 165 pruned atom pairs is 0.252 angstroms; (across all 273 pairs:
    10359 36.940) 
    10360  
    10361 Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with Alpha Fold
    10362 Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
    10363 score = 567.2 
    10364 RMSD between 5 pruned atom pairs is 1.242 angstroms; (across all 269 pairs:
    10365 26.754) 
    10366  
    10367 Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with Alpha Fold
    10368 Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
    10369 992.6 
    10370 RMSD between 162 pruned atom pairs is 0.383 angstroms; (across all 255 pairs:
    10371 42.412) 
    10372  
    10373 Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with Ndumu virus
    10374 Alphafold.pdb, chain A (#15), sequence alignment score = 812.5 
    10375 RMSD between 147 pruned atom pairs is 0.649 angstroms; (across all 265 pairs:
    10376 39.998) 
    10377  
    10378 Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with Everglades virus
    10379 Alphafold.pdb, chain A (#16), sequence alignment score = 1238.2 
    10380 RMSD between 165 pruned atom pairs is 0.252 angstroms; (across all 273 pairs:
    10381 36.940) 
    10382  
    10383 Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with Bebaru virus
    10384 Alphafold.pdb, chain A (#17), sequence alignment score = 803.3 
    10385 RMSD between 13 pruned atom pairs is 1.246 angstroms; (across all 257 pairs:
    10386 34.843) 
    10387  
    10388 Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with Caaingua virus
    10389 AlphaFold.pdb, chain A (#18), sequence alignment score = 703.7 
    10390 RMSD between 149 pruned atom pairs is 0.682 angstroms; (across all 261 pairs:
    10391 25.890) 
    10392  
    10393 Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with 6xo4.pdb, chain C
    10394 (#5), sequence alignment score = 693.4 
    10395 RMSD between 104 pruned atom pairs is 1.218 angstroms; (across all 151 pairs:
    10396 2.050) 
    10397  
    10398 Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with 1vcp.pdb, chain C
    10399 (#7), sequence alignment score = 557.1 
    10400 RMSD between 147 pruned atom pairs is 0.589 angstroms; (across all 149 pairs:
    10401 0.717) 
    10402  
    10403 Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with 2yew.pdb, chain G
    10404 (#8), sequence alignment score = 512.3 
    10405 RMSD between 54 pruned atom pairs is 1.264 angstroms; (across all 171 pairs:
    10406 9.925) 
    10407  
    10408 
    10409 > show #18 models
    10410 
    10411 > hide #18 models
    10412 
    10413 > color #19 #aaff7fff
    10414 
    10415 > color #19 #92d96cff
    10416 
    10417 > color #19 #90d56aff
    10418 
    10419 > color #19 #88ca65ff
    10420 
    10421 > color #19 #8fd46aff
    10422 
    10423 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    10424 > UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
    10425 
    10426 ——— End of log from Fri Jun 9 12:21:12 2023 ———
    10427 
    10428 opened ChimeraX session 
    10429 
    10430 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    10431 > UASLP/Lab Virología/Alpha fold/Eilat virus Alphafold.pdb"
    10432 
    10433 Chain information for Eilat virus Alphafold.pdb #20 
    10434 --- 
    10435 Chain | Description 
    10436 A | No description available 
    10437  
    10438 
    10439 > ui tool show Matchmaker
    10440 
    10441 > matchmaker #2-4,6,9-19#!5,7-8 to #20
    10442 
    10443 Parameters 
    10444 --- 
    10445 Chain pairing | bb 
    10446 Alignment algorithm | Needleman-Wunsch 
    10447 Similarity matrix | BLOSUM-62 
    10448 SS fraction | 0.3 
    10449 Gap open (HH/SS/other) | 18/18/6 
    10450 Gap extend | 1 
    10451 SS matrix |  |  | H | S | O 
    10452 ---|---|---|--- 
    10453 H | 6 | -9 | -6 
    10454 S |  | 6 | -6 
    10455 O |  |  | 4 
    10456 Iteration cutoff | 2 
    10457  
    10458 Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with 3j2w.pdb, chain I
    10459 (#2), sequence alignment score = 459.1 
    10460 RMSD between 145 pruned atom pairs is 0.743 angstroms; (across all 149 pairs:
    10461 0.843) 
    10462  
    10463 Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with 1kxf.pdb, chain A
    10464 (#3), sequence alignment score = 618.2 
    10465 RMSD between 148 pruned atom pairs is 0.717 angstroms; (across all 159 pairs:
    10466 1.840) 
    10467  
    10468 Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with 7sfu.pdb, chain I
    10469 (#4), sequence alignment score = 520.6 
    10470 RMSD between 138 pruned atom pairs is 0.873 angstroms; (across all 162 pairs:
    10471 2.526) 
    10472  
    10473 Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with 4agk.pdb, chain A
    10474 (#6), sequence alignment score = 660.7 
    10475 RMSD between 150 pruned atom pairs is 0.630 angstroms; (across all 152 pairs:
    10476 0.685) 
    10477  
    10478 Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with 7ko8.pdb, chain G
    10479 (#9), sequence alignment score = 491.3 
    10480 RMSD between 125 pruned atom pairs is 1.096 angstroms; (across all 152 pairs:
    10481 1.726) 
    10482  
    10483 Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with AlphFold Colaboratory
    10484 Ross River.pdb, chain A (#10), sequence alignment score = 688.4 
    10485 RMSD between 151 pruned atom pairs is 0.721 angstroms; (across all 251 pairs:
    10486 32.337) 
    10487  
    10488 Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with AlphaFold
    10489 Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
    10490 705.8 
    10491 RMSD between 7 pruned atom pairs is 1.275 angstroms; (across all 248 pairs:
    10492 30.093) 
    10493  
    10494 Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with AlphaFold
    10495 Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
    10496 706.4 
    10497 RMSD between 10 pruned atom pairs is 1.510 angstroms; (across all 254 pairs:
    10498 29.648) 
    10499  
    10500 Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with Alpha Fold
    10501 Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
    10502 score = 512.7 
    10503 RMSD between 5 pruned atom pairs is 1.118 angstroms; (across all 251 pairs:
    10504 27.761) 
    10505  
    10506 Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with Alpha Fold
    10507 Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
    10508 719.5 
    10509 RMSD between 151 pruned atom pairs is 0.659 angstroms; (across all 245 pairs:
    10510 31.518) 
    10511  
    10512 Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with Ndumu virus
    10513 Alphafold.pdb, chain A (#15), sequence alignment score = 640.6 
    10514 RMSD between 149 pruned atom pairs is 0.662 angstroms; (across all 252 pairs:
    10515 29.525) 
    10516  
    10517 Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with Everglades virus
    10518 Alphafold.pdb, chain A (#16), sequence alignment score = 706.4 
    10519 RMSD between 10 pruned atom pairs is 1.511 angstroms; (across all 254 pairs:
    10520 29.647) 
    10521  
    10522 Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with Bebaru virus
    10523 Alphafold.pdb, chain A (#17), sequence alignment score = 702.4 
    10524 RMSD between 127 pruned atom pairs is 0.613 angstroms; (across all 251 pairs:
    10525 36.013) 
    10526  
    10527 Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with Caaingua virus
    10528 AlphaFold.pdb, chain A (#18), sequence alignment score = 647.9 
    10529 RMSD between 142 pruned atom pairs is 0.759 angstroms; (across all 242 pairs:
    10530 33.358) 
    10531  
    10532 Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with Cabassou virus
    10533 Alphafold.pdb, chain A (#19), sequence alignment score = 707.1 
    10534 RMSD between 148 pruned atom pairs is 0.716 angstroms; (across all 253 pairs:
    10535 23.904) 
    10536  
    10537 Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with 6xo4.pdb, chain C
    10538 (#5), sequence alignment score = 441.5 
    10539 RMSD between 91 pruned atom pairs is 1.178 angstroms; (across all 150 pairs:
    10540 2.235) 
    10541  
    10542 Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with 1vcp.pdb, chain C
    10543 (#7), sequence alignment score = 506.2 
    10544 RMSD between 144 pruned atom pairs is 0.683 angstroms; (across all 149 pairs:
    10545 0.855) 
    10546  
    10547 Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with 2yew.pdb, chain G
    10548 (#8), sequence alignment score = 461.4 
    10549 RMSD between 55 pruned atom pairs is 1.242 angstroms; (across all 171 pairs:
    10550 7.961) 
    10551  
    10552 
    10553 > color #20 #55aa00ff
    10554 
    10555 > color #20 #00aa7fff
    10556 
    10557 > color #20 #00b182ff
    10558 
    10559 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    10560 > UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
    10561 
    10562 > hide #20 models
    10563 
    10564 > show #20 models
    10565 
    10566 > hide #20 models
    10567 
    10568 > ui mousemode right select
    10569 
    10570 > select #2/I:126
    10571 
    10572 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10573 
    10574 > select #19/A:133
    10575 
    10576 12 atoms, 11 bonds, 1 residue, 1 model selected 
    10577 Alignment identifier is 19/A 
    10578 
    10579 > style sel stick
    10580 
    10581 Changed 12 atom styles 
    10582 
    10583 > show sel atoms
    10584 
    10585 > color sel red
    10586 
    10587 > select #2/I:128
    10588 
    10589 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10590 
    10591 > select #19/A:135
    10592 
    10593 22 atoms, 21 bonds, 1 residue, 1 model selected 
    10594 
    10595 > style sel stick
    10596 
    10597 Changed 22 atom styles 
    10598 
    10599 > show sel atoms
    10600 
    10601 > color sel blue
    10602 
    10603 > select clear
    10604 
    10605 > ui mousemode right translate
    10606 
    10607 > ui mousemode right select
    10608 
    10609 > select clear
    10610 
    10611 Drag select of 2 residues 
    10612 
    10613 > ui mousemode right translate
    10614 
    10615 > ui mousemode right select
    10616 
    10617 > select #19/A:45
    10618 
    10619 17 atoms, 16 bonds, 1 residue, 1 model selected 
    10620 
    10621 > select #2/I:240
    10622 
    10623 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10624 
    10625 > ui mousemode right translate
    10626 
    10627 [Repeated 1 time(s)]
    10628 
    10629 > ui mousemode right rotate
    10630 
    10631 > ui mousemode right select
    10632 
    10633 > select #2/I:126
    10634 
    10635 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10636 
    10637 > select #19/A:133
    10638 
    10639 12 atoms, 11 bonds, 1 residue, 1 model selected 
    10640 
    10641 > ui mousemode right translate
    10642 
    10643 > ui mousemode right select
    10644 
    10645 > select #2/I:240
    10646 
    10647 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10648 
    10649 > select #19/A:247
    10650 
    10651 15 atoms, 14 bonds, 1 residue, 1 model selected 
    10652 
    10653 > style sel stick
    10654 
    10655 Changed 15 atom styles 
    10656 
    10657 > show sel atoms
    10658 
    10659 > color sel red
    10660 
    10661 > select clear
    10662 
    10663 > ui mousemode right translate
    10664 
    10665 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    10666 > UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
    10667 
    10668 > ui mousemode right select
    10669 
    10670 > select #2/I:190
    10671 
    10672 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10673 
    10674 > select #19/A:197
    10675 
    10676 17 atoms, 16 bonds, 1 residue, 1 model selected 
    10677 
    10678 > select #19/A:197
    10679 
    10680 17 atoms, 16 bonds, 1 residue, 1 model selected 
    10681 
    10682 > select #19/A:198
    10683 
    10684 7 atoms, 6 bonds, 1 residue, 1 model selected 
    10685 
    10686 > select #19/A:197
    10687 
    10688 17 atoms, 16 bonds, 1 residue, 1 model selected 
    10689 
    10690 > style sel stick
    10691 
    10692 Changed 17 atom styles 
    10693 
    10694 > show sel atoms
    10695 
    10696 > ui mousemode right select
    10697 
    10698 > select #19/A:198
    10699 
    10700 7 atoms, 6 bonds, 1 residue, 1 model selected 
    10701 
    10702 > select #19/A:197
    10703 
    10704 17 atoms, 16 bonds, 1 residue, 1 model selected 
    10705 
    10706 > select #2/I:190
    10707 
    10708 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10709 
    10710 > select #19/A:197
    10711 
    10712 17 atoms, 16 bonds, 1 residue, 1 model selected 
    10713 
    10714 > color sel orange
    10715 
    10716 > ui mousemode right translate
    10717 
    10718 [Repeated 1 time(s)]
    10719 
    10720 > ui mousemode right rotate
    10721 
    10722 > ui mousemode right select
    10723 
    10724 > select clear
    10725 
    10726 > select #2/I:183
    10727 
    10728 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10729 
    10730 > select #19/A:190
    10731 
    10732 24 atoms, 23 bonds, 1 residue, 1 model selected 
    10733 
    10734 > select #19/A:189
    10735 
    10736 20 atoms, 20 bonds, 1 residue, 1 model selected 
    10737 
    10738 > select #2/I:184
    10739 
    10740 11 atoms, 11 bonds, 1 residue, 1 model selected 
    10741 
    10742 > select #19/A:191
    10743 
    10744 21 atoms, 21 bonds, 1 residue, 1 model selected 
    10745 
    10746 > select #19/A:190
    10747 
    10748 24 atoms, 23 bonds, 1 residue, 1 model selected 
    10749 
    10750 > style sel stick
    10751 
    10752 Changed 24 atom styles 
    10753 
    10754 > show sel atoms
    10755 
    10756 > color sel blue
    10757 
    10758 > select #2/I:183
    10759 
    10760 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10761 
    10762 > ui mousemode right rotate
    10763 
    10764 > ui mousemode right translate
    10765 
    10766 > ui mousemode right select
    10767 
    10768 > select #2/I:178
    10769 
    10770 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10771 Drag select of 2 residues 
    10772 
    10773 > select #19/A:185
    10774 
    10775 24 atoms, 23 bonds, 1 residue, 1 model selected 
    10776 
    10777 > select #2/I:178
    10778 
    10779 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10780 
    10781 > select #19/A:185
    10782 
    10783 24 atoms, 23 bonds, 1 residue, 1 model selected 
    10784 
    10785 > style sel stick
    10786 
    10787 Changed 24 atom styles 
    10788 
    10789 > show sel atoms
    10790 
    10791 > color sel blue
    10792 
    10793 > select #19/A:184
    10794 
    10795 17 atoms, 16 bonds, 1 residue, 1 model selected 
    10796 
    10797 > select #2/I:178
    10798 
    10799 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10800 
    10801 > select #19/A:185
    10802 
    10803 24 atoms, 23 bonds, 1 residue, 1 model selected 
    10804 
    10805 > select clear
    10806 
    10807 > ui mousemode right translate
    10808 
    10809 > ui mousemode right select
    10810 
    10811 > select #2/I:157
    10812 
    10813 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10814 
    10815 > select #19/A:164
    10816 
    10817 10 atoms, 9 bonds, 1 residue, 1 model selected 
    10818 
    10819 > style sel stick
    10820 
    10821 Changed 10 atom styles 
    10822 
    10823 > show sel atoms
    10824 
    10825 > color sel gray
    10826 
    10827 Drag select of 2 residues 
    10828 
    10829 > select #19/A:164
    10830 
    10831 10 atoms, 9 bonds, 1 residue, 1 model selected 
    10832 
    10833 > ui mousemode right translate
    10834 
    10835 > ui mousemode right select
    10836 
    10837 > select #2/I:154
    10838 
    10839 8 atoms, 7 bonds, 1 residue, 1 model selected 
    10840 
    10841 > select #19/A:161
    10842 
    10843 14 atoms, 13 bonds, 1 residue, 1 model selected 
    10844 
    10845 > style sel stick
    10846 
    10847 Changed 14 atom styles 
    10848 
    10849 > show sel atoms
    10850 
    10851 > color sel orange
    10852 
    10853 > ui mousemode right translate
    10854 
    10855 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    10856 > UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
    10857 
    10858 > show #18 models
    10859 
    10860 > hide #18 models
    10861 
    10862 > ui mousemode right translate
    10863 
    10864 > ui mousemode right select
    10865 
    10866 > select #2/I:128
    10867 
    10868 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10869 
    10870 > select #19/A:135
    10871 
    10872 22 atoms, 21 bonds, 1 residue, 1 model selected 
    10873 
    10874 > select #19/A:135
    10875 
    10876 22 atoms, 21 bonds, 1 residue, 1 model selected 
    10877 
    10878 > select #19/A:135
    10879 
    10880 22 atoms, 21 bonds, 1 residue, 1 model selected 
    10881 
    10882 > select #2/I:126
    10883 
    10884 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10885 
    10886 > select #19/A:133
    10887 
    10888 12 atoms, 11 bonds, 1 residue, 1 model selected 
    10889 
    10890 > select #2/I:240
    10891 
    10892 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10893 
    10894 > select #19/A:247
    10895 
    10896 15 atoms, 14 bonds, 1 residue, 1 model selected 
    10897 
    10898 > select #2/I:190
    10899 
    10900 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10901 
    10902 > select #19/A:197
    10903 
    10904 17 atoms, 16 bonds, 1 residue, 1 model selected 
    10905 
    10906 > select #2/I:183
    10907 
    10908 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10909 
    10910 > select #19/A:190
    10911 
    10912 24 atoms, 23 bonds, 1 residue, 1 model selected 
    10913 
    10914 > select #2/I:178
    10915 
    10916 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10917 
    10918 > select #19/A:185
    10919 
    10920 24 atoms, 23 bonds, 1 residue, 1 model selected 
    10921 
    10922 > select #2/I:157
    10923 
    10924 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10925 
    10926 > select #19/A:164
    10927 
    10928 10 atoms, 9 bonds, 1 residue, 1 model selected 
    10929 
    10930 > select #2/I:154
    10931 
    10932 8 atoms, 7 bonds, 1 residue, 1 model selected 
    10933 
    10934 > select #19/A:161
    10935 
    10936 14 atoms, 13 bonds, 1 residue, 1 model selected 
    10937 
    10938 > hide #19 models
    10939 
    10940 > show #20 models
    10941 
    10942 Drag select of 1 atoms, 5 residues 
    10943 
    10944 > ui mousemode right translate
    10945 
    10946 > ui mousemode right select
    10947 
    10948 > select #2/I:126
    10949 
    10950 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10951 
    10952 > select #20/A:113
    10953 
    10954 22 atoms, 21 bonds, 1 residue, 1 model selected 
    10955 
    10956 > select #20/A:112
    10957 
    10958 12 atoms, 11 bonds, 1 residue, 1 model selected 
    10959 
    10960 > select #20/A:113
    10961 
    10962 22 atoms, 21 bonds, 1 residue, 1 model selected 
    10963 Alignment identifier is 20/A 
    10964 
    10965 > style sel stick
    10966 
    10967 Changed 22 atom styles 
    10968 
    10969 > show sel atoms
    10970 
    10971 Drag select of 1 bonds 
    10972 
    10973 > ui mousemode right translate
    10974 
    10975 > ui mousemode right select
    10976 
    10977 > select #20/A:113
    10978 
    10979 22 atoms, 21 bonds, 1 residue, 1 model selected 
    10980 
    10981 > select #2/I:126
    10982 
    10983 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10984 
    10985 > select #20/A:113
    10986 
    10987 22 atoms, 21 bonds, 1 residue, 1 model selected 
    10988 
    10989 > color sel blue
    10990 
    10991 > select #2/I:128
    10992 
    10993 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10994 
    10995 > select #20/A:113
    10996 
    10997 22 atoms, 21 bonds, 1 residue, 1 model selected 
    10998 
    10999 > select #2/I:126
    11000 
    11001 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11002 
    11003 > select #2/I:128
    11004 
    11005 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11006 
    11007 > select #20/A:115
    11008 
    11009 16 atoms, 15 bonds, 1 residue, 1 model selected 
    11010 
    11011 > select #2/I:128
    11012 
    11013 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11014 
    11015 > select #20/A:115
    11016 
    11017 16 atoms, 15 bonds, 1 residue, 1 model selected 
    11018 
    11019 > style sel stick
    11020 
    11021 Changed 16 atom styles 
    11022 
    11023 > show sel atoms
    11024 
    11025 > color sel gray
    11026 
    11027 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    11028 > UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
    11029 
    11030 > ui mousemode right translate
    11031 
    11032 > ui mousemode right select
    11033 
    11034 > select #20/A:227
    11035 
    11036 15 atoms, 14 bonds, 1 residue, 1 model selected 
    11037 
    11038 > select #2/I:240
    11039 
    11040 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11041 
    11042 > select #20/A:227
    11043 
    11044 15 atoms, 14 bonds, 1 residue, 1 model selected 
    11045 
    11046 > style sel stick
    11047 
    11048 Changed 15 atom styles 
    11049 
    11050 > show sel atoms
    11051 
    11052 > color sel red
    11053 
    11054 > ui mousemode right translate
    11055 
    11056 > ui mousemode right select
    11057 
    11058 > select #2/I:190
    11059 
    11060 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11061 
    11062 > select #20/A:177
    11063 
    11064 12 atoms, 11 bonds, 1 residue, 1 model selected 
    11065 
    11066 > style sel stick
    11067 
    11068 Changed 12 atom styles 
    11069 
    11070 > show sel atoms
    11071 
    11072 > color sel red
    11073 
    11074 > select clear
    11075 
    11076 > ui mousemode right translate
    11077 
    11078 > ui mousemode right select
    11079 
    11080 > select #2/I:183
    11081 
    11082 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11083 
    11084 > select #2/I:183
    11085 
    11086 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11087 
    11088 > select #20/A:170
    11089 
    11090 10 atoms, 9 bonds, 1 residue, 1 model selected 
    11091 
    11092 > style sel stick
    11093 
    11094 Changed 10 atom styles 
    11095 
    11096 > show sel atoms
    11097 
    11098 > color sel gray
    11099 
    11100 Drag select of 4 residues 
    11101 
    11102 > ui mousemode right translate
    11103 
    11104 > ui mousemode right select
    11105 
    11106 > select #2/I:178
    11107 
    11108 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11109 
    11110 > select #20/A:165
    11111 
    11112 24 atoms, 23 bonds, 1 residue, 1 model selected 
    11113 
    11114 > select #20/A:164
    11115 
    11116 17 atoms, 16 bonds, 1 residue, 1 model selected 
    11117 
    11118 > select #20/A:165
    11119 
    11120 24 atoms, 23 bonds, 1 residue, 1 model selected 
    11121 
    11122 > style sel stick
    11123 
    11124 Changed 24 atom styles 
    11125 
    11126 > show sel atoms
    11127 
    11128 > color sel blue
    11129 
    11130 Drag select of 12 atoms, 40 residues, 8 bonds 
    11131 
    11132 > ui mousemode right translate
    11133 
    11134 > ui mousemode right rotate
    11135 
    11136 > ui mousemode right select
    11137 
    11138 > select #2/I:157
    11139 
    11140 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11141 
    11142 > select #20/A:144
    11143 
    11144 11 atoms, 10 bonds, 1 residue, 1 model selected 
    11145 
    11146 > color sel orange
    11147 
    11148 > style sel stick
    11149 
    11150 Changed 11 atom styles 
    11151 
    11152 > show sel atoms
    11153 
    11154 > select #2/I:154
    11155 
    11156 8 atoms, 7 bonds, 1 residue, 1 model selected 
    11157 
    11158 > ui mousemode right select
    11159 
    11160 > select #2/I:154
    11161 
    11162 8 atoms, 7 bonds, 1 residue, 1 model selected 
    11163 
    11164 > select #20/A:141
    11165 
    11166 19 atoms, 18 bonds, 1 residue, 1 model selected 
    11167 
    11168 > color sel gray
    11169 
    11170 > style sel stick
    11171 
    11172 Changed 19 atom styles 
    11173 
    11174 > show sel atoms
    11175 
    11176 > ui mousemode right translate
    11177 
    11178 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    11179 > UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
    11180 
    11181 ——— End of log from Fri Jun 9 15:09:21 2023 ———
    11182 
    11183 opened ChimeraX session 
    11184 
    11185 > hide #20 models
    11186 
    11187 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    11188 > UASLP/Lab Virología/Alpha fold/Highlands J. virus Alphafold.pdb"
    11189 
    11190 Chain information for Highlands J. virus Alphafold.pdb #21 
    11191 --- 
    11192 Chain | Description 
    11193 A | No description available 
    11194  
    11195 
    11196 > ui tool show Matchmaker
    11197 
    11198 > matchmaker #2-4,6,9-20#!5,7-8 to #21
    11199 
    11200 Parameters 
    11201 --- 
    11202 Chain pairing | bb 
    11203 Alignment algorithm | Needleman-Wunsch 
    11204 Similarity matrix | BLOSUM-62 
    11205 SS fraction | 0.3 
    11206 Gap open (HH/SS/other) | 18/18/6 
    11207 Gap extend | 1 
    11208 SS matrix |  |  | H | S | O 
    11209 ---|---|---|--- 
    11210 H | 6 | -9 | -6 
    11211 S |  | 6 | -6 
    11212 O |  |  | 4 
    11213 Iteration cutoff | 2 
    11214  
    11215 Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with 3j2w.pdb,
    11216 chain I (#2), sequence alignment score = 534.6 
    11217 RMSD between 147 pruned atom pairs is 0.672 angstroms; (across all 149 pairs:
    11218 0.755) 
    11219  
    11220 Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with 1kxf.pdb,
    11221 chain A (#3), sequence alignment score = 584.9 
    11222 RMSD between 150 pruned atom pairs is 0.630 angstroms; (across all 158 pairs:
    11223 2.143) 
    11224  
    11225 Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with 7sfu.pdb,
    11226 chain F (#4), sequence alignment score = 704.2 
    11227 RMSD between 148 pruned atom pairs is 0.808 angstroms; (across all 162 pairs:
    11228 2.057) 
    11229  
    11230 Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with 4agk.pdb,
    11231 chain A (#6), sequence alignment score = 563.1 
    11232 RMSD between 150 pruned atom pairs is 0.643 angstroms; (across all 151 pairs:
    11233 0.671) 
    11234  
    11235 Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with 7ko8.pdb,
    11236 chain G (#9), sequence alignment score = 593.5 
    11237 RMSD between 134 pruned atom pairs is 1.109 angstroms; (across all 152 pairs:
    11238 1.587) 
    11239  
    11240 Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with AlphFold
    11241 Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 804.8 
    11242 RMSD between 148 pruned atom pairs is 0.558 angstroms; (across all 257 pairs:
    11243 26.440) 
    11244  
    11245 Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with AlphaFold
    11246 Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
    11247 818.8 
    11248 RMSD between 151 pruned atom pairs is 0.625 angstroms; (across all 258 pairs:
    11249 21.384) 
    11250  
    11251 Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with AlphaFold
    11252 Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
    11253 996.4 
    11254 RMSD between 163 pruned atom pairs is 0.346 angstroms; (across all 254 pairs:
    11255 15.033) 
    11256  
    11257 Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with Alpha Fold
    11258 Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
    11259 score = 539.8 
    11260 RMSD between 132 pruned atom pairs is 0.906 angstroms; (across all 256 pairs:
    11261 30.694) 
    11262  
    11263 Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with Alpha Fold
    11264 Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
    11265 1232.6 
    11266 RMSD between 164 pruned atom pairs is 0.338 angstroms; (across all 259 pairs:
    11267 25.527) 
    11268  
    11269 Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with Ndumu virus
    11270 Alphafold.pdb, chain A (#15), sequence alignment score = 774.7 
    11271 RMSD between 147 pruned atom pairs is 0.592 angstroms; (across all 251 pairs:
    11272 32.099) 
    11273  
    11274 Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with Everglades
    11275 virus Alphafold.pdb, chain A (#16), sequence alignment score = 996.4 
    11276 RMSD between 163 pruned atom pairs is 0.346 angstroms; (across all 254 pairs:
    11277 15.031) 
    11278  
    11279 Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with Bebaru virus
    11280 Alphafold.pdb, chain A (#17), sequence alignment score = 830.6 
    11281 RMSD between 151 pruned atom pairs is 0.547 angstroms; (across all 256 pairs:
    11282 26.017) 
    11283  
    11284 Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with Caaingua virus
    11285 AlphaFold.pdb, chain A (#18), sequence alignment score = 698.7 
    11286 RMSD between 151 pruned atom pairs is 0.680 angstroms; (across all 248 pairs:
    11287 24.738) 
    11288  
    11289 Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with Cabassou virus
    11290 Alphafold.pdb, chain A (#19), sequence alignment score = 1000.3 
    11291 RMSD between 159 pruned atom pairs is 0.253 angstroms; (across all 255 pairs:
    11292 39.413) 
    11293  
    11294 Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with Eilat virus
    11295 Alphafold.pdb, chain A (#20), sequence alignment score = 734.7 
    11296 RMSD between 151 pruned atom pairs is 0.665 angstroms; (across all 244 pairs:
    11297 36.300) 
    11298  
    11299 Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with 6xo4.pdb,
    11300 chain C (#5), sequence alignment score = 922.1 
    11301 RMSD between 103 pruned atom pairs is 1.185 angstroms; (across all 151 pairs:
    11302 2.034) 
    11303  
    11304 Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with 1vcp.pdb,
    11305 chain C (#7), sequence alignment score = 566.4 
    11306 RMSD between 147 pruned atom pairs is 0.527 angstroms; (across all 149 pairs:
    11307 0.665) 
    11308  
    11309 Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with 2yew.pdb,
    11310 chain G (#8), sequence alignment score = 540.8 
    11311 RMSD between 53 pruned atom pairs is 1.232 angstroms; (across all 169 pairs:
    11312 7.986) 
    11313  
    11314 
    11315 > color #21 #00aaffff
    11316 
    11317 > color #21 #007cbaff
    11318 
    11319 > select add #20
    11320 
    11321 3966 atoms, 4011 bonds, 255 residues, 1 model selected 
    11322 
    11323 > select subtract #20
    11324 
    11325 Nothing selected 
    11326 
    11327 > show #20 models
    11328 
    11329 > hide #20 models
    11330 
    11331 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    11332 > UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
    11333 
    11334 ——— End of log from Mon Jun 12 10:47:51 2023 ———
    11335 
    11336 opened ChimeraX session 
    11337 
    11338 > ui mousemode right select
    11339 
    11340 > select #2/I:126
    11341 
    11342 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11343 
    11344 > select #21/A:117
    11345 
    11346 14 atoms, 13 bonds, 1 residue, 1 model selected 
    11347 
    11348 > select clear
    11349 
    11350 > select #21/A:117
    11351 
    11352 14 atoms, 13 bonds, 1 residue, 1 model selected 
    11353 
    11354 > style sel stick
    11355 
    11356 Changed 14 atom styles 
    11357 
    11358 > show sel atoms
    11359 
    11360 > color sel red
    11361 
    11362 > select #2/I:126
    11363 
    11364 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11365 Destroying pre-existing alignment with identifier 2/I 
    11366 Alignment identifier is 2/I 
    11367 
    11368 > select #21/A:117
    11369 
    11370 14 atoms, 13 bonds, 1 residue, 1 model selected 
    11371 Alignment identifier is 21/A 
    11372 
    11373 > select #2/I:126
    11374 
    11375 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11376 
    11377 > select #21/A:117
    11378 
    11379 14 atoms, 13 bonds, 1 residue, 1 model selected 
    11380 
    11381 > color sel orange
    11382 
    11383 > select #2/I:128
    11384 
    11385 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11386 
    11387 > select #21/A:119
    11388 
    11389 17 atoms, 16 bonds, 1 residue, 1 model selected 
    11390 
    11391 > select #2/I:128
    11392 
    11393 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11394 
    11395 > select clear
    11396 
    11397 > select #21/A:119
    11398 
    11399 17 atoms, 16 bonds, 1 residue, 1 model selected 
    11400 
    11401 > color sel orange
    11402 
    11403 > style sel stick
    11404 
    11405 Changed 17 atom styles 
    11406 
    11407 > show sel atoms
    11408 
    11409 Drag select of 8 atoms, 6 bonds 
    11410 
    11411 > ui mousemode right translate
    11412 
    11413 > ui mousemode right select
    11414 
    11415 > select #2/I:240
    11416 
    11417 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11418 
    11419 > select #21/A:231
    11420 
    11421 15 atoms, 14 bonds, 1 residue, 1 model selected 
    11422 
    11423 > style sel stick
    11424 
    11425 Changed 15 atom styles 
    11426 
    11427 > show sel atoms
    11428 
    11429 > color sel red
    11430 
    11431 > ui mousemode right translate
    11432 
    11433 > ui mousemode right rotate
    11434 
    11435 > ui mousemode right select
    11436 
    11437 > select #2/I:190
    11438 
    11439 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11440 
    11441 > select #21/A:181
    11442 
    11443 14 atoms, 14 bonds, 1 residue, 1 model selected 
    11444 
    11445 > select #21/A:181
    11446 
    11447 14 atoms, 14 bonds, 1 residue, 1 model selected 
    11448 
    11449 > style sel stick
    11450 
    11451 Changed 14 atom styles 
    11452 
    11453 > show sel atoms
    11454 
    11455 > color sel magenta
    11456 
    11457 Drag select of 1 atoms, 9 residues 
    11458 
    11459 > ui mousemode right translate
    11460 
    11461 > ui mousemode right select
    11462 
    11463 > select #2/I:183
    11464 
    11465 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11466 
    11467 > select #21/A:174
    11468 
    11469 17 atoms, 16 bonds, 1 residue, 1 model selected 
    11470 
    11471 > select #21/A:175
    11472 
    11473 21 atoms, 21 bonds, 1 residue, 1 model selected 
    11474 
    11475 > select #21/A:174
    11476 
    11477 17 atoms, 16 bonds, 1 residue, 1 model selected 
    11478 
    11479 > select clear
    11480 
    11481 > select #2/I:183
    11482 
    11483 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11484 
    11485 > select #21/A:174
    11486 
    11487 17 atoms, 16 bonds, 1 residue, 1 model selected 
    11488 
    11489 > style sel stick
    11490 
    11491 Changed 17 atom styles 
    11492 
    11493 > show sel atoms
    11494 
    11495 > color sel orange
    11496 
    11497 Drag select of 2 residues 
    11498 
    11499 > select clear
    11500 
    11501 [Repeated 3 time(s)]
    11502 
    11503 > ui mousemode right translate
    11504 
    11505 > ui mousemode right select
    11506 
    11507 > select #2/I:178
    11508 
    11509 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11510 
    11511 > select #21/A:169
    11512 
    11513 22 atoms, 21 bonds, 1 residue, 1 model selected 
    11514 
    11515 > style sel stick
    11516 
    11517 Changed 22 atom styles 
    11518 
    11519 > show sel atoms
    11520 
    11521 > color sel blue
    11522 
    11523 > ui mousemode right translate
    11524 
    11525 > ui mousemode right select
    11526 
    11527 > select #2/I:154
    11528 
    11529 8 atoms, 7 bonds, 1 residue, 1 model selected 
    11530 
    11531 > select #21/A:145
    11532 
    11533 17 atoms, 16 bonds, 1 residue, 1 model selected 
    11534 
    11535 > select #2/I:154
    11536 
    11537 8 atoms, 7 bonds, 1 residue, 1 model selected 
    11538 
    11539 > select #21/A:145
    11540 
    11541 17 atoms, 16 bonds, 1 residue, 1 model selected 
    11542 
    11543 > style sel stick
    11544 
    11545 Changed 17 atom styles 
    11546 
    11547 > show sel atoms
    11548 
    11549 > color sel orange
    11550 
    11551 > select #2/I:157
    11552 
    11553 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11554 Drag select of 1 residues 
    11555 
    11556 > select clear
    11557 
    11558 > select #21/A:148
    11559 
    11560 10 atoms, 9 bonds, 1 residue, 1 model selected 
    11561 
    11562 > style sel stick
    11563 
    11564 Changed 10 atom styles 
    11565 
    11566 > show sel atoms
    11567 
    11568 > color sel gray
    11569 
    11570 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    11571 > UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
    11572 
    11573 Drag select of 6 residues 
    11574 
    11575 > ui mousemode right translate
    11576 
    11577 > ui mousemode right select
    11578 
    11579 > ui mousemode right translate
    11580 
    11581 > ui mousemode right select
    11582 
    11583 > select #2/I:126
    11584 
    11585 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11586 
    11587 > select #21/A:117
    11588 
    11589 14 atoms, 13 bonds, 1 residue, 1 model selected 
    11590 
    11591 > select clear
    11592 
    11593 > select #2/I:128
    11594 
    11595 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11596 
    11597 > select #21/A:119
    11598 
    11599 17 atoms, 16 bonds, 1 residue, 1 model selected 
    11600 
    11601 > select #2/I:240
    11602 
    11603 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11604 
    11605 > select #21/A:231
    11606 
    11607 15 atoms, 14 bonds, 1 residue, 1 model selected 
    11608 
    11609 > ui mousemode right translate
    11610 
    11611 > ui mousemode right select
    11612 
    11613 > select #2/I:190
    11614 
    11615 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11616 
    11617 > select #21/A:181
    11618 
    11619 14 atoms, 14 bonds, 1 residue, 1 model selected 
    11620 
    11621 > select #2/I:183
    11622 
    11623 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11624 Drag select of 1 residues 
    11625 
    11626 > select clear
    11627 
    11628 > ui mousemode right translate
    11629 
    11630 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    11631 > UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
    11632 
    11633 ——— End of log from Mon Jun 12 13:04:04 2023 ———
    11634 
    11635 opened ChimeraX session 
    11636 
    11637 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    11638 > UASLP/Lab Virología/prediction Madariaga virus.zip"
    11639 
    11640 Unrecognized file suffix '.zip' 
    11641 
    11642 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    11643 > UASLP/Lab Virología/AlphaFold/Madariaga virus Alpha Fold.pdb"
    11644 
    11645 Chain information for Madariaga virus Alpha Fold.pdb #22 
    11646 --- 
    11647 Chain | Description 
    11648 A | No description available 
    11649  
    11650 
    11651 > ui tool show Matchmaker
    11652 
    11653 > matchmaker #2-4,6,9-21#!5,7-8 to #22
    11654 
    11655 Parameters 
    11656 --- 
    11657 Chain pairing | bb 
    11658 Alignment algorithm | Needleman-Wunsch 
    11659 Similarity matrix | BLOSUM-62 
    11660 SS fraction | 0.3 
    11661 Gap open (HH/SS/other) | 18/18/6 
    11662 Gap extend | 1 
    11663 SS matrix |  |  | H | S | O 
    11664 ---|---|---|--- 
    11665 H | 6 | -9 | -6 
    11666 S |  | 6 | -6 
    11667 O |  |  | 4 
    11668 Iteration cutoff | 2 
    11669  
    11670 Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with 3j2w.pdb, chain
    11671 I (#2), sequence alignment score = 522 
    11672 RMSD between 147 pruned atom pairs is 0.696 angstroms; (across all 149 pairs:
    11673 0.789) 
    11674  
    11675 Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with 1kxf.pdb, chain
    11676 A (#3), sequence alignment score = 569.7 
    11677 RMSD between 150 pruned atom pairs is 0.715 angstroms; (across all 158 pairs:
    11678 2.187) 
    11679  
    11680 Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with 7sfu.pdb, chain
    11681 F (#4), sequence alignment score = 693.9 
    11682 RMSD between 145 pruned atom pairs is 0.763 angstroms; (across all 162 pairs:
    11683 2.000) 
    11684  
    11685 Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with 4agk.pdb, chain
    11686 A (#6), sequence alignment score = 550.5 
    11687 RMSD between 150 pruned atom pairs is 0.691 angstroms; (across all 151 pairs:
    11688 0.721) 
    11689  
    11690 Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with 7ko8.pdb, chain
    11691 G (#9), sequence alignment score = 589.5 
    11692 RMSD between 133 pruned atom pairs is 1.135 angstroms; (across all 152 pairs:
    11693 1.607) 
    11694  
    11695 Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with AlphFold
    11696 Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 785.6 
    11697 RMSD between 150 pruned atom pairs is 0.551 angstroms; (across all 253 pairs:
    11698 30.619) 
    11699  
    11700 Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with AlphaFold
    11701 Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
    11702 784.8 
    11703 RMSD between 149 pruned atom pairs is 0.602 angstroms; (across all 253 pairs:
    11704 31.010) 
    11705  
    11706 Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with AlphaFold
    11707 Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
    11708 991.5 
    11709 RMSD between 147 pruned atom pairs is 0.277 angstroms; (across all 256 pairs:
    11710 36.174) 
    11711  
    11712 Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Alpha Fold
    11713 Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
    11714 score = 557.2 
    11715 RMSD between 107 pruned atom pairs is 0.830 angstroms; (across all 260 pairs:
    11716 49.521) 
    11717  
    11718 Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Alpha Fold
    11719 Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
    11720 1201.4 
    11721 RMSD between 171 pruned atom pairs is 0.328 angstroms; (across all 259 pairs:
    11722 11.288) 
    11723  
    11724 Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Ndumu virus
    11725 Alphafold.pdb, chain A (#15), sequence alignment score = 767.1 
    11726 RMSD between 148 pruned atom pairs is 0.604 angstroms; (across all 253 pairs:
    11727 21.396) 
    11728  
    11729 Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Everglades virus
    11730 Alphafold.pdb, chain A (#16), sequence alignment score = 991.5 
    11731 RMSD between 147 pruned atom pairs is 0.278 angstroms; (across all 256 pairs:
    11732 36.175) 
    11733  
    11734 Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Bebaru virus
    11735 Alphafold.pdb, chain A (#17), sequence alignment score = 810.1 
    11736 RMSD between 150 pruned atom pairs is 0.536 angstroms; (across all 249 pairs:
    11737 25.607) 
    11738  
    11739 Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Caaingua virus
    11740 AlphaFold.pdb, chain A (#18), sequence alignment score = 679.6 
    11741 RMSD between 84 pruned atom pairs is 0.443 angstroms; (across all 250 pairs:
    11742 38.023) 
    11743  
    11744 Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Cabassou virus
    11745 Alphafold.pdb, chain A (#19), sequence alignment score = 996.6 
    11746 RMSD between 158 pruned atom pairs is 0.330 angstroms; (across all 257 pairs:
    11747 38.933) 
    11748  
    11749 Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Eilat virus
    11750 Alphafold.pdb, chain A (#20), sequence alignment score = 719.3 
    11751 RMSD between 148 pruned atom pairs is 0.691 angstroms; (across all 243 pairs:
    11752 28.968) 
    11753  
    11754 Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Highlands J.
    11755 virus Alphafold.pdb, chain A (#21), sequence alignment score = 1253.2 
    11756 RMSD between 119 pruned atom pairs is 0.235 angstroms; (across all 259 pairs:
    11757 32.666) 
    11758  
    11759 Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with 6xo4.pdb, chain
    11760 C (#5), sequence alignment score = 1014.1 
    11761 RMSD between 100 pruned atom pairs is 1.163 angstroms; (across all 151 pairs:
    11762 2.109) 
    11763  
    11764 Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with 1vcp.pdb, chain
    11765 C (#7), sequence alignment score = 555.2 
    11766 RMSD between 147 pruned atom pairs is 0.560 angstroms; (across all 149 pairs:
    11767 0.708) 
    11768  
    11769 Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with 2yew.pdb, chain
    11770 G (#8), sequence alignment score = 534.1 
    11771 RMSD between 54 pruned atom pairs is 1.237 angstroms; (across all 171 pairs:
    11772 10.062) 
    11773  
    11774 
    11775 > hide #21 models
    11776 
    11777 > show #21 models
    11778 
    11779 > hide #22 models
    11780 
    11781 > show #22 models
    11782 
    11783 > hide #21 models
    11784 
    11785 > color #22 #ff5500ff
    11786 
    11787 > color #22 #eb4e00ff
    11788 
    11789 > ui mousemode right select
    11790 
    11791 > select #2/I:126
    11792 
    11793 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11794 
    11795 > select #22/A:118
    11796 
    11797 19 atoms, 18 bonds, 1 residue, 1 model selected 
    11798 Alignment identifier is 22/A 
    11799 
    11800 > select #22/A:119
    11801 
    11802 14 atoms, 13 bonds, 1 residue, 1 model selected 
    11803 
    11804 > select #22/A:119
    11805 
    11806 14 atoms, 13 bonds, 1 residue, 1 model selected 
    11807 
    11808 > select #2/I:126
    11809 
    11810 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11811 
    11812 > select #22/A:119
    11813 
    11814 14 atoms, 13 bonds, 1 residue, 1 model selected 
    11815 
    11816 > select #2/I:126
    11817 
    11818 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11819 
    11820 > select #2/I:126
    11821 
    11822 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11823 
    11824 > select #22/A:119
    11825 
    11826 14 atoms, 13 bonds, 1 residue, 1 model selected 
    11827 
    11828 > style sel stick
    11829 
    11830 Changed 14 atom styles 
    11831 
    11832 > show sel atoms
    11833 
    11834 > color sel orange
    11835 
    11836 > ui mousemode right translate
    11837 
    11838 > ui mousemode right select
    11839 
    11840 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    11841 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    11842 
    11843 > select #22/A:121
    11844 
    11845 17 atoms, 16 bonds, 1 residue, 1 model selected 
    11846 
    11847 > select #2/I:128
    11848 
    11849 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11850 
    11851 > select #22/A:121
    11852 
    11853 17 atoms, 16 bonds, 1 residue, 1 model selected 
    11854 
    11855 > color sel orange
    11856 
    11857 > style sel stick
    11858 
    11859 Changed 17 atom styles 
    11860 
    11861 > show sel atoms
    11862 
    11863 > hide sel atoms
    11864 
    11865 > style sel stick
    11866 
    11867 Changed 17 atom styles 
    11868 
    11869 > show sel atoms
    11870 
    11871 > ui mousemode right translate
    11872 
    11873 > ui mousemode right select
    11874 
    11875 > select #2/I:240
    11876 
    11877 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11878 
    11879 > ui mousemode right translate
    11880 
    11881 > ui mousemode right select
    11882 
    11883 > select #22/A:233
    11884 
    11885 15 atoms, 14 bonds, 1 residue, 1 model selected 
    11886 
    11887 > select #2/I:240
    11888 
    11889 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11890 
    11891 > select #22/A:233
    11892 
    11893 15 atoms, 14 bonds, 1 residue, 1 model selected 
    11894 
    11895 > select #22/A:233
    11896 
    11897 15 atoms, 14 bonds, 1 residue, 1 model selected 
    11898 
    11899 > select #2/I:240
    11900 
    11901 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11902 
    11903 > select #22/A:233
    11904 
    11905 15 atoms, 14 bonds, 1 residue, 1 model selected 
    11906 
    11907 > style sel stick
    11908 
    11909 Changed 15 atom styles 
    11910 
    11911 > show sel atoms
    11912 
    11913 > color sel red
    11914 
    11915 > hide sel atoms
    11916 
    11917 > show sel atoms
    11918 
    11919 > ui mousemode right translate
    11920 
    11921 > ui mousemode right select
    11922 
    11923 > select #2/I:190
    11924 
    11925 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11926 
    11927 > select #22/A:183
    11928 
    11929 14 atoms, 14 bonds, 1 residue, 1 model selected 
    11930 
    11931 > style sel stick
    11932 
    11933 Changed 14 atom styles 
    11934 
    11935 > show sel atoms
    11936 
    11937 > color sel magenta
    11938 
    11939 > ui mousemode right translate
    11940 
    11941 > color #22 #ffaa7fff
    11942 
    11943 > color #22 #ee9e77ff
    11944 
    11945 > color #22 #ffaa00ff
    11946 
    11947 > color #22 #cc8800ff
    11948 
    11949 > color #22 #b37700ff
    11950 
    11951 > color #22 #b57900ff
    11952 
    11953 > color #22 #ce8900ff
    11954 
    11955 > color #22 #ff5500ff
    11956 
    11957 > ui mousemode right select
    11958 
    11959 > select #22/A:119
    11960 
    11961 14 atoms, 13 bonds, 1 residue, 1 model selected 
    11962 
    11963 > select #22/A:121
    11964 
    11965 17 atoms, 16 bonds, 1 residue, 1 model selected 
    11966 
    11967 > color sel orange
    11968 
    11969 > select #22/A:119
    11970 
    11971 14 atoms, 13 bonds, 1 residue, 1 model selected 
    11972 
    11973 > color sel orange
    11974 
    11975 > select clear
    11976 
    11977 [Repeated 1 time(s)]
    11978 
    11979 > ui mousemode right translate
    11980 
    11981 > ui mousemode right select
    11982 
    11983 > select #22/A:233
    11984 
    11985 15 atoms, 14 bonds, 1 residue, 1 model selected 
    11986 
    11987 > color sel red
    11988 
    11989 > ui mousemode right translate
    11990 
    11991 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    11992 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    11993 
    11994 ——— End of log from Tue Jun 13 11:14:29 2023 ———
    11995 
    11996 opened ChimeraX session 
    11997 
    11998 > select #22/A:1-30
    11999 
    12000 505 atoms, 519 bonds, 30 residues, 1 model selected 
    12001 
    12002 > select #22/A:1-30
    12003 
    12004 505 atoms, 519 bonds, 30 residues, 1 model selected 
    12005 
    12006 > ui mousemode right select
    12007 
    12008 > select #2/I:126
    12009 
    12010 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12011 
    12012 > select #22/A:119
    12013 
    12014 14 atoms, 13 bonds, 1 residue, 1 model selected 
    12015 
    12016 > select #2/I:128
    12017 
    12018 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12019 
    12020 > select #22/A:121
    12021 
    12022 17 atoms, 16 bonds, 1 residue, 1 model selected 
    12023 
    12024 > ui mousemode right translate
    12025 
    12026 > ui mousemode right select
    12027 
    12028 > select #2/I:240
    12029 
    12030 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12031 
    12032 > select #22/A:233
    12033 
    12034 15 atoms, 14 bonds, 1 residue, 1 model selected 
    12035 
    12036 > ui mousemode right translate
    12037 
    12038 > ui mousemode right select
    12039 
    12040 > select #2/I:190
    12041 
    12042 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12043 
    12044 > select #22/A:183
    12045 
    12046 14 atoms, 14 bonds, 1 residue, 1 model selected 
    12047 
    12048 > color sel magenta
    12049 
    12050 > ui mousemode right translate
    12051 
    12052 > ui mousemode right select
    12053 
    12054 > select #2/I:183
    12055 
    12056 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12057 
    12058 > select #22/A:176
    12059 
    12060 17 atoms, 16 bonds, 1 residue, 1 model selected 
    12061 
    12062 > select #22/A:176
    12063 
    12064 17 atoms, 16 bonds, 1 residue, 1 model selected 
    12065 
    12066 > select #2/I:183
    12067 
    12068 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12069 
    12070 > select #22/A:176
    12071 
    12072 17 atoms, 16 bonds, 1 residue, 1 model selected 
    12073 
    12074 > select #22/A:176
    12075 
    12076 17 atoms, 16 bonds, 1 residue, 1 model selected 
    12077 
    12078 > style sel stick
    12079 
    12080 Changed 17 atom styles 
    12081 
    12082 > show sel atoms
    12083 
    12084 > color sel orange
    12085 
    12086 > ui mousemode right translate
    12087 
    12088 > ui mousemode right rotate
    12089 
    12090 > ui mousemode right select
    12091 
    12092 > select #2/I:178
    12093 
    12094 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12095 
    12096 > select #22/A:171
    12097 
    12098 22 atoms, 21 bonds, 1 residue, 1 model selected 
    12099 
    12100 > select #22/A:170
    12101 
    12102 17 atoms, 16 bonds, 1 residue, 1 model selected 
    12103 
    12104 > select #22/A:171
    12105 
    12106 22 atoms, 21 bonds, 1 residue, 1 model selected 
    12107 
    12108 > select #2/I:178
    12109 
    12110 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12111 
    12112 > select #22/A:171
    12113 
    12114 22 atoms, 21 bonds, 1 residue, 1 model selected 
    12115 
    12116 > style sel stick
    12117 
    12118 Changed 22 atom styles 
    12119 
    12120 > show sel atoms
    12121 
    12122 > color sel blue
    12123 
    12124 Drag select of 5 residues 
    12125 
    12126 > ui mousemode right translate
    12127 
    12128 > ui mousemode right select
    12129 
    12130 > select #2/I:154
    12131 
    12132 8 atoms, 7 bonds, 1 residue, 1 model selected 
    12133 
    12134 > select #22/A:147
    12135 
    12136 17 atoms, 16 bonds, 1 residue, 1 model selected 
    12137 
    12138 > color sel orange
    12139 
    12140 > style sel stick
    12141 
    12142 Changed 17 atom styles 
    12143 
    12144 > show sel atoms
    12145 
    12146 > select #2/I:154
    12147 
    12148 8 atoms, 7 bonds, 1 residue, 1 model selected 
    12149 
    12150 > select #22/A:147
    12151 
    12152 17 atoms, 16 bonds, 1 residue, 1 model selected 
    12153 
    12154 > select #2/I:157
    12155 
    12156 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12157 
    12158 > select #22/A:150
    12159 
    12160 10 atoms, 9 bonds, 1 residue, 1 model selected 
    12161 
    12162 > select #22/A:149
    12163 
    12164 10 atoms, 9 bonds, 1 residue, 1 model selected 
    12165 
    12166 > select #22/A:150
    12167 
    12168 10 atoms, 9 bonds, 1 residue, 1 model selected 
    12169 
    12170 > style sel stick
    12171 
    12172 Changed 10 atom styles 
    12173 
    12174 > show sel atoms
    12175 
    12176 Drag select of 3 residues, 2 atoms, 4 bonds 
    12177 
    12178 > select #22/A:150
    12179 
    12180 10 atoms, 9 bonds, 1 residue, 1 model selected 
    12181 
    12182 > color sel gray
    12183 
    12184 > ui mousemode right translate
    12185 
    12186 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    12187 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    12188 
    12189 ——— End of log from Tue Jun 13 12:23:11 2023 ———
    12190 
    12191 opened ChimeraX session 
    12192 
    12193 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    12194 > UASLP/Lab Virología/AlphaFold/Mosso das Pedras virus AlphaFold.pdb"
    12195 
    12196 Chain information for Mosso das Pedras virus AlphaFold.pdb #23 
    12197 --- 
    12198 Chain | Description 
    12199 A | No description available 
    12200  
    12201 
    12202 > ui tool show Matchmaker
    12203 
    12204 > matchmaker #2-4,6,9-22#!5,7-8 to #23
    12205 
    12206 Parameters 
    12207 --- 
    12208 Chain pairing | bb 
    12209 Alignment algorithm | Needleman-Wunsch 
    12210 Similarity matrix | BLOSUM-62 
    12211 SS fraction | 0.3 
    12212 Gap open (HH/SS/other) | 18/18/6 
    12213 Gap extend | 1 
    12214 SS matrix |  |  | H | S | O 
    12215 ---|---|---|--- 
    12216 H | 6 | -9 | -6 
    12217 S |  | 6 | -6 
    12218 O |  |  | 4 
    12219 Iteration cutoff | 2 
    12220  
    12221 Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with 3j2w.pdb,
    12222 chain I (#2), sequence alignment score = 525 
    12223 RMSD between 147 pruned atom pairs is 0.747 angstroms; (across all 149 pairs:
    12224 0.843) 
    12225  
    12226 Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with 1kxf.pdb,
    12227 chain A (#3), sequence alignment score = 555.1 
    12228 RMSD between 150 pruned atom pairs is 0.697 angstroms; (across all 158 pairs:
    12229 2.182) 
    12230  
    12231 Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with 7sfu.pdb,
    12232 chain F (#4), sequence alignment score = 774.4 
    12233 RMSD between 146 pruned atom pairs is 0.748 angstroms; (across all 162 pairs:
    12234 2.048) 
    12235  
    12236 Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with 4agk.pdb,
    12237 chain A (#6), sequence alignment score = 564 
    12238 RMSD between 151 pruned atom pairs is 0.736 angstroms; (across all 151 pairs:
    12239 0.736) 
    12240  
    12241 Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with 7ko8.pdb,
    12242 chain G (#9), sequence alignment score = 530.6 
    12243 RMSD between 138 pruned atom pairs is 1.162 angstroms; (across all 152 pairs:
    12244 1.566) 
    12245  
    12246 Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with AlphFold
    12247 Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 796.6 
    12248 RMSD between 151 pruned atom pairs is 0.563 angstroms; (across all 261 pairs:
    12249 34.344) 
    12250  
    12251 Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with AlphaFold
    12252 Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
    12253 791.9 
    12254 RMSD between 135 pruned atom pairs is 0.567 angstroms; (across all 263 pairs:
    12255 37.641) 
    12256  
    12257 Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with AlphaFold
    12258 Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
    12259 1181.5 
    12260 RMSD between 13 pruned atom pairs is 1.031 angstroms; (across all 272 pairs:
    12261 39.100) 
    12262  
    12263 Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Alpha Fold
    12264 Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
    12265 score = 560.8 
    12266 RMSD between 25 pruned atom pairs is 0.636 angstroms; (across all 270 pairs:
    12267 41.007) 
    12268  
    12269 Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Alpha Fold
    12270 Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
    12271 979.8 
    12272 RMSD between 164 pruned atom pairs is 0.325 angstroms; (across all 255 pairs:
    12273 31.044) 
    12274  
    12275 Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Ndumu
    12276 virus Alphafold.pdb, chain A (#15), sequence alignment score = 808.2 
    12277 RMSD between 149 pruned atom pairs is 0.627 angstroms; (across all 267 pairs:
    12278 30.210) 
    12279  
    12280 Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Everglades
    12281 virus Alphafold.pdb, chain A (#16), sequence alignment score = 1181.5 
    12282 RMSD between 13 pruned atom pairs is 1.030 angstroms; (across all 272 pairs:
    12283 39.103) 
    12284  
    12285 Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Bebaru
    12286 virus Alphafold.pdb, chain A (#17), sequence alignment score = 796.3 
    12287 RMSD between 147 pruned atom pairs is 0.540 angstroms; (across all 258 pairs:
    12288 32.949) 
    12289  
    12290 Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Caaingua
    12291 virus AlphaFold.pdb, chain A (#18), sequence alignment score = 669.3 
    12292 RMSD between 143 pruned atom pairs is 0.659 angstroms; (across all 254 pairs:
    12293 36.135) 
    12294  
    12295 Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Cabassou
    12296 virus Alphafold.pdb, chain A (#19), sequence alignment score = 1176 
    12297 RMSD between 165 pruned atom pairs is 0.262 angstroms; (across all 274 pairs:
    12298 29.984) 
    12299  
    12300 Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Eilat
    12301 virus Alphafold.pdb, chain A (#20), sequence alignment score = 704.1 
    12302 RMSD between 148 pruned atom pairs is 0.693 angstroms; (across all 253 pairs:
    12303 13.728) 
    12304  
    12305 Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Highlands
    12306 J. virus Alphafold.pdb, chain A (#21), sequence alignment score = 962.3 
    12307 RMSD between 12 pruned atom pairs is 1.277 angstroms; (across all 255 pairs:
    12308 27.902) 
    12309  
    12310 Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Madariaga
    12311 virus Alpha Fold.pdb, chain A (#22), sequence alignment score = 976.4 
    12312 RMSD between 163 pruned atom pairs is 0.314 angstroms; (across all 257 pairs:
    12313 25.593) 
    12314  
    12315 Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with 6xo4.pdb,
    12316 chain C (#5), sequence alignment score = 680.4 
    12317 RMSD between 103 pruned atom pairs is 1.187 angstroms; (across all 151 pairs:
    12318 2.065) 
    12319  
    12320 Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with 1vcp.pdb,
    12321 chain C (#7), sequence alignment score = 558.9 
    12322 RMSD between 147 pruned atom pairs is 0.584 angstroms; (across all 149 pairs:
    12323 0.736) 
    12324  
    12325 Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with 2yew.pdb,
    12326 chain G (#8), sequence alignment score = 499.1 
    12327 RMSD between 55 pruned atom pairs is 1.261 angstroms; (across all 170 pairs:
    12328 9.233) 
    12329  
    12330 
    12331 > hide #22 models
    12332 
    12333 > select add #22
    12334 
    12335 4167 atoms, 4228 bonds, 261 residues, 1 model selected 
    12336 
    12337 > select subtract #22
    12338 
    12339 Nothing selected 
    12340 
    12341 > color #23 #aaaa7fff
    12342 
    12343 > color #23 #999972ff
    12344 
    12345 > color #23 #94946eff
    12346 
    12347 > color #23 #9e9e76ff
    12348 
    12349 > color #23 #a3a379ff
    12350 
    12351 > color #23 #a5a57bff
    12352 
    12353 > color #23 #a1a178ff
    12354 
    12355 > ui mousemode right select
    12356 
    12357 > select #2/I:126
    12358 
    12359 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12360 
    12361 > select #23/A:137
    12362 
    12363 12 atoms, 11 bonds, 1 residue, 1 model selected 
    12364 
    12365 > style sel stick
    12366 
    12367 Changed 12 atom styles 
    12368 
    12369 > show sel atoms
    12370 
    12371 Alignment identifier is 23/A 
    12372 
    12373 > color sel red
    12374 
    12375 > select #2/I:128
    12376 
    12377 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12378 
    12379 > select #23/A:139
    12380 
    12381 22 atoms, 21 bonds, 1 residue, 1 model selected 
    12382 
    12383 > style sel stick
    12384 
    12385 Changed 22 atom styles 
    12386 
    12387 > show sel atoms
    12388 
    12389 > color sel blue
    12390 
    12391 > select clear
    12392 
    12393 > ui mousemode right translate
    12394 
    12395 > ui mousemode right select
    12396 
    12397 > select #2/I:240
    12398 
    12399 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12400 
    12401 > select #23/A:251
    12402 
    12403 15 atoms, 14 bonds, 1 residue, 1 model selected 
    12404 
    12405 > style sel stick
    12406 
    12407 Changed 15 atom styles 
    12408 
    12409 > show sel atoms
    12410 
    12411 > color sel red
    12412 
    12413 > ui mousemode right translate
    12414 
    12415 > ui mousemode right select
    12416 
    12417 > select #2/I:190
    12418 
    12419 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12420 
    12421 > select #23/A:201
    12422 
    12423 24 atoms, 23 bonds, 1 residue, 1 model selected 
    12424 
    12425 > select #2/I:190
    12426 
    12427 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12428 
    12429 > select #23/A:201
    12430 
    12431 24 atoms, 23 bonds, 1 residue, 1 model selected 
    12432 
    12433 > style sel stick
    12434 
    12435 Changed 24 atom styles 
    12436 
    12437 > show sel atoms
    12438 
    12439 > color sel blue
    12440 
    12441 > select #2/I:190
    12442 
    12443 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12444 
    12445 > select #23/A:201
    12446 
    12447 24 atoms, 23 bonds, 1 residue, 1 model selected 
    12448 
    12449 > select clear
    12450 
    12451 > ui mousemode right translate
    12452 
    12453 > ui mousemode right select
    12454 
    12455 > select #2/I:183
    12456 
    12457 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12458 
    12459 > select #23/A:194
    12460 
    12461 22 atoms, 21 bonds, 1 residue, 1 model selected 
    12462 
    12463 > select #2/I:183
    12464 
    12465 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12466 
    12467 > select #23/A:194
    12468 
    12469 22 atoms, 21 bonds, 1 residue, 1 model selected 
    12470 
    12471 > style sel stick
    12472 
    12473 Changed 22 atom styles 
    12474 
    12475 > show sel atoms
    12476 
    12477 > color sel blue
    12478 
    12479 > select #2/I:183
    12480 
    12481 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12482 
    12483 > select #23/A:194
    12484 
    12485 22 atoms, 21 bonds, 1 residue, 1 model selected 
    12486 
    12487 > ui mousemode right translate
    12488 
    12489 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    12490 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    12491 
    12492 > ui mousemode right select
    12493 
    12494 > select #2/I:178
    12495 
    12496 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12497 
    12498 > select #23/A:189
    12499 
    12500 24 atoms, 23 bonds, 1 residue, 1 model selected 
    12501 
    12502 > style sel stick
    12503 
    12504 Changed 24 atom styles 
    12505 
    12506 > show sel atoms
    12507 
    12508 > color sel blue
    12509 
    12510 > ui mousemode right translate
    12511 
    12512 > ui mousemode right select
    12513 
    12514 > select #2/I:157
    12515 
    12516 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12517 
    12518 > select #23/A:168
    12519 
    12520 10 atoms, 9 bonds, 1 residue, 1 model selected 
    12521 
    12522 > style sel stick
    12523 
    12524 Changed 10 atom styles 
    12525 
    12526 > show sel atoms
    12527 
    12528 > color sel gray
    12529 
    12530 > select #2/I:154
    12531 
    12532 8 atoms, 7 bonds, 1 residue, 1 model selected 
    12533 
    12534 > select #23/A:165
    12535 
    12536 19 atoms, 18 bonds, 1 residue, 1 model selected 
    12537 
    12538 > select #23/A:168
    12539 
    12540 10 atoms, 9 bonds, 1 residue, 1 model selected 
    12541 
    12542 > select #23/A:165
    12543 
    12544 19 atoms, 18 bonds, 1 residue, 1 model selected 
    12545 
    12546 > style sel stick
    12547 
    12548 Changed 19 atom styles 
    12549 
    12550 > show sel atoms
    12551 
    12552 > color sel gray
    12553 
    12554 > ui mousemode right translate
    12555 
    12556 [Repeated 1 time(s)]
    12557 
    12558 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    12559 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    12560 
    12561 > ui mousemode right select
    12562 
    12563 > select #2/I:126
    12564 
    12565 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12566 
    12567 > select #23/A:137
    12568 
    12569 12 atoms, 11 bonds, 1 residue, 1 model selected 
    12570 
    12571 > select #23/A:139
    12572 
    12573 22 atoms, 21 bonds, 1 residue, 1 model selected 
    12574 
    12575 > ui mousemode right translate
    12576 
    12577 > ui mousemode right rotate
    12578 
    12579 > ui mousemode right select
    12580 
    12581 > select #23/A:251
    12582 
    12583 15 atoms, 14 bonds, 1 residue, 1 model selected 
    12584 
    12585 > select #2/I:190
    12586 
    12587 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12588 
    12589 > ui mousemode right translate
    12590 
    12591 > ui mousemode right select
    12592 
    12593 > select #23/A:201
    12594 
    12595 24 atoms, 23 bonds, 1 residue, 1 model selected 
    12596 
    12597 > select #2/I:190
    12598 
    12599 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12600 
    12601 > ui mousemode right translate
    12602 
    12603 > ui mousemode right select
    12604 
    12605 > select #2/I:183@CA
    12606 
    12607 1 atom, 1 residue, 1 model selected 
    12608 
    12609 > select #23/A:194
    12610 
    12611 22 atoms, 21 bonds, 1 residue, 1 model selected 
    12612 
    12613 > select #2/I:183
    12614 
    12615 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12616 
    12617 > select #23/A:194
    12618 
    12619 22 atoms, 21 bonds, 1 residue, 1 model selected 
    12620 
    12621 > select #23/A:194
    12622 
    12623 22 atoms, 21 bonds, 1 residue, 1 model selected 
    12624 
    12625 > select #2/I:178
    12626 
    12627 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12628 
    12629 > select #23/A:189
    12630 
    12631 24 atoms, 23 bonds, 1 residue, 1 model selected 
    12632 
    12633 > ui mousemode right translate
    12634 
    12635 > ui mousemode right select
    12636 
    12637 > select #23/A:168@CA
    12638 
    12639 1 atom, 1 residue, 1 model selected 
    12640 
    12641 > select #23/A:165
    12642 
    12643 19 atoms, 18 bonds, 1 residue, 1 model selected 
    12644 
    12645 > ui mousemode right translate
    12646 
    12647 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    12648 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    12649 
    12650 ——— End of log from Wed Jun 14 15:40:04 2023 ———
    12651 
    12652 opened ChimeraX session 
    12653 
    12654 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    12655 > UASLP/Lab Virología/AlphaFold/Southern Elephant Seal virus AlphaFold.pdb"
    12656 
    12657 Chain information for Southern Elephant Seal virus AlphaFold.pdb #24 
    12658 --- 
    12659 Chain | Description 
    12660 A | No description available 
    12661  
    12662 
    12663 > ui tool show Matchmaker
    12664 
    12665 > matchmaker #2-4,6,9-23#!5,7-8 to #24
    12666 
    12667 Parameters 
    12668 --- 
    12669 Chain pairing | bb 
    12670 Alignment algorithm | Needleman-Wunsch 
    12671 Similarity matrix | BLOSUM-62 
    12672 SS fraction | 0.3 
    12673 Gap open (HH/SS/other) | 18/18/6 
    12674 Gap extend | 1 
    12675 SS matrix |  |  | H | S | O 
    12676 ---|---|---|--- 
    12677 H | 6 | -9 | -6 
    12678 S |  | 6 | -6 
    12679 O |  |  | 4 
    12680 Iteration cutoff | 2 
    12681  
    12682 Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
    12683 3j2w.pdb, chain I (#2), sequence alignment score = 595.1 
    12684 RMSD between 149 pruned atom pairs is 0.700 angstroms; (across all 149 pairs:
    12685 0.700) 
    12686  
    12687 Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
    12688 1kxf.pdb, chain A (#3), sequence alignment score = 543.6 
    12689 RMSD between 147 pruned atom pairs is 0.771 angstroms; (across all 157 pairs:
    12690 1.959) 
    12691  
    12692 Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
    12693 7sfu.pdb, chain I (#4), sequence alignment score = 577.8 
    12694 RMSD between 143 pruned atom pairs is 0.786 angstroms; (across all 161 pairs:
    12695 2.477) 
    12696  
    12697 Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
    12698 4agk.pdb, chain A (#6), sequence alignment score = 575.4 
    12699 RMSD between 147 pruned atom pairs is 0.663 angstroms; (across all 150 pairs:
    12700 0.772) 
    12701  
    12702 Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
    12703 7ko8.pdb, chain D (#9), sequence alignment score = 657.3 
    12704 RMSD between 133 pruned atom pairs is 1.065 angstroms; (across all 152 pairs:
    12705 1.706) 
    12706  
    12707 Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
    12708 AlphFold Colaboratory Ross River.pdb, chain A (#10), sequence alignment score
    12709 = 914 
    12710 RMSD between 154 pruned atom pairs is 0.396 angstroms; (across all 251 pairs:
    12711 23.072) 
    12712  
    12713 Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
    12714 AlphaFold Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment
    12715 score = 910.1 
    12716 RMSD between 156 pruned atom pairs is 0.463 angstroms; (across all 251 pairs:
    12717 24.684) 
    12718  
    12719 Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
    12720 AlphaFold Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment
    12721 score = 745.1 
    12722 RMSD between 147 pruned atom pairs is 0.547 angstroms; (across all 258 pairs:
    12723 29.865) 
    12724  
    12725 Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
    12726 Alpha Fold Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence
    12727 alignment score = 561.1 
    12728 RMSD between 132 pruned atom pairs is 0.772 angstroms; (across all 265 pairs:
    12729 33.702) 
    12730  
    12731 Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
    12732 Alpha Fold Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence
    12733 alignment score = 747.2 
    12734 RMSD between 150 pruned atom pairs is 0.471 angstroms; (across all 258 pairs:
    12735 22.727) 
    12736  
    12737 Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
    12738 Ndumu virus Alphafold.pdb, chain A (#15), sequence alignment score = 876.2 
    12739 RMSD between 153 pruned atom pairs is 0.454 angstroms; (across all 260 pairs:
    12740 16.995) 
    12741  
    12742 Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
    12743 Everglades virus Alphafold.pdb, chain A (#16), sequence alignment score =
    12744 745.1 
    12745 RMSD between 147 pruned atom pairs is 0.547 angstroms; (across all 258 pairs:
    12746 29.865) 
    12747  
    12748 Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
    12749 Bebaru virus Alphafold.pdb, chain A (#17), sequence alignment score = 885.6 
    12750 RMSD between 154 pruned atom pairs is 0.323 angstroms; (across all 250 pairs:
    12751 25.775) 
    12752  
    12753 Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
    12754 Caaingua virus AlphaFold.pdb, chain A (#18), sequence alignment score = 686.5 
    12755 RMSD between 101 pruned atom pairs is 0.541 angstroms; (across all 257 pairs:
    12756 34.122) 
    12757  
    12758 Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
    12759 Cabassou virus Alphafold.pdb, chain A (#19), sequence alignment score = 746.3 
    12760 RMSD between 5 pruned atom pairs is 0.781 angstroms; (across all 261 pairs:
    12761 39.736) 
    12762  
    12763 Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
    12764 Eilat virus Alphafold.pdb, chain A (#20), sequence alignment score = 688.6 
    12765 RMSD between 154 pruned atom pairs is 0.690 angstroms; (across all 238 pairs:
    12766 27.995) 
    12767  
    12768 Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
    12769 Highlands J. virus Alphafold.pdb, chain A (#21), sequence alignment score =
    12770 761.8 
    12771 RMSD between 150 pruned atom pairs is 0.515 angstroms; (across all 252 pairs:
    12772 24.621) 
    12773  
    12774 Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
    12775 Madariaga virus Alpha Fold.pdb, chain A (#22), sequence alignment score =
    12776 744.9 
    12777 RMSD between 150 pruned atom pairs is 0.532 angstroms; (across all 254 pairs:
    12778 26.232) 
    12779  
    12780 Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
    12781 Mosso das Pedras virus AlphaFold.pdb, chain A (#23), sequence alignment score
    12782 = 761.8 
    12783 RMSD between 150 pruned atom pairs is 0.559 angstroms; (across all 260 pairs:
    12784 36.762) 
    12785  
    12786 Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
    12787 6xo4.pdb, chain C (#5), sequence alignment score = 496.9 
    12788 RMSD between 101 pruned atom pairs is 1.204 angstroms; (across all 150 pairs:
    12789 2.038) 
    12790  
    12791 Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
    12792 1vcp.pdb, chain C (#7), sequence alignment score = 628.6 
    12793 RMSD between 149 pruned atom pairs is 0.536 angstroms; (across all 149 pairs:
    12794 0.536) 
    12795  
    12796 Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
    12797 2yew.pdb, chain G (#8), sequence alignment score = 628.5 
    12798 RMSD between 56 pruned atom pairs is 1.258 angstroms; (across all 171 pairs:
    12799 5.304) 
    12800  
    12801 
    12802 > hide #23 models
    12803 
    12804 > select add #23
    12805 
    12806 4449 atoms, 4504 bonds, 279 residues, 1 model selected 
    12807 
    12808 > select subtract #23
    12809 
    12810 Nothing selected 
    12811 
    12812 > show #23 models
    12813 
    12814 > hide #23 models
    12815 
    12816 > color #24 #555500ff
    12817 
    12818 > color #24 black
    12819 
    12820 > color #24 #550000ff
    12821 
    12822 > color #24 #aaaa7fff
    12823 
    12824 > color #24 #aaaa00ff
    12825 
    12826 > color #24 #555500ff
    12827 
    12828 > color #24 #6c6c00ff
    12829 
    12830 > color #24 #7f7f00ff
    12831 
    12832 > color #24 #666600ff
    12833 
    12834 > color #24 #aaaa7fff
    12835 
    12836 > color #24 #757557ff
    12837 
    12838 > color #24 #707053ff
    12839 
    12840 > color #24 #68684dff
    12841 
    12842 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    12843 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    12844 
    12845 > ui mousemode right select
    12846 
    12847 > select #2/I:126
    12848 
    12849 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12850 
    12851 > select #2/I:126
    12852 
    12853 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12854 
    12855 > select #24/A:127
    12856 
    12857 12 atoms, 11 bonds, 1 residue, 1 model selected 
    12858 Alignment identifier is 24/A 
    12859 
    12860 > select #2/I:126
    12861 
    12862 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12863 Drag select of 1 residues 
    12864 
    12865 > style sel stick
    12866 
    12867 Changed 12 atom styles 
    12868 
    12869 > show sel atoms
    12870 
    12871 > color sel red
    12872 
    12873 > select #2/I:128
    12874 
    12875 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12876 
    12877 > select #24/A:129
    12878 
    12879 19 atoms, 18 bonds, 1 residue, 1 model selected 
    12880 
    12881 > style sel stick
    12882 
    12883 Changed 19 atom styles 
    12884 
    12885 > show sel atoms
    12886 
    12887 > color sel blue
    12888 
    12889 > ui mousemode right translate
    12890 
    12891 > ui mousemode right select
    12892 
    12893 > select #2/I:240
    12894 
    12895 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12896 
    12897 > select #24/A:241
    12898 
    12899 15 atoms, 14 bonds, 1 residue, 1 model selected 
    12900 
    12901 > ui mousemode right translate
    12902 
    12903 > style sel stick
    12904 
    12905 Changed 15 atom styles 
    12906 
    12907 > show sel atoms
    12908 
    12909 > ui mousemode right select
    12910 
    12911 > select #2/I:240
    12912 
    12913 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12914 
    12915 > select #24/A:241
    12916 
    12917 15 atoms, 14 bonds, 1 residue, 1 model selected 
    12918 
    12919 > color sel red
    12920 
    12921 > ui mousemode right translate
    12922 
    12923 > ui mousemode right select
    12924 
    12925 > select #2/I:190
    12926 
    12927 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12928 
    12929 > select #24/A:191
    12930 
    12931 15 atoms, 14 bonds, 1 residue, 1 model selected 
    12932 
    12933 > style sel stick
    12934 
    12935 Changed 15 atom styles 
    12936 
    12937 > show sel atoms
    12938 
    12939 > color sel red
    12940 
    12941 > select clear
    12942 
    12943 > ui mousemode right translate
    12944 
    12945 > ui mousemode right select
    12946 
    12947 > select #2/I:183
    12948 
    12949 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12950 
    12951 > select #24/A:184
    12952 
    12953 22 atoms, 21 bonds, 1 residue, 1 model selected 
    12954 
    12955 > style sel stick
    12956 
    12957 Changed 22 atom styles 
    12958 
    12959 > show sel atoms
    12960 
    12961 > color sel blue
    12962 
    12963 > ui mousemode right translate
    12964 
    12965 > ui mousemode right select
    12966 
    12967 > select #2/I:178
    12968 
    12969 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12970 
    12971 > select #24/A:179
    12972 
    12973 24 atoms, 23 bonds, 1 residue, 1 model selected 
    12974 
    12975 > style sel stick
    12976 
    12977 Changed 24 atom styles 
    12978 
    12979 > show sel atoms
    12980 
    12981 > color sel blue
    12982 
    12983 > set bgColor black
    12984 
    12985 > set bgColor white
    12986 
    12987 > ui mousemode right translate
    12988 
    12989 > ui mousemode right rotate
    12990 
    12991 > ui mousemode right select
    12992 
    12993 > select #2/I:157
    12994 
    12995 9 atoms, 8 bonds, 1 residue, 1 model selected 
    12996 
    12997 > select #24/A:158
    12998 
    12999 22 atoms, 21 bonds, 1 residue, 1 model selected 
    13000 
    13001 > ui mousemode right translate
    13002 
    13003 > style sel stick
    13004 
    13005 Changed 22 atom styles 
    13006 
    13007 > show sel atoms
    13008 
    13009 > color sel blue
    13010 
    13011 > ui mousemode right select
    13012 
    13013 > ui mousemode right translate
    13014 
    13015 > ui mousemode right select
    13016 
    13017 > select #2/I:154
    13018 
    13019 8 atoms, 7 bonds, 1 residue, 1 model selected 
    13020 
    13021 > ui mousemode right translate
    13022 
    13023 > ui mousemode right select
    13024 
    13025 > select #2/I:154
    13026 
    13027 8 atoms, 7 bonds, 1 residue, 1 model selected 
    13028 
    13029 > select #24/A:155
    13030 
    13031 19 atoms, 18 bonds, 1 residue, 1 model selected 
    13032 
    13033 > style sel stick
    13034 
    13035 Changed 19 atom styles 
    13036 
    13037 > show sel atoms
    13038 
    13039 > color sel gray
    13040 
    13041 > ui mousemode right translate
    13042 
    13043 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    13044 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    13045 
    13046 > ui mousemode right select
    13047 
    13048 > select #2/I:128
    13049 
    13050 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13051 
    13052 > select #24/A:129
    13053 
    13054 19 atoms, 18 bonds, 1 residue, 1 model selected 
    13055 
    13056 > select #2/I:128
    13057 
    13058 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13059 
    13060 > select #24/A:129
    13061 
    13062 19 atoms, 18 bonds, 1 residue, 1 model selected 
    13063 
    13064 > color sel gray
    13065 
    13066 > ui mousemode right translate
    13067 
    13068 > ui mousemode right select
    13069 
    13070 > select #2/I:240
    13071 
    13072 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13073 
    13074 > select #24/A:241
    13075 
    13076 15 atoms, 14 bonds, 1 residue, 1 model selected 
    13077 
    13078 > ui mousemode right translate
    13079 
    13080 > ui mousemode right select
    13081 
    13082 > select #2/I:183
    13083 
    13084 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13085 
    13086 > select #24/A:184
    13087 
    13088 22 atoms, 21 bonds, 1 residue, 1 model selected 
    13089 
    13090 > select #2/I:183
    13091 
    13092 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13093 
    13094 > select #2/I:178
    13095 
    13096 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13097 
    13098 > select #24/A:179
    13099 
    13100 24 atoms, 23 bonds, 1 residue, 1 model selected 
    13101 
    13102 > ui mousemode right translate
    13103 
    13104 > ui mousemode right select
    13105 
    13106 > select #2/I:157
    13107 
    13108 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13109 
    13110 > select #24/A:158
    13111 
    13112 22 atoms, 21 bonds, 1 residue, 1 model selected 
    13113 
    13114 > select #2/I:154
    13115 
    13116 8 atoms, 7 bonds, 1 residue, 1 model selected 
    13117 
    13118 > select #2/I:154
    13119 
    13120 8 atoms, 7 bonds, 1 residue, 1 model selected 
    13121 
    13122 > select #24/A:155
    13123 
    13124 19 atoms, 18 bonds, 1 residue, 1 model selected 
    13125 
    13126 > ui mousemode right translate
    13127 
    13128 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    13129 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    13130 
    13131 ——— End of log from Thu Jun 15 13:33:00 2023 ———
    13132 
    13133 opened ChimeraX session 
    13134 
    13135 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    13136 > UASLP/Lab Virología/AlphaFold/Mucambo virus AlphaFold.pdb"
    13137 
    13138 Chain information for Mucambo virus AlphaFold.pdb #25 
    13139 --- 
    13140 Chain | Description 
    13141 A | No description available 
    13142  
    13143 
    13144 > ui tool show Matchmaker
    13145 
    13146 [Repeated 1 time(s)]
    13147 
    13148 > matchmaker #2-4,6,9-24#!5,7-8 to #25
    13149 
    13150 Parameters 
    13151 --- 
    13152 Chain pairing | bb 
    13153 Alignment algorithm | Needleman-Wunsch 
    13154 Similarity matrix | BLOSUM-62 
    13155 SS fraction | 0.3 
    13156 Gap open (HH/SS/other) | 18/18/6 
    13157 Gap extend | 1 
    13158 SS matrix |  |  | H | S | O 
    13159 ---|---|---|--- 
    13160 H | 6 | -9 | -6 
    13161 S |  | 6 | -6 
    13162 O |  |  | 4 
    13163 Iteration cutoff | 2 
    13164  
    13165 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 3j2w.pdb, chain I
    13166 (#2), sequence alignment score = 529.5 
    13167 RMSD between 148 pruned atom pairs is 0.719 angstroms; (across all 149 pairs:
    13168 0.763) 
    13169  
    13170 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 1kxf.pdb, chain A
    13171 (#3), sequence alignment score = 561.4 
    13172 RMSD between 150 pruned atom pairs is 0.671 angstroms; (across all 158 pairs:
    13173 1.955) 
    13174  
    13175 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 7sfu.pdb, chain F
    13176 (#4), sequence alignment score = 791.4 
    13177 RMSD between 148 pruned atom pairs is 0.732 angstroms; (across all 162 pairs:
    13178 2.042) 
    13179  
    13180 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 4agk.pdb, chain A
    13181 (#6), sequence alignment score = 559.3 
    13182 RMSD between 150 pruned atom pairs is 0.713 angstroms; (across all 151 pairs:
    13183 0.739) 
    13184  
    13185 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 7ko8.pdb, chain G
    13186 (#9), sequence alignment score = 568.5 
    13187 RMSD between 129 pruned atom pairs is 1.055 angstroms; (across all 152 pairs:
    13188 1.523) 
    13189  
    13190 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with AlphFold
    13191 Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 797.8 
    13192 RMSD between 148 pruned atom pairs is 0.605 angstroms; (across all 261 pairs:
    13193 27.742) 
    13194  
    13195 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with AlphaFold
    13196 Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
    13197 775.8 
    13198 RMSD between 151 pruned atom pairs is 0.653 angstroms; (across all 262 pairs:
    13199 24.551) 
    13200  
    13201 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with AlphaFold
    13202 Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
    13203 1240.9 
    13204 RMSD between 152 pruned atom pairs is 0.330 angstroms; (across all 274 pairs:
    13205 24.227) 
    13206  
    13207 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Alpha Fold
    13208 Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
    13209 score = 569.6 
    13210 RMSD between 132 pruned atom pairs is 0.920 angstroms; (across all 267 pairs:
    13211 15.674) 
    13212  
    13213 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Alpha Fold
    13214 Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
    13215 974.5 
    13216 RMSD between 155 pruned atom pairs is 0.353 angstroms; (across all 255 pairs:
    13217 37.484) 
    13218  
    13219 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Ndumu virus
    13220 Alphafold.pdb, chain A (#15), sequence alignment score = 830.2 
    13221 RMSD between 137 pruned atom pairs is 0.550 angstroms; (across all 267 pairs:
    13222 41.448) 
    13223  
    13224 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Everglades virus
    13225 Alphafold.pdb, chain A (#16), sequence alignment score = 1240.9 
    13226 RMSD between 152 pruned atom pairs is 0.330 angstroms; (across all 274 pairs:
    13227 24.231) 
    13228  
    13229 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Bebaru virus
    13230 Alphafold.pdb, chain A (#17), sequence alignment score = 795.9 
    13231 RMSD between 146 pruned atom pairs is 0.593 angstroms; (across all 258 pairs:
    13232 29.444) 
    13233  
    13234 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Caaingua virus
    13235 AlphaFold.pdb, chain A (#18), sequence alignment score = 680.9 
    13236 RMSD between 130 pruned atom pairs is 0.713 angstroms; (across all 261 pairs:
    13237 27.031) 
    13238  
    13239 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Cabassou virus
    13240 Alphafold.pdb, chain A (#19), sequence alignment score = 1287 
    13241 RMSD between 13 pruned atom pairs is 0.146 angstroms; (across all 274 pairs:
    13242 25.862) 
    13243  
    13244 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Eilat virus
    13245 Alphafold.pdb, chain A (#20), sequence alignment score = 686.9 
    13246 RMSD between 11 pruned atom pairs is 1.306 angstroms; (across all 254 pairs:
    13247 32.777) 
    13248  
    13249 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Highlands J. virus
    13250 Alphafold.pdb, chain A (#21), sequence alignment score = 984.3 
    13251 RMSD between 156 pruned atom pairs is 0.293 angstroms; (across all 255 pairs:
    13252 25.661) 
    13253  
    13254 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Madariaga virus
    13255 Alpha Fold.pdb, chain A (#22), sequence alignment score = 988.9 
    13256 RMSD between 135 pruned atom pairs is 0.294 angstroms; (across all 257 pairs:
    13257 42.924) 
    13258  
    13259 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Mosso das Pedras
    13260 virus AlphaFold.pdb, chain A (#23), sequence alignment score = 1167.1 
    13261 RMSD between 20 pruned atom pairs is 1.361 angstroms; (across all 274 pairs:
    13262 38.794) 
    13263  
    13264 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Southern Elephant
    13265 Seal virus AlphaFold.pdb, chain A (#24), sequence alignment score = 764.6 
    13266 RMSD between 147 pruned atom pairs is 0.552 angstroms; (across all 262 pairs:
    13267 31.695) 
    13268  
    13269 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 6xo4.pdb, chain C
    13270 (#5), sequence alignment score = 701.7 
    13271 RMSD between 104 pruned atom pairs is 1.212 angstroms; (across all 151 pairs:
    13272 2.018) 
    13273  
    13274 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 1vcp.pdb, chain C
    13275 (#7), sequence alignment score = 563.4 
    13276 RMSD between 147 pruned atom pairs is 0.576 angstroms; (across all 149 pairs:
    13277 0.688) 
    13278  
    13279 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 2yew.pdb, chain G
    13280 (#8), sequence alignment score = 508.8 
    13281 RMSD between 54 pruned atom pairs is 1.257 angstroms; (across all 171 pairs:
    13282 5.382) 
    13283  
    13284 
    13285 > hide #24 models
    13286 
    13287 > color #25 #ff557fff
    13288 
    13289 > color #25 #f4517aff
    13290 
    13291 > color #25 #e64d73ff
    13292 
    13293 > color #25 #da496dff
    13294 
    13295 > color #25 #e34c72ff
    13296 
    13297 > color #25 #f8537cff
    13298 
    13299 > color #25 #ff007fff
    13300 
    13301 > color #25 #ff557fff
    13302 
    13303 > color #25 #be3f5fff
    13304 
    13305 > color #25 #e14b71ff
    13306 
    13307 > color #25 #ef5078ff
    13308 
    13309 > color #25 #ffaaffff
    13310 
    13311 > color #25 #ff557fff
    13312 
    13313 > color #25 #ff679cff
    13314 
    13315 > color #25 #ff82baff
    13316 
    13317 > color #25 #ff97dbff
    13318 
    13319 > color #25 #ff86c7ff
    13320 
    13321 > color #25 #ff81d9ff
    13322 
    13323 > color #25 #ff7bcaff
    13324 
    13325 > ui mousemode right select
    13326 
    13327 > select #2/I:126
    13328 
    13329 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13330 
    13331 > select #25/A:133
    13332 
    13333 12 atoms, 11 bonds, 1 residue, 1 model selected 
    13334 Alignment identifier is 25/A 
    13335 
    13336 > select #2/I:126
    13337 
    13338 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13339 
    13340 > select #2/I:126
    13341 
    13342 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13343 Alignment identifier is 2/I 
    13344 
    13345 > select #25/A:133
    13346 
    13347 12 atoms, 11 bonds, 1 residue, 1 model selected 
    13348 
    13349 > style sel stick
    13350 
    13351 Changed 12 atom styles 
    13352 
    13353 > show sel atoms
    13354 
    13355 > color sel red
    13356 
    13357 > select #2/I:128
    13358 
    13359 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13360 
    13361 > select #25/A:135
    13362 
    13363 22 atoms, 21 bonds, 1 residue, 1 model selected 
    13364 
    13365 > select #2/I:128
    13366 
    13367 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13368 
    13369 > select #25/A:135
    13370 
    13371 22 atoms, 21 bonds, 1 residue, 1 model selected 
    13372 
    13373 > style sel stick
    13374 
    13375 Changed 22 atom styles 
    13376 
    13377 > show sel atoms
    13378 
    13379 > color sel blue
    13380 
    13381 > ui mousemode right translate
    13382 
    13383 > ui mousemode right select
    13384 
    13385 > select #2/I:240
    13386 
    13387 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13388 
    13389 > select #25/A:247
    13390 
    13391 15 atoms, 14 bonds, 1 residue, 1 model selected 
    13392 
    13393 > ui mousemode right translate
    13394 
    13395 > style sel stick
    13396 
    13397 Changed 15 atom styles 
    13398 
    13399 > show sel atoms
    13400 
    13401 > color sel red
    13402 
    13403 > style sel stick
    13404 
    13405 Changed 15 atom styles 
    13406 
    13407 > ui mousemode right rotate
    13408 
    13409 > ui mousemode right select
    13410 
    13411 > select #2/I:190
    13412 
    13413 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13414 
    13415 > select #25/A:197
    13416 
    13417 17 atoms, 16 bonds, 1 residue, 1 model selected 
    13418 
    13419 > style sel stick
    13420 
    13421 Changed 17 atom styles 
    13422 
    13423 > show sel atoms
    13424 
    13425 > color sel orange
    13426 
    13427 > ui mousemode right translate
    13428 
    13429 > ui mousemode right select
    13430 
    13431 > ui mousemode right translate
    13432 
    13433 > ui mousemode right select
    13434 
    13435 > select #2/I:183
    13436 
    13437 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13438 
    13439 > select #25/A:190
    13440 
    13441 22 atoms, 21 bonds, 1 residue, 1 model selected 
    13442 
    13443 > style sel stick
    13444 
    13445 Changed 22 atom styles 
    13446 
    13447 > show sel atoms
    13448 
    13449 > color sel blue
    13450 
    13451 > ui mousemode right translate
    13452 
    13453 > ui mousemode right select
    13454 
    13455 > select #2/I:178
    13456 
    13457 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13458 
    13459 > select #25/A:185
    13460 
    13461 24 atoms, 23 bonds, 1 residue, 1 model selected 
    13462 
    13463 > style sel stick
    13464 
    13465 Changed 24 atom styles 
    13466 
    13467 > show sel atoms
    13468 
    13469 > color sel blue
    13470 
    13471 > select #25/A:190
    13472 
    13473 22 atoms, 21 bonds, 1 residue, 1 model selected 
    13474 
    13475 > ui mousemode right translate
    13476 
    13477 > ui mousemode right select
    13478 
    13479 > select #2/I:157
    13480 
    13481 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13482 
    13483 > select #25/A:164
    13484 
    13485 11 atoms, 10 bonds, 1 residue, 1 model selected 
    13486 
    13487 > select #25/A:164
    13488 
    13489 11 atoms, 10 bonds, 1 residue, 1 model selected 
    13490 
    13491 > style sel stick
    13492 
    13493 Changed 11 atom styles 
    13494 
    13495 > hide sel atoms
    13496 
    13497 > show sel atoms
    13498 
    13499 > style sel stick
    13500 
    13501 Changed 11 atom styles 
    13502 
    13503 > color sel orange
    13504 
    13505 > select #2/I:154
    13506 
    13507 8 atoms, 7 bonds, 1 residue, 1 model selected 
    13508 
    13509 > select #25/A:161
    13510 
    13511 14 atoms, 13 bonds, 1 residue, 1 model selected 
    13512 
    13513 > style sel stick
    13514 
    13515 Changed 14 atom styles 
    13516 
    13517 > show sel atoms
    13518 
    13519 > color sel orange
    13520 
    13521 > ui mousemode right translate
    13522 
    13523 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    13524 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    13525 
    13526 ——— End of log from Fri Jun 16 15:07:56 2023 ———
    13527 
    13528 opened ChimeraX session 
    13529 
    13530 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    13531 > UASLP/Lab Virología/AlphaFold/Onyong-nyong virus AlphaFold.pdb"
    13532 
    13533 Chain information for Onyong-nyong virus AlphaFold.pdb #26 
    13534 --- 
    13535 Chain | Description 
    13536 A | No description available 
    13537  
    13538 
    13539 > select add #25
    13540 
    13541 4421 atoms, 4479 bonds, 275 residues, 1 model selected 
    13542 
    13543 > hide #25 models
    13544 
    13545 > select subtract #25
    13546 
    13547 Nothing selected 
    13548 
    13549 > ui tool show Matchmaker
    13550 
    13551 > matchmaker #2-4,6,9-25#!5,7-8 to #26
    13552 
    13553 Parameters 
    13554 --- 
    13555 Chain pairing | bb 
    13556 Alignment algorithm | Needleman-Wunsch 
    13557 Similarity matrix | BLOSUM-62 
    13558 SS fraction | 0.3 
    13559 Gap open (HH/SS/other) | 18/18/6 
    13560 Gap extend | 1 
    13561 SS matrix |  |  | H | S | O 
    13562 ---|---|---|--- 
    13563 H | 6 | -9 | -6 
    13564 S |  | 6 | -6 
    13565 O |  |  | 4 
    13566 Iteration cutoff | 2 
    13567  
    13568 Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with 3j2w.pdb,
    13569 chain I (#2), sequence alignment score = 693.1 
    13570 RMSD between 145 pruned atom pairs is 0.692 angstroms; (across all 149 pairs:
    13571 0.928) 
    13572  
    13573 Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with 1kxf.pdb,
    13574 chain A (#3), sequence alignment score = 550.8 
    13575 RMSD between 145 pruned atom pairs is 0.764 angstroms; (across all 157 pairs:
    13576 1.974) 
    13577  
    13578 Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with 7sfu.pdb,
    13579 chain I (#4), sequence alignment score = 571.5 
    13580 RMSD between 141 pruned atom pairs is 0.808 angstroms; (across all 161 pairs:
    13581 2.633) 
    13582  
    13583 Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with 4agk.pdb,
    13584 chain A (#6), sequence alignment score = 554.2 
    13585 RMSD between 145 pruned atom pairs is 0.645 angstroms; (across all 150 pairs:
    13586 0.967) 
    13587  
    13588 Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with 7ko8.pdb,
    13589 chain D (#9), sequence alignment score = 789.3 
    13590 RMSD between 135 pruned atom pairs is 1.096 angstroms; (across all 152 pairs:
    13591 1.761) 
    13592  
    13593 Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with AlphFold
    13594 Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 1011.1 
    13595 RMSD between 161 pruned atom pairs is 0.532 angstroms; (across all 259 pairs:
    13596 26.498) 
    13597  
    13598 Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with AlphaFold
    13599 Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
    13600 990.1 
    13601 RMSD between 166 pruned atom pairs is 0.493 angstroms; (across all 260 pairs:
    13602 12.774) 
    13603  
    13604 Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with AlphaFold
    13605 Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
    13606 745.5 
    13607 RMSD between 148 pruned atom pairs is 0.549 angstroms; (across all 253 pairs:
    13608 25.234) 
    13609  
    13610 Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Alpha Fold
    13611 Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
    13612 score = 521 
    13613 RMSD between 129 pruned atom pairs is 0.751 angstroms; (across all 253 pairs:
    13614 34.504) 
    13615  
    13616 Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Alpha Fold
    13617 Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
    13618 761.6 
    13619 RMSD between 148 pruned atom pairs is 0.466 angstroms; (across all 257 pairs:
    13620 22.771) 
    13621  
    13622 Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Ndumu virus
    13623 Alphafold.pdb, chain A (#15), sequence alignment score = 883 
    13624 RMSD between 153 pruned atom pairs is 0.307 angstroms; (across all 255 pairs:
    13625 28.508) 
    13626  
    13627 Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Everglades
    13628 virus Alphafold.pdb, chain A (#16), sequence alignment score = 745.5 
    13629 RMSD between 148 pruned atom pairs is 0.549 angstroms; (across all 253 pairs:
    13630 25.235) 
    13631  
    13632 Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Bebaru virus
    13633 Alphafold.pdb, chain A (#17), sequence alignment score = 1010.1 
    13634 RMSD between 168 pruned atom pairs is 0.393 angstroms; (across all 256 pairs:
    13635 13.447) 
    13636  
    13637 Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Caaingua virus
    13638 AlphaFold.pdb, chain A (#18), sequence alignment score = 714.7 
    13639 RMSD between 131 pruned atom pairs is 0.592 angstroms; (across all 248 pairs:
    13640 30.461) 
    13641  
    13642 Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Cabassou virus
    13643 Alphafold.pdb, chain A (#19), sequence alignment score = 737.3 
    13644 RMSD between 12 pruned atom pairs is 0.503 angstroms; (across all 255 pairs:
    13645 37.820) 
    13646  
    13647 Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Eilat virus
    13648 Alphafold.pdb, chain A (#20), sequence alignment score = 665.2 
    13649 RMSD between 146 pruned atom pairs is 0.659 angstroms; (across all 248 pairs:
    13650 33.950) 
    13651  
    13652 Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Highlands J.
    13653 virus Alphafold.pdb, chain A (#21), sequence alignment score = 778.5 
    13654 RMSD between 148 pruned atom pairs is 0.516 angstroms; (across all 257 pairs:
    13655 23.355) 
    13656  
    13657 Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Madariaga
    13658 virus Alpha Fold.pdb, chain A (#22), sequence alignment score = 752.9 
    13659 RMSD between 148 pruned atom pairs is 0.535 angstroms; (across all 255 pairs:
    13660 24.725) 
    13661  
    13662 Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Mosso das
    13663 Pedras virus AlphaFold.pdb, chain A (#23), sequence alignment score = 734.5 
    13664 RMSD between 148 pruned atom pairs is 0.559 angstroms; (across all 255 pairs:
    13665 31.406) 
    13666  
    13667 Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Southern
    13668 Elephant Seal virus AlphaFold.pdb, chain A (#24), sequence alignment score =
    13669 881.1 
    13670 RMSD between 151 pruned atom pairs is 0.324 angstroms; (across all 248 pairs:
    13671 23.757) 
    13672  
    13673 Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Mucambo virus
    13674 AlphaFold.pdb, chain A (#25), sequence alignment score = 737.4 
    13675 RMSD between 147 pruned atom pairs is 0.545 angstroms; (across all 256 pairs:
    13676 32.618) 
    13677  
    13678 Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with 6xo4.pdb,
    13679 chain C (#5), sequence alignment score = 495.9 
    13680 RMSD between 99 pruned atom pairs is 1.202 angstroms; (across all 150 pairs:
    13681 2.096) 
    13682  
    13683 Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with 1vcp.pdb,
    13684 chain C (#7), sequence alignment score = 720.3 
    13685 RMSD between 145 pruned atom pairs is 0.504 angstroms; (across all 149 pairs:
    13686 0.805) 
    13687  
    13688 Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with 2yew.pdb,
    13689 chain G (#8), sequence alignment score = 682.7 
    13690 RMSD between 54 pruned atom pairs is 1.188 angstroms; (across all 171 pairs:
    13691 9.494) 
    13692  
    13693 
    13694 > color #26 #55557fff
    13695 
    13696 > color #26 #67679aff
    13697 
    13698 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    13699 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    13700 
    13701 ——— End of log from Sat Jun 17 16:13:53 2023 ———
    13702 
    13703 opened ChimeraX session 
    13704 
    13705 > ui mousemode right select
    13706 
    13707 > select #2/I:126
    13708 
    13709 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13710 
    13711 > select #26/A:119
    13712 
    13713 15 atoms, 14 bonds, 1 residue, 1 model selected 
    13714 Alignment identifier is 26/A 
    13715 
    13716 > select #2/I:126
    13717 
    13718 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13719 
    13720 > select clear
    13721 
    13722 > select #26/A:119
    13723 
    13724 15 atoms, 14 bonds, 1 residue, 1 model selected 
    13725 
    13726 > select #2/I:126
    13727 
    13728 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13729 
    13730 > select #26/A:119
    13731 
    13732 15 atoms, 14 bonds, 1 residue, 1 model selected 
    13733 
    13734 > style sel stick
    13735 
    13736 Changed 15 atom styles 
    13737 
    13738 > show sel atoms
    13739 
    13740 > color sel red
    13741 
    13742 > ui mousemode right translate
    13743 
    13744 > ui mousemode right select
    13745 
    13746 > select #2/I:128
    13747 
    13748 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13749 
    13750 > select #26/A:121
    13751 
    13752 22 atoms, 21 bonds, 1 residue, 1 model selected 
    13753 
    13754 > style sel stick
    13755 
    13756 Changed 22 atom styles 
    13757 
    13758 > show sel atoms
    13759 
    13760 > color sel blue
    13761 
    13762 > ui mousemode right translate
    13763 
    13764 > ui mousemode right select
    13765 
    13766 > select #2/I:240
    13767 
    13768 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13769 
    13770 > select #26/A:233
    13771 
    13772 15 atoms, 14 bonds, 1 residue, 1 model selected 
    13773 
    13774 > style sel stick
    13775 
    13776 Changed 15 atom styles 
    13777 
    13778 > show sel atoms
    13779 
    13780 > color sel red
    13781 
    13782 > ui mousemode right translate
    13783 
    13784 > ui mousemode right select
    13785 
    13786 > select #2/I:190
    13787 
    13788 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13789 
    13790 > select #26/A:183
    13791 
    13792 15 atoms, 14 bonds, 1 residue, 1 model selected 
    13793 
    13794 > style sel stick
    13795 
    13796 Changed 15 atom styles 
    13797 
    13798 > show sel atoms
    13799 
    13800 > color sel red
    13801 
    13802 > ui mousemode right translate
    13803 
    13804 > ui mousemode right rotate
    13805 
    13806 > ui mousemode right select
    13807 
    13808 > select #2/I:183
    13809 
    13810 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13811 
    13812 > select #26/A:176
    13813 
    13814 22 atoms, 21 bonds, 1 residue, 1 model selected 
    13815 
    13816 > style sel stick
    13817 
    13818 Changed 22 atom styles 
    13819 
    13820 > show sel atoms
    13821 
    13822 > color sel blue
    13823 
    13824 > select #2/I:183@CA
    13825 
    13826 1 atom, 1 residue, 1 model selected 
    13827 
    13828 > select #26/A:176
    13829 
    13830 22 atoms, 21 bonds, 1 residue, 1 model selected 
    13831 
    13832 > select #26/A:176
    13833 
    13834 22 atoms, 21 bonds, 1 residue, 1 model selected 
    13835 
    13836 > ui mousemode right translate
    13837 
    13838 > ui mousemode right select
    13839 
    13840 > select #2/I:178
    13841 
    13842 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13843 
    13844 > select #26/A:171
    13845 
    13846 22 atoms, 21 bonds, 1 residue, 1 model selected 
    13847 
    13848 > select #2/I:178
    13849 
    13850 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13851 
    13852 > select #26/A:171
    13853 
    13854 22 atoms, 21 bonds, 1 residue, 1 model selected 
    13855 
    13856 > select #26/A:171
    13857 
    13858 22 atoms, 21 bonds, 1 residue, 1 model selected 
    13859 
    13860 > style sel stick
    13861 
    13862 Changed 22 atom styles 
    13863 
    13864 > show sel atoms
    13865 
    13866 > color sel blue
    13867 
    13868 > ui mousemode right translate
    13869 
    13870 > ui mousemode right select
    13871 
    13872 > select #2/I:157
    13873 
    13874 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13875 
    13876 > select #26/A:150
    13877 
    13878 22 atoms, 21 bonds, 1 residue, 1 model selected 
    13879 
    13880 > select #2/I:157
    13881 
    13882 9 atoms, 8 bonds, 1 residue, 1 model selected 
    13883 
    13884 > select #26/A:150
    13885 
    13886 22 atoms, 21 bonds, 1 residue, 1 model selected 
    13887 
    13888 > style sel stick
    13889 
    13890 Changed 22 atom styles 
    13891 
    13892 > show sel atoms
    13893 
    13894 > color sel blue
    13895 
    13896 > ui mousemode right translate
    13897 
    13898 > ui mousemode right select
    13899 
    13900 > select #2/I:154
    13901 
    13902 8 atoms, 7 bonds, 1 residue, 1 model selected 
    13903 
    13904 > select #26/A:147
    13905 
    13906 12 atoms, 11 bonds, 1 residue, 1 model selected 
    13907 
    13908 > style sel stick
    13909 
    13910 Changed 12 atom styles 
    13911 
    13912 > show sel atoms
    13913 
    13914 > color sel red
    13915 
    13916 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    13917 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    13918 
    13919 Drag select of 9 residues 
    13920 
    13921 > ui mousemode right translate
    13922 
    13923 > ui mousemode right select
    13924 
    13925 > select #2/I:237
    13926 
    13927 4 atoms, 3 bonds, 1 residue, 1 model selected 
    13928 
    13929 > ui mousemode right translate
    13930 
    13931 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    13932 > UASLP/Lab Virología/AlphaFold/Pixuna virus AlphaFold.pdb"
    13933 
    13934 Chain information for Pixuna virus AlphaFold.pdb #27 
    13935 --- 
    13936 Chain | Description 
    13937 A | No description available 
    13938  
    13939 
    13940 > ui tool show Matchmaker
    13941 
    13942 > matchmaker #2-4,6,9-26#!5,7-8 to #27
    13943 
    13944 Parameters 
    13945 --- 
    13946 Chain pairing | bb 
    13947 Alignment algorithm | Needleman-Wunsch 
    13948 Similarity matrix | BLOSUM-62 
    13949 SS fraction | 0.3 
    13950 Gap open (HH/SS/other) | 18/18/6 
    13951 Gap extend | 1 
    13952 SS matrix |  |  | H | S | O 
    13953 ---|---|---|--- 
    13954 H | 6 | -9 | -6 
    13955 S |  | 6 | -6 
    13956 O |  |  | 4 
    13957 Iteration cutoff | 2 
    13958  
    13959 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 3j2w.pdb, chain I
    13960 (#2), sequence alignment score = 521 
    13961 RMSD between 147 pruned atom pairs is 0.730 angstroms; (across all 149 pairs:
    13962 0.820) 
    13963  
    13964 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 1kxf.pdb, chain A
    13965 (#3), sequence alignment score = 570.9 
    13966 RMSD between 149 pruned atom pairs is 0.684 angstroms; (across all 158 pairs:
    13967 1.897) 
    13968  
    13969 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 7sfu.pdb, chain F
    13970 (#4), sequence alignment score = 784.4 
    13971 RMSD between 148 pruned atom pairs is 0.745 angstroms; (across all 162 pairs:
    13972 2.028) 
    13973  
    13974 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 4agk.pdb, chain A
    13975 (#6), sequence alignment score = 557.4 
    13976 RMSD between 149 pruned atom pairs is 0.706 angstroms; (across all 151 pairs:
    13977 0.770) 
    13978  
    13979 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 7ko8.pdb, chain G
    13980 (#9), sequence alignment score = 555.5 
    13981 RMSD between 135 pruned atom pairs is 1.130 angstroms; (across all 152 pairs:
    13982 1.573) 
    13983  
    13984 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphFold
    13985 Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 768.3 
    13986 RMSD between 150 pruned atom pairs is 0.552 angstroms; (across all 258 pairs:
    13987 31.415) 
    13988  
    13989 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphaFold
    13990 Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
    13991 757.5 
    13992 RMSD between 140 pruned atom pairs is 0.581 angstroms; (across all 263 pairs:
    13993 32.104) 
    13994  
    13995 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphaFold
    13996 Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
    13997 1176.1 
    13998 RMSD between 24 pruned atom pairs is 0.507 angstroms; (across all 273 pairs:
    13999 32.005) 
    14000  
    14001 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Alpha Fold
    14002 Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
    14003 score = 600.2 
    14004 RMSD between 92 pruned atom pairs is 0.792 angstroms; (across all 268 pairs:
    14005 45.726) 
    14006  
    14007 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Alpha Fold
    14008 Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
    14009 931.2 
    14010 RMSD between 153 pruned atom pairs is 0.312 angstroms; (across all 255 pairs:
    14011 24.821) 
    14012  
    14013 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Ndumu virus
    14014 Alphafold.pdb, chain A (#15), sequence alignment score = 849.5 
    14015 RMSD between 148 pruned atom pairs is 0.597 angstroms; (across all 266 pairs:
    14016 16.320) 
    14017  
    14018 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Everglades virus
    14019 Alphafold.pdb, chain A (#16), sequence alignment score = 1176.1 
    14020 RMSD between 24 pruned atom pairs is 0.507 angstroms; (across all 273 pairs:
    14021 32.005) 
    14022  
    14023 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Bebaru virus
    14024 Alphafold.pdb, chain A (#17), sequence alignment score = 755.1 
    14025 RMSD between 140 pruned atom pairs is 0.521 angstroms; (across all 258 pairs:
    14026 26.677) 
    14027  
    14028 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Caaingua virus
    14029 AlphaFold.pdb, chain A (#18), sequence alignment score = 629.3 
    14030 RMSD between 10 pruned atom pairs is 0.489 angstroms; (across all 258 pairs:
    14031 31.729) 
    14032  
    14033 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Cabassou virus
    14034 Alphafold.pdb, chain A (#19), sequence alignment score = 1205.6 
    14035 RMSD between 149 pruned atom pairs is 0.247 angstroms; (across all 274 pairs:
    14036 39.936) 
    14037  
    14038 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Eilat virus
    14039 Alphafold.pdb, chain A (#20), sequence alignment score = 645.7 
    14040 RMSD between 152 pruned atom pairs is 0.709 angstroms; (across all 247 pairs:
    14041 22.031) 
    14042  
    14043 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Highlands J. virus
    14044 Alphafold.pdb, chain A (#21), sequence alignment score = 931.4 
    14045 RMSD between 139 pruned atom pairs is 0.323 angstroms; (across all 254 pairs:
    14046 36.964) 
    14047  
    14048 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Madariaga virus
    14049 Alpha Fold.pdb, chain A (#22), sequence alignment score = 930.4 
    14050 RMSD between 155 pruned atom pairs is 0.321 angstroms; (across all 256 pairs:
    14051 20.809) 
    14052  
    14053 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Mosso das Pedras
    14054 virus AlphaFold.pdb, chain A (#23), sequence alignment score = 1156 
    14055 RMSD between 144 pruned atom pairs is 0.209 angstroms; (across all 275 pairs:
    14056 22.847) 
    14057  
    14058 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Southern Elephant
    14059 Seal virus AlphaFold.pdb, chain A (#24), sequence alignment score = 743.4 
    14060 RMSD between 148 pruned atom pairs is 0.534 angstroms; (across all 265 pairs:
    14061 24.355) 
    14062  
    14063 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Mucambo virus
    14064 AlphaFold.pdb, chain A (#25), sequence alignment score = 1188.8 
    14065 RMSD between 41 pruned atom pairs is 0.760 angstroms; (across all 274 pairs:
    14066 36.851) 
    14067  
    14068 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Onyong-nyong virus
    14069 AlphaFold.pdb, chain A (#26), sequence alignment score = 689.8 
    14070 RMSD between 144 pruned atom pairs is 0.546 angstroms; (across all 255 pairs:
    14071 28.486) 
    14072  
    14073 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 6xo4.pdb, chain C
    14074 (#5), sequence alignment score = 676.1 
    14075 RMSD between 104 pruned atom pairs is 1.210 angstroms; (across all 151 pairs:
    14076 2.057) 
    14077  
    14078 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 1vcp.pdb, chain C
    14079 (#7), sequence alignment score = 554.2 
    14080 RMSD between 147 pruned atom pairs is 0.608 angstroms; (across all 149 pairs:
    14081 0.747) 
    14082  
    14083 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 2yew.pdb, chain G
    14084 (#8), sequence alignment score = 518.2 
    14085 RMSD between 51 pruned atom pairs is 1.245 angstroms; (across all 171 pairs:
    14086 6.032) 
    14087  
    14088 
    14089 > hide #26 models
    14090 
    14091 > color #27 #ff5500ff
    14092 
    14093 > color #27 #aa007fff
    14094 
    14095 > color #27 #a7007dff
    14096 
    14097 > color #27 #a10079ff
    14098 
    14099 > ui mousemode right select
    14100 
    14101 > select #2/I:126
    14102 
    14103 9 atoms, 8 bonds, 1 residue, 1 model selected 
    14104 
    14105 > select #27/A:133
    14106 
    14107 15 atoms, 14 bonds, 1 residue, 1 model selected 
    14108 Alignment identifier is 27/A 
    14109 
    14110 > style sel stick
    14111 
    14112 Changed 15 atom styles 
    14113 
    14114 > show sel atoms
    14115 
    14116 > color sel red
    14117 
    14118 > select #2/I:128
    14119 
    14120 9 atoms, 8 bonds, 1 residue, 1 model selected 
    14121 
    14122 > select #27/A:135
    14123 
    14124 24 atoms, 23 bonds, 1 residue, 1 model selected 
    14125 
    14126 > select #2/I:128
    14127 
    14128 9 atoms, 8 bonds, 1 residue, 1 model selected 
    14129 
    14130 > select #27/A:135
    14131 
    14132 24 atoms, 23 bonds, 1 residue, 1 model selected 
    14133 
    14134 > style sel stick
    14135 
    14136 Changed 24 atom styles 
    14137 
    14138 > show sel atoms
    14139 
    14140 > color sel blue
    14141 
    14142 > ui mousemode right translate
    14143 
    14144 > ui mousemode right select
    14145 
    14146 > select #2/I:240@CA
    14147 
    14148 1 atom, 1 residue, 1 model selected 
    14149 
    14150 > select #27/A:247
    14151 
    14152 15 atoms, 14 bonds, 1 residue, 1 model selected 
    14153 
    14154 > select #2/I:240@CA
    14155 
    14156 1 atom, 1 residue, 1 model selected 
    14157 
    14158 > select #27/A:247
    14159 
    14160 15 atoms, 14 bonds, 1 residue, 1 model selected 
    14161 
    14162 > hide sel cartoons
    14163 
    14164 > style sel stick
    14165 
    14166 Changed 15 atom styles 
    14167 
    14168 > show sel cartoons
    14169 
    14170 > style sel stick
    14171 
    14172 Changed 15 atom styles 
    14173 
    14174 > show sel atoms
    14175 
    14176 > color sel red
    14177 
    14178 > ui mousemode right translate
    14179 
    14180 > ui mousemode right select
    14181 
    14182 > select #2/I:190
    14183 
    14184 9 atoms, 8 bonds, 1 residue, 1 model selected 
    14185 
    14186 > select #27/A:197
    14187 
    14188 17 atoms, 16 bonds, 1 residue, 1 model selected 
    14189 
    14190 > style sel stick
    14191 
    14192 Changed 17 atom styles 
    14193 
    14194 > show sel atoms
    14195 
    14196 > color sel orange
    14197 
    14198 > ui mousemode right translate
    14199 
    14200 > ui mousemode right select
    14201 
    14202 > select #2/I:183@CA
    14203 
    14204 1 atom, 1 residue, 1 model selected 
    14205 
    14206 > select #27/A:190
    14207 
    14208 22 atoms, 21 bonds, 1 residue, 1 model selected 
    14209 
    14210 > style sel stick
    14211 
    14212 Changed 22 atom styles 
    14213 
    14214 > show sel atoms
    14215 
    14216 > color sel blue
    14217 
    14218 > ui mousemode right translate
    14219 
    14220 > ui mousemode right select
    14221 
    14222 > select #2/I:178
    14223 
    14224 9 atoms, 8 bonds, 1 residue, 1 model selected 
    14225 
    14226 > select #27/A:185
    14227 
    14228 24 atoms, 23 bonds, 1 residue, 1 model selected 
    14229 
    14230 > select #27/A:185
    14231 
    14232 24 atoms, 23 bonds, 1 residue, 1 model selected 
    14233 
    14234 > select #2/I:178
    14235 
    14236 9 atoms, 8 bonds, 1 residue, 1 model selected 
    14237 
    14238 > select #27/A:185
    14239 
    14240 24 atoms, 23 bonds, 1 residue, 1 model selected 
    14241 
    14242 > style sel stick
    14243 
    14244 Changed 24 atom styles 
    14245 
    14246 > show sel atoms
    14247 
    14248 > color sel blue
    14249 
    14250 > ui mousemode right translate
    14251 
    14252 > ui mousemode right select
    14253 
    14254 > select #2/I:157
    14255 
    14256 9 atoms, 8 bonds, 1 residue, 1 model selected 
    14257 
    14258 > select #27/A:164
    14259 
    14260 10 atoms, 9 bonds, 1 residue, 1 model selected 
    14261 
    14262 > select #27/A:164
    14263 
    14264 10 atoms, 9 bonds, 1 residue, 1 model selected 
    14265 
    14266 > style sel stick
    14267 
    14268 Changed 10 atom styles 
    14269 
    14270 > show sel atoms
    14271 
    14272 > color sel gray
    14273 
    14274 > ui mousemode right translate
    14275 
    14276 > ui mousemode right select
    14277 
    14278 > select #2/I:154
    14279 
    14280 8 atoms, 7 bonds, 1 residue, 1 model selected 
    14281 
    14282 > select #27/A:161
    14283 
    14284 10 atoms, 9 bonds, 1 residue, 1 model selected 
    14285 
    14286 > style sel stick
    14287 
    14288 Changed 10 atom styles 
    14289 
    14290 > show sel atoms
    14291 
    14292 > ui mousemode right translate
    14293 
    14294 > color sel gray
    14295 
    14296 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    14297 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    14298 
    14299 ——— End of log from Mon Jun 19 14:50:40 2023 ———
    14300 
    14301 opened ChimeraX session 
    14302 
    14303 > hide #27 models
    14304 
    14305 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    14306 > UASLP/Lab Virología/AlphaFold/RioNegro virus AlphaFold.pdb"
    14307 
    14308 Chain information for RioNegro virus AlphaFold.pdb #28 
    14309 --- 
    14310 Chain | Description 
    14311 A | No description available 
    14312  
    14313 
    14314 > ui tool show Matchmaker
    14315 
    14316 > matchmaker #2-4,6,9-27#!5,7-8 to #28
    14317 
    14318 Parameters 
    14319 --- 
    14320 Chain pairing | bb 
    14321 Alignment algorithm | Needleman-Wunsch 
    14322 Similarity matrix | BLOSUM-62 
    14323 SS fraction | 0.3 
    14324 Gap open (HH/SS/other) | 18/18/6 
    14325 Gap extend | 1 
    14326 SS matrix |  |  | H | S | O 
    14327 ---|---|---|--- 
    14328 H | 6 | -9 | -6 
    14329 S |  | 6 | -6 
    14330 O |  |  | 4 
    14331 Iteration cutoff | 2 
    14332  
    14333 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 3j2w.pdb, chain I
    14334 (#2), sequence alignment score = 527.8 
    14335 RMSD between 147 pruned atom pairs is 0.698 angstroms; (across all 149 pairs:
    14336 0.789) 
    14337  
    14338 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 1kxf.pdb, chain A
    14339 (#3), sequence alignment score = 566.3 
    14340 RMSD between 150 pruned atom pairs is 0.681 angstroms; (across all 158 pairs:
    14341 1.969) 
    14342  
    14343 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 7sfu.pdb, chain F
    14344 (#4), sequence alignment score = 787.7 
    14345 RMSD between 147 pruned atom pairs is 0.760 angstroms; (across all 162 pairs:
    14346 2.092) 
    14347  
    14348 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 4agk.pdb, chain A
    14349 (#6), sequence alignment score = 560.5 
    14350 RMSD between 150 pruned atom pairs is 0.690 angstroms; (across all 151 pairs:
    14351 0.725) 
    14352  
    14353 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 7ko8.pdb, chain G
    14354 (#9), sequence alignment score = 543.1 
    14355 RMSD between 136 pruned atom pairs is 1.140 angstroms; (across all 152 pairs:
    14356 1.558) 
    14357  
    14358 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with AlphFold
    14359 Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 810.7 
    14360 RMSD between 149 pruned atom pairs is 0.612 angstroms; (across all 260 pairs:
    14361 26.607) 
    14362  
    14363 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with AlphaFold
    14364 Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
    14365 814.9 
    14366 RMSD between 150 pruned atom pairs is 0.655 angstroms; (across all 262 pairs:
    14367 19.991) 
    14368  
    14369 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with AlphaFold
    14370 Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
    14371 1186.9 
    14372 RMSD between 153 pruned atom pairs is 0.275 angstroms; (across all 273 pairs:
    14373 22.699) 
    14374  
    14375 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Alpha Fold
    14376 Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
    14377 score = 570 
    14378 RMSD between 129 pruned atom pairs is 0.916 angstroms; (across all 274 pairs:
    14379 14.045) 
    14380  
    14381 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Alpha Fold
    14382 Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
    14383 971.5 
    14384 RMSD between 153 pruned atom pairs is 0.346 angstroms; (across all 255 pairs:
    14385 34.468) 
    14386  
    14387 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Ndumu virus
    14388 Alphafold.pdb, chain A (#15), sequence alignment score = 805.7 
    14389 RMSD between 110 pruned atom pairs is 0.481 angstroms; (across all 266 pairs:
    14390 39.937) 
    14391  
    14392 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Everglades virus
    14393 Alphafold.pdb, chain A (#16), sequence alignment score = 1186.9 
    14394 RMSD between 153 pruned atom pairs is 0.275 angstroms; (across all 273 pairs:
    14395 22.702) 
    14396  
    14397 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Bebaru virus
    14398 Alphafold.pdb, chain A (#17), sequence alignment score = 803.1 
    14399 RMSD between 150 pruned atom pairs is 0.602 angstroms; (across all 255 pairs:
    14400 27.125) 
    14401  
    14402 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Caaingua virus
    14403 AlphaFold.pdb, chain A (#18), sequence alignment score = 690.7 
    14404 RMSD between 142 pruned atom pairs is 0.666 angstroms; (across all 260 pairs:
    14405 24.522) 
    14406  
    14407 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Cabassou virus
    14408 Alphafold.pdb, chain A (#19), sequence alignment score = 1172 
    14409 RMSD between 14 pruned atom pairs is 1.444 angstroms; (across all 275 pairs:
    14410 24.262) 
    14411  
    14412 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Eilat virus
    14413 Alphafold.pdb, chain A (#20), sequence alignment score = 686 
    14414 RMSD between 13 pruned atom pairs is 1.555 angstroms; (across all 251 pairs:
    14415 32.745) 
    14416  
    14417 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Highlands J. virus
    14418 Alphafold.pdb, chain A (#21), sequence alignment score = 974.3 
    14419 RMSD between 154 pruned atom pairs is 0.271 angstroms; (across all 255 pairs:
    14420 21.224) 
    14421  
    14422 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Madariaga virus
    14423 Alpha Fold.pdb, chain A (#22), sequence alignment score = 972.7 
    14424 RMSD between 133 pruned atom pairs is 0.245 angstroms; (across all 257 pairs:
    14425 43.677) 
    14426  
    14427 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Mosso das Pedras
    14428 virus AlphaFold.pdb, chain A (#23), sequence alignment score = 1260.3 
    14429 RMSD between 23 pruned atom pairs is 1.168 angstroms; (across all 278 pairs:
    14430 34.771) 
    14431  
    14432 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Southern Elephant
    14433 Seal virus AlphaFold.pdb, chain A (#24), sequence alignment score = 777 
    14434 RMSD between 148 pruned atom pairs is 0.570 angstroms; (across all 265 pairs:
    14435 31.463) 
    14436  
    14437 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Mucambo virus
    14438 AlphaFold.pdb, chain A (#25), sequence alignment score = 1175.9 
    14439 RMSD between 159 pruned atom pairs is 0.307 angstroms; (across all 274 pairs:
    14440 6.018) 
    14441  
    14442 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Onyong-nyong virus
    14443 AlphaFold.pdb, chain A (#26), sequence alignment score = 731.4 
    14444 RMSD between 148 pruned atom pairs is 0.584 angstroms; (across all 255 pairs:
    14445 29.382) 
    14446  
    14447 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Pixuna virus
    14448 AlphaFold.pdb, chain A (#27), sequence alignment score = 1160.6 
    14449 RMSD between 44 pruned atom pairs is 1.121 angstroms; (across all 275 pairs:
    14450 35.129) 
    14451  
    14452 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 6xo4.pdb, chain C
    14453 (#5), sequence alignment score = 670.2 
    14454 RMSD between 100 pruned atom pairs is 1.164 angstroms; (across all 151 pairs:
    14455 2.092) 
    14456  
    14457 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 1vcp.pdb, chain C
    14458 (#7), sequence alignment score = 561.7 
    14459 RMSD between 146 pruned atom pairs is 0.547 angstroms; (across all 149 pairs:
    14460 0.720) 
    14461  
    14462 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 2yew.pdb, chain G
    14463 (#8), sequence alignment score = 489.8 
    14464 RMSD between 57 pruned atom pairs is 1.297 angstroms; (across all 171 pairs:
    14465 6.267) 
    14466  
    14467 
    14468 > color #28 #55557fff
    14469 
    14470 > color #28 #55007fff
    14471 
    14472 > color #28 black
    14473 
    14474 > color #28 #545454ff
    14475 
    14476 > color #28 #868686ff
    14477 
    14478 > color #28 #212121ff
    14479 
    14480 > color #28 #414141ff
    14481 
    14482 > color #28 #4c4c4cff
    14483 
    14484 > color #28 #55557fff
    14485 
    14486 > color #28 #4e4e75ff
    14487 
    14488 > color #28 #414161ff
    14489 
    14490 > color #28 black
    14491 
    14492 > color #28 #2c2c2cff
    14493 
    14494 > color #28 #474747ff
    14495 
    14496 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    14497 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    14498 
    14499 ——— End of log from Tue Jun 20 13:21:24 2023 ———
    14500 
    14501 opened ChimeraX session 
    14502 Alignment identifier is 27/A 
    14503 
    14504 > select add #27
    14505 
    14506 4429 atoms, 4485 bonds, 275 residues, 1 model selected 
    14507 
    14508 > select subtract #27
    14509 
    14510 Nothing selected 
    14511 
    14512 > select add #28
    14513 
    14514 4421 atoms, 4477 bonds, 278 residues, 1 model selected 
    14515 Alignment identifier is 28/A 
    14516 
    14517 > select subtract #28
    14518 
    14519 Nothing selected 
    14520 
    14521 > ui mousemode right rotate
    14522 
    14523 > ui mousemode right select
    14524 
    14525 > select #2/I:126
    14526 
    14527 9 atoms, 8 bonds, 1 residue, 1 model selected 
    14528 
    14529 > select #28/A:136
    14530 
    14531 12 atoms, 11 bonds, 1 residue, 1 model selected 
    14532 
    14533 > style sel stick
    14534 
    14535 Changed 12 atom styles 
    14536 
    14537 > hide sel atoms
    14538 
    14539 > show sel atoms
    14540 
    14541 > color sel red
    14542 
    14543 > select #2/I:128
    14544 
    14545 9 atoms, 8 bonds, 1 residue, 1 model selected 
    14546 
    14547 > select #28/A:138
    14548 
    14549 24 atoms, 23 bonds, 1 residue, 1 model selected 
    14550 
    14551 > style sel stick
    14552 
    14553 Changed 24 atom styles 
    14554 
    14555 > show sel atoms
    14556 
    14557 > color sel blue
    14558 
    14559 > ui mousemode right translate
    14560 
    14561 > ui mousemode right select
    14562 
    14563 > select #2/I:128
    14564 
    14565 9 atoms, 8 bonds, 1 residue, 1 model selected 
    14566 
    14567 > ui mousemode right translate
    14568 
    14569 > ui mousemode right select
    14570 
    14571 > select #2/I:240
    14572 
    14573 9 atoms, 8 bonds, 1 residue, 1 model selected 
    14574 
    14575 > select #28/A:250
    14576 
    14577 15 atoms, 14 bonds, 1 residue, 1 model selected 
    14578 
    14579 > ui mousemode right translate
    14580 
    14581 > style sel stick
    14582 
    14583 Changed 15 atom styles 
    14584 
    14585 > show sel atoms
    14586 
    14587 > color sel red
    14588 
    14589 > ui mousemode right select
    14590 
    14591 > select #2/I:190
    14592 
    14593 9 atoms, 8 bonds, 1 residue, 1 model selected 
    14594 
    14595 > select #28/A:200
    14596 
    14597 17 atoms, 16 bonds, 1 residue, 1 model selected 
    14598 
    14599 > style sel stick
    14600 
    14601 Changed 17 atom styles 
    14602 
    14603 > show sel atoms
    14604 
    14605 > color sel orange
    14606 
    14607 > ui mousemode right translate
    14608 
    14609 > ui mousemode right select
    14610 
    14611 > select #2/I:190
    14612 
    14613 9 atoms, 8 bonds, 1 residue, 1 model selected 
    14614 
    14615 > ui mousemode right translate
    14616 
    14617 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    14618 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    14619 
    14620 > ui mousemode right select
    14621 
    14622 > select #2/I:183
    14623 
    14624 9 atoms, 8 bonds, 1 residue, 1 model selected 
    14625 
    14626 > select #28/A:193
    14627 
    14628 22 atoms, 21 bonds, 1 residue, 1 model selected 
    14629 
    14630 > select #2/I:183
    14631 
    14632 9 atoms, 8 bonds, 1 residue, 1 model selected 
    14633 
    14634 > select #28/A:193
    14635 
    14636 22 atoms, 21 bonds, 1 residue, 1 model selected 
    14637 
    14638 > style sel stick
    14639 
    14640 Changed 22 atom styles 
    14641 
    14642 > show sel atoms
    14643 
    14644 > color sel blue
    14645 
    14646 > ui mousemode right translate
    14647 
    14648 > ui mousemode right select
    14649 
    14650 > select #2/I:178
    14651 
    14652 9 atoms, 8 bonds, 1 residue, 1 model selected 
    14653 
    14654 > select #28/A:188
    14655 
    14656 24 atoms, 23 bonds, 1 residue, 1 model selected 
    14657 
    14658 > style sel stick
    14659 
    14660 Changed 24 atom styles 
    14661 
    14662 > show sel atoms
    14663 
    14664 > color sel blue
    14665 
    14666 > ui mousemode right translate
    14667 
    14668 > ui mousemode right select
    14669 
    14670 > select #2/I:157
    14671 
    14672 9 atoms, 8 bonds, 1 residue, 1 model selected 
    14673 
    14674 > select #28/A:167
    14675 
    14676 14 atoms, 13 bonds, 1 residue, 1 model selected 
    14677 
    14678 > style sel stick
    14679 
    14680 Changed 14 atom styles 
    14681 
    14682 > show sel atoms
    14683 
    14684 > color sel orange
    14685 
    14686 > ui mousemode right translate
    14687 
    14688 > ui mousemode right select
    14689 
    14690 > select #2/I:154
    14691 
    14692 8 atoms, 7 bonds, 1 residue, 1 model selected 
    14693 
    14694 > select #28/A:164
    14695 
    14696 16 atoms, 15 bonds, 1 residue, 1 model selected 
    14697 
    14698 > style sel stick
    14699 
    14700 Changed 16 atom styles 
    14701 
    14702 > show sel atoms
    14703 
    14704 > color sel gray
    14705 
    14706 > ui mousemode right translate
    14707 
    14708 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    14709 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    14710 
    14711 > hide #28 models
    14712 
    14713 > show #28 models
    14714 
    14715 > hide #28 models
    14716 
    14717 > show #27 models
    14718 
    14719 > select add #28
    14720 
    14721 4421 atoms, 4477 bonds, 278 residues, 1 model selected 
    14722 
    14723 > select subtract #28
    14724 
    14725 Nothing selected 
    14726 
    14727 > show #26 models
    14728 
    14729 > hide #26 models
    14730 
    14731 > hide #27 models
    14732 
    14733 > show #27 models
    14734 
    14735 > ui tool show Matchmaker
    14736 
    14737 > matchmaker #2-4,6,9-26,28#!5,7-8 to #27
    14738 
    14739 Parameters 
    14740 --- 
    14741 Chain pairing | bb 
    14742 Alignment algorithm | Needleman-Wunsch 
    14743 Similarity matrix | BLOSUM-62 
    14744 SS fraction | 0.3 
    14745 Gap open (HH/SS/other) | 18/18/6 
    14746 Gap extend | 1 
    14747 SS matrix |  |  | H | S | O 
    14748 ---|---|---|--- 
    14749 H | 6 | -9 | -6 
    14750 S |  | 6 | -6 
    14751 O |  |  | 4 
    14752 Iteration cutoff | 2 
    14753  
    14754 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 3j2w.pdb, chain I
    14755 (#2), sequence alignment score = 521 
    14756 RMSD between 147 pruned atom pairs is 0.730 angstroms; (across all 149 pairs:
    14757 0.820) 
    14758  
    14759 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 1kxf.pdb, chain A
    14760 (#3), sequence alignment score = 570.9 
    14761 RMSD between 149 pruned atom pairs is 0.684 angstroms; (across all 158 pairs:
    14762 1.897) 
    14763  
    14764 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 7sfu.pdb, chain F
    14765 (#4), sequence alignment score = 784.4 
    14766 RMSD between 148 pruned atom pairs is 0.745 angstroms; (across all 162 pairs:
    14767 2.028) 
    14768  
    14769 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 4agk.pdb, chain A
    14770 (#6), sequence alignment score = 557.4 
    14771 RMSD between 149 pruned atom pairs is 0.706 angstroms; (across all 151 pairs:
    14772 0.770) 
    14773  
    14774 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 7ko8.pdb, chain G
    14775 (#9), sequence alignment score = 555.5 
    14776 RMSD between 135 pruned atom pairs is 1.130 angstroms; (across all 152 pairs:
    14777 1.573) 
    14778  
    14779 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphFold
    14780 Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 768.3 
    14781 RMSD between 150 pruned atom pairs is 0.552 angstroms; (across all 258 pairs:
    14782 31.415) 
    14783  
    14784 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphaFold
    14785 Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
    14786 757.5 
    14787 RMSD between 140 pruned atom pairs is 0.581 angstroms; (across all 263 pairs:
    14788 32.104) 
    14789  
    14790 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphaFold
    14791 Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
    14792 1176.1 
    14793 RMSD between 24 pruned atom pairs is 0.507 angstroms; (across all 273 pairs:
    14794 32.005) 
    14795  
    14796 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Alpha Fold
    14797 Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
    14798 score = 600.2 
    14799 RMSD between 92 pruned atom pairs is 0.792 angstroms; (across all 268 pairs:
    14800 45.726) 
    14801  
    14802 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Alpha Fold
    14803 Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
    14804 931.2 
    14805 RMSD between 153 pruned atom pairs is 0.312 angstroms; (across all 255 pairs:
    14806 24.821) 
    14807  
    14808 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Ndumu virus
    14809 Alphafold.pdb, chain A (#15), sequence alignment score = 849.5 
    14810 RMSD between 148 pruned atom pairs is 0.597 angstroms; (across all 266 pairs:
    14811 16.320) 
    14812  
    14813 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Everglades virus
    14814 Alphafold.pdb, chain A (#16), sequence alignment score = 1176.1 
    14815 RMSD between 24 pruned atom pairs is 0.507 angstroms; (across all 273 pairs:
    14816 32.005) 
    14817  
    14818 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Bebaru virus
    14819 Alphafold.pdb, chain A (#17), sequence alignment score = 755.1 
    14820 RMSD between 140 pruned atom pairs is 0.521 angstroms; (across all 258 pairs:
    14821 26.677) 
    14822  
    14823 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Caaingua virus
    14824 AlphaFold.pdb, chain A (#18), sequence alignment score = 629.3 
    14825 RMSD between 10 pruned atom pairs is 0.489 angstroms; (across all 258 pairs:
    14826 31.729) 
    14827  
    14828 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Cabassou virus
    14829 Alphafold.pdb, chain A (#19), sequence alignment score = 1205.6 
    14830 RMSD between 149 pruned atom pairs is 0.247 angstroms; (across all 274 pairs:
    14831 39.936) 
    14832  
    14833 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Eilat virus
    14834 Alphafold.pdb, chain A (#20), sequence alignment score = 645.7 
    14835 RMSD between 152 pruned atom pairs is 0.709 angstroms; (across all 247 pairs:
    14836 22.031) 
    14837  
    14838 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Highlands J. virus
    14839 Alphafold.pdb, chain A (#21), sequence alignment score = 931.4 
    14840 RMSD between 139 pruned atom pairs is 0.323 angstroms; (across all 254 pairs:
    14841 36.964) 
    14842  
    14843 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Madariaga virus
    14844 Alpha Fold.pdb, chain A (#22), sequence alignment score = 930.4 
    14845 RMSD between 155 pruned atom pairs is 0.321 angstroms; (across all 256 pairs:
    14846 20.809) 
    14847  
    14848 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Mosso das Pedras
    14849 virus AlphaFold.pdb, chain A (#23), sequence alignment score = 1156 
    14850 RMSD between 144 pruned atom pairs is 0.209 angstroms; (across all 275 pairs:
    14851 22.847) 
    14852  
    14853 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Southern Elephant
    14854 Seal virus AlphaFold.pdb, chain A (#24), sequence alignment score = 743.4 
    14855 RMSD between 148 pruned atom pairs is 0.534 angstroms; (across all 265 pairs:
    14856 24.355) 
    14857  
    14858 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Mucambo virus
    14859 AlphaFold.pdb, chain A (#25), sequence alignment score = 1188.8 
    14860 RMSD between 41 pruned atom pairs is 0.760 angstroms; (across all 274 pairs:
    14861 36.851) 
    14862  
    14863 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Onyong-nyong virus
    14864 AlphaFold.pdb, chain A (#26), sequence alignment score = 689.8 
    14865 RMSD between 144 pruned atom pairs is 0.546 angstroms; (across all 255 pairs:
    14866 28.486) 
    14867  
    14868 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with RioNegro virus
    14869 AlphaFold.pdb, chain A (#28), sequence alignment score = 1160.6 
    14870 RMSD between 44 pruned atom pairs is 1.121 angstroms; (across all 275 pairs:
    14871 35.129) 
    14872  
    14873 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 6xo4.pdb, chain C
    14874 (#5), sequence alignment score = 676.1 
    14875 RMSD between 104 pruned atom pairs is 1.210 angstroms; (across all 151 pairs:
    14876 2.057) 
    14877  
    14878 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 1vcp.pdb, chain C
    14879 (#7), sequence alignment score = 554.2 
    14880 RMSD between 147 pruned atom pairs is 0.608 angstroms; (across all 149 pairs:
    14881 0.747) 
    14882  
    14883 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 2yew.pdb, chain G
    14884 (#8), sequence alignment score = 518.2 
    14885 RMSD between 51 pruned atom pairs is 1.245 angstroms; (across all 171 pairs:
    14886 6.032) 
    14887  
    14888 
    14889 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    14890 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    14891 
    14892 ——— End of log from Tue Jun 20 13:33:55 2023 ———
    14893 
    14894 opened ChimeraX session 
    14895 
    14896 > hide #27 models
    14897 
    14898 > show #28 models
    14899 
    14900 > show #26 models
    14901 
    14902 > hide #26 models
    14903 
    14904 > ui tool show Matchmaker
    14905 
    14906 > matchmaker #2-4,6,9-27#!5,7-8 to #28
    14907 
    14908 Parameters 
    14909 --- 
    14910 Chain pairing | bb 
    14911 Alignment algorithm | Needleman-Wunsch 
    14912 Similarity matrix | BLOSUM-62 
    14913 SS fraction | 0.3 
    14914 Gap open (HH/SS/other) | 18/18/6 
    14915 Gap extend | 1 
    14916 SS matrix |  |  | H | S | O 
    14917 ---|---|---|--- 
    14918 H | 6 | -9 | -6 
    14919 S |  | 6 | -6 
    14920 O |  |  | 4 
    14921 Iteration cutoff | 2 
    14922  
    14923 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 3j2w.pdb, chain I
    14924 (#2), sequence alignment score = 527.8 
    14925 RMSD between 147 pruned atom pairs is 0.698 angstroms; (across all 149 pairs:
    14926 0.789) 
    14927  
    14928 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 1kxf.pdb, chain A
    14929 (#3), sequence alignment score = 566.3 
    14930 RMSD between 150 pruned atom pairs is 0.681 angstroms; (across all 158 pairs:
    14931 1.969) 
    14932  
    14933 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 7sfu.pdb, chain F
    14934 (#4), sequence alignment score = 787.7 
    14935 RMSD between 147 pruned atom pairs is 0.760 angstroms; (across all 162 pairs:
    14936 2.092) 
    14937  
    14938 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 4agk.pdb, chain A
    14939 (#6), sequence alignment score = 560.5 
    14940 RMSD between 150 pruned atom pairs is 0.690 angstroms; (across all 151 pairs:
    14941 0.725) 
    14942  
    14943 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 7ko8.pdb, chain G
    14944 (#9), sequence alignment score = 543.1 
    14945 RMSD between 136 pruned atom pairs is 1.140 angstroms; (across all 152 pairs:
    14946 1.558) 
    14947  
    14948 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with AlphFold
    14949 Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 810.7 
    14950 RMSD between 149 pruned atom pairs is 0.612 angstroms; (across all 260 pairs:
    14951 26.607) 
    14952  
    14953 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with AlphaFold
    14954 Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
    14955 814.9 
    14956 RMSD between 150 pruned atom pairs is 0.655 angstroms; (across all 262 pairs:
    14957 19.991) 
    14958  
    14959 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with AlphaFold
    14960 Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
    14961 1186.9 
    14962 RMSD between 153 pruned atom pairs is 0.275 angstroms; (across all 273 pairs:
    14963 22.699) 
    14964  
    14965 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Alpha Fold
    14966 Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
    14967 score = 570 
    14968 RMSD between 129 pruned atom pairs is 0.916 angstroms; (across all 274 pairs:
    14969 14.045) 
    14970  
    14971 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Alpha Fold
    14972 Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
    14973 971.5 
    14974 RMSD between 153 pruned atom pairs is 0.346 angstroms; (across all 255 pairs:
    14975 34.468) 
    14976  
    14977 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Ndumu virus
    14978 Alphafold.pdb, chain A (#15), sequence alignment score = 805.7 
    14979 RMSD between 110 pruned atom pairs is 0.481 angstroms; (across all 266 pairs:
    14980 39.937) 
    14981  
    14982 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Everglades virus
    14983 Alphafold.pdb, chain A (#16), sequence alignment score = 1186.9 
    14984 RMSD between 153 pruned atom pairs is 0.275 angstroms; (across all 273 pairs:
    14985 22.702) 
    14986  
    14987 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Bebaru virus
    14988 Alphafold.pdb, chain A (#17), sequence alignment score = 803.1 
    14989 RMSD between 150 pruned atom pairs is 0.602 angstroms; (across all 255 pairs:
    14990 27.125) 
    14991  
    14992 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Caaingua virus
    14993 AlphaFold.pdb, chain A (#18), sequence alignment score = 690.7 
    14994 RMSD between 142 pruned atom pairs is 0.666 angstroms; (across all 260 pairs:
    14995 24.522) 
    14996  
    14997 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Cabassou virus
    14998 Alphafold.pdb, chain A (#19), sequence alignment score = 1172 
    14999 RMSD between 14 pruned atom pairs is 1.444 angstroms; (across all 275 pairs:
    15000 24.262) 
    15001  
    15002 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Eilat virus
    15003 Alphafold.pdb, chain A (#20), sequence alignment score = 686 
    15004 RMSD between 13 pruned atom pairs is 1.555 angstroms; (across all 251 pairs:
    15005 32.745) 
    15006  
    15007 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Highlands J. virus
    15008 Alphafold.pdb, chain A (#21), sequence alignment score = 974.3 
    15009 RMSD between 154 pruned atom pairs is 0.271 angstroms; (across all 255 pairs:
    15010 21.224) 
    15011  
    15012 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Madariaga virus
    15013 Alpha Fold.pdb, chain A (#22), sequence alignment score = 972.7 
    15014 RMSD between 133 pruned atom pairs is 0.245 angstroms; (across all 257 pairs:
    15015 43.677) 
    15016  
    15017 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Mosso das Pedras
    15018 virus AlphaFold.pdb, chain A (#23), sequence alignment score = 1260.3 
    15019 RMSD between 23 pruned atom pairs is 1.168 angstroms; (across all 278 pairs:
    15020 34.771) 
    15021  
    15022 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Southern Elephant
    15023 Seal virus AlphaFold.pdb, chain A (#24), sequence alignment score = 777 
    15024 RMSD between 148 pruned atom pairs is 0.570 angstroms; (across all 265 pairs:
    15025 31.463) 
    15026  
    15027 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Mucambo virus
    15028 AlphaFold.pdb, chain A (#25), sequence alignment score = 1175.9 
    15029 RMSD between 159 pruned atom pairs is 0.307 angstroms; (across all 274 pairs:
    15030 6.018) 
    15031  
    15032 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Onyong-nyong virus
    15033 AlphaFold.pdb, chain A (#26), sequence alignment score = 731.4 
    15034 RMSD between 148 pruned atom pairs is 0.584 angstroms; (across all 255 pairs:
    15035 29.382) 
    15036  
    15037 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Pixuna virus
    15038 AlphaFold.pdb, chain A (#27), sequence alignment score = 1160.6 
    15039 RMSD between 44 pruned atom pairs is 1.121 angstroms; (across all 275 pairs:
    15040 35.129) 
    15041  
    15042 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 6xo4.pdb, chain C
    15043 (#5), sequence alignment score = 670.2 
    15044 RMSD between 100 pruned atom pairs is 1.164 angstroms; (across all 151 pairs:
    15045 2.092) 
    15046  
    15047 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 1vcp.pdb, chain C
    15048 (#7), sequence alignment score = 561.7 
    15049 RMSD between 146 pruned atom pairs is 0.547 angstroms; (across all 149 pairs:
    15050 0.720) 
    15051  
    15052 Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 2yew.pdb, chain G
    15053 (#8), sequence alignment score = 489.8 
    15054 RMSD between 57 pruned atom pairs is 1.297 angstroms; (across all 171 pairs:
    15055 6.267) 
    15056  
    15057 
    15058 > show #26 models
    15059 
    15060 > hide #26 models
    15061 
    15062 > hide #28 models
    15063 
    15064 > show #27 models
    15065 
    15066 > ui tool show Matchmaker
    15067 
    15068 > matchmaker #2-4,6,9-26,28#!5,7-8 to #27
    15069 
    15070 Parameters 
    15071 --- 
    15072 Chain pairing | bb 
    15073 Alignment algorithm | Needleman-Wunsch 
    15074 Similarity matrix | BLOSUM-62 
    15075 SS fraction | 0.3 
    15076 Gap open (HH/SS/other) | 18/18/6 
    15077 Gap extend | 1 
    15078 SS matrix |  |  | H | S | O 
    15079 ---|---|---|--- 
    15080 H | 6 | -9 | -6 
    15081 S |  | 6 | -6 
    15082 O |  |  | 4 
    15083 Iteration cutoff | 2 
    15084  
    15085 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 3j2w.pdb, chain I
    15086 (#2), sequence alignment score = 521 
    15087 RMSD between 147 pruned atom pairs is 0.730 angstroms; (across all 149 pairs:
    15088 0.820) 
    15089  
    15090 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 1kxf.pdb, chain A
    15091 (#3), sequence alignment score = 570.9 
    15092 RMSD between 149 pruned atom pairs is 0.684 angstroms; (across all 158 pairs:
    15093 1.897) 
    15094  
    15095 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 7sfu.pdb, chain F
    15096 (#4), sequence alignment score = 784.4 
    15097 RMSD between 148 pruned atom pairs is 0.745 angstroms; (across all 162 pairs:
    15098 2.028) 
    15099  
    15100 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 4agk.pdb, chain A
    15101 (#6), sequence alignment score = 557.4 
    15102 RMSD between 149 pruned atom pairs is 0.706 angstroms; (across all 151 pairs:
    15103 0.770) 
    15104  
    15105 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 7ko8.pdb, chain G
    15106 (#9), sequence alignment score = 555.5 
    15107 RMSD between 135 pruned atom pairs is 1.130 angstroms; (across all 152 pairs:
    15108 1.573) 
    15109  
    15110 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphFold
    15111 Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 768.3 
    15112 RMSD between 150 pruned atom pairs is 0.552 angstroms; (across all 258 pairs:
    15113 31.415) 
    15114  
    15115 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphaFold
    15116 Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
    15117 757.5 
    15118 RMSD between 140 pruned atom pairs is 0.581 angstroms; (across all 263 pairs:
    15119 32.104) 
    15120  
    15121 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphaFold
    15122 Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
    15123 1176.1 
    15124 RMSD between 24 pruned atom pairs is 0.507 angstroms; (across all 273 pairs:
    15125 32.005) 
    15126  
    15127 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Alpha Fold
    15128 Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
    15129 score = 600.2 
    15130 RMSD between 92 pruned atom pairs is 0.792 angstroms; (across all 268 pairs:
    15131 45.726) 
    15132  
    15133 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Alpha Fold
    15134 Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
    15135 931.2 
    15136 RMSD between 153 pruned atom pairs is 0.312 angstroms; (across all 255 pairs:
    15137 24.821) 
    15138  
    15139 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Ndumu virus
    15140 Alphafold.pdb, chain A (#15), sequence alignment score = 849.5 
    15141 RMSD between 148 pruned atom pairs is 0.597 angstroms; (across all 266 pairs:
    15142 16.320) 
    15143  
    15144 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Everglades virus
    15145 Alphafold.pdb, chain A (#16), sequence alignment score = 1176.1 
    15146 RMSD between 24 pruned atom pairs is 0.507 angstroms; (across all 273 pairs:
    15147 32.005) 
    15148  
    15149 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Bebaru virus
    15150 Alphafold.pdb, chain A (#17), sequence alignment score = 755.1 
    15151 RMSD between 140 pruned atom pairs is 0.521 angstroms; (across all 258 pairs:
    15152 26.677) 
    15153  
    15154 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Caaingua virus
    15155 AlphaFold.pdb, chain A (#18), sequence alignment score = 629.3 
    15156 RMSD between 10 pruned atom pairs is 0.489 angstroms; (across all 258 pairs:
    15157 31.729) 
    15158  
    15159 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Cabassou virus
    15160 Alphafold.pdb, chain A (#19), sequence alignment score = 1205.6 
    15161 RMSD between 149 pruned atom pairs is 0.247 angstroms; (across all 274 pairs:
    15162 39.936) 
    15163  
    15164 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Eilat virus
    15165 Alphafold.pdb, chain A (#20), sequence alignment score = 645.7 
    15166 RMSD between 152 pruned atom pairs is 0.709 angstroms; (across all 247 pairs:
    15167 22.031) 
    15168  
    15169 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Highlands J. virus
    15170 Alphafold.pdb, chain A (#21), sequence alignment score = 931.4 
    15171 RMSD between 139 pruned atom pairs is 0.323 angstroms; (across all 254 pairs:
    15172 36.964) 
    15173  
    15174 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Madariaga virus
    15175 Alpha Fold.pdb, chain A (#22), sequence alignment score = 930.4 
    15176 RMSD between 155 pruned atom pairs is 0.321 angstroms; (across all 256 pairs:
    15177 20.809) 
    15178  
    15179 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Mosso das Pedras
    15180 virus AlphaFold.pdb, chain A (#23), sequence alignment score = 1156 
    15181 RMSD between 144 pruned atom pairs is 0.209 angstroms; (across all 275 pairs:
    15182 22.847) 
    15183  
    15184 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Southern Elephant
    15185 Seal virus AlphaFold.pdb, chain A (#24), sequence alignment score = 743.4 
    15186 RMSD between 148 pruned atom pairs is 0.534 angstroms; (across all 265 pairs:
    15187 24.355) 
    15188  
    15189 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Mucambo virus
    15190 AlphaFold.pdb, chain A (#25), sequence alignment score = 1188.8 
    15191 RMSD between 41 pruned atom pairs is 0.760 angstroms; (across all 274 pairs:
    15192 36.851) 
    15193  
    15194 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Onyong-nyong virus
    15195 AlphaFold.pdb, chain A (#26), sequence alignment score = 689.8 
    15196 RMSD between 144 pruned atom pairs is 0.546 angstroms; (across all 255 pairs:
    15197 28.486) 
    15198  
    15199 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with RioNegro virus
    15200 AlphaFold.pdb, chain A (#28), sequence alignment score = 1160.6 
    15201 RMSD between 44 pruned atom pairs is 1.121 angstroms; (across all 275 pairs:
    15202 35.129) 
    15203  
    15204 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 6xo4.pdb, chain C
    15205 (#5), sequence alignment score = 676.1 
    15206 RMSD between 104 pruned atom pairs is 1.210 angstroms; (across all 151 pairs:
    15207 2.057) 
    15208  
    15209 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 1vcp.pdb, chain C
    15210 (#7), sequence alignment score = 554.2 
    15211 RMSD between 147 pruned atom pairs is 0.608 angstroms; (across all 149 pairs:
    15212 0.747) 
    15213  
    15214 Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 2yew.pdb, chain G
    15215 (#8), sequence alignment score = 518.2 
    15216 RMSD between 51 pruned atom pairs is 1.245 angstroms; (across all 171 pairs:
    15217 6.032) 
    15218  
    15219 
    15220 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    15221 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    15222 
    15223 > hide #27 models
    15224 
    15225 > show #26 models
    15226 
    15227 > hide #26 models
    15228 
    15229 > show #26 models
    15230 
    15231 > hide #26 models
    15232 
    15233 > show #25 models
    15234 
    15235 > show #24 models
    15236 
    15237 > hide #24 models
    15238 
    15239 > show #23 models
    15240 
    15241 > hide #23 models
    15242 
    15243 > ui tool show Matchmaker
    15244 
    15245 > matchmaker #2-4,6,9-24,26-28#!5,7-8 to #25
    15246 
    15247 Parameters 
    15248 --- 
    15249 Chain pairing | bb 
    15250 Alignment algorithm | Needleman-Wunsch 
    15251 Similarity matrix | BLOSUM-62 
    15252 SS fraction | 0.3 
    15253 Gap open (HH/SS/other) | 18/18/6 
    15254 Gap extend | 1 
    15255 SS matrix |  |  | H | S | O 
    15256 ---|---|---|--- 
    15257 H | 6 | -9 | -6 
    15258 S |  | 6 | -6 
    15259 O |  |  | 4 
    15260 Iteration cutoff | 2 
    15261  
    15262 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 3j2w.pdb, chain I
    15263 (#2), sequence alignment score = 529.5 
    15264 RMSD between 148 pruned atom pairs is 0.719 angstroms; (across all 149 pairs:
    15265 0.763) 
    15266  
    15267 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 1kxf.pdb, chain A
    15268 (#3), sequence alignment score = 561.4 
    15269 RMSD between 150 pruned atom pairs is 0.671 angstroms; (across all 158 pairs:
    15270 1.955) 
    15271  
    15272 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 7sfu.pdb, chain F
    15273 (#4), sequence alignment score = 791.4 
    15274 RMSD between 148 pruned atom pairs is 0.732 angstroms; (across all 162 pairs:
    15275 2.042) 
    15276  
    15277 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 4agk.pdb, chain A
    15278 (#6), sequence alignment score = 559.3 
    15279 RMSD between 150 pruned atom pairs is 0.713 angstroms; (across all 151 pairs:
    15280 0.739) 
    15281  
    15282 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 7ko8.pdb, chain G
    15283 (#9), sequence alignment score = 568.5 
    15284 RMSD between 129 pruned atom pairs is 1.055 angstroms; (across all 152 pairs:
    15285 1.523) 
    15286  
    15287 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with AlphFold
    15288 Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 797.8 
    15289 RMSD between 148 pruned atom pairs is 0.605 angstroms; (across all 261 pairs:
    15290 27.742) 
    15291  
    15292 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with AlphaFold
    15293 Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
    15294 775.8 
    15295 RMSD between 151 pruned atom pairs is 0.653 angstroms; (across all 262 pairs:
    15296 24.551) 
    15297  
    15298 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with AlphaFold
    15299 Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
    15300 1240.9 
    15301 RMSD between 152 pruned atom pairs is 0.330 angstroms; (across all 274 pairs:
    15302 24.227) 
    15303  
    15304 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Alpha Fold
    15305 Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
    15306 score = 569.6 
    15307 RMSD between 132 pruned atom pairs is 0.920 angstroms; (across all 267 pairs:
    15308 15.674) 
    15309  
    15310 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Alpha Fold
    15311 Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
    15312 974.5 
    15313 RMSD between 155 pruned atom pairs is 0.353 angstroms; (across all 255 pairs:
    15314 37.484) 
    15315  
    15316 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Ndumu virus
    15317 Alphafold.pdb, chain A (#15), sequence alignment score = 830.2 
    15318 RMSD between 137 pruned atom pairs is 0.550 angstroms; (across all 267 pairs:
    15319 41.448) 
    15320  
    15321 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Everglades virus
    15322 Alphafold.pdb, chain A (#16), sequence alignment score = 1240.9 
    15323 RMSD between 152 pruned atom pairs is 0.330 angstroms; (across all 274 pairs:
    15324 24.231) 
    15325  
    15326 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Bebaru virus
    15327 Alphafold.pdb, chain A (#17), sequence alignment score = 795.9 
    15328 RMSD between 146 pruned atom pairs is 0.593 angstroms; (across all 258 pairs:
    15329 29.444) 
    15330  
    15331 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Caaingua virus
    15332 AlphaFold.pdb, chain A (#18), sequence alignment score = 680.9 
    15333 RMSD between 130 pruned atom pairs is 0.713 angstroms; (across all 261 pairs:
    15334 27.031) 
    15335  
    15336 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Cabassou virus
    15337 Alphafold.pdb, chain A (#19), sequence alignment score = 1287 
    15338 RMSD between 13 pruned atom pairs is 0.146 angstroms; (across all 274 pairs:
    15339 25.862) 
    15340  
    15341 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Eilat virus
    15342 Alphafold.pdb, chain A (#20), sequence alignment score = 686.9 
    15343 RMSD between 11 pruned atom pairs is 1.306 angstroms; (across all 254 pairs:
    15344 32.777) 
    15345  
    15346 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Highlands J. virus
    15347 Alphafold.pdb, chain A (#21), sequence alignment score = 984.3 
    15348 RMSD between 156 pruned atom pairs is 0.293 angstroms; (across all 255 pairs:
    15349 25.661) 
    15350  
    15351 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Madariaga virus
    15352 Alpha Fold.pdb, chain A (#22), sequence alignment score = 988.9 
    15353 RMSD between 135 pruned atom pairs is 0.294 angstroms; (across all 257 pairs:
    15354 42.924) 
    15355  
    15356 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Mosso das Pedras
    15357 virus AlphaFold.pdb, chain A (#23), sequence alignment score = 1167.1 
    15358 RMSD between 20 pruned atom pairs is 1.361 angstroms; (across all 274 pairs:
    15359 38.794) 
    15360  
    15361 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Southern Elephant
    15362 Seal virus AlphaFold.pdb, chain A (#24), sequence alignment score = 764.6 
    15363 RMSD between 147 pruned atom pairs is 0.552 angstroms; (across all 262 pairs:
    15364 31.695) 
    15365  
    15366 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Onyong-nyong virus
    15367 AlphaFold.pdb, chain A (#26), sequence alignment score = 737.4 
    15368 RMSD between 147 pruned atom pairs is 0.545 angstroms; (across all 256 pairs:
    15369 32.618) 
    15370  
    15371 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Pixuna virus
    15372 AlphaFold.pdb, chain A (#27), sequence alignment score = 1188.8 
    15373 RMSD between 41 pruned atom pairs is 0.760 angstroms; (across all 274 pairs:
    15374 36.851) 
    15375  
    15376 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with RioNegro virus
    15377 AlphaFold.pdb, chain A (#28), sequence alignment score = 1175.9 
    15378 RMSD between 159 pruned atom pairs is 0.307 angstroms; (across all 274 pairs:
    15379 6.018) 
    15380  
    15381 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 6xo4.pdb, chain C
    15382 (#5), sequence alignment score = 701.7 
    15383 RMSD between 104 pruned atom pairs is 1.212 angstroms; (across all 151 pairs:
    15384 2.018) 
    15385  
    15386 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 1vcp.pdb, chain C
    15387 (#7), sequence alignment score = 563.4 
    15388 RMSD between 147 pruned atom pairs is 0.576 angstroms; (across all 149 pairs:
    15389 0.688) 
    15390  
    15391 Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 2yew.pdb, chain G
    15392 (#8), sequence alignment score = 508.8 
    15393 RMSD between 54 pruned atom pairs is 1.257 angstroms; (across all 171 pairs:
    15394 5.382) 
    15395  
    15396 
    15397 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    15398 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    15399 
    15400 ——— End of log from Tue Jun 20 13:41:59 2023 ———
    15401 
    15402 opened ChimeraX session 
    15403 
    15404 > hide #25 models
    15405 
    15406 > show #28 models
    15407 
    15408 > hide #28 models
    15409 
    15410 > show #28 models
    15411 
    15412 > hide #28 models
    15413 
    15414 > show #27 models
    15415 
    15416 > show #26 models
    15417 
    15418 > hide #26 models
    15419 
    15420 > show #25 models
    15421 
    15422 > hide #25 models
    15423 
    15424 > hide #27 models
    15425 
    15426 > show #28 models
    15427 
    15428 > show #26 models
    15429 
    15430 > hide #26 models
    15431 
    15432 > show #27 models
    15433 
    15434 > hide #28 models
    15435 
    15436 > ui tool show Matchmaker
    15437 
    15438 > matchmaker #27 to #2
    15439 
    15440 Parameters 
    15441 --- 
    15442 Chain pairing | bb 
    15443 Alignment algorithm | Needleman-Wunsch 
    15444 Similarity matrix | BLOSUM-62 
    15445 SS fraction | 0.3 
    15446 Gap open (HH/SS/other) | 18/18/6 
    15447 Gap extend | 1 
    15448 SS matrix |  |  | H | S | O 
    15449 ---|---|---|--- 
    15450 H | 6 | -9 | -6 
    15451 S |  | 6 | -6 
    15452 O |  |  | 4 
    15453 Iteration cutoff | 2 
    15454  
    15455 Matchmaker 3j2w.pdb, chain I (#2) with Pixuna virus AlphaFold.pdb, chain A
    15456 (#27), sequence alignment score = 521 
    15457 RMSD between 147 pruned atom pairs is 0.730 angstroms; (across all 149 pairs:
    15458 0.820) 
    15459  
    15460 
    15461 > show #28 models
    15462 
    15463 > hide #28 models
    15464 
    15465 > show #28 models
    15466 
    15467 > hide #28 models
    15468 
    15469 > show #28 models
    15470 
    15471 > show #26 models
    15472 
    15473 > hide #28 models
    15474 
    15475 > hide #26 models
    15476 
    15477 > show #26 models
    15478 
    15479 > hide #27 models
    15480 
    15481 > show #25 models
    15482 
    15483 > hide #26 models
    15484 
    15485 > show #24 models
    15486 
    15487 > hide #25 models
    15488 
    15489 > show #13 models
    15490 
    15491 > hide #24 models
    15492 
    15493 > show #25 models
    15494 
    15495 > show #26 models
    15496 
    15497 > hide #26 models
    15498 
    15499 > hide #25 models
    15500 
    15501 > show #27 models
    15502 
    15503 > show #28 models
    15504 
    15505 > hide #28 models
    15506 
    15507 > show #28 models
    15508 
    15509 > hide #28 models
    15510 
    15511 > hide #27 models
    15512 
    15513 > hide #13 models
    15514 
    15515 > show #28 models
    15516 
    15517 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    15518 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    15519 
    15520 ——— End of log from Tue Jun 20 13:59:27 2023 ———
    15521 
    15522 opened ChimeraX session 
    15523 
    15524 > show #27 models
    15525 
    15526 > hide #27 models
    15527 
    15528 > hide #28 models
    15529 
    15530 > show #28 models
    15531 
    15532 > hide #28 models
    15533 
    15534 > show #27 models
    15535 
    15536 > hide #27 models
    15537 
    15538 > show #28 models
    15539 
    15540 > show #26 models
    15541 
    15542 > show #25 models
    15543 
    15544 > hide #25 models
    15545 
    15546 > hide #26 models
    15547 
    15548 > hide #28 models
    15549 
    15550 > show #28 models
    15551 
    15552 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    15553 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    15554 
    15555 ——— End of log from Tue Jun 20 14:01:06 2023 ———
    15556 
    15557 opened ChimeraX session 
    15558 
    15559 > show #27 models
    15560 
    15561 > hide #27 models
    15562 
    15563 > show #26 models
    15564 
    15565 > hide #26 models
    15566 
    15567 > show #25 models
    15568 
    15569 > hide #25 models
    15570 
    15571 > hide #28 models
    15572 
    15573 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    15574 > UASLP/Lab Virología/AlphaFold/Tonate virus AlphaFold.pdb"
    15575 
    15576 Chain information for Tonate virus AlphaFold.pdb #29 
    15577 --- 
    15578 Chain | Description 
    15579 A | No description available 
    15580  
    15581 
    15582 > ui tool show Matchmaker
    15583 
    15584 > matchmaker #29 to #2
    15585 
    15586 Parameters 
    15587 --- 
    15588 Chain pairing | bb 
    15589 Alignment algorithm | Needleman-Wunsch 
    15590 Similarity matrix | BLOSUM-62 
    15591 SS fraction | 0.3 
    15592 Gap open (HH/SS/other) | 18/18/6 
    15593 Gap extend | 1 
    15594 SS matrix |  |  | H | S | O 
    15595 ---|---|---|--- 
    15596 H | 6 | -9 | -6 
    15597 S |  | 6 | -6 
    15598 O |  |  | 4 
    15599 Iteration cutoff | 2 
    15600  
    15601 Matchmaker 3j2w.pdb, chain I (#2) with Tonate virus AlphaFold.pdb, chain A
    15602 (#29), sequence alignment score = 516.2 
    15603 RMSD between 147 pruned atom pairs is 0.812 angstroms; (across all 149 pairs:
    15604 0.929) 
    15605  
    15606 
    15607 > color #29 #555500ff
    15608 
    15609 > color #29 #550000ff
    15610 
    15611 > color #29 #0055ffff
    15612 
    15613 > color #29 #0042c7ff
    15614 
    15615 > color #29 #00007fff
    15616 
    15617 > color #29 #0000a6ff
    15618 
    15619 > color #29 #0000ecff
    15620 
    15621 > color #29 #00007cff
    15622 
    15623 > color #29 #200e7cff
    15624 
    15625 > color #29 #27167cff
    15626 
    15627 > color #29 #2e1e7cff
    15628 
    15629 > color #29 #36287cff
    15630 
    15631 > color #29 #40237cff
    15632 
    15633 > color #29 #3b2e7cff
    15634 
    15635 > color #29 #5240adff
    15636 
    15637 > color #29 #3638adff
    15638 
    15639 > color #29 #585cadff
    15640 
    15641 > color #29 #4b54adff
    15642 
    15643 > color #29 #333a76ff
    15644 
    15645 > color #29 #404894ff
    15646 
    15647 > color #29 #616ee1ff
    15648 
    15649 > color #29 #434c9cff
    15650 
    15651 > color #29 #3d458dff
    15652 
    15653 > color #29 #394084ff
    15654 
    15655 > color #29 #363d7dff
    15656 
    15657 > ui mousemode right select
    15658 
    15659 > select #2/I:126
    15660 
    15661 9 atoms, 8 bonds, 1 residue, 1 model selected 
    15662 
    15663 > select #29/A:133
    15664 
    15665 12 atoms, 11 bonds, 1 residue, 1 model selected 
    15666 
    15667 > style sel stick
    15668 
    15669 Changed 12 atom styles 
    15670 
    15671 > show sel atoms
    15672 
    15673 Alignment identifier is 29/A 
    15674 
    15675 > ui mousemode right translate
    15676 
    15677 > ui mousemode right select
    15678 
    15679 > select #2/I:126
    15680 
    15681 9 atoms, 8 bonds, 1 residue, 1 model selected 
    15682 
    15683 > select #29/A:133
    15684 
    15685 12 atoms, 11 bonds, 1 residue, 1 model selected 
    15686 
    15687 > color sel red
    15688 
    15689 > select #2/I:128
    15690 
    15691 9 atoms, 8 bonds, 1 residue, 1 model selected 
    15692 
    15693 > select #29/A:135
    15694 
    15695 22 atoms, 21 bonds, 1 residue, 1 model selected 
    15696 
    15697 > style sel stick
    15698 
    15699 Changed 22 atom styles 
    15700 
    15701 > show sel atoms
    15702 
    15703 > color sel blue
    15704 
    15705 > ui mousemode right translate
    15706 
    15707 > ui mousemode right select
    15708 
    15709 > select #2/I:240@CA
    15710 
    15711 1 atom, 1 residue, 1 model selected 
    15712 
    15713 > select #29/A:247
    15714 
    15715 15 atoms, 14 bonds, 1 residue, 1 model selected 
    15716 
    15717 > style sel stick
    15718 
    15719 Changed 15 atom styles 
    15720 
    15721 > show sel atoms
    15722 
    15723 > color sel red
    15724 
    15725 > ui mousemode right translate
    15726 
    15727 > ui mousemode right select
    15728 
    15729 > select #2/I:190
    15730 
    15731 9 atoms, 8 bonds, 1 residue, 1 model selected 
    15732 
    15733 > select #29/A:197
    15734 
    15735 17 atoms, 16 bonds, 1 residue, 1 model selected 
    15736 
    15737 > style sel stick
    15738 
    15739 Changed 17 atom styles 
    15740 
    15741 > show sel atoms
    15742 
    15743 > color sel orange
    15744 
    15745 > ui mousemode right zoom
    15746 
    15747 > ui mousemode right translate
    15748 
    15749 > ui mousemode right select
    15750 
    15751 > select #2/I:183
    15752 
    15753 9 atoms, 8 bonds, 1 residue, 1 model selected 
    15754 
    15755 > select #29/A:190
    15756 
    15757 22 atoms, 21 bonds, 1 residue, 1 model selected 
    15758 
    15759 > style sel stick
    15760 
    15761 Changed 22 atom styles 
    15762 
    15763 > show sel atoms
    15764 
    15765 > color sel blue
    15766 
    15767 > ui mousemode right translate
    15768 
    15769 > ui mousemode right select
    15770 
    15771 > select #2/I:178
    15772 
    15773 9 atoms, 8 bonds, 1 residue, 1 model selected 
    15774 
    15775 > select #29/A:190
    15776 
    15777 22 atoms, 21 bonds, 1 residue, 1 model selected 
    15778 
    15779 > select #2/I:183
    15780 
    15781 9 atoms, 8 bonds, 1 residue, 1 model selected 
    15782 
    15783 > select #2/I:178
    15784 
    15785 9 atoms, 8 bonds, 1 residue, 1 model selected 
    15786 
    15787 > select #29/A:185
    15788 
    15789 24 atoms, 23 bonds, 1 residue, 1 model selected 
    15790 
    15791 > style sel stick
    15792 
    15793 Changed 24 atom styles 
    15794 
    15795 > show sel atoms
    15796 
    15797 > color sel blue
    15798 
    15799 > ui mousemode right translate
    15800 
    15801 > ui mousemode right select
    15802 
    15803 > select #2/I:157
    15804 
    15805 9 atoms, 8 bonds, 1 residue, 1 model selected 
    15806 
    15807 > select #29/A:164
    15808 
    15809 10 atoms, 9 bonds, 1 residue, 1 model selected 
    15810 
    15811 > ui mousemode right translate
    15812 
    15813 > ui mousemode right select
    15814 
    15815 > select #29/A:163
    15816 
    15817 10 atoms, 9 bonds, 1 residue, 1 model selected 
    15818 
    15819 > select #29/A:164
    15820 
    15821 10 atoms, 9 bonds, 1 residue, 1 model selected 
    15822 
    15823 > select clear
    15824 
    15825 > select #2/I:154
    15826 
    15827 8 atoms, 7 bonds, 1 residue, 1 model selected 
    15828 
    15829 > select #29/A:161
    15830 
    15831 14 atoms, 13 bonds, 1 residue, 1 model selected 
    15832 
    15833 > select #29/A:164
    15834 
    15835 10 atoms, 9 bonds, 1 residue, 1 model selected 
    15836 
    15837 > style sel stick
    15838 
    15839 Changed 10 atom styles 
    15840 
    15841 > show sel atoms
    15842 
    15843 > color sel gray
    15844 
    15845 > select #29/A:161
    15846 
    15847 14 atoms, 13 bonds, 1 residue, 1 model selected 
    15848 
    15849 > style sel stick
    15850 
    15851 Changed 14 atom styles 
    15852 
    15853 > show sel atoms
    15854 
    15855 > color sel orange
    15856 
    15857 > ui mousemode right translate
    15858 
    15859 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    15860 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    15861 
    15862 > show #27 models
    15863 
    15864 > hide #2 models
    15865 
    15866 > show #2 models
    15867 
    15868 > hide #27 models
    15869 
    15870 > select add #29
    15871 
    15872 4432 atoms, 4487 bonds, 275 residues, 1 model selected 
    15873 
    15874 > select subtract #29
    15875 
    15876 Nothing selected 
    15877 
    15878 > hide #29 models
    15879 
    15880 > show #17 models
    15881 
    15882 > ui tool show Matchmaker
    15883 
    15884 > matchmaker #17 to #2
    15885 
    15886 Parameters 
    15887 --- 
    15888 Chain pairing | bb 
    15889 Alignment algorithm | Needleman-Wunsch 
    15890 Similarity matrix | BLOSUM-62 
    15891 SS fraction | 0.3 
    15892 Gap open (HH/SS/other) | 18/18/6 
    15893 Gap extend | 1 
    15894 SS matrix |  |  | H | S | O 
    15895 ---|---|---|--- 
    15896 H | 6 | -9 | -6 
    15897 S |  | 6 | -6 
    15898 O |  |  | 4 
    15899 Iteration cutoff | 2 
    15900  
    15901 Matchmaker 3j2w.pdb, chain I (#2) with Bebaru virus Alphafold.pdb, chain A
    15902 (#17), sequence alignment score = 675.4 
    15903 RMSD between 148 pruned atom pairs is 0.764 angstroms; (across all 149 pairs:
    15904 0.786) 
    15905  
    15906 
    15907 > show #29 models
    15908 
    15909 > hide #29 models
    15910 
    15911 > show #14 models
    15912 
    15913 > hide #17 models
    15914 
    15915 > hide #14 models
    15916 
    15917 > show #29 models
    15918 
    15919 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    15920 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    15921 
    15922 ——— End of log from Wed Jun 21 13:00:17 2023 ———
    15923 
    15924 opened ChimeraX session 
    15925 
    15926 > ui tool show Registration
    15927 
    15928 > hide #29 models
    15929 
    15930 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    15931 > UASLP/Lab Virología/AlphaFold/Trocara virus AlphaFold.pdb"
    15932 
    15933 Chain information for Trocara virus AlphaFold.pdb #30 
    15934 --- 
    15935 Chain | Description 
    15936 A | No description available 
    15937  
    15938 
    15939 > ui tool show Matchmaker
    15940 
    15941 > matchmaker #30 to #2
    15942 
    15943 Parameters 
    15944 --- 
    15945 Chain pairing | bb 
    15946 Alignment algorithm | Needleman-Wunsch 
    15947 Similarity matrix | BLOSUM-62 
    15948 SS fraction | 0.3 
    15949 Gap open (HH/SS/other) | 18/18/6 
    15950 Gap extend | 1 
    15951 SS matrix |  |  | H | S | O 
    15952 ---|---|---|--- 
    15953 H | 6 | -9 | -6 
    15954 S |  | 6 | -6 
    15955 O |  |  | 4 
    15956 Iteration cutoff | 2 
    15957  
    15958 Matchmaker 3j2w.pdb, chain I (#2) with Trocara virus AlphaFold.pdb, chain A
    15959 (#30), sequence alignment score = 500.7 
    15960 RMSD between 144 pruned atom pairs is 0.680 angstroms; (across all 149 pairs:
    15961 0.933) 
    15962  
    15963 
    15964 > color #30 #550000ff
    15965 
    15966 > color #30 #670000ff
    15967 
    15968 > color #30 #740000ff
    15969 
    15970 > color #30 #940000ff
    15971 
    15972 > color #30 #750000ff
    15973 
    15974 > color #30 #750b0bff
    15975 
    15976 > color #30 #752616ff
    15977 
    15978 > color #30 #752620ff
    15979 
    15980 > color #30 #751414ff
    15981 
    15982 > color #30 #750b0bff
    15983 
    15984 > color #30 #b51212ff
    15985 
    15986 > color #30 #620a0aff
    15987 
    15988 > color #30 #810d0dff
    15989 
    15990 > color #30 #8f0e0eff
    15991 
    15992 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    15993 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    15994 
    15995 > ui mousemode right translate
    15996 
    15997 > ui mousemode right select
    15998 
    15999 > select #2/I:126
    16000 
    16001 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16002 
    16003 > select #30/A:121
    16004 
    16005 15 atoms, 14 bonds, 1 residue, 1 model selected 
    16006 Alignment identifier is 30/A 
    16007 
    16008 > style sel stick
    16009 
    16010 Changed 15 atom styles 
    16011 
    16012 > show sel atoms
    16013 
    16014 > color sel red
    16015 
    16016 Drag select of 1 bonds 
    16017 
    16018 > select #30/A:121
    16019 
    16020 15 atoms, 14 bonds, 1 residue, 1 model selected 
    16021 
    16022 > select #2/I:126
    16023 
    16024 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16025 
    16026 > select #30/A:121
    16027 
    16028 15 atoms, 14 bonds, 1 residue, 1 model selected 
    16029 
    16030 > select clear
    16031 
    16032 > ui mousemode right translate
    16033 
    16034 > ui mousemode right select
    16035 
    16036 > select #2/I:128
    16037 
    16038 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16039 
    16040 > select #30/A:124
    16041 
    16042 22 atoms, 21 bonds, 1 residue, 1 model selected 
    16043 
    16044 > select #2/I:128
    16045 
    16046 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16047 
    16048 > select #30/A:124
    16049 
    16050 22 atoms, 21 bonds, 1 residue, 1 model selected 
    16051 
    16052 > style sel stick
    16053 
    16054 Changed 22 atom styles 
    16055 
    16056 > show sel atoms
    16057 
    16058 > color sel blue
    16059 
    16060 > ui mousemode right translate
    16061 
    16062 > ui mousemode right select
    16063 
    16064 > select #2/I:240@CA
    16065 
    16066 1 atom, 1 residue, 1 model selected 
    16067 
    16068 > select #30/A:236
    16069 
    16070 17 atoms, 16 bonds, 1 residue, 1 model selected 
    16071 
    16072 > select #2/I:240
    16073 
    16074 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16075 
    16076 > select #30/A:236
    16077 
    16078 17 atoms, 16 bonds, 1 residue, 1 model selected 
    16079 
    16080 > style sel stick
    16081 
    16082 Changed 17 atom styles 
    16083 
    16084 > show sel atoms
    16085 
    16086 > color sel orange
    16087 
    16088 > ui mousemode right translate
    16089 
    16090 > ui mousemode right select
    16091 
    16092 > select #2/I:190@CA
    16093 
    16094 1 atom, 1 residue, 1 model selected 
    16095 
    16096 > select #30/A:186
    16097 
    16098 15 atoms, 14 bonds, 1 residue, 1 model selected 
    16099 
    16100 > style sel stick
    16101 
    16102 Changed 15 atom styles 
    16103 
    16104 > show sel atoms
    16105 
    16106 > color sel red
    16107 
    16108 > ui mousemode right translate
    16109 
    16110 > ui mousemode right select
    16111 
    16112 > select #2/I:183
    16113 
    16114 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16115 
    16116 > select #30/A:179
    16117 
    16118 22 atoms, 21 bonds, 1 residue, 1 model selected 
    16119 
    16120 > select #2/I:183
    16121 
    16122 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16123 
    16124 > select #30/A:179
    16125 
    16126 22 atoms, 21 bonds, 1 residue, 1 model selected 
    16127 
    16128 > style sel stick
    16129 
    16130 Changed 22 atom styles 
    16131 
    16132 > show sel atoms
    16133 
    16134 > color sel blue
    16135 
    16136 > ui mousemode right translate
    16137 
    16138 > ui mousemode right select
    16139 
    16140 > select #2/I:178
    16141 
    16142 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16143 
    16144 > select #30/A:174
    16145 
    16146 24 atoms, 23 bonds, 1 residue, 1 model selected 
    16147 
    16148 > style sel stick
    16149 
    16150 Changed 24 atom styles 
    16151 
    16152 > show sel atoms
    16153 
    16154 > color sel blue
    16155 
    16156 > ui mousemode right translate
    16157 
    16158 > ui mousemode right select
    16159 
    16160 > select #2/I:178
    16161 
    16162 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16163 
    16164 > select #30/A:174
    16165 
    16166 24 atoms, 23 bonds, 1 residue, 1 model selected 
    16167 
    16168 > select #30/A:153
    16169 
    16170 22 atoms, 21 bonds, 1 residue, 1 model selected 
    16171 
    16172 > select #2/I:157
    16173 
    16174 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16175 
    16176 > select #30/A:153
    16177 
    16178 22 atoms, 21 bonds, 1 residue, 1 model selected 
    16179 
    16180 > style sel stick
    16181 
    16182 Changed 22 atom styles 
    16183 
    16184 > show sel atoms
    16185 
    16186 > color sel blue
    16187 
    16188 > ui mousemode right translate
    16189 
    16190 > ui mousemode right select
    16191 
    16192 > select #2/I:154
    16193 
    16194 8 atoms, 7 bonds, 1 residue, 1 model selected 
    16195 
    16196 > select #30/A:150
    16197 
    16198 10 atoms, 9 bonds, 1 residue, 1 model selected 
    16199 
    16200 > style sel stick
    16201 
    16202 Changed 10 atom styles 
    16203 
    16204 > show sel atoms
    16205 
    16206 > color sel gray
    16207 
    16208 > ui mousemode right translate
    16209 
    16210 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    16211 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    16212 
    16213 > show #28 models
    16214 
    16215 > hide #28 models
    16216 
    16217 > show #28 models
    16218 
    16219 > show #27 models
    16220 
    16221 > hide #27 models
    16222 
    16223 > hide #28 models
    16224 
    16225 > select add #30
    16226 
    16227 4192 atoms, 4243 bonds, 264 residues, 1 model selected 
    16228 
    16229 > select subtract #30
    16230 
    16231 Nothing selected 
    16232 
    16233 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    16234 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    16235 
    16236 ——— End of log from Thu Jun 22 13:48:19 2023 ———
    16237 
    16238 opened ChimeraX session 
    16239 
    16240 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    16241 > UASLP/Lab Virología/AlphaFold/Una virus AlphaFold.pdb"
    16242 
    16243 Chain information for Una virus AlphaFold.pdb #31 
    16244 --- 
    16245 Chain | Description 
    16246 A | No description available 
    16247  
    16248 
    16249 > hide #30 models
    16250 
    16251 > ui tool show Matchmaker
    16252 
    16253 > matchmaker #31 to #2
    16254 
    16255 Parameters 
    16256 --- 
    16257 Chain pairing | bb 
    16258 Alignment algorithm | Needleman-Wunsch 
    16259 Similarity matrix | BLOSUM-62 
    16260 SS fraction | 0.3 
    16261 Gap open (HH/SS/other) | 18/18/6 
    16262 Gap extend | 1 
    16263 SS matrix |  |  | H | S | O 
    16264 ---|---|---|--- 
    16265 H | 6 | -9 | -6 
    16266 S |  | 6 | -6 
    16267 O |  |  | 4 
    16268 Iteration cutoff | 2 
    16269  
    16270 Matchmaker 3j2w.pdb, chain I (#2) with Una virus AlphaFold.pdb, chain A (#31),
    16271 sequence alignment score = 668.1 
    16272 RMSD between 144 pruned atom pairs is 0.726 angstroms; (across all 149 pairs:
    16273 0.900) 
    16274  
    16275 
    16276 > color #31 #ff557fff
    16277 
    16278 > color #31 #ff007fff
    16279 
    16280 > color #31 #55557fff
    16281 
    16282 > color #31 #ff557fff
    16283 
    16284 > color #31 #ff5580ff
    16285 
    16286 > color #31 #ffaaffff
    16287 
    16288 > color #31 #ff557fff
    16289 
    16290 > color #31 #ff5a99ff
    16291 
    16292 > color #31 #ff5ea4ff
    16293 
    16294 > color #31 #ff67abff
    16295 
    16296 > color #31 #ff69a2ff
    16297 
    16298 > color #31 #ff5496ff
    16299 
    16300 > color #31 #ff557fff
    16301 
    16302 > color #31 #ff5892ff
    16303 
    16304 > color #31 #ff4f8dff
    16305 
    16306 > color #31 #ff52a6ff
    16307 
    16308 > color #31 #ff54a1ff
    16309 
    16310 > ui mousemode right select
    16311 
    16312 Drag select of 2 atoms, 1 bonds 
    16313 
    16314 > ui mousemode right translate
    16315 
    16316 > ui mousemode right select
    16317 
    16318 > select #2/I:126
    16319 
    16320 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16321 
    16322 > select #31/A:122
    16323 
    16324 12 atoms, 11 bonds, 1 residue, 1 model selected 
    16325 Alignment identifier is 31/A 
    16326 
    16327 > style sel stick
    16328 
    16329 Changed 12 atom styles 
    16330 
    16331 > show sel atoms
    16332 
    16333 > color sel red
    16334 
    16335 > select clear
    16336 
    16337 > select #2/I:128
    16338 
    16339 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16340 
    16341 > select #31/A:124
    16342 
    16343 22 atoms, 21 bonds, 1 residue, 1 model selected 
    16344 
    16345 > style sel stick
    16346 
    16347 Changed 22 atom styles 
    16348 
    16349 > show sel atoms
    16350 
    16351 > color sel blue
    16352 
    16353 > ui mousemode right translate
    16354 
    16355 > ui mousemode right select
    16356 
    16357 > select #2/I:240
    16358 
    16359 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16360 
    16361 > select #31/A:236
    16362 
    16363 15 atoms, 14 bonds, 1 residue, 1 model selected 
    16364 
    16365 > style sel stick
    16366 
    16367 Changed 15 atom styles 
    16368 
    16369 > show sel atoms
    16370 
    16371 > color sel red
    16372 
    16373 > select clear
    16374 
    16375 > ui mousemode right rotate
    16376 
    16377 > ui mousemode right translate
    16378 
    16379 > ui mousemode right select
    16380 
    16381 > select #2/I:190
    16382 
    16383 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16384 
    16385 > select #31/A:186
    16386 
    16387 15 atoms, 14 bonds, 1 residue, 1 model selected 
    16388 
    16389 > style sel stick
    16390 
    16391 Changed 15 atom styles 
    16392 
    16393 > show sel atoms
    16394 
    16395 > color sel red
    16396 
    16397 > ui mousemode right translate
    16398 
    16399 > ui mousemode right select
    16400 
    16401 > select #2/I:183
    16402 
    16403 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16404 
    16405 > select #31/A:179
    16406 
    16407 22 atoms, 21 bonds, 1 residue, 1 model selected 
    16408 
    16409 > style sel stick
    16410 
    16411 Changed 22 atom styles 
    16412 
    16413 > show sel atoms
    16414 
    16415 > color sel blue
    16416 
    16417 Drag select of 6 residues 
    16418 
    16419 > ui mousemode right translate
    16420 
    16421 > ui mousemode right select
    16422 
    16423 > select #2/I:178
    16424 
    16425 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16426 Drag select of 1 residues 
    16427 
    16428 > style sel stick
    16429 
    16430 Changed 24 atom styles 
    16431 
    16432 > show sel atoms
    16433 
    16434 > color sel blue
    16435 
    16436 > ui mousemode right translate
    16437 
    16438 > ui mousemode right select
    16439 
    16440 > select #2/I:157
    16441 
    16442 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16443 
    16444 > select #2/I:157
    16445 
    16446 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16447 
    16448 > select #31/A:153
    16449 
    16450 22 atoms, 21 bonds, 1 residue, 1 model selected 
    16451 
    16452 > style sel stick
    16453 
    16454 Changed 22 atom styles 
    16455 
    16456 > show sel atoms
    16457 
    16458 > color sel blue
    16459 
    16460 Drag select of 19 residues 
    16461 
    16462 > ui mousemode right translate
    16463 
    16464 > ui mousemode right select
    16465 
    16466 > select #2/I:154
    16467 
    16468 8 atoms, 7 bonds, 1 residue, 1 model selected 
    16469 
    16470 > select #31/A:150
    16471 
    16472 12 atoms, 11 bonds, 1 residue, 1 model selected 
    16473 
    16474 > ui mousemode right translate
    16475 
    16476 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    16477 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    16478 
    16479 > show #30 models
    16480 
    16481 > hide #31 models
    16482 
    16483 > ui mousemode right select
    16484 
    16485 > select #2/I:157
    16486 
    16487 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16488 
    16489 > select #30/A:153
    16490 
    16491 22 atoms, 21 bonds, 1 residue, 1 model selected 
    16492 
    16493 > select #2/I:154
    16494 
    16495 8 atoms, 7 bonds, 1 residue, 1 model selected 
    16496 
    16497 > select #30/A:150
    16498 
    16499 10 atoms, 9 bonds, 1 residue, 1 model selected 
    16500 
    16501 > ui mousemode right translate
    16502 
    16503 > ui mousemode right select
    16504 
    16505 > select #2/I:240
    16506 
    16507 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16508 
    16509 > select #30/A:236
    16510 
    16511 17 atoms, 16 bonds, 1 residue, 1 model selected 
    16512 
    16513 > hide #30 models
    16514 
    16515 > show #31 models
    16516 
    16517 > ui mousemode right translate
    16518 
    16519 > show #30 models
    16520 
    16521 > show #29 models
    16522 
    16523 > hide #29 models
    16524 
    16525 > hide #30 models
    16526 
    16527 > hide #31 models
    16528 
    16529 > show #31 models
    16530 
    16531 > select add #30
    16532 
    16533 4192 atoms, 4243 bonds, 264 residues, 1 model selected 
    16534 
    16535 > select subtract #30
    16536 
    16537 Nothing selected 
    16538 
    16539 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    16540 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    16541 
    16542 ——— End of log from Fri Jun 23 14:27:32 2023 ———
    16543 
    16544 opened ChimeraX session 
    16545 
    16546 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    16547 > UASLP/Lab Virología/AlphaFold/Whataroa virus AlphaFold.pdb"
    16548 
    16549 Chain information for Whataroa virus AlphaFold.pdb #32 
    16550 --- 
    16551 Chain | Description 
    16552 A | No description available 
    16553  
    16554 
    16555 > ui tool show Matchmaker
    16556 
    16557 > matchmaker #32 to #2
    16558 
    16559 Parameters 
    16560 --- 
    16561 Chain pairing | bb 
    16562 Alignment algorithm | Needleman-Wunsch 
    16563 Similarity matrix | BLOSUM-62 
    16564 SS fraction | 0.3 
    16565 Gap open (HH/SS/other) | 18/18/6 
    16566 Gap extend | 1 
    16567 SS matrix |  |  | H | S | O 
    16568 ---|---|---|--- 
    16569 H | 6 | -9 | -6 
    16570 S |  | 6 | -6 
    16571 O |  |  | 4 
    16572 Iteration cutoff | 2 
    16573  
    16574 Matchmaker 3j2w.pdb, chain I (#2) with Whataroa virus AlphaFold.pdb, chain A
    16575 (#32), sequence alignment score = 516.5 
    16576 RMSD between 146 pruned atom pairs is 0.667 angstroms; (across all 149 pairs:
    16577 0.786) 
    16578  
    16579 
    16580 > hide #31 models
    16581 
    16582 > color #32 #ffaa7fff
    16583 
    16584 > color #32 #ffaa00ff
    16585 
    16586 > color #32 #ffff7fff
    16587 
    16588 > color #32 yellow
    16589 
    16590 > color #32 #ffcb0eff
    16591 
    16592 > color #32 #ffcd07ff
    16593 
    16594 > color #32 #ffca0cff
    16595 
    16596 > color #32 #ffd711ff
    16597 
    16598 > ui mousemode right select
    16599 
    16600 > select #2/I:126
    16601 
    16602 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16603 
    16604 > select #32/A:123
    16605 
    16606 15 atoms, 14 bonds, 1 residue, 1 model selected 
    16607 Alignment identifier is 32/A 
    16608 
    16609 > style sel stick
    16610 
    16611 Changed 15 atom styles 
    16612 
    16613 > show sel atoms
    16614 
    16615 > color sel red
    16616 
    16617 > select #2/I:128
    16618 
    16619 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16620 
    16621 > select #32/A:126
    16622 
    16623 12 atoms, 11 bonds, 1 residue, 1 model selected 
    16624 
    16625 > style sel stick
    16626 
    16627 Changed 12 atom styles 
    16628 
    16629 > show sel atoms
    16630 
    16631 > color sel red
    16632 
    16633 > ui mousemode right translate
    16634 
    16635 > ui mousemode right select
    16636 
    16637 > select #2/I:240
    16638 
    16639 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16640 
    16641 > select #32/A:238
    16642 
    16643 15 atoms, 14 bonds, 1 residue, 1 model selected 
    16644 
    16645 > style sel stick
    16646 
    16647 Changed 15 atom styles 
    16648 
    16649 > show sel atoms
    16650 
    16651 > color sel red
    16652 
    16653 > ui mousemode right translate
    16654 
    16655 > ui mousemode right rotate
    16656 
    16657 > ui mousemode right select
    16658 
    16659 > select #2/I:190
    16660 
    16661 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16662 
    16663 > select #32/A:188
    16664 
    16665 15 atoms, 14 bonds, 1 residue, 1 model selected 
    16666 
    16667 > style sel stick
    16668 
    16669 Changed 15 atom styles 
    16670 
    16671 > show sel atoms
    16672 
    16673 > color sel red
    16674 
    16675 Drag select of 2 atoms, 2 residues, 3 bonds 
    16676 
    16677 > ui mousemode right translate
    16678 
    16679 > ui mousemode right select
    16680 
    16681 > select #2/I:183
    16682 
    16683 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16684 
    16685 > select #32/A:181
    16686 
    16687 14 atoms, 13 bonds, 1 residue, 1 model selected 
    16688 
    16689 > ui mousemode right translate
    16690 
    16691 > style sel stick
    16692 
    16693 Changed 14 atom styles 
    16694 
    16695 > show sel atoms
    16696 
    16697 > color sel orange
    16698 
    16699 > color #32 #ffec20ff
    16700 
    16701 > color #32 #ffd70cff
    16702 
    16703 > color #32 #ffff7fff
    16704 
    16705 > color #32 #ffaa00ff
    16706 
    16707 > color #32 #ffff7fff
    16708 
    16709 > color #32 #ffff5cff
    16710 
    16711 > color #32 #fcff4aff
    16712 
    16713 > color #32 #ddff43ff
    16714 
    16715 > color #32 #ffff38ff
    16716 
    16717 > color #32 #ff9cd9ff
    16718 
    16719 > color #32 #ffa7d2ff
    16720 
    16721 > color #32 #ffa4d3ff
    16722 
    16723 > color #32 #fcff39ff
    16724 
    16725 > color #32 #ffef3aff
    16726 
    16727 > style sel stick
    16728 
    16729 Changed 14 atom styles 
    16730 
    16731 > hide sel atoms
    16732 
    16733 > show sel atoms
    16734 
    16735 > color sel orange
    16736 
    16737 > ui mousemode right select
    16738 
    16739 > select #32/A:123
    16740 
    16741 15 atoms, 14 bonds, 1 residue, 1 model selected 
    16742 
    16743 > color sel red
    16744 
    16745 > select #32/A:126
    16746 
    16747 12 atoms, 11 bonds, 1 residue, 1 model selected 
    16748 
    16749 > color sel red
    16750 
    16751 > select #32/A:123
    16752 
    16753 15 atoms, 14 bonds, 1 residue, 1 model selected 
    16754 
    16755 > ui mousemode right translate
    16756 
    16757 > ui mousemode right select
    16758 
    16759 > select #32/A:238
    16760 
    16761 15 atoms, 14 bonds, 1 residue, 1 model selected 
    16762 
    16763 > color sel red
    16764 
    16765 > ui mousemode right translate
    16766 
    16767 > ui mousemode right select
    16768 
    16769 > select #32/A:188
    16770 
    16771 15 atoms, 14 bonds, 1 residue, 1 model selected 
    16772 
    16773 > color sel red
    16774 
    16775 > ui mousemode right translate
    16776 
    16777 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    16778 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    16779 
    16780 > ui mousemode right rotate
    16781 
    16782 > ui mousemode right select
    16783 
    16784 > select #2/I:178
    16785 
    16786 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16787 
    16788 > select #2/I:178
    16789 
    16790 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16791 
    16792 > select #32/A:176
    16793 
    16794 22 atoms, 21 bonds, 1 residue, 1 model selected 
    16795 
    16796 > style sel stick
    16797 
    16798 Changed 22 atom styles 
    16799 
    16800 > show sel atoms
    16801 
    16802 > color sel blue
    16803 
    16804 > select clear
    16805 
    16806 > ui mousemode right translate
    16807 
    16808 > ui mousemode right select
    16809 
    16810 > select #2/I:154
    16811 
    16812 8 atoms, 7 bonds, 1 residue, 1 model selected 
    16813 
    16814 > select #32/A:152
    16815 
    16816 16 atoms, 15 bonds, 1 residue, 1 model selected 
    16817 
    16818 > select #2/I:154
    16819 
    16820 8 atoms, 7 bonds, 1 residue, 1 model selected 
    16821 
    16822 > select #32/A:152
    16823 
    16824 16 atoms, 15 bonds, 1 residue, 1 model selected 
    16825 
    16826 > style sel stick
    16827 
    16828 Changed 16 atom styles 
    16829 
    16830 > hide sel atoms
    16831 
    16832 > show sel atoms
    16833 
    16834 > color sel gray
    16835 
    16836 > select #32/A:155
    16837 
    16838 22 atoms, 21 bonds, 1 residue, 1 model selected 
    16839 
    16840 > select #2/I:157
    16841 
    16842 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16843 
    16844 > select #32/A:155
    16845 
    16846 22 atoms, 21 bonds, 1 residue, 1 model selected 
    16847 
    16848 > style sel stick
    16849 
    16850 Changed 22 atom styles 
    16851 
    16852 > show sel atoms
    16853 
    16854 > color sel blue
    16855 
    16856 > ui mousemode right translate
    16857 
    16858 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    16859 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    16860 
    16861 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    16862 > UASLP/Lab Virología/AlphaFold/AguaSalud alphavirus AlphaFold.pdb"
    16863 
    16864 Chain information for AguaSalud alphavirus AlphaFold.pdb #33 
    16865 --- 
    16866 Chain | Description 
    16867 A | No description available 
    16868  
    16869 
    16870 > ui tool show Matchmaker
    16871 
    16872 > matchmaker #33 to #2
    16873 
    16874 Parameters 
    16875 --- 
    16876 Chain pairing | bb 
    16877 Alignment algorithm | Needleman-Wunsch 
    16878 Similarity matrix | BLOSUM-62 
    16879 SS fraction | 0.3 
    16880 Gap open (HH/SS/other) | 18/18/6 
    16881 Gap extend | 1 
    16882 SS matrix |  |  | H | S | O 
    16883 ---|---|---|--- 
    16884 H | 6 | -9 | -6 
    16885 S |  | 6 | -6 
    16886 O |  |  | 4 
    16887 Iteration cutoff | 2 
    16888  
    16889 Matchmaker 3j2w.pdb, chain I (#2) with AguaSalud alphavirus AlphaFold.pdb,
    16890 chain A (#33), sequence alignment score = 497.5 
    16891 RMSD between 147 pruned atom pairs is 0.696 angstroms; (across all 149 pairs:
    16892 0.798) 
    16893  
    16894 
    16895 > hide #32 models
    16896 
    16897 > select add #32
    16898 
    16899 4214 atoms, 4273 bonds, 266 residues, 1 model selected 
    16900 
    16901 > select subtract #32
    16902 
    16903 Nothing selected 
    16904 
    16905 > color #33 #56344dff
    16906 
    16907 > color #33 #4e3256ff
    16908 
    16909 > color #33 #562651ff
    16910 
    16911 > color #33 #561b3cff
    16912 
    16913 > color #33 #ffaaffff
    16914 
    16915 > color #33 #f78affff
    16916 
    16917 > color #33 #ff66f0ff
    16918 
    16919 > color #33 #f352ffff
    16920 
    16921 > color #33 #55ffffff
    16922 
    16923 > color #33 #ffaaffff
    16924 
    16925 > color #33 #ffb3feff
    16926 
    16927 > color #33 #fcb0ffff
    16928 
    16929 > color #33 #ffa1efff
    16930 
    16931 > color #33 #ffb9e9ff
    16932 
    16933 > color #33 #ffb2e7ff
    16934 
    16935 > color #33 #ffaed8ff
    16936 
    16937 > ui mousemode right select
    16938 
    16939 > select #2/I:126
    16940 
    16941 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16942 
    16943 > select #33/A:123
    16944 
    16945 11 atoms, 10 bonds, 1 residue, 1 model selected 
    16946 Alignment identifier is 33/A 
    16947 
    16948 > select #33/A:124
    16949 
    16950 12 atoms, 11 bonds, 1 residue, 1 model selected 
    16951 
    16952 > select #33/A:123
    16953 
    16954 11 atoms, 10 bonds, 1 residue, 1 model selected 
    16955 
    16956 > select #33/A:124
    16957 
    16958 12 atoms, 11 bonds, 1 residue, 1 model selected 
    16959 
    16960 > style sel stick
    16961 
    16962 Changed 12 atom styles 
    16963 
    16964 > show sel atoms
    16965 
    16966 > color sel red
    16967 
    16968 > set bgColor black
    16969 
    16970 [Repeated 1 time(s)]
    16971 
    16972 > set bgColor white
    16973 
    16974 > select #2/I:128
    16975 
    16976 9 atoms, 8 bonds, 1 residue, 1 model selected 
    16977 
    16978 > select #33/A:126
    16979 
    16980 17 atoms, 16 bonds, 1 residue, 1 model selected 
    16981 
    16982 > select #33/A:127
    16983 
    16984 16 atoms, 15 bonds, 1 residue, 1 model selected 
    16985 
    16986 > select #33/A:126
    16987 
    16988 17 atoms, 16 bonds, 1 residue, 1 model selected 
    16989 
    16990 > ui mousemode right translate
    16991 
    16992 > style sel stick
    16993 
    16994 Changed 17 atom styles 
    16995 
    16996 > show sel atoms
    16997 
    16998 > color sel orange
    16999 
    17000 > ui mousemode right select
    17001 
    17002 > select #2/I:240
    17003 
    17004 9 atoms, 8 bonds, 1 residue, 1 model selected 
    17005 
    17006 > select #33/A:238
    17007 
    17008 15 atoms, 14 bonds, 1 residue, 1 model selected 
    17009 
    17010 > show #32 models
    17011 
    17012 > select #32/A:238
    17013 
    17014 15 atoms, 14 bonds, 1 residue, 1 model selected 
    17015 
    17016 > hide #32 models
    17017 
    17018 > select add #32
    17019 
    17020 4214 atoms, 4273 bonds, 266 residues, 1 model selected 
    17021 
    17022 > select subtract #32
    17023 
    17024 Nothing selected 
    17025 
    17026 > select #33/A:238
    17027 
    17028 15 atoms, 14 bonds, 1 residue, 1 model selected 
    17029 
    17030 > ui mousemode right translate
    17031 
    17032 > style sel stick
    17033 
    17034 Changed 15 atom styles 
    17035 
    17036 > show sel atoms
    17037 
    17038 > color sel red
    17039 
    17040 > ui mousemode right select
    17041 
    17042 > select #2/I:190@CA
    17043 
    17044 1 atom, 1 residue, 1 model selected 
    17045 
    17046 > select #33/A:188
    17047 
    17048 15 atoms, 14 bonds, 1 residue, 1 model selected 
    17049 
    17050 > style sel stick
    17051 
    17052 Changed 15 atom styles 
    17053 
    17054 > show sel atoms
    17055 
    17056 > color sel red
    17057 
    17058 Drag select of 2 residues 
    17059 
    17060 > ui mousemode right translate
    17061 
    17062 > ui mousemode right select
    17063 
    17064 > select #2/I:183
    17065 
    17066 9 atoms, 8 bonds, 1 residue, 1 model selected 
    17067 
    17068 > select #33/A:181
    17069 
    17070 24 atoms, 23 bonds, 1 residue, 1 model selected 
    17071 
    17072 > hide sel cartoons
    17073 
    17074 > style sel stick
    17075 
    17076 Changed 24 atom styles 
    17077 
    17078 > hide sel cartoons
    17079 
    17080 > show sel cartoons
    17081 
    17082 > style sel stick
    17083 
    17084 Changed 24 atom styles 
    17085 
    17086 > show sel atoms
    17087 
    17088 > color sel blue
    17089 
    17090 > ui mousemode right translate
    17091 
    17092 > ui mousemode right select
    17093 
    17094 > select #2/I:178
    17095 
    17096 9 atoms, 8 bonds, 1 residue, 1 model selected 
    17097 
    17098 > select #33/A:176
    17099 
    17100 22 atoms, 21 bonds, 1 residue, 1 model selected 
    17101 
    17102 > style sel stick
    17103 
    17104 Changed 22 atom styles 
    17105 
    17106 > show sel atoms
    17107 
    17108 > color sel blue
    17109 
    17110 > select #2/I:178
    17111 
    17112 9 atoms, 8 bonds, 1 residue, 1 model selected 
    17113 
    17114 > select #33/A:176
    17115 
    17116 22 atoms, 21 bonds, 1 residue, 1 model selected 
    17117 
    17118 > ui mousemode right translate
    17119 
    17120 > ui mousemode right select
    17121 
    17122 > select #2/I:157
    17123 
    17124 9 atoms, 8 bonds, 1 residue, 1 model selected 
    17125 
    17126 > select #33/A:155
    17127 
    17128 22 atoms, 21 bonds, 1 residue, 1 model selected 
    17129 
    17130 > style sel stick
    17131 
    17132 Changed 22 atom styles 
    17133 
    17134 > show sel atoms
    17135 
    17136 > color sel blue
    17137 
    17138 > select #2/I:154
    17139 
    17140 8 atoms, 7 bonds, 1 residue, 1 model selected 
    17141 
    17142 > select #33/A:152
    17143 
    17144 19 atoms, 18 bonds, 1 residue, 1 model selected 
    17145 
    17146 > style sel stick
    17147 
    17148 Changed 19 atom styles 
    17149 
    17150 > show sel atoms
    17151 
    17152 > color sel gray
    17153 
    17154 > ui mousemode right translate
    17155 
    17156 > show #32 models
    17157 
    17158 > hide #33 models
    17159 
    17160 > show #33 models
    17161 
    17162 > hide #32 models
    17163 
    17164 > select add #33
    17165 
    17166 4198 atoms, 4258 bonds, 266 residues, 1 model selected 
    17167 
    17168 > select subtract #33
    17169 
    17170 Nothing selected 
    17171 
    17172 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    17173 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    17174 
    17175 [Repeated 1 time(s)]
    17176 
    17177 ——— End of log from Mon Jun 26 10:11:19 2023 ———
    17178 
    17179 opened ChimeraX session 
    17180 
    17181 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    17182 > UASLP/Lab Virología/AlphaFold/Comber alphavirus AlphaFold.pdb"
    17183 
    17184 Chain information for Comber alphavirus AlphaFold.pdb #34 
    17185 --- 
    17186 Chain | Description 
    17187 A | No description available 
    17188  
    17189 
    17190 > hide #33 models
    17191 
    17192 > ui tool show Matchmaker
    17193 
    17194 > matchmaker #34 to #2
    17195 
    17196 Parameters 
    17197 --- 
    17198 Chain pairing | bb 
    17199 Alignment algorithm | Needleman-Wunsch 
    17200 Similarity matrix | BLOSUM-62 
    17201 SS fraction | 0.3 
    17202 Gap open (HH/SS/other) | 18/18/6 
    17203 Gap extend | 1 
    17204 SS matrix |  |  | H | S | O 
    17205 ---|---|---|--- 
    17206 H | 6 | -9 | -6 
    17207 S |  | 6 | -6 
    17208 O |  |  | 4 
    17209 Iteration cutoff | 2 
    17210  
    17211 Matchmaker 3j2w.pdb, chain I (#2) with Comber alphavirus AlphaFold.pdb, chain
    17212 A (#34), sequence alignment score = 336.5 
    17213 RMSD between 118 pruned atom pairs is 0.991 angstroms; (across all 144 pairs:
    17214 3.924) 
    17215  
    17216 
    17217 > color #34 #cd7248ff
    17218 
    17219 > color #34 #cd4a33ff
    17220 
    17221 > color #34 #cd5647ff
    17222 
    17223 > color #34 #cd7d44ff
    17224 
    17225 > color #34 #bd733fff
    17226 
    17227 > color #34 #b36d3cff
    17228 
    17229 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    17230 > UASLP/Lab Virología/AlphaFold/Harbor porpoise alphavirus AlphaFold.pdb"
    17231 
    17232 Chain information for Harbor porpoise alphavirus AlphaFold.pdb #35 
    17233 --- 
    17234 Chain | Description 
    17235 A | No description available 
    17236  
    17237 
    17238 > ui tool show Matchmaker
    17239 
    17240 > matchmaker #35 to #2
    17241 
    17242 Parameters 
    17243 --- 
    17244 Chain pairing | bb 
    17245 Alignment algorithm | Needleman-Wunsch 
    17246 Similarity matrix | BLOSUM-62 
    17247 SS fraction | 0.3 
    17248 Gap open (HH/SS/other) | 18/18/6 
    17249 Gap extend | 1 
    17250 SS matrix |  |  | H | S | O 
    17251 ---|---|---|--- 
    17252 H | 6 | -9 | -6 
    17253 S |  | 6 | -6 
    17254 O |  |  | 4 
    17255 Iteration cutoff | 2 
    17256  
    17257 Matchmaker 3j2w.pdb, chain I (#2) with Harbor porpoise alphavirus
    17258 AlphaFold.pdb, chain A (#35), sequence alignment score = 612.2 
    17259 RMSD between 146 pruned atom pairs is 0.708 angstroms; (across all 149 pairs:
    17260 0.922) 
    17261  
    17262 
    17263 > hide #34 models
    17264 
    17265 > color #35 #ff557fff
    17266 
    17267 > color #35 #ffff7fff
    17268 
    17269 > color #35 yellow
    17270 
    17271 > color #35 #ffff7fff
    17272 
    17273 > color #35 #fff049ff
    17274 
    17275 > color #35 #f6ff42ff
    17276 
    17277 > color #35 #e0ff6eff
    17278 
    17279 > color #35 #d3ff73ff
    17280 
    17281 > color #35 #ddff61ff
    17282 
    17283 > color #35 #cbea59ff
    17284 
    17285 > color #35 #bcd953ff
    17286 
    17287 > color #35 #bad94aff
    17288 
    17289 > color #35 #c9d93cff
    17290 
    17291 > color #35 #bdd92fff
    17292 
    17293 > color #35 #c0d941ff
    17294 
    17295 > color #35 #cad946ff
    17296 
    17297 > color #35 #d1d93cff
    17298 
    17299 > color #35 #bad931ff
    17300 
    17301 > color #35 #d9d93fff
    17302 
    17303 > color #35 #bfd93cff
    17304 
    17305 > color #35 #d1d93cff
    17306 
    17307 > color #35 #b7d93cff
    17308 
    17309 > color #35 #bfd93cff
    17310 
    17311 > color #35 #bed938ff
    17312 
    17313 > color #35 #cae63cff
    17314 
    17315 > color #35 #c2e640ff
    17316 
    17317 > color #35 #cae63eff
    17318 
    17319 > color #35 #c9e53eff
    17320 
    17321 > show #34 models
    17322 
    17323 > hide #35 models
    17324 
    17325 > ui mousemode right select
    17326 
    17327 > select #2/I:126
    17328 
    17329 9 atoms, 8 bonds, 1 residue, 1 model selected 
    17330 
    17331 > select #34/A:161
    17332 
    17333 15 atoms, 14 bonds, 1 residue, 1 model selected 
    17334 Alignment identifier is 34/A 
    17335 
    17336 > style sel stick
    17337 
    17338 Changed 15 atom styles 
    17339 
    17340 > show sel atoms
    17341 
    17342 > color sel red
    17343 
    17344 > select #2/I:128
    17345 
    17346 9 atoms, 8 bonds, 1 residue, 1 model selected 
    17347 
    17348 > select #34/A:163
    17349 
    17350 14 atoms, 13 bonds, 1 residue, 1 model selected 
    17351 
    17352 > style sel stick
    17353 
    17354 Changed 14 atom styles 
    17355 
    17356 > show sel atoms
    17357 
    17358 > color sel blue
    17359 
    17360 > color sel orange
    17361 
    17362 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    17363 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    17364 
    17365 > ui mousemode right translate
    17366 
    17367 > ui mousemode right select
    17368 
    17369 > select #2/I:240
    17370 
    17371 9 atoms, 8 bonds, 1 residue, 1 model selected 
    17372 
    17373 > select clear
    17374 
    17375 > select #34/A:274
    17376 
    17377 11 atoms, 10 bonds, 1 residue, 1 model selected 
    17378 Drag select of 1 atoms, 2 residues 
    17379 
    17380 > ui mousemode right translate
    17381 
    17382 > ui mousemode right select
    17383 
    17384 > select #34/A:274
    17385 
    17386 11 atoms, 10 bonds, 1 residue, 1 model selected 
    17387 
    17388 > style sel stick
    17389 
    17390 Changed 11 atom styles 
    17391 
    17392 > show sel atoms
    17393 
    17394 > color sel orange
    17395 
    17396 > ui mousemode right translate
    17397 
    17398 > ui mousemode right select
    17399 
    17400 > select #2/I:190
    17401 
    17402 9 atoms, 8 bonds, 1 residue, 1 model selected 
    17403 
    17404 > select #34/A:225
    17405 
    17406 7 atoms, 6 bonds, 1 residue, 1 model selected 
    17407 
    17408 > select #34/A:224
    17409 
    17410 12 atoms, 11 bonds, 1 residue, 1 model selected 
    17411 
    17412 > select #34/A:225
    17413 
    17414 7 atoms, 6 bonds, 1 residue, 1 model selected 
    17415 
    17416 > select #34/A:224
    17417 
    17418 12 atoms, 11 bonds, 1 residue, 1 model selected 
    17419 
    17420 > select #34/A:225
    17421 
    17422 7 atoms, 6 bonds, 1 residue, 1 model selected 
    17423 
    17424 > select #34/A:224
    17425 
    17426 12 atoms, 11 bonds, 1 residue, 1 model selected 
    17427 
    17428 > select #34/A:225
    17429 
    17430 7 atoms, 6 bonds, 1 residue, 1 model selected 
    17431 
    17432 > select #2/I:190
    17433 
    17434 9 atoms, 8 bonds, 1 residue, 1 model selected 
    17435 
    17436 > select #34/A:225
    17437 
    17438 7 atoms, 6 bonds, 1 residue, 1 model selected 
    17439 
    17440 > select clear
    17441 
    17442 > select #34/A:225
    17443 
    17444 7 atoms, 6 bonds, 1 residue, 1 model selected 
    17445 
    17446 > select #34/A:224
    17447 
    17448 12 atoms, 11 bonds, 1 residue, 1 model selected 
    17449 
    17450 > select #34/A:225
    17451 
    17452 7 atoms, 6 bonds, 1 residue, 1 model selected 
    17453 
    17454 > style sel stick
    17455 
    17456 Changed 7 atom styles 
    17457 
    17458 > show sel atoms
    17459 
    17460 [Repeated 1 time(s)]
    17461 
    17462 > hide sel atoms
    17463 
    17464 > style sel stick
    17465 
    17466 Changed 7 atom styles 
    17467 
    17468 > hide sel atoms
    17469 
    17470 > show sel atoms
    17471 
    17472 > select #34/A:225
    17473 
    17474 7 atoms, 6 bonds, 1 residue, 1 model selected 
    17475 
    17476 > select #2/I:190@CA
    17477 
    17478 1 atom, 1 residue, 1 model selected 
    17479 
    17480 > select #34/A:225
    17481 
    17482 7 atoms, 6 bonds, 1 residue, 1 model selected 
    17483 
    17484 > style sel stick
    17485 
    17486 Changed 7 atom styles 
    17487 
    17488 > show sel atoms
    17489 
    17490 > hide sel atoms
    17491 
    17492 > hide sel cartoons
    17493 
    17494 [Repeated 1 time(s)]
    17495 
    17496 > show sel cartoons
    17497 
    17498 > show sel atoms
    17499 
    17500 > hide sel atoms
    17501 
    17502 [Repeated 1 time(s)]
    17503 
    17504 > show sel atoms
    17505 
    17506 > hide sel cartoons
    17507 
    17508 > show sel cartoons
    17509 
    17510 > show sel atoms
    17511 
    17512 > color sel magenta
    17513 
    17514 > ui mousemode right translate
    17515 
    17516 > ui mousemode right select
    17517 
    17518 > select #2/I:183
    17519 
    17520 9 atoms, 8 bonds, 1 residue, 1 model selected 
    17521 
    17522 > select #34/A:218
    17523 
    17524 22 atoms, 21 bonds, 1 residue, 1 model selected 
    17525 
    17526 > style sel stick
    17527 
    17528 Changed 22 atom styles 
    17529 
    17530 > show sel atoms
    17531 
    17532 > color sel blue
    17533 
    17534 > ui mousemode right translate
    17535 
    17536 > ui mousemode right select
    17537 
    17538 > select #34/A:225
    17539 
    17540 7 atoms, 6 bonds, 1 residue, 1 model selected 
    17541 
    17542 > show sel atoms
    17543 
    17544 > hide sel atoms
    17545 
    17546 > show sel cartoons
    17547 
    17548 > hide sel cartoons
    17549 
    17550 > show sel cartoons
    17551 
    17552 > show sel atoms
    17553 
    17554 > style sel stick
    17555 
    17556 Changed 7 atom styles 
    17557 
    17558 > show sel atoms
    17559 
    17560 > ui mousemode right zoom
    17561 
    17562 > ui mousemode right translate
    17563 
    17564 > ui mousemode right select
    17565 
    17566 > select #2/I:178
    17567 
    17568 9 atoms, 8 bonds, 1 residue, 1 model selected 
    17569 
    17570 > select #34/A:213
    17571 
    17572 22 atoms, 21 bonds, 1 residue, 1 model selected 
    17573 
    17574 > style sel stick
    17575 
    17576 Changed 22 atom styles 
    17577 
    17578 > show sel atoms
    17579 
    17580 > color sel blue
    17581 
    17582 > select clear
    17583 
    17584 > ui mousemode right translate
    17585 
    17586 > ui mousemode right select
    17587 
    17588 > select #2/I:157@CA
    17589 
    17590 1 atom, 1 residue, 1 model selected 
    17591 
    17592 > select #34/A:192
    17593 
    17594 22 atoms, 21 bonds, 1 residue, 1 model selected 
    17595 
    17596 > select #2/I:157
    17597 
    17598 9 atoms, 8 bonds, 1 residue, 1 model selected 
    17599 
    17600 > select #34/A:192
    17601 
    17602 22 atoms, 21 bonds, 1 residue, 1 model selected 
    17603 
    17604 > style sel stick
    17605 
    17606 Changed 22 atom styles 
    17607 
    17608 > show sel atoms
    17609 
    17610 > color sel blue
    17611 
    17612 > select #2/I:154
    17613 
    17614 8 atoms, 7 bonds, 1 residue, 1 model selected 
    17615 
    17616 > select #34/A:189
    17617 
    17618 15 atoms, 14 bonds, 1 residue, 1 model selected 
    17619 
    17620 > style sel stick
    17621 
    17622 Changed 15 atom styles 
    17623 
    17624 > show sel atoms
    17625 
    17626 > color sel red
    17627 
    17628 > ui mousemode right translate
    17629 
    17630 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    17631 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    17632 
    17633 ——— End of log from Tue Jun 27 12:45:33 2023 ———
    17634 
    17635 opened ChimeraX session 
    17636 
    17637 > ui mousemode right select
    17638 
    17639 > select #34/A:225
    17640 
    17641 7 atoms, 6 bonds, 1 residue, 1 model selected 
    17642 
    17643 > style sel stick
    17644 
    17645 Changed 7 atom styles 
    17646 
    17647 > show sel atoms
    17648 
    17649 > hide sel atoms
    17650 
    17651 > show sel atoms
    17652 
    17653 > hide #34 models
    17654 
    17655 > select add #34
    17656 
    17657 4798 atoms, 4847 bonds, 303 residues, 1 model selected 
    17658 
    17659 > select subtract #34
    17660 
    17661 Nothing selected 
    17662 
    17663 > show #35 models
    17664 
    17665 > ui mousemode right rotate
    17666 
    17667 > ui mousemode right translate
    17668 
    17669 > ui mousemode right select
    17670 
    17671 > select #35/A:95
    17672 
    17673 12 atoms, 11 bonds, 1 residue, 1 model selected 
    17674 
    17675 > select #2/I:126
    17676 
    17677 9 atoms, 8 bonds, 1 residue, 1 model selected 
    17678 
    17679 > select #35/A:95
    17680 
    17681 12 atoms, 11 bonds, 1 residue, 1 model selected 
    17682 
    17683 > select #2/I:126
    17684 
    17685 9 atoms, 8 bonds, 1 residue, 1 model selected 
    17686 
    17687 > select #35/A:95
    17688 
    17689 12 atoms, 11 bonds, 1 residue, 1 model selected 
    17690 
    17691 > interfaces select & ~solvent
    17692 
    17693 Missing or invalid "atoms" argument: invalid atoms specifier 
    17694 Alignment identifier is 35/A 
    17695 
    17696 > style sel stick
    17697 
    17698 Changed 12 atom styles 
    17699 
    17700 > show sel atoms
    17701 
    17702 > color sel red
    17703 
    17704 > select #2/I:128
    17705 
    17706 9 atoms, 8 bonds, 1 residue, 1 model selected 
    17707 
    17708 > select #35/A:97
    17709 
    17710 22 atoms, 21 bonds, 1 residue, 1 model selected 
    17711 
    17712 > style sel stick
    17713 
    17714 Changed 22 atom styles 
    17715 
    17716 > show sel atoms
    17717 
    17718 > color sel blue
    17719 
    17720 > ui mousemode right translate
    17721 
    17722 > ui mousemode right select
    17723 
    17724 > select #2/I:240
    17725 
    17726 9 atoms, 8 bonds, 1 residue, 1 model selected 
    17727 
    17728 > select #35/A:209
    17729 
    17730 15 atoms, 14 bonds, 1 residue, 1 model selected 
    17731 
    17732 > style sel stick
    17733 
    17734 Changed 15 atom styles 
    17735 
    17736 > show sel atoms
    17737 
    17738 > color sel red
    17739 
    17740 > ui mousemode right translate
    17741 
    17742 > ui mousemode right select
    17743 
    17744 > select #2/I:190
    17745 
    17746 9 atoms, 8 bonds, 1 residue, 1 model selected 
    17747 
    17748 > select #35/A:159
    17749 
    17750 12 atoms, 11 bonds, 1 residue, 1 model selected 
    17751 
    17752 > style sel stick
    17753 
    17754 Changed 12 atom styles 
    17755 
    17756 > show sel atoms
    17757 
    17758 > color sel red
    17759 
    17760 > ui mousemode right translate
    17761 
    17762 > ui mousemode right select
    17763 
    17764 > select #2/I:183
    17765 
    17766 9 atoms, 8 bonds, 1 residue, 1 model selected 
    17767 
    17768 > select #2/I:183
    17769 
    17770 9 atoms, 8 bonds, 1 residue, 1 model selected 
    17771 
    17772 > select clear
    17773 
    17774 > select #35/A:152
    17775 
    17776 22 atoms, 21 bonds, 1 residue, 1 model selected 
    17777 
    17778 > style sel stick
    17779 
    17780 Changed 22 atom styles 
    17781 
    17782 > hide sel atoms
    17783 
    17784 > show sel atoms
    17785 
    17786 > color sel blue
    17787 
    17788 > ui mousemode right translate
    17789 
    17790 > ui mousemode right select
    17791 
    17792 > select #2/I:178
    17793 
    17794 9 atoms, 8 bonds, 1 residue, 1 model selected 
    17795 
    17796 > select #35/A:147
    17797 
    17798 22 atoms, 21 bonds, 1 residue, 1 model selected 
    17799 
    17800 > style sel stick
    17801 
    17802 Changed 22 atom styles 
    17803 
    17804 > show sel atoms
    17805 
    17806 > color sel blue
    17807 
    17808 > select clear
    17809 
    17810 > ui mousemode right translate
    17811 
    17812 > ui mousemode right select
    17813 
    17814 > select #2/I:157
    17815 
    17816 9 atoms, 8 bonds, 1 residue, 1 model selected 
    17817 
    17818 > select #35/A:126
    17819 
    17820 22 atoms, 21 bonds, 1 residue, 1 model selected 
    17821 
    17822 > style sel stick
    17823 
    17824 Changed 22 atom styles 
    17825 
    17826 > show sel atoms
    17827 
    17828 > color sel blue
    17829 
    17830 Drag select of 1 residues 
    17831 
    17832 > select #2/I:154
    17833 
    17834 8 atoms, 7 bonds, 1 residue, 1 model selected 
    17835 
    17836 > select #35/A:123
    17837 
    17838 16 atoms, 15 bonds, 1 residue, 1 model selected 
    17839 
    17840 > select #2/I:154
    17841 
    17842 8 atoms, 7 bonds, 1 residue, 1 model selected 
    17843 
    17844 > select #35/A:123
    17845 
    17846 16 atoms, 15 bonds, 1 residue, 1 model selected 
    17847 
    17848 > hide sel cartoons
    17849 
    17850 > show sel cartoons
    17851 
    17852 > style sel stick
    17853 
    17854 Changed 16 atom styles 
    17855 
    17856 > show sel atoms
    17857 
    17858 > color sel gray
    17859 
    17860 > ui mousemode right translate
    17861 
    17862 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    17863 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    17864 
    17865 ——— End of log from Tue Jun 27 13:05:48 2023 ———
    17866 
    17867 opened ChimeraX session 
    17868 
    17869 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    17870 > UASLP/Lab Virología/AlphaFold/Mwinilunga alphavirus AlphaFold.pdb"
    17871 
    17872 Chain information for Mwinilunga alphavirus AlphaFold.pdb #36 
    17873 --- 
    17874 Chain | Description 
    17875 A | No description available 
    17876  
    17877 
    17878 > hide #35 models
    17879 
    17880 > select add #35
    17881 
    17882 3771 atoms, 3815 bonds, 236 residues, 1 model selected 
    17883 
    17884 > select subtract #35
    17885 
    17886 Nothing selected 
    17887 
    17888 > color #36 #cd4e7aff
    17889 
    17890 > color #36 #cd4355ff
    17891 
    17892 > color #36 #8d81cdff
    17893 
    17894 > color #36 #7867cdff
    17895 
    17896 > color #36 #574fcdff
    17897 
    17898 > color #36 #7272cdff
    17899 
    17900 > color #36 #8383ebff
    17901 
    17902 > color #36 #888debff
    17903 
    17904 > ui tool show Angles/Torsions
    17905 
    17906 > ui tool show Matchmaker
    17907 
    17908 > matchmaker #36 to #2
    17909 
    17910 Parameters 
    17911 --- 
    17912 Chain pairing | bb 
    17913 Alignment algorithm | Needleman-Wunsch 
    17914 Similarity matrix | BLOSUM-62 
    17915 SS fraction | 0.3 
    17916 Gap open (HH/SS/other) | 18/18/6 
    17917 Gap extend | 1 
    17918 SS matrix |  |  | H | S | O 
    17919 ---|---|---|--- 
    17920 H | 6 | -9 | -6 
    17921 S |  | 6 | -6 
    17922 O |  |  | 4 
    17923 Iteration cutoff | 2 
    17924  
    17925 Matchmaker 3j2w.pdb, chain I (#2) with Mwinilunga alphavirus AlphaFold.pdb,
    17926 chain A (#36), sequence alignment score = 461.6 
    17927 RMSD between 143 pruned atom pairs is 0.699 angstroms; (across all 149 pairs:
    17928 0.975) 
    17929  
    17930 
    17931 > color #36 #8086dcff
    17932 
    17933 > ui mousemode right select
    17934 
    17935 > select #2/I:126
    17936 
    17937 9 atoms, 8 bonds, 1 residue, 1 model selected 
    17938 
    17939 > select #36/A:113
    17940 
    17941 12 atoms, 11 bonds, 1 residue, 1 model selected 
    17942 Alignment identifier is 36/A 
    17943 
    17944 > select #2/I:126
    17945 
    17946 9 atoms, 8 bonds, 1 residue, 1 model selected 
    17947 
    17948 > select #36/A:113
    17949 
    17950 12 atoms, 11 bonds, 1 residue, 1 model selected 
    17951 
    17952 > style sel stick
    17953 
    17954 Changed 12 atom styles 
    17955 
    17956 > show sel atoms
    17957 
    17958 > color sel red
    17959 
    17960 > select clear
    17961 
    17962 > select #2/I:128
    17963 
    17964 9 atoms, 8 bonds, 1 residue, 1 model selected 
    17965 
    17966 > select #36/A:116
    17967 
    17968 10 atoms, 9 bonds, 1 residue, 1 model selected 
    17969 
    17970 > style sel stick
    17971 
    17972 Changed 10 atom styles 
    17973 
    17974 > show sel atoms
    17975 
    17976 > color sel gray
    17977 
    17978 > ui mousemode right translate
    17979 
    17980 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    17981 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    17982 
    17983 > ui mousemode right select
    17984 
    17985 > select #2/I:240
    17986 
    17987 9 atoms, 8 bonds, 1 residue, 1 model selected 
    17988 
    17989 > select #36/A:228
    17990 
    17991 15 atoms, 14 bonds, 1 residue, 1 model selected 
    17992 
    17993 > style sel stick
    17994 
    17995 Changed 15 atom styles 
    17996 
    17997 > show sel atoms
    17998 
    17999 > color sel red
    18000 
    18001 > ui mousemode right translate
    18002 
    18003 > ui mousemode right select
    18004 
    18005 > select #36/A:178
    18006 
    18007 12 atoms, 11 bonds, 1 residue, 1 model selected 
    18008 
    18009 > style sel stick
    18010 
    18011 Changed 12 atom styles 
    18012 
    18013 > show sel atoms
    18014 
    18015 > color sel red
    18016 
    18017 > ui mousemode right translate
    18018 
    18019 > ui mousemode right select
    18020 
    18021 > select #2/I:183
    18022 
    18023 9 atoms, 8 bonds, 1 residue, 1 model selected 
    18024 
    18025 > select #36/A:171
    18026 
    18027 14 atoms, 13 bonds, 1 residue, 1 model selected 
    18028 
    18029 > select #36/A:172
    18030 
    18031 21 atoms, 21 bonds, 1 residue, 1 model selected 
    18032 
    18033 > select #36/A:171
    18034 
    18035 14 atoms, 13 bonds, 1 residue, 1 model selected 
    18036 
    18037 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    18038 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    18039 
    18040 ——— End of log from Wed Jun 28 16:04:54 2023 ———
    18041 
    18042 opened ChimeraX session 
    18043 
    18044 > ui mousemode right select
    18045 
    18046 > select #36/A:178
    18047 
    18048 12 atoms, 11 bonds, 1 residue, 1 model selected 
    18049 
    18050 > ui mousemode right translate
    18051 
    18052 > ui mousemode right select
    18053 
    18054 > select #2/I:183
    18055 
    18056 9 atoms, 8 bonds, 1 residue, 1 model selected 
    18057 
    18058 > select #36/A:171
    18059 
    18060 14 atoms, 13 bonds, 1 residue, 1 model selected 
    18061 
    18062 > style sel stick
    18063 
    18064 Changed 14 atom styles 
    18065 
    18066 > show sel atoms
    18067 
    18068 > ui mousemode right translate
    18069 
    18070 > color sel orange
    18071 
    18072 > ui mousemode right select
    18073 
    18074 > select #2/I:178
    18075 
    18076 9 atoms, 8 bonds, 1 residue, 1 model selected 
    18077 
    18078 > select #36/A:166
    18079 
    18080 24 atoms, 23 bonds, 1 residue, 1 model selected 
    18081 
    18082 > style sel stick
    18083 
    18084 Changed 24 atom styles 
    18085 
    18086 > style sel stick
    18087 
    18088 Changed 24 atom styles 
    18089 
    18090 > ui mousemode right translate
    18091 
    18092 > show sel atoms
    18093 
    18094 > color sel blue
    18095 
    18096 > ui mousemode right select
    18097 
    18098 > select #2/I:157
    18099 
    18100 9 atoms, 8 bonds, 1 residue, 1 model selected 
    18101 
    18102 > select #36/A:145
    18103 
    18104 14 atoms, 13 bonds, 1 residue, 1 model selected 
    18105 
    18106 > select #36/A:145
    18107 
    18108 14 atoms, 13 bonds, 1 residue, 1 model selected 
    18109 
    18110 > style sel stick
    18111 
    18112 Changed 14 atom styles 
    18113 
    18114 > show sel atoms
    18115 
    18116 > color sel orange
    18117 
    18118 > select #2/I:154
    18119 
    18120 8 atoms, 7 bonds, 1 residue, 1 model selected 
    18121 
    18122 > select #36/A:142
    18123 
    18124 19 atoms, 18 bonds, 1 residue, 1 model selected 
    18125 
    18126 > style sel stick
    18127 
    18128 Changed 19 atom styles 
    18129 
    18130 > show sel atoms
    18131 
    18132 > color sel gray
    18133 
    18134 > set bgColor white
    18135 
    18136 > ui mousemode right translate
    18137 
    18138 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    18139 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    18140 
    18141 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    18142 > UASLP/Lab Virología/AlphaFold/selected_prediction Pirahy virus.pdb"
    18143 
    18144 Chain information for selected_prediction Pirahy virus.pdb #37 
    18145 --- 
    18146 Chain | Description 
    18147 A | No description available 
    18148  
    18149 
    18150 > hide #36 models
    18151 
    18152 > select add #36
    18153 
    18154 3980 atoms, 4027 bonds, 256 residues, 1 model selected 
    18155 
    18156 > select subtract #36
    18157 
    18158 Nothing selected 
    18159 
    18160 > ui tool show Matchmaker
    18161 
    18162 > matchmaker #37 to #2
    18163 
    18164 Parameters 
    18165 --- 
    18166 Chain pairing | bb 
    18167 Alignment algorithm | Needleman-Wunsch 
    18168 Similarity matrix | BLOSUM-62 
    18169 SS fraction | 0.3 
    18170 Gap open (HH/SS/other) | 18/18/6 
    18171 Gap extend | 1 
    18172 SS matrix |  |  | H | S | O 
    18173 ---|---|---|--- 
    18174 H | 6 | -9 | -6 
    18175 S |  | 6 | -6 
    18176 O |  |  | 4 
    18177 Iteration cutoff | 2 
    18178  
    18179 Matchmaker 3j2w.pdb, chain I (#2) with selected_prediction Pirahy virus.pdb,
    18180 chain A (#37), sequence alignment score = 544.4 
    18181 RMSD between 147 pruned atom pairs is 0.769 angstroms; (across all 149 pairs:
    18182 0.873) 
    18183  
    18184 
    18185 > color #37 #55557fff
    18186 
    18187 > color #37 #550000ff
    18188 
    18189 > color #37 #0055ffff
    18190 
    18191 > color #37 #aaff7fff
    18192 
    18193 > color #37 #55ff00ff
    18194 
    18195 > color #37 #4ade00ff
    18196 
    18197 > color #37 #4cde0dff
    18198 
    18199 > color #37 #47de1dff
    18200 
    18201 > color #37 #65de39ff
    18202 
    18203 > color #37 #6bde41ff
    18204 
    18205 > ui mousemode right select
    18206 
    18207 > select #2/I:126
    18208 
    18209 9 atoms, 8 bonds, 1 residue, 1 model selected 
    18210 
    18211 > select #37/A:134
    18212 
    18213 12 atoms, 11 bonds, 1 residue, 1 model selected 
    18214 
    18215 > interfaces select & ~solvent
    18216 
    18217 Missing or invalid "atoms" argument: invalid atoms specifier 
    18218 Alignment identifier is 37/A 
    18219 
    18220 > ui mousemode right translate
    18221 
    18222 > style sel stick
    18223 
    18224 Changed 12 atom styles 
    18225 
    18226 > show sel atoms
    18227 
    18228 > color sel red
    18229 
    18230 > ui mousemode right select
    18231 
    18232 > select #2/I:128
    18233 
    18234 9 atoms, 8 bonds, 1 residue, 1 model selected 
    18235 
    18236 > select #37/A:136
    18237 
    18238 22 atoms, 21 bonds, 1 residue, 1 model selected 
    18239 
    18240 > select #2/I:128
    18241 
    18242 9 atoms, 8 bonds, 1 residue, 1 model selected 
    18243 
    18244 > select #37/A:136
    18245 
    18246 22 atoms, 21 bonds, 1 residue, 1 model selected 
    18247 
    18248 > style sel stick
    18249 
    18250 Changed 22 atom styles 
    18251 
    18252 > show sel atoms
    18253 
    18254 > color sel blue
    18255 
    18256 > ui mousemode right zoom
    18257 
    18258 > ui mousemode right translate
    18259 
    18260 > ui mousemode right select
    18261 
    18262 > select #2/I:240
    18263 
    18264 9 atoms, 8 bonds, 1 residue, 1 model selected 
    18265 
    18266 > select #37/A:248
    18267 
    18268 15 atoms, 14 bonds, 1 residue, 1 model selected 
    18269 
    18270 > select #2/I:240
    18271 
    18272 9 atoms, 8 bonds, 1 residue, 1 model selected 
    18273 
    18274 > select #37/A:248
    18275 
    18276 15 atoms, 14 bonds, 1 residue, 1 model selected 
    18277 
    18278 > ui mousemode right translate
    18279 
    18280 > style sel stick
    18281 
    18282 Changed 15 atom styles 
    18283 
    18284 > show sel atoms
    18285 
    18286 > color sel red
    18287 
    18288 > ui mousemode right select
    18289 
    18290 > select #2/I:190
    18291 
    18292 9 atoms, 8 bonds, 1 residue, 1 model selected 
    18293 
    18294 > select #37/A:198
    18295 
    18296 17 atoms, 16 bonds, 1 residue, 1 model selected 
    18297 
    18298 > ui mousemode right translate
    18299 
    18300 > style sel stick
    18301 
    18302 Changed 17 atom styles 
    18303 
    18304 > show sel atoms
    18305 
    18306 > color sel orange
    18307 
    18308 [Repeated 1 time(s)]
    18309 
    18310 > ui mousemode right select
    18311 
    18312 > select #2/I:183
    18313 
    18314 9 atoms, 8 bonds, 1 residue, 1 model selected 
    18315 
    18316 > select clear
    18317 
    18318 > select #37/A:191
    18319 
    18320 22 atoms, 21 bonds, 1 residue, 1 model selected 
    18321 
    18322 > style sel stick
    18323 
    18324 Changed 22 atom styles 
    18325 
    18326 > show sel atoms
    18327 
    18328 > color sel blue
    18329 
    18330 > ui mousemode right translate
    18331 
    18332 > ui mousemode right select
    18333 
    18334 > select #2/I:178
    18335 
    18336 9 atoms, 8 bonds, 1 residue, 1 model selected 
    18337 
    18338 > select #37/A:186
    18339 
    18340 24 atoms, 23 bonds, 1 residue, 1 model selected 
    18341 
    18342 > select #37/A:185
    18343 
    18344 17 atoms, 16 bonds, 1 residue, 1 model selected 
    18345 
    18346 > select #37/A:186
    18347 
    18348 24 atoms, 23 bonds, 1 residue, 1 model selected 
    18349 
    18350 > style sel stick
    18351 
    18352 Changed 24 atom styles 
    18353 
    18354 > show sel atoms
    18355 
    18356 > color sel blue
    18357 
    18358 > select #2/I:178
    18359 
    18360 9 atoms, 8 bonds, 1 residue, 1 model selected 
    18361 
    18362 > select #2/I:178
    18363 
    18364 9 atoms, 8 bonds, 1 residue, 1 model selected 
    18365 
    18366 > select #37/A:186
    18367 
    18368 24 atoms, 23 bonds, 1 residue, 1 model selected 
    18369 
    18370 > ui mousemode right rotate
    18371 
    18372 > ui mousemode right translate
    18373 
    18374 > ui mousemode right select
    18375 
    18376 > select #2/I:157
    18377 
    18378 9 atoms, 8 bonds, 1 residue, 1 model selected 
    18379 
    18380 > select #37/A:165
    18381 
    18382 11 atoms, 10 bonds, 1 residue, 1 model selected 
    18383 
    18384 > ui mousemode right translate
    18385 
    18386 > style sel stick
    18387 
    18388 Changed 11 atom styles 
    18389 
    18390 > show sel atoms
    18391 
    18392 > color sel orange
    18393 
    18394 > ui mousemode right select
    18395 
    18396 > select #2/I:154
    18397 
    18398 8 atoms, 7 bonds, 1 residue, 1 model selected 
    18399 
    18400 > select #37/A:162
    18401 
    18402 14 atoms, 13 bonds, 1 residue, 1 model selected 
    18403 
    18404 > style sel stick
    18405 
    18406 Changed 14 atom styles 
    18407 
    18408 > show sel atoms
    18409 
    18410 > color sel orange
    18411 
    18412 > ui mousemode right translate
    18413 
    18414 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    18415 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    18416 
    18417 > hide #37 models
    18418 
    18419 > select add #37
    18420 
    18421 4402 atoms, 4459 bonds, 276 residues, 1 model selected 
    18422 
    18423 > show #37 models
    18424 
    18425 > select subtract #37
    18426 
    18427 Nothing selected 
    18428 
    18429 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    18430 > UASLP/Lab Virología/AlphaFold/selected_prediction tai forest alphavirus
    18431 > .pdb"
    18432 
    18433 Chain information for selected_prediction tai forest alphavirus .pdb #38 
    18434 --- 
    18435 Chain | Description 
    18436 A | No description available 
    18437  
    18438 
    18439 > ui tool show Matchmaker
    18440 
    18441 > matchmaker #38 to #2
    18442 
    18443 Parameters 
    18444 --- 
    18445 Chain pairing | bb 
    18446 Alignment algorithm | Needleman-Wunsch 
    18447 Similarity matrix | BLOSUM-62 
    18448 SS fraction | 0.3 
    18449 Gap open (HH/SS/other) | 18/18/6 
    18450 Gap extend | 1 
    18451 SS matrix |  |  | H | S | O 
    18452 ---|---|---|--- 
    18453 H | 6 | -9 | -6 
    18454 S |  | 6 | -6 
    18455 O |  |  | 4 
    18456 Iteration cutoff | 2 
    18457  
    18458 Matchmaker 3j2w.pdb, chain I (#2) with selected_prediction tai forest
    18459 alphavirus .pdb, chain A (#38), sequence alignment score = 454.7 
    18460 RMSD between 140 pruned atom pairs is 0.831 angstroms; (across all 149 pairs:
    18461 1.170) 
    18462  
    18463 
    18464 > hide #37 models
    18465 
    18466 > color #38 #348d22ff
    18467 
    18468 > color #38 #aaaa00ff
    18469 
    18470 > color #38 #aaaa7fff
    18471 
    18472 > color #38 #93936eff
    18473 
    18474 > color #38 #939362ff
    18475 
    18476 > color #38 #939360ff
    18477 
    18478 > color #38 #938f54ff
    18479 
    18480 > color #38 #93934bff
    18481 
    18482 > color #38 #a6a655ff
    18483 
    18484 > ui mousemode right select
    18485 
    18486 > select #2/I:126
    18487 
    18488 9 atoms, 8 bonds, 1 residue, 1 model selected 
    18489 
    18490 > select #38/A:115
    18491 
    18492 17 atoms, 16 bonds, 1 residue, 1 model selected 
    18493 Alignment identifier is 38/A 
    18494 
    18495 > select #38/A:114
    18496 
    18497 12 atoms, 11 bonds, 1 residue, 1 model selected 
    18498 Drag select of 12 residues 
    18499 
    18500 > select clear
    18501 
    18502 > select #38/A:114
    18503 
    18504 12 atoms, 11 bonds, 1 residue, 1 model selected 
    18505 Destroying pre-existing alignment with identifier 38/A 
    18506 Alignment identifier is 38/A 
    18507 
    18508 > ui mousemode right zoom
    18509 
    18510 > ui mousemode right translate
    18511 
    18512 > style sel stick
    18513 
    18514 Changed 12 atom styles 
    18515 
    18516 > show sel atoms
    18517 
    18518 > color sel red
    18519 
    18520 > ui mousemode right select
    18521 
    18522 > select clear
    18523 
    18524 > select #2/I:128
    18525 
    18526 9 atoms, 8 bonds, 1 residue, 1 model selected 
    18527 
    18528 > select #38/A:117
    18529 
    18530 16 atoms, 15 bonds, 1 residue, 1 model selected 
    18531 
    18532 > style sel stick
    18533 
    18534 Changed 16 atom styles 
    18535 
    18536 > show sel atoms
    18537 
    18538 > ui mousemode right translate
    18539 
    18540 > color sel gray
    18541 
    18542 > ui mousemode right select
    18543 
    18544 > select #2/I:240
    18545 
    18546 9 atoms, 8 bonds, 1 residue, 1 model selected 
    18547 
    18548 > select #38/A:229
    18549 
    18550 15 atoms, 14 bonds, 1 residue, 1 model selected 
    18551 
    18552 > style sel stick
    18553 
    18554 Changed 15 atom styles 
    18555 
    18556 > show sel atoms
    18557 
    18558 > color sel red
    18559 
    18560 > ui mousemode right translate
    18561 
    18562 > ui mousemode right select
    18563 
    18564 > select #2/I:190
    18565 
    18566 9 atoms, 8 bonds, 1 residue, 1 model selected 
    18567 
    18568 > select #38/A:179
    18569 
    18570 12 atoms, 11 bonds, 1 residue, 1 model selected 
    18571 
    18572 > ui mousemode right translate
    18573 
    18574 > style sel stick
    18575 
    18576 Changed 12 atom styles 
    18577 
    18578 > show sel atoms
    18579 
    18580 > color sel red
    18581 
    18582 > ui mousemode right select
    18583 
    18584 > select #2/I:183
    18585 
    18586 9 atoms, 8 bonds, 1 residue, 1 model selected 
    18587 
    18588 > select #38/A:172
    18589 
    18590 11 atoms, 10 bonds, 1 residue, 1 model selected 
    18591 
    18592 > ui mousemode right translate
    18593 
    18594 > style sel stick
    18595 
    18596 Changed 11 atom styles 
    18597 
    18598 > show sel atoms
    18599 
    18600 > color sel orange
    18601 
    18602 > ui mousemode right rotate
    18603 
    18604 > ui mousemode right select
    18605 
    18606 > select #2/I:178
    18607 
    18608 9 atoms, 8 bonds, 1 residue, 1 model selected 
    18609 
    18610 > select #38/A:167
    18611 
    18612 24 atoms, 23 bonds, 1 residue, 1 model selected 
    18613 
    18614 > style sel stick
    18615 
    18616 Changed 24 atom styles 
    18617 
    18618 > show sel atoms
    18619 
    18620 > color sel blue
    18621 
    18622 > select clear
    18623 
    18624 > ui mousemode right translate
    18625 
    18626 > ui mousemode right rotate
    18627 
    18628 > ui mousemode right select
    18629 
    18630 Drag select of 1 atoms, 6 residues 
    18631 
    18632 > select clear
    18633 
    18634 > select #38/A:146
    18635 
    18636 11 atoms, 10 bonds, 1 residue, 1 model selected 
    18637 
    18638 > style sel sphere
    18639 
    18640 Changed 11 atom styles 
    18641 
    18642 > style sel stick
    18643 
    18644 Changed 11 atom styles 
    18645 
    18646 > show sel atoms
    18647 
    18648 > color sel orange
    18649 
    18650 > select #38/A:147
    18651 
    18652 19 atoms, 18 bonds, 1 residue, 1 model selected 
    18653 
    18654 > ui mousemode right translate
    18655 
    18656 > ui mousemode right select
    18657 
    18658 > select #2/I:154
    18659 
    18660 8 atoms, 7 bonds, 1 residue, 1 model selected 
    18661 
    18662 > select #38/A:143
    18663 
    18664 19 atoms, 18 bonds, 1 residue, 1 model selected 
    18665 
    18666 > style sel stick
    18667 
    18668 Changed 19 atom styles 
    18669 
    18670 > show sel atoms
    18671 
    18672 > color sel gray
    18673 
    18674 > ui mousemode right translate
    18675 
    18676 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    18677 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    18678 
    18679 ——— End of log from Wed Jun 28 17:55:43 2023 ———
    18680 
    18681 opened ChimeraX session 
    18682 
    18683 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    18684 > UASLP/Lab Virología/AlphaFold/selected_prediction Weglinng hagfish
    18685 > alphavirus consensus.pdb"
    18686 
    18687 Chain information for selected_prediction Weglinng hagfish alphavirus
    18688 consensus.pdb #39 
    18689 --- 
    18690 Chain | Description 
    18691 A | No description available 
    18692  
    18693 
    18694 > hide #38 models
    18695 
    18696 > select add #38
    18697 
    18698 4010 atoms, 4055 bonds, 257 residues, 1 model selected 
    18699 
    18700 > select subtract #38
    18701 
    18702 Nothing selected 
    18703 
    18704 > color #39 #550000ff
    18705 
    18706 > color #39 #aa5500ff
    18707 
    18708 > color #39 #550000ff
    18709 
    18710 > color #39 #6b0000ff
    18711 
    18712 > color #39 #810000ff
    18713 
    18714 > color #39 #814a3dff
    18715 
    18716 > ui tool show Matchmaker
    18717 
    18718 > matchmaker #39 to #2
    18719 
    18720 Parameters 
    18721 --- 
    18722 Chain pairing | bb 
    18723 Alignment algorithm | Needleman-Wunsch 
    18724 Similarity matrix | BLOSUM-62 
    18725 SS fraction | 0.3 
    18726 Gap open (HH/SS/other) | 18/18/6 
    18727 Gap extend | 1 
    18728 SS matrix |  |  | H | S | O 
    18729 ---|---|---|--- 
    18730 H | 6 | -9 | -6 
    18731 S |  | 6 | -6 
    18732 O |  |  | 4 
    18733 Iteration cutoff | 2 
    18734  
    18735 Matchmaker 3j2w.pdb, chain I (#2) with selected_prediction Weglinng hagfish
    18736 alphavirus consensus.pdb, chain A (#39), sequence alignment score = 364.7 
    18737 RMSD between 66 pruned atom pairs is 0.877 angstroms; (across all 134 pairs:
    18738 4.771) 
    18739  
    18740 
    18741 > set bgColor white
    18742 
    18743 > ui mousemode right select
    18744 
    18745 > select #2/I:126
    18746 
    18747 9 atoms, 8 bonds, 1 residue, 1 model selected 
    18748 
    18749 > select #39/A:186
    18750 
    18751 15 atoms, 14 bonds, 1 residue, 1 model selected 
    18752 Alignment identifier is 39/A 
    18753 
    18754 > style sel stick
    18755 
    18756 Changed 15 atom styles 
    18757 
    18758 > show sel atoms
    18759 
    18760 > color sel red
    18761 
    18762 > select #39/A:188
    18763 
    18764 7 atoms, 6 bonds, 1 residue, 1 model selected 
    18765 
    18766 > style sel stick
    18767 
    18768 Changed 7 atom styles 
    18769 
    18770 > show sel atoms
    18771 
    18772 > color sel magenta
    18773 
    18774 > show sel atoms
    18775 
    18776 [Repeated 1 time(s)]
    18777 
    18778 > ui mousemode right translate
    18779 
    18780 > ui mousemode right select
    18781 
    18782 > select #39/A:300
    18783 
    18784 7 atoms, 6 bonds, 1 residue, 1 model selected 
    18785 
    18786 > ui mousemode right translate
    18787 
    18788 > ui mousemode right select
    18789 
    18790 > select #39/A:299
    18791 
    18792 12 atoms, 11 bonds, 1 residue, 1 model selected 
    18793 
    18794 > ui mousemode right translate
    18795 
    18796 > style sel stick
    18797 
    18798 Changed 12 atom styles 
    18799 
    18800 > show sel atoms
    18801 
    18802 > color sel red
    18803 
    18804 > ui mousemode right select
    18805 
    18806 > select #2/I:190
    18807 
    18808 9 atoms, 8 bonds, 1 residue, 1 model selected 
    18809 
    18810 > select #39/A:249
    18811 
    18812 12 atoms, 11 bonds, 1 residue, 1 model selected 
    18813 
    18814 > select #39/A:250
    18815 
    18816 7 atoms, 6 bonds, 1 residue, 1 model selected 
    18817 
    18818 > select #39/A:249
    18819 
    18820 12 atoms, 11 bonds, 1 residue, 1 model selected 
    18821 
    18822 > select #39/A:263
    18823 
    18824 12 atoms, 11 bonds, 1 residue, 1 model selected 
    18825 
    18826 > select #39/A:249
    18827 
    18828 12 atoms, 11 bonds, 1 residue, 1 model selected 
    18829 
    18830 > style sel stick
    18831 
    18832 Changed 12 atom styles 
    18833 
    18834 > show sel atoms
    18835 
    18836 > color sel red
    18837 
    18838 > ui mousemode right translate
    18839 
    18840 > ui mousemode right select
    18841 
    18842 > select #2/I:183
    18843 
    18844 9 atoms, 8 bonds, 1 residue, 1 model selected 
    18845 
    18846 > select #2/I:190
    18847 
    18848 9 atoms, 8 bonds, 1 residue, 1 model selected 
    18849 
    18850 > select #39/A:249
    18851 
    18852 12 atoms, 11 bonds, 1 residue, 1 model selected 
    18853 
    18854 > ui mousemode right translate
    18855 
    18856 > ui mousemode right select
    18857 
    18858 > select #39/A:299
    18859 
    18860 12 atoms, 11 bonds, 1 residue, 1 model selected 
    18861 
    18862 > ui mousemode right translate
    18863 
    18864 > ui mousemode right select
    18865 
    18866 > select #2/I:183@CA
    18867 
    18868 1 atom, 1 residue, 1 model selected 
    18869 
    18870 > select #39/A:243
    18871 
    18872 22 atoms, 21 bonds, 1 residue, 1 model selected 
    18873 
    18874 > ui mousemode right translate
    18875 
    18876 > style sel stick
    18877 
    18878 Changed 22 atom styles 
    18879 
    18880 > show sel atoms
    18881 
    18882 > color sel blue
    18883 
    18884 > ui mousemode right select
    18885 
    18886 > select #39/A:238
    18887 
    18888 24 atoms, 23 bonds, 1 residue, 1 model selected 
    18889 
    18890 > select #2/I:178
    18891 
    18892 9 atoms, 8 bonds, 1 residue, 1 model selected 
    18893 
    18894 > select #39/A:238
    18895 
    18896 24 atoms, 23 bonds, 1 residue, 1 model selected 
    18897 
    18898 > ui mousemode right translate
    18899 
    18900 > style sel stick
    18901 
    18902 Changed 24 atom styles 
    18903 
    18904 > show sel atoms
    18905 
    18906 > color sel blue
    18907 
    18908 > ui mousemode right select
    18909 
    18910 > select #2/I:157
    18911 
    18912 9 atoms, 8 bonds, 1 residue, 1 model selected 
    18913 
    18914 > select #39/A:217
    18915 
    18916 14 atoms, 13 bonds, 1 residue, 1 model selected 
    18917 
    18918 > style sel stick
    18919 
    18920 Changed 14 atom styles 
    18921 
    18922 > show sel atoms
    18923 
    18924 > color sel orange
    18925 
    18926 > select #2/I:154
    18927 
    18928 8 atoms, 7 bonds, 1 residue, 1 model selected 
    18929 
    18930 > select #39/A:214
    18931 
    18932 12 atoms, 11 bonds, 1 residue, 1 model selected 
    18933 
    18934 > style sel stick
    18935 
    18936 Changed 12 atom styles 
    18937 
    18938 > show sel atoms
    18939 
    18940 > color sel red
    18941 
    18942 > ui mousemode right translate
    18943 
    18944 > color #39 #965647ff
    18945 
    18946 > color #39 #ba6a58ff
    18947 
    18948 > color #39 #7f483cff
    18949 
    18950 > color #39 #8f5043ff
    18951 
    18952 > color #39 #8c4e42ff
    18953 
    18954 > color #39 #8c5444ff
    18955 
    18956 > color #39 #8c4545ff
    18957 
    18958 > color #39 #8c4b49ff
    18959 
    18960 > color #39 #9d5452ff
    18961 
    18962 > color #39 #96514eff
    18963 
    18964 > ui mousemode right select
    18965 
    18966 > select #2/I:126
    18967 
    18968 9 atoms, 8 bonds, 1 residue, 1 model selected 
    18969 
    18970 > select #39/A:186
    18971 
    18972 15 atoms, 14 bonds, 1 residue, 1 model selected 
    18973 
    18974 > style sel stick
    18975 
    18976 Changed 15 atom styles 
    18977 
    18978 > color sel red
    18979 
    18980 > select #2/I:128
    18981 
    18982 9 atoms, 8 bonds, 1 residue, 1 model selected 
    18983 
    18984 > select #39/A:188
    18985 
    18986 7 atoms, 6 bonds, 1 residue, 1 model selected 
    18987 
    18988 > color sel magenta
    18989 
    18990 > ui mousemode right translate
    18991 
    18992 > ui mousemode right select
    18993 
    18994 > select #39/A:300
    18995 
    18996 7 atoms, 6 bonds, 1 residue, 1 model selected 
    18997 
    18998 > select #39/A:299
    18999 
    19000 12 atoms, 11 bonds, 1 residue, 1 model selected 
    19001 
    19002 > hide sel atoms
    19003 
    19004 > show sel atoms
    19005 
    19006 > color sel red
    19007 
    19008 > ui mousemode right translate
    19009 
    19010 > ui mousemode right select
    19011 
    19012 > select #39/A:249
    19013 
    19014 12 atoms, 11 bonds, 1 residue, 1 model selected 
    19015 
    19016 > color sel red
    19017 
    19018 > set bgColor black
    19019 
    19020 > set bgColor white
    19021 
    19022 > ui mousemode right translate
    19023 
    19024 > ui mousemode right select
    19025 
    19026 > select clear
    19027 
    19028 > select #39/A:243
    19029 
    19030 22 atoms, 21 bonds, 1 residue, 1 model selected 
    19031 
    19032 > ui mousemode right translate
    19033 
    19034 > color sel blue
    19035 
    19036 > ui mousemode right select
    19037 
    19038 > select #39/A:238
    19039 
    19040 24 atoms, 23 bonds, 1 residue, 1 model selected 
    19041 
    19042 > color sel blue
    19043 
    19044 Drag select of 4 residues 
    19045 
    19046 > ui mousemode right translate
    19047 
    19048 > ui mousemode right select
    19049 
    19050 > select #2/I:154
    19051 
    19052 8 atoms, 7 bonds, 1 residue, 1 model selected 
    19053 
    19054 > select #39/A:214
    19055 
    19056 12 atoms, 11 bonds, 1 residue, 1 model selected 
    19057 
    19058 > ui mousemode right rotate
    19059 
    19060 > ui mousemode right translate
    19061 
    19062 > color sel red
    19063 
    19064 > ui mousemode right select
    19065 
    19066 > select #2/I:157
    19067 
    19068 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19069 
    19070 > select #39/A:217
    19071 
    19072 14 atoms, 13 bonds, 1 residue, 1 model selected 
    19073 
    19074 > color sel orange
    19075 
    19076 [Repeated 1 time(s)]
    19077 
    19078 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    19079 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    19080 
    19081 Drag select of 44 residues 
    19082 
    19083 > select #39/A:187
    19084 
    19085 7 atoms, 6 bonds, 1 residue, 1 model selected 
    19086 
    19087 > ui mousemode right translate
    19088 
    19089 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    19090 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    19091 
    19092 ——— End of log from Wed Jun 28 18:20:41 2023 ———
    19093 
    19094 opened ChimeraX session 
    19095 
    19096 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    19097 > UASLP/Lab Virología/AlphaFold/Norwegian salmonid alphavirus AlphaFold.pdb"
    19098 
    19099 Chain information for Norwegian salmonid alphavirus AlphaFold.pdb #40 
    19100 --- 
    19101 Chain | Description 
    19102 A | No description available 
    19103  
    19104 
    19105 > ui tool show Matchmaker
    19106 
    19107 > matchmaker #40 to #2
    19108 
    19109 Parameters 
    19110 --- 
    19111 Chain pairing | bb 
    19112 Alignment algorithm | Needleman-Wunsch 
    19113 Similarity matrix | BLOSUM-62 
    19114 SS fraction | 0.3 
    19115 Gap open (HH/SS/other) | 18/18/6 
    19116 Gap extend | 1 
    19117 SS matrix |  |  | H | S | O 
    19118 ---|---|---|--- 
    19119 H | 6 | -9 | -6 
    19120 S |  | 6 | -6 
    19121 O |  |  | 4 
    19122 Iteration cutoff | 2 
    19123  
    19124 Matchmaker 3j2w.pdb, chain I (#2) with Norwegian salmonid alphavirus
    19125 AlphaFold.pdb, chain A (#40), sequence alignment score = 379.7 
    19126 RMSD between 128 pruned atom pairs is 0.984 angstroms; (across all 148 pairs:
    19127 1.791) 
    19128  
    19129 
    19130 > hide #39 models
    19131 
    19132 > select add #39
    19133 
    19134 4950 atoms, 4999 bonds, 312 residues, 1 model selected 
    19135 
    19136 > select subtract #39
    19137 
    19138 Nothing selected 
    19139 
    19140 > color #40 #cd8444ff
    19141 
    19142 > color #40 #cd6c58ff
    19143 
    19144 > color #40 #cd8b4aff
    19145 
    19146 > color #40 #966636ff
    19147 
    19148 > color #40 #ba7f43ff
    19149 
    19150 > color #40 #b57b41ff
    19151 
    19152 > color #40 #b58a34ff
    19153 
    19154 > color #40 #9e782dff
    19155 
    19156 > color #40 #ba8e35ff
    19157 
    19158 > color #40 #b08632ff
    19159 
    19160 > ui mousemode right select
    19161 
    19162 > select #2/I:126
    19163 
    19164 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19165 
    19166 > select #40/A:141
    19167 
    19168 7 atoms, 6 bonds, 1 residue, 1 model selected 
    19169 
    19170 > select #40/A:140
    19171 
    19172 12 atoms, 11 bonds, 1 residue, 1 model selected 
    19173 Alignment identifier is 40/A 
    19174 
    19175 > style sel stick
    19176 
    19177 Changed 12 atom styles 
    19178 
    19179 > show sel atoms
    19180 
    19181 > color sel red
    19182 
    19183 > select #2/I:128
    19184 
    19185 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19186 
    19187 > select #40/A:142
    19188 
    19189 10 atoms, 9 bonds, 1 residue, 1 model selected 
    19190 
    19191 > style sel stick
    19192 
    19193 Changed 10 atom styles 
    19194 
    19195 > show sel atoms
    19196 
    19197 > color sel gray
    19198 
    19199 > ui mousemode right translate
    19200 
    19201 > ui mousemode right select
    19202 
    19203 > select #2/I:240
    19204 
    19205 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19206 
    19207 > select #40/A:253
    19208 
    19209 12 atoms, 11 bonds, 1 residue, 1 model selected 
    19210 
    19211 > style sel stick
    19212 
    19213 Changed 12 atom styles 
    19214 
    19215 > show sel atoms
    19216 
    19217 > color sel red
    19218 
    19219 > ui mousemode right translate
    19220 
    19221 > ui mousemode right select
    19222 
    19223 > select #2/I:190
    19224 
    19225 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19226 
    19227 > select #40/A:204
    19228 
    19229 7 atoms, 6 bonds, 1 residue, 1 model selected 
    19230 
    19231 > select #40/A:203
    19232 
    19233 12 atoms, 11 bonds, 1 residue, 1 model selected 
    19234 
    19235 > select #40/A:204
    19236 
    19237 7 atoms, 6 bonds, 1 residue, 1 model selected 
    19238 
    19239 > select #40/A:203
    19240 
    19241 12 atoms, 11 bonds, 1 residue, 1 model selected 
    19242 
    19243 > ui mousemode right translate
    19244 
    19245 > style sel stick
    19246 
    19247 Changed 12 atom styles 
    19248 
    19249 > show sel atoms
    19250 
    19251 > color sel red
    19252 
    19253 > set bgColor white
    19254 
    19255 > ui mousemode right select
    19256 
    19257 > select #2/I:183
    19258 
    19259 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19260 
    19261 > select #40/A:197
    19262 
    19263 15 atoms, 14 bonds, 1 residue, 1 model selected 
    19264 
    19265 > select #2/I:183
    19266 
    19267 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19268 
    19269 > select #40/A:197
    19270 
    19271 15 atoms, 14 bonds, 1 residue, 1 model selected 
    19272 
    19273 > style sel stick
    19274 
    19275 Changed 15 atom styles 
    19276 
    19277 > show sel atoms
    19278 
    19279 > color sel red
    19280 
    19281 > ui mousemode right translate
    19282 
    19283 > ui mousemode right select
    19284 
    19285 > select #2/I:178
    19286 
    19287 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19288 
    19289 > select #40/A:192
    19290 
    19291 24 atoms, 23 bonds, 1 residue, 1 model selected 
    19292 
    19293 > style sel stick
    19294 
    19295 Changed 24 atom styles 
    19296 
    19297 > show sel atoms
    19298 
    19299 > color sel red
    19300 
    19301 > ui mousemode right translate
    19302 
    19303 > ui mousemode right select
    19304 
    19305 > select #40/A:140
    19306 
    19307 12 atoms, 11 bonds, 1 residue, 1 model selected 
    19308 
    19309 > select #40/A:142
    19310 
    19311 10 atoms, 9 bonds, 1 residue, 1 model selected 
    19312 
    19313 > select #40/A:253
    19314 
    19315 12 atoms, 11 bonds, 1 residue, 1 model selected 
    19316 
    19317 > ui mousemode right translate
    19318 
    19319 > ui mousemode right select
    19320 
    19321 > select #40/A:203
    19322 
    19323 12 atoms, 11 bonds, 1 residue, 1 model selected 
    19324 
    19325 > ui mousemode right translate
    19326 
    19327 > ui mousemode right select
    19328 
    19329 > select #40/A:197
    19330 
    19331 15 atoms, 14 bonds, 1 residue, 1 model selected 
    19332 
    19333 > select #40/A:192
    19334 
    19335 24 atoms, 23 bonds, 1 residue, 1 model selected 
    19336 
    19337 > ui mousemode right translate
    19338 
    19339 > ui mousemode right select
    19340 
    19341 > select #2/I:157
    19342 
    19343 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19344 
    19345 > select #40/A:171
    19346 
    19347 12 atoms, 11 bonds, 1 residue, 1 model selected 
    19348 
    19349 > style sel stick
    19350 
    19351 Changed 12 atom styles 
    19352 
    19353 > show sel atoms
    19354 
    19355 > color sel red
    19356 
    19357 > ui mousemode right translate
    19358 
    19359 > ui mousemode right select
    19360 
    19361 > select #2/I:154
    19362 
    19363 8 atoms, 7 bonds, 1 residue, 1 model selected 
    19364 
    19365 > select #40/A:167
    19366 
    19367 14 atoms, 14 bonds, 1 residue, 1 model selected 
    19368 
    19369 > select #40/A:168
    19370 
    19371 15 atoms, 14 bonds, 1 residue, 1 model selected 
    19372 
    19373 > select #2/I:154
    19374 
    19375 8 atoms, 7 bonds, 1 residue, 1 model selected 
    19376 
    19377 > select #40/A:168
    19378 
    19379 15 atoms, 14 bonds, 1 residue, 1 model selected 
    19380 
    19381 > style sel stick
    19382 
    19383 Changed 15 atom styles 
    19384 
    19385 > show sel atoms
    19386 
    19387 > color sel red
    19388 
    19389 > select #40/A:171
    19390 
    19391 12 atoms, 11 bonds, 1 residue, 1 model selected 
    19392 
    19393 > select #2/I:154
    19394 
    19395 8 atoms, 7 bonds, 1 residue, 1 model selected 
    19396 
    19397 > select #40/A:167
    19398 
    19399 14 atoms, 14 bonds, 1 residue, 1 model selected 
    19400 
    19401 > select #40/A:168
    19402 
    19403 15 atoms, 14 bonds, 1 residue, 1 model selected 
    19404 
    19405 > ui mousemode right translate
    19406 
    19407 > ui mousemode right select
    19408 
    19409 > select #40/A:203
    19410 
    19411 12 atoms, 11 bonds, 1 residue, 1 model selected 
    19412 
    19413 > select #40/A:197
    19414 
    19415 15 atoms, 14 bonds, 1 residue, 1 model selected 
    19416 
    19417 > ui mousemode right translate
    19418 
    19419 > ui mousemode right select
    19420 
    19421 > select #40/A:192
    19422 
    19423 24 atoms, 23 bonds, 1 residue, 1 model selected 
    19424 
    19425 > color sel blue
    19426 
    19427 > ui mousemode right translate
    19428 
    19429 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    19430 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    19431 
    19432 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    19433 > UASLP/Lab Virología/AlphaFold/selected_prediction Wenling fish
    19434 > alphavirus.pdb"
    19435 
    19436 Chain information for selected_prediction Wenling fish alphavirus.pdb #41 
    19437 --- 
    19438 Chain | Description 
    19439 A | No description available 
    19440  
    19441 
    19442 > ui tool show Matchmaker
    19443 
    19444 > matchmaker #41 to #2
    19445 
    19446 Parameters 
    19447 --- 
    19448 Chain pairing | bb 
    19449 Alignment algorithm | Needleman-Wunsch 
    19450 Similarity matrix | BLOSUM-62 
    19451 SS fraction | 0.3 
    19452 Gap open (HH/SS/other) | 18/18/6 
    19453 Gap extend | 1 
    19454 SS matrix |  |  | H | S | O 
    19455 ---|---|---|--- 
    19456 H | 6 | -9 | -6 
    19457 S |  | 6 | -6 
    19458 O |  |  | 4 
    19459 Iteration cutoff | 2 
    19460  
    19461 Matchmaker 3j2w.pdb, chain I (#2) with selected_prediction Wenling fish
    19462 alphavirus.pdb, chain A (#41), sequence alignment score = 320.8 
    19463 RMSD between 130 pruned atom pairs is 0.918 angstroms; (across all 148 pairs:
    19464 1.592) 
    19465  
    19466 
    19467 > hide #40 models
    19468 
    19469 > select add #40
    19470 
    19471 4420 atoms, 4461 bonds, 281 residues, 1 model selected 
    19472 
    19473 > select subtract #40
    19474 
    19475 Nothing selected 
    19476 
    19477 > color #41 #286b1aff
    19478 
    19479 > ui mousemode right select
    19480 
    19481 > select #2/I:126
    19482 
    19483 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19484 
    19485 > select #41/A:156
    19486 
    19487 22 atoms, 21 bonds, 1 residue, 1 model selected 
    19488 
    19489 > select #41/A:155
    19490 
    19491 14 atoms, 13 bonds, 1 residue, 1 model selected 
    19492 
    19493 > select #41/A:156
    19494 
    19495 22 atoms, 21 bonds, 1 residue, 1 model selected 
    19496 
    19497 > select #41/A:155
    19498 
    19499 14 atoms, 13 bonds, 1 residue, 1 model selected 
    19500 
    19501 > select #41/A:156
    19502 
    19503 22 atoms, 21 bonds, 1 residue, 1 model selected 
    19504 Alignment identifier is 41/A 
    19505 
    19506 > style sel stick
    19507 
    19508 Changed 22 atom styles 
    19509 
    19510 > show sel atoms
    19511 
    19512 > color sel blue
    19513 
    19514 > ui mousemode right translate
    19515 
    19516 > ui mousemode right select
    19517 
    19518 > select #2/I:128
    19519 
    19520 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19521 
    19522 > select #41/A:158
    19523 
    19524 14 atoms, 13 bonds, 1 residue, 1 model selected 
    19525 
    19526 > ui mousemode right translate
    19527 
    19528 > hide #41 models
    19529 
    19530 > select add #41
    19531 
    19532 4748 atoms, 4801 bonds, 296 residues, 1 model selected 
    19533 
    19534 > select subtract #41
    19535 
    19536 Nothing selected 
    19537 
    19538 > show #26 models
    19539 
    19540 > hide #26 models
    19541 
    19542 > show #39 models
    19543 
    19544 > show #40 models
    19545 
    19546 > hide #39 models
    19547 
    19548 > show #38 models
    19549 
    19550 > hide #40 models
    19551 
    19552 > hide #38 models
    19553 
    19554 > show #41 models
    19555 
    19556 > ui mousemode right select
    19557 
    19558 > select #41/A:158
    19559 
    19560 14 atoms, 13 bonds, 1 residue, 1 model selected 
    19561 
    19562 > select #2/I:128
    19563 
    19564 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19565 
    19566 > select #41/A:158
    19567 
    19568 14 atoms, 13 bonds, 1 residue, 1 model selected 
    19569 
    19570 > style sel stick
    19571 
    19572 Changed 14 atom styles 
    19573 
    19574 > show sel atoms
    19575 
    19576 > color sel orange
    19577 
    19578 > ui mousemode right translate
    19579 
    19580 > ui mousemode right select
    19581 
    19582 > select clear
    19583 
    19584 > select #2/I:240
    19585 
    19586 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19587 
    19588 > select #41/A:269
    19589 
    19590 15 atoms, 14 bonds, 1 residue, 1 model selected 
    19591 
    19592 > style sel stick
    19593 
    19594 Changed 15 atom styles 
    19595 
    19596 > show sel atoms
    19597 
    19598 > color sel red
    19599 
    19600 Drag select of 1 residues 
    19601 
    19602 > ui mousemode right translate
    19603 
    19604 > ui mousemode right rotate
    19605 
    19606 > ui mousemode right select
    19607 
    19608 > select #41/A:219
    19609 
    19610 15 atoms, 14 bonds, 1 residue, 1 model selected 
    19611 
    19612 > select #2/I:190
    19613 
    19614 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19615 
    19616 > select #41/A:219
    19617 
    19618 15 atoms, 14 bonds, 1 residue, 1 model selected 
    19619 
    19620 > style sel stick
    19621 
    19622 Changed 15 atom styles 
    19623 
    19624 > show sel atoms
    19625 
    19626 > color sel red
    19627 
    19628 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    19629 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    19630 
    19631 ——— End of log from Thu Jun 29 15:37:27 2023 ———
    19632 
    19633 opened ChimeraX session 
    19634 
    19635 > ui mousemode right select
    19636 
    19637 > select #2/I:183
    19638 
    19639 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19640 
    19641 > select #41/A:138
    19642 
    19643 19 atoms, 18 bonds, 1 residue, 1 model selected 
    19644 
    19645 > select clear
    19646 
    19647 > ui mousemode right translate
    19648 
    19649 > ui mousemode right select
    19650 
    19651 > select #2/I:183
    19652 
    19653 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19654 
    19655 > select #41/A:213
    19656 
    19657 10 atoms, 9 bonds, 1 residue, 1 model selected 
    19658 
    19659 > ui mousemode right translate
    19660 
    19661 > style sel stick
    19662 
    19663 Changed 10 atom styles 
    19664 
    19665 > show sel atoms
    19666 
    19667 > color sel gray
    19668 
    19669 > ui mousemode right select
    19670 
    19671 > select #2/I:178
    19672 
    19673 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19674 
    19675 > select #41/A:208
    19676 
    19677 17 atoms, 17 bonds, 1 residue, 1 model selected 
    19678 
    19679 > ui mousemode right translate
    19680 
    19681 > style sel stick
    19682 
    19683 Changed 17 atom styles 
    19684 
    19685 > show sel atoms
    19686 
    19687 > color sel blue
    19688 
    19689 > ui mousemode right select
    19690 
    19691 > select #2/I:157
    19692 
    19693 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19694 
    19695 > select #41/A:187
    19696 
    19697 15 atoms, 14 bonds, 1 residue, 1 model selected 
    19698 
    19699 > select #2/I:157
    19700 
    19701 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19702 
    19703 > select #41/A:187
    19704 
    19705 15 atoms, 14 bonds, 1 residue, 1 model selected 
    19706 
    19707 > style sel sphere
    19708 
    19709 Changed 15 atom styles 
    19710 
    19711 > style sel stick
    19712 
    19713 Changed 15 atom styles 
    19714 
    19715 > show sel atoms
    19716 
    19717 > color sel red
    19718 
    19719 Drag select of 3 atoms, 6 residues, 2 bonds 
    19720 
    19721 > select clear
    19722 
    19723 > ui mousemode right translate
    19724 
    19725 > ui mousemode right select
    19726 
    19727 > select #2/I:154
    19728 
    19729 8 atoms, 7 bonds, 1 residue, 1 model selected 
    19730 
    19731 > select #41/A:184
    19732 
    19733 19 atoms, 18 bonds, 1 residue, 1 model selected 
    19734 
    19735 > ui mousemode right translate
    19736 
    19737 > style sel stick
    19738 
    19739 Changed 19 atom styles 
    19740 
    19741 > show sel atoms
    19742 
    19743 > color sel gray
    19744 
    19745 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    19746 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    19747 
    19748 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    19749 > UASLP/Lab Virología/AlphaFold/Yada yada virus AlphaFold.pdb"
    19750 
    19751 Chain information for Yada yada virus AlphaFold.pdb #42 
    19752 --- 
    19753 Chain | Description 
    19754 A | No description available 
    19755  
    19756 
    19757 > color #42 #5555ffff
    19758 
    19759 > color #42 #5500ffff
    19760 
    19761 > color #42 #ff007fff
    19762 
    19763 > color #42 #ca0065ff
    19764 
    19765 > color #42 #5dcac6ff
    19766 
    19767 > color #42 #6647caff
    19768 
    19769 > color #42 #ca6d89ff
    19770 
    19771 > color #42 #ca758cff
    19772 
    19773 > color #42 #ca7585ff
    19774 
    19775 > color #42 #77ca53ff
    19776 
    19777 > color #42 #ca78c3ff
    19778 
    19779 > color #42 #ca7894ff
    19780 
    19781 > color #42 #ca6d83ff
    19782 
    19783 > color #42 magenta
    19784 
    19785 > color #42 #ff2ad8ff
    19786 
    19787 > color #42 #ff1ebbff
    19788 
    19789 > color #42 #b623ffff
    19790 
    19791 > color #42 #da23ffff
    19792 
    19793 > color #42 #e837ffff
    19794 
    19795 > color #42 #ff4c91ff
    19796 
    19797 > color #42 #ff3acaff
    19798 
    19799 > color #42 #ff2fd2ff
    19800 
    19801 > color #42 #ff11b4ff
    19802 
    19803 > color #42 #c30d89ff
    19804 
    19805 > color #42 #c340abff
    19806 
    19807 > color #42 #5d6fc3ff
    19808 
    19809 > color #42 #7a73c3ff
    19810 
    19811 > color #42 #c35344ff
    19812 
    19813 > color #42 #a8473bff
    19814 
    19815 > color #42 #a84e37ff
    19816 
    19817 > color #42 #a8412fff
    19818 
    19819 > color #42 #a83931ff
    19820 
    19821 > color #42 #b63d35ff
    19822 
    19823 > color #42 #b6877bff
    19824 
    19825 > color #42 #b67d6fff
    19826 
    19827 > color #42 #b65b5bff
    19828 
    19829 > color #42 #a65353ff
    19830 
    19831 > color #42 #b15959ff
    19832 
    19833 > color #42 #b13e3aff
    19834 
    19835 > color #42 #b13227ff
    19836 
    19837 > color #42 #89b19eff
    19838 
    19839 > ui tool show Matchmaker
    19840 
    19841 > matchmaker #42 to #2
    19842 
    19843 Parameters 
    19844 --- 
    19845 Chain pairing | bb 
    19846 Alignment algorithm | Needleman-Wunsch 
    19847 Similarity matrix | BLOSUM-62 
    19848 SS fraction | 0.3 
    19849 Gap open (HH/SS/other) | 18/18/6 
    19850 Gap extend | 1 
    19851 SS matrix |  |  | H | S | O 
    19852 ---|---|---|--- 
    19853 H | 6 | -9 | -6 
    19854 S |  | 6 | -6 
    19855 O |  |  | 4 
    19856 Iteration cutoff | 2 
    19857  
    19858 Matchmaker 3j2w.pdb, chain I (#2) with Yada yada virus AlphaFold.pdb, chain A
    19859 (#42), sequence alignment score = 480 
    19860 RMSD between 140 pruned atom pairs is 0.706 angstroms; (across all 149 pairs:
    19861 0.975) 
    19862  
    19863 
    19864 > hide #41 models
    19865 
    19866 > select add #41
    19867 
    19868 4748 atoms, 4801 bonds, 296 residues, 1 model selected 
    19869 
    19870 > select subtract #41
    19871 
    19872 Nothing selected 
    19873 
    19874 > ui mousemode right select
    19875 
    19876 > select #2/I:126
    19877 
    19878 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19879 
    19880 > select #42/A:125
    19881 
    19882 15 atoms, 14 bonds, 1 residue, 1 model selected 
    19883 Alignment identifier is 42/A 
    19884 
    19885 > style sel stick
    19886 
    19887 Changed 15 atom styles 
    19888 
    19889 > show sel atoms
    19890 
    19891 > color sel red
    19892 
    19893 > ui mousemode right translate
    19894 
    19895 > ui mousemode right select
    19896 
    19897 > select #2/I:128
    19898 
    19899 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19900 
    19901 > select #42/A:128
    19902 
    19903 24 atoms, 23 bonds, 1 residue, 1 model selected 
    19904 
    19905 > ui mousemode right translate
    19906 
    19907 > style sel stick
    19908 
    19909 Changed 24 atom styles 
    19910 
    19911 > show sel atoms
    19912 
    19913 > color sel blue
    19914 
    19915 > ui mousemode right select
    19916 
    19917 > select #2/I:240
    19918 
    19919 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19920 
    19921 > select #42/A:240
    19922 
    19923 15 atoms, 14 bonds, 1 residue, 1 model selected 
    19924 
    19925 > style sel stick
    19926 
    19927 Changed 15 atom styles 
    19928 
    19929 > show sel atoms
    19930 
    19931 > color sel red
    19932 
    19933 > select clear
    19934 
    19935 Drag select of 1 atoms, 1 bonds 
    19936 
    19937 > ui mousemode right translate
    19938 
    19939 > ui mousemode right select
    19940 
    19941 > select #2/I:190
    19942 
    19943 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19944 
    19945 > select #42/A:190
    19946 
    19947 12 atoms, 11 bonds, 1 residue, 1 model selected 
    19948 
    19949 > ui mousemode right translate
    19950 
    19951 > style sel stick
    19952 
    19953 Changed 12 atom styles 
    19954 
    19955 > show sel atoms
    19956 
    19957 > color sel red
    19958 
    19959 > ui mousemode right select
    19960 
    19961 > ui mousemode right translate
    19962 
    19963 > ui mousemode right select
    19964 
    19965 > select clear
    19966 
    19967 > select #2/I:183
    19968 
    19969 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19970 
    19971 > select #42/A:183
    19972 
    19973 10 atoms, 9 bonds, 1 residue, 1 model selected 
    19974 
    19975 > ui mousemode right translate
    19976 
    19977 > style sel stick
    19978 
    19979 Changed 10 atom styles 
    19980 
    19981 > show sel atoms
    19982 
    19983 > color sel gray
    19984 
    19985 > color #42 #a5d6beff
    19986 
    19987 > color #42 #9eccb6ff
    19988 
    19989 > color sel gray
    19990 
    19991 > ui mousemode right select
    19992 
    19993 > select #2/I:178
    19994 
    19995 9 atoms, 8 bonds, 1 residue, 1 model selected 
    19996 
    19997 > select #42/A:178
    19998 
    19999 24 atoms, 23 bonds, 1 residue, 1 model selected 
    20000 
    20001 > style sel stick
    20002 
    20003 Changed 24 atom styles 
    20004 
    20005 > show sel atoms
    20006 
    20007 > color sel red
    20008 
    20009 > color sel blue
    20010 
    20011 > select #2/I:178
    20012 
    20013 9 atoms, 8 bonds, 1 residue, 1 model selected 
    20014 
    20015 > select #42/A:178
    20016 
    20017 24 atoms, 23 bonds, 1 residue, 1 model selected 
    20018 
    20019 > ui mousemode right translate
    20020 
    20021 > ui mousemode right select
    20022 
    20023 > select #42/A:128
    20024 
    20025 24 atoms, 23 bonds, 1 residue, 1 model selected 
    20026 
    20027 > select clear
    20028 
    20029 > select #2/I:128
    20030 
    20031 9 atoms, 8 bonds, 1 residue, 1 model selected 
    20032 
    20033 > select #42/A:125
    20034 
    20035 15 atoms, 14 bonds, 1 residue, 1 model selected 
    20036 
    20037 > color sel red
    20038 
    20039 > select #42/A:128
    20040 
    20041 24 atoms, 23 bonds, 1 residue, 1 model selected 
    20042 
    20043 > ui mousemode right translate
    20044 
    20045 > color sel blue
    20046 
    20047 > ui mousemode right select
    20048 
    20049 > select #42/A:240
    20050 
    20051 15 atoms, 14 bonds, 1 residue, 1 model selected 
    20052 
    20053 > ui mousemode right translate
    20054 
    20055 > color sel red
    20056 
    20057 > ui mousemode right select
    20058 
    20059 > select #42/A:190
    20060 
    20061 12 atoms, 11 bonds, 1 residue, 1 model selected 
    20062 
    20063 > color sel red
    20064 
    20065 > select #42/A:240
    20066 
    20067 15 atoms, 14 bonds, 1 residue, 1 model selected 
    20068 
    20069 > ui mousemode right translate
    20070 
    20071 > ui mousemode right select
    20072 
    20073 > select #2/I:157
    20074 
    20075 9 atoms, 8 bonds, 1 residue, 1 model selected 
    20076 
    20077 > select #42/A:157
    20078 
    20079 11 atoms, 10 bonds, 1 residue, 1 model selected 
    20080 
    20081 > style sel stick
    20082 
    20083 Changed 11 atom styles 
    20084 
    20085 > show sel atoms
    20086 
    20087 > color sel orange
    20088 
    20089 > select #2/I:154
    20090 
    20091 8 atoms, 7 bonds, 1 residue, 1 model selected 
    20092 
    20093 > select #42/A:154
    20094 
    20095 14 atoms, 13 bonds, 1 residue, 1 model selected 
    20096 
    20097 > select #2/I:154
    20098 
    20099 8 atoms, 7 bonds, 1 residue, 1 model selected 
    20100 
    20101 > select #42/A:154
    20102 
    20103 14 atoms, 13 bonds, 1 residue, 1 model selected 
    20104 
    20105 > ui mousemode right translate
    20106 
    20107 > style sel stick
    20108 
    20109 Changed 14 atom styles 
    20110 
    20111 > show sel atoms
    20112 
    20113 > color sel orange
    20114 
    20115 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    20116 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    20117 
    20118 ——— End of log from Thu Jun 29 18:48:25 2023 ———
    20119 
    20120 opened ChimeraX session 
    20121 
    20122 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    20123 > UASLP/Lab Virología/AlphaFold/Aura virus AlphaFold.pdb"
    20124 
    20125 Chain information for Aura virus AlphaFold.pdb #43 
    20126 --- 
    20127 Chain | Description 
    20128 A | No description available 
    20129  
    20130 
    20131 > ui tool show Matchmaker
    20132 
    20133 > matchmaker #43 to #2
    20134 
    20135 Parameters 
    20136 --- 
    20137 Chain pairing | bb 
    20138 Alignment algorithm | Needleman-Wunsch 
    20139 Similarity matrix | BLOSUM-62 
    20140 SS fraction | 0.3 
    20141 Gap open (HH/SS/other) | 18/18/6 
    20142 Gap extend | 1 
    20143 SS matrix |  |  | H | S | O 
    20144 ---|---|---|--- 
    20145 H | 6 | -9 | -6 
    20146 S |  | 6 | -6 
    20147 O |  |  | 4 
    20148 Iteration cutoff | 2 
    20149  
    20150 Matchmaker 3j2w.pdb, chain I (#2) with Aura virus AlphaFold.pdb, chain A
    20151 (#43), sequence alignment score = 493.2 
    20152 RMSD between 143 pruned atom pairs is 0.738 angstroms; (across all 149 pairs:
    20153 1.063) 
    20154  
    20155 
    20156 > color #43 #55007fff
    20157 
    20158 > color #43 #8d00d3ff
    20159 
    20160 > hide #42 models
    20161 
    20162 > select add #42
    20163 
    20164 4151 atoms, 4199 bonds, 268 residues, 1 model selected 
    20165 
    20166 > select subtract #42
    20167 
    20168 Nothing selected 
    20169 
    20170 > ui mousemode right select
    20171 
    20172 > select #43/A:124
    20173 
    20174 15 atoms, 14 bonds, 1 residue, 1 model selected 
    20175 Alignment identifier is 43/A 
    20176 
    20177 > select #43/A:125
    20178 
    20179 12 atoms, 11 bonds, 1 residue, 1 model selected 
    20180 
    20181 > select #43/A:124
    20182 
    20183 15 atoms, 14 bonds, 1 residue, 1 model selected 
    20184 Drag select of 15 residues 
    20185 
    20186 > select clear
    20187 
    20188 Drag select of 31 residues 
    20189 
    20190 > ui mousemode right translate
    20191 
    20192 > ui mousemode right select
    20193 
    20194 > select #43/A:125
    20195 
    20196 12 atoms, 11 bonds, 1 residue, 1 model selected 
    20197 
    20198 > ui mousemode right rotate
    20199 
    20200 > ui mousemode right translate
    20201 
    20202 > style sel stick
    20203 
    20204 Changed 12 atom styles 
    20205 
    20206 > show sel atoms
    20207 
    20208 > color sel red
    20209 
    20210 > ui mousemode right select
    20211 
    20212 > select #43/A:127
    20213 
    20214 22 atoms, 21 bonds, 1 residue, 1 model selected 
    20215 
    20216 > select #2/I:128
    20217 
    20218 9 atoms, 8 bonds, 1 residue, 1 model selected 
    20219 
    20220 > select #43/A:127
    20221 
    20222 22 atoms, 21 bonds, 1 residue, 1 model selected 
    20223 
    20224 > ui mousemode right rotate
    20225 
    20226 > ui mousemode right select
    20227 
    20228 > style sel stick
    20229 
    20230 Changed 22 atom styles 
    20231 
    20232 > show sel atoms
    20233 
    20234 > color sel light sea green
    20235 
    20236 > color sel blue
    20237 
    20238 > ui mousemode right translate
    20239 
    20240 > ui mousemode right select
    20241 
    20242 > select clear
    20243 
    20244 > select #2/I:240
    20245 
    20246 9 atoms, 8 bonds, 1 residue, 1 model selected 
    20247 
    20248 > select #43/A:239
    20249 
    20250 15 atoms, 14 bonds, 1 residue, 1 model selected 
    20251 
    20252 > style sel stick
    20253 
    20254 Changed 15 atom styles 
    20255 
    20256 > show sel atoms
    20257 
    20258 > color sel red
    20259 
    20260 > ui mousemode right translate
    20261 
    20262 > ui mousemode right select
    20263 
    20264 > select #43/A:189
    20265 
    20266 15 atoms, 14 bonds, 1 residue, 1 model selected 
    20267 
    20268 > select #2/I:190
    20269 
    20270 9 atoms, 8 bonds, 1 residue, 1 model selected 
    20271 
    20272 > select #43/A:189
    20273 
    20274 15 atoms, 14 bonds, 1 residue, 1 model selected 
    20275 
    20276 > style sel stick
    20277 
    20278 Changed 15 atom styles 
    20279 
    20280 > show sel atoms
    20281 
    20282 > color sel red
    20283 
    20284 > ui mousemode right translate
    20285 
    20286 > ui mousemode right select
    20287 
    20288 > select #43/A:182
    20289 
    20290 7 atoms, 6 bonds, 1 residue, 1 model selected 
    20291 
    20292 > style sel stick
    20293 
    20294 Changed 7 atom styles 
    20295 
    20296 > show sel atoms
    20297 
    20298 > color sel magenta
    20299 
    20300 > style sel stick
    20301 
    20302 Changed 7 atom styles 
    20303 
    20304 > show sel atoms
    20305 
    20306 > hide sel atoms
    20307 
    20308 [Repeated 1 time(s)]
    20309 
    20310 > hide sel cartoons
    20311 
    20312 [Repeated 1 time(s)]
    20313 
    20314 > show sel cartoons
    20315 
    20316 > show sel atoms
    20317 
    20318 [Repeated 3 time(s)]
    20319 
    20320 > hide sel atoms
    20321 
    20322 > show sel atoms
    20323 
    20324 > style sel stick
    20325 
    20326 Changed 7 atom styles 
    20327 
    20328 > show sel atoms
    20329 
    20330 > color sel magenta
    20331 
    20332 > ui mousemode right translate
    20333 
    20334 > ui mousemode right select
    20335 
    20336 > select #2/I:178
    20337 
    20338 9 atoms, 8 bonds, 1 residue, 1 model selected 
    20339 
    20340 > select #43/A:177
    20341 
    20342 22 atoms, 21 bonds, 1 residue, 1 model selected 
    20343 
    20344 > ui mousemode right translate
    20345 
    20346 > style sel stick
    20347 
    20348 Changed 22 atom styles 
    20349 
    20350 > show sel atoms
    20351 
    20352 > color sel blue
    20353 
    20354 > color #43 #ff55ffff
    20355 
    20356 > color #43 #aaaaffff
    20357 
    20358 > color #43 #8d8dd3ff
    20359 
    20360 > color #43 #9696e1ff
    20361 
    20362 > color #43 #a391e1ff
    20363 
    20364 > color #43 #b58ae1ff
    20365 
    20366 > color #43 #bb8ee8ff
    20367 
    20368 > color sel blue
    20369 
    20370 > ui mousemode right select
    20371 
    20372 > select #43/A:182
    20373 
    20374 7 atoms, 6 bonds, 1 residue, 1 model selected 
    20375 
    20376 > style sel stick
    20377 
    20378 Changed 7 atom styles 
    20379 
    20380 > hide sel atoms
    20381 
    20382 > show sel atoms
    20383 
    20384 [Repeated 1 time(s)]
    20385 
    20386 > style sel stick
    20387 
    20388 Changed 7 atom styles 
    20389 
    20390 > show sel atoms
    20391 
    20392 > color sel magenta
    20393 
    20394 > ui mousemode right translate
    20395 
    20396 > color #43 #c797f7ff
    20397 
    20398 > color sel magenta
    20399 
    20400 > color sel blue
    20401 
    20402 > color sel magenta
    20403 
    20404 > ui mousemode right select
    20405 
    20406 > select #43/A:177
    20407 
    20408 22 atoms, 21 bonds, 1 residue, 1 model selected 
    20409 
    20410 > color sel blue
    20411 
    20412 > ui mousemode right translate
    20413 
    20414 > ui mousemode right select
    20415 
    20416 > select #2/I:190
    20417 
    20418 9 atoms, 8 bonds, 1 residue, 1 model selected 
    20419 
    20420 > select #43/A:189@CA
    20421 
    20422 1 atom, 1 residue, 1 model selected 
    20423 
    20424 > select #43/A:189
    20425 
    20426 15 atoms, 14 bonds, 1 residue, 1 model selected 
    20427 
    20428 > color sel red
    20429 
    20430 > ui mousemode right translate
    20431 
    20432 > ui mousemode right select
    20433 
    20434 > select #43/A:239
    20435 
    20436 15 atoms, 14 bonds, 1 residue, 1 model selected 
    20437 
    20438 > color sel red
    20439 
    20440 > ui mousemode right translate
    20441 
    20442 > ui mousemode right select
    20443 
    20444 > select #43/A:127
    20445 
    20446 22 atoms, 21 bonds, 1 residue, 1 model selected 
    20447 
    20448 > color sel blue
    20449 
    20450 > select #43/A:125
    20451 
    20452 12 atoms, 11 bonds, 1 residue, 1 model selected 
    20453 
    20454 > color sel red
    20455 
    20456 > select #43/A:127
    20457 
    20458 22 atoms, 21 bonds, 1 residue, 1 model selected 
    20459 
    20460 > select #43/A:239
    20461 
    20462 15 atoms, 14 bonds, 1 residue, 1 model selected 
    20463 
    20464 > select #2/I:190
    20465 
    20466 9 atoms, 8 bonds, 1 residue, 1 model selected 
    20467 
    20468 > ui mousemode right translate
    20469 
    20470 > ui mousemode right select
    20471 
    20472 > select #2/I:157
    20473 
    20474 9 atoms, 8 bonds, 1 residue, 1 model selected 
    20475 
    20476 > select #43/A:156
    20477 
    20478 22 atoms, 21 bonds, 1 residue, 1 model selected 
    20479 
    20480 > style sel stick
    20481 
    20482 Changed 22 atom styles 
    20483 
    20484 > show sel atoms
    20485 
    20486 > color sel blue
    20487 
    20488 > select #43/A:153
    20489 
    20490 10 atoms, 9 bonds, 1 residue, 1 model selected 
    20491 
    20492 > ui mousemode right translate
    20493 
    20494 > style sel stick
    20495 
    20496 Changed 10 atom styles 
    20497 
    20498 > show sel atoms
    20499 
    20500 > color sel gray
    20501 
    20502 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    20503 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    20504 
    20505 ——— End of log from Mon Jul 3 21:54:16 2023 ———
    20506 
    20507 opened ChimeraX session 
    20508 
    20509 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    20510 > UASLP/Lab Virología/AlphaFold/BFV AlphaFold.pdb"
    20511 
    20512 Chain information for BFV AlphaFold.pdb #44 
    20513 --- 
    20514 Chain | Description 
    20515 A | No description available 
    20516  
    20517 
    20518 > hide #43 models
    20519 
    20520 > select add #43
    20521 
    20522 4223 atoms, 4279 bonds, 267 residues, 1 model selected 
    20523 
    20524 > select subtract #43
    20525 
    20526 Nothing selected 
    20527 
    20528 > color #44 #ffaa7fff
    20529 
    20530 > color #44 #ffb375ff
    20531 
    20532 > color #44 #ffa77bff
    20533 
    20534 > color #44 #ffae6cff
    20535 
    20536 > color #44 #c78854ff
    20537 
    20538 > color #44 #d18f59ff
    20539 
    20540 > color #44 #dc965dff
    20541 
    20542 > color #44 #cf8d58ff
    20543 
    20544 > color #44 #d18f59ff
    20545 
    20546 > ui tool show Matchmaker
    20547 
    20548 > matchmaker #44 to #2
    20549 
    20550 Parameters 
    20551 --- 
    20552 Chain pairing | bb 
    20553 Alignment algorithm | Needleman-Wunsch 
    20554 Similarity matrix | BLOSUM-62 
    20555 SS fraction | 0.3 
    20556 Gap open (HH/SS/other) | 18/18/6 
    20557 Gap extend | 1 
    20558 SS matrix |  |  | H | S | O 
    20559 ---|---|---|--- 
    20560 H | 6 | -9 | -6 
    20561 S |  | 6 | -6 
    20562 O |  |  | 4 
    20563 Iteration cutoff | 2 
    20564  
    20565 Matchmaker 3j2w.pdb, chain I (#2) with BFV AlphaFold.pdb, chain A (#44),
    20566 sequence alignment score = 630.2 
    20567 RMSD between 144 pruned atom pairs is 0.775 angstroms; (across all 149 pairs:
    20568 1.027) 
    20569  
    20570 
    20571 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    20572 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    20573 
    20574 > ui mousemode right rotate
    20575 
    20576 > ui mousemode right select
    20577 
    20578 > select #2/I:126
    20579 
    20580 9 atoms, 8 bonds, 1 residue, 1 model selected 
    20581 
    20582 > select #44/A:112
    20583 
    20584 12 atoms, 11 bonds, 1 residue, 1 model selected 
    20585 Alignment identifier is 44/A 
    20586 
    20587 > style sel stick
    20588 
    20589 Changed 12 atom styles 
    20590 
    20591 > show sel atoms
    20592 
    20593 > color sel red
    20594 
    20595 > select #44/A:114
    20596 
    20597 22 atoms, 21 bonds, 1 residue, 1 model selected 
    20598 
    20599 > style sel stick
    20600 
    20601 Changed 22 atom styles 
    20602 
    20603 > show sel atoms
    20604 
    20605 > color sel blue
    20606 
    20607 > ui mousemode right translate
    20608 
    20609 > ui mousemode right select
    20610 
    20611 > select #44/A:226
    20612 
    20613 15 atoms, 14 bonds, 1 residue, 1 model selected 
    20614 
    20615 > ui mousemode right translate
    20616 
    20617 > style sel stick
    20618 
    20619 Changed 15 atom styles 
    20620 
    20621 > show sel atoms
    20622 
    20623 > color sel red
    20624 
    20625 > set bgColor black
    20626 
    20627 > set bgColor white
    20628 
    20629 > ui mousemode right select
    20630 
    20631 Drag select of 1 residues 
    20632 
    20633 > select #44/A:176
    20634 
    20635 15 atoms, 14 bonds, 1 residue, 1 model selected 
    20636 
    20637 > ui mousemode right translate
    20638 
    20639 > style sel stick
    20640 
    20641 Changed 15 atom styles 
    20642 
    20643 > show sel atoms
    20644 
    20645 > color sel red
    20646 
    20647 > ui mousemode right select
    20648 
    20649 > select #2/I:183
    20650 
    20651 9 atoms, 8 bonds, 1 residue, 1 model selected 
    20652 
    20653 > select #44/A:169
    20654 
    20655 22 atoms, 21 bonds, 1 residue, 1 model selected 
    20656 
    20657 > style sel stick
    20658 
    20659 Changed 22 atom styles 
    20660 
    20661 > show sel atoms
    20662 
    20663 > color sel blue
    20664 
    20665 Drag select of 3 residues 
    20666 
    20667 > select clear
    20668 
    20669 > ui mousemode right translate
    20670 
    20671 > ui mousemode right select
    20672 
    20673 > select clear
    20674 
    20675 > select #2/I:178
    20676 
    20677 9 atoms, 8 bonds, 1 residue, 1 model selected 
    20678 
    20679 > select #44/A:164
    20680 
    20681 22 atoms, 21 bonds, 1 residue, 1 model selected 
    20682 
    20683 > ui mousemode right translate
    20684 
    20685 > style sel stick
    20686 
    20687 Changed 22 atom styles 
    20688 
    20689 > show sel atoms
    20690 
    20691 > color sel blue
    20692 
    20693 > ui mousemode right select
    20694 
    20695 > select #2/I:157
    20696 
    20697 9 atoms, 8 bonds, 1 residue, 1 model selected 
    20698 
    20699 > select #44/A:143
    20700 
    20701 22 atoms, 21 bonds, 1 residue, 1 model selected 
    20702 
    20703 > ui mousemode right translate
    20704 
    20705 > style sel stick
    20706 
    20707 Changed 22 atom styles 
    20708 
    20709 > show sel atoms
    20710 
    20711 > color sel blue
    20712 
    20713 > ui mousemode right select
    20714 
    20715 > select #2/I:154
    20716 
    20717 8 atoms, 7 bonds, 1 residue, 1 model selected 
    20718 
    20719 > select #44/A:140
    20720 
    20721 15 atoms, 14 bonds, 1 residue, 1 model selected 
    20722 
    20723 > select #2/I:154
    20724 
    20725 8 atoms, 7 bonds, 1 residue, 1 model selected 
    20726 
    20727 > select #44/A:140
    20728 
    20729 15 atoms, 14 bonds, 1 residue, 1 model selected 
    20730 
    20731 > select #44/A:140
    20732 
    20733 15 atoms, 14 bonds, 1 residue, 1 model selected 
    20734 
    20735 > style sel stick
    20736 
    20737 Changed 15 atom styles 
    20738 
    20739 > show sel atoms
    20740 
    20741 > color sel red
    20742 
    20743 > ui mousemode right translate
    20744 
    20745 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    20746 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    20747 
    20748 ——— End of log from Mon Jul 3 22:05:56 2023 ———
    20749 
    20750 opened ChimeraX session 
    20751 
    20752 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    20753 > UASLP/Lab Virología/AlphaFold/WEEV AlphaFold.pdb"
    20754 
    20755 Chain information for WEEV AlphaFold.pdb #45 
    20756 --- 
    20757 Chain | Description 
    20758 A | No description available 
    20759  
    20760 
    20761 > color #45 #00aaffff
    20762 
    20763 > color #45 blue
    20764 
    20765 > color #45 #00007fff
    20766 
    20767 > color #45 #5500ffff
    20768 
    20769 > color #45 #00aaffff
    20770 
    20771 > color #45 #0093ddff
    20772 
    20773 > color #45 #0083c5ff
    20774 
    20775 > color #45 #0079b6ff
    20776 
    20777 > hide #44 models
    20778 
    20779 > color #45 #0084c6ff
    20780 
    20781 > color #45 #2f78c6ff
    20782 
    20783 > color #45 #4075c6ff
    20784 
    20785 > color #45 #5581c6ff
    20786 
    20787 > color #45 #6a92c6ff
    20788 
    20789 > show #36 models
    20790 
    20791 > hide #36 models
    20792 
    20793 > select add #44
    20794 
    20795 4047 atoms, 4099 bonds, 253 residues, 1 model selected 
    20796 
    20797 > select subtract #44
    20798 
    20799 Nothing selected 
    20800 
    20801 > ui tool show Matchmaker
    20802 
    20803 > matchmaker #45 to #2
    20804 
    20805 Parameters 
    20806 --- 
    20807 Chain pairing | bb 
    20808 Alignment algorithm | Needleman-Wunsch 
    20809 Similarity matrix | BLOSUM-62 
    20810 SS fraction | 0.3 
    20811 Gap open (HH/SS/other) | 18/18/6 
    20812 Gap extend | 1 
    20813 SS matrix |  |  | H | S | O 
    20814 ---|---|---|--- 
    20815 H | 6 | -9 | -6 
    20816 S |  | 6 | -6 
    20817 O |  |  | 4 
    20818 Iteration cutoff | 2 
    20819  
    20820 Matchmaker 3j2w.pdb, chain I (#2) with WEEV AlphaFold.pdb, chain A (#45),
    20821 sequence alignment score = 514.5 
    20822 RMSD between 148 pruned atom pairs is 0.714 angstroms; (across all 149 pairs:
    20823 0.757) 
    20824  
    20825 
    20826 > ui mousemode right select
    20827 
    20828 > select #45/A:117
    20829 
    20830 14 atoms, 13 bonds, 1 residue, 1 model selected 
    20831 Alignment identifier is 45/A 
    20832 
    20833 > ui mousemode right translate
    20834 
    20835 > style sel stick
    20836 
    20837 Changed 14 atom styles 
    20838 
    20839 > show sel atoms
    20840 
    20841 > color sel orange
    20842 
    20843 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    20844 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    20845 
    20846 > ui mousemode right select
    20847 
    20848 > select #45/A:119
    20849 
    20850 17 atoms, 16 bonds, 1 residue, 1 model selected 
    20851 
    20852 > select #2/I:128
    20853 
    20854 9 atoms, 8 bonds, 1 residue, 1 model selected 
    20855 
    20856 > select #45/A:119
    20857 
    20858 17 atoms, 16 bonds, 1 residue, 1 model selected 
    20859 
    20860 > style sel stick
    20861 
    20862 Changed 17 atom styles 
    20863 
    20864 > show sel atoms
    20865 
    20866 > color sel orange
    20867 
    20868 > ui mousemode right translate
    20869 
    20870 > ui mousemode right select
    20871 
    20872 > select clear
    20873 
    20874 > select #45/A:119
    20875 
    20876 17 atoms, 16 bonds, 1 residue, 1 model selected 
    20877 
    20878 > ui mousemode right translate
    20879 
    20880 > ui mousemode right select
    20881 
    20882 > select #2/I:240
    20883 
    20884 9 atoms, 8 bonds, 1 residue, 1 model selected 
    20885 Drag select of 2 residues 
    20886 
    20887 > select #2/I:239
    20888 
    20889 8 atoms, 7 bonds, 1 residue, 1 model selected 
    20890 
    20891 > ui mousemode right translate
    20892 
    20893 > ui mousemode right select
    20894 
    20895 > select #45/A:231
    20896 
    20897 15 atoms, 14 bonds, 1 residue, 1 model selected 
    20898 
    20899 > style sel sphere
    20900 
    20901 Changed 15 atom styles 
    20902 
    20903 > style sel stick
    20904 
    20905 Changed 15 atom styles 
    20906 
    20907 > show sel atoms
    20908 
    20909 > color sel red
    20910 
    20911 > ui mousemode right translate
    20912 
    20913 > ui mousemode right select
    20914 
    20915 > select #2/I:190
    20916 
    20917 9 atoms, 8 bonds, 1 residue, 1 model selected 
    20918 
    20919 > select clear
    20920 
    20921 > select #45/A:181
    20922 
    20923 14 atoms, 14 bonds, 1 residue, 1 model selected 
    20924 
    20925 > style sel stick
    20926 
    20927 Changed 14 atom styles 
    20928 
    20929 > show sel atoms
    20930 
    20931 > color sel magenta
    20932 
    20933 > ui mousemode right translate
    20934 
    20935 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    20936 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    20937 
    20938 ——— End of log from Tue Jul 4 13:42:21 2023 ———
    20939 
    20940 opened ChimeraX session 
    20941 
    20942 > ui mousemode right select
    20943 
    20944 > select #2/I:183
    20945 
    20946 9 atoms, 8 bonds, 1 residue, 1 model selected 
    20947 
    20948 > select #45/A:174
    20949 
    20950 17 atoms, 16 bonds, 1 residue, 1 model selected 
    20951 
    20952 > style sel stick
    20953 
    20954 Changed 17 atom styles 
    20955 
    20956 > show sel atoms
    20957 
    20958 > color sel orange
    20959 
    20960 > ui mousemode right translate
    20961 
    20962 > ui mousemode right select
    20963 
    20964 > select #2/I:178
    20965 
    20966 9 atoms, 8 bonds, 1 residue, 1 model selected 
    20967 
    20968 > select #45/A:169
    20969 
    20970 22 atoms, 21 bonds, 1 residue, 1 model selected 
    20971 
    20972 > select #45/A:169
    20973 
    20974 22 atoms, 21 bonds, 1 residue, 1 model selected 
    20975 
    20976 > style sel stick
    20977 
    20978 Changed 22 atom styles 
    20979 
    20980 > show sel atoms
    20981 
    20982 > color sel blue
    20983 
    20984 > ui mousemode right translate
    20985 
    20986 > ui mousemode right select
    20987 
    20988 > select #2/I:157
    20989 
    20990 9 atoms, 8 bonds, 1 residue, 1 model selected 
    20991 
    20992 > select #45/A:148
    20993 
    20994 10 atoms, 9 bonds, 1 residue, 1 model selected 
    20995 
    20996 > ui mousemode right translate
    20997 
    20998 > style sel stick
    20999 
    21000 Changed 10 atom styles 
    21001 
    21002 > show sel atoms
    21003 
    21004 [Repeated 1 time(s)]
    21005 
    21006 > color sel gray
    21007 
    21008 > ui mousemode right select
    21009 
    21010 > select #2/I:154
    21011 
    21012 8 atoms, 7 bonds, 1 residue, 1 model selected 
    21013 
    21014 > select #45/A:145
    21015 
    21016 17 atoms, 16 bonds, 1 residue, 1 model selected 
    21017 
    21018 > ui mousemode right translate
    21019 
    21020 > style sel stick
    21021 
    21022 Changed 17 atom styles 
    21023 
    21024 > show sel atoms
    21025 
    21026 > color sel orange
    21027 
    21028 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    21029 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    21030 
    21031 ——— End of log from Tue Jul 4 14:24:08 2023 ———
    21032 
    21033 opened ChimeraX session 
    21034 
    21035 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    21036 > UASLP/Lab Virología/AlphaFold/EEEV AlphaFold.pdb"
    21037 
    21038 Chain information for EEEV AlphaFold.pdb #46 
    21039 --- 
    21040 Chain | Description 
    21041 A | No description available 
    21042  
    21043 
    21044 > ui tool show Matchmaker
    21045 
    21046 > matchmaker #46 to #2
    21047 
    21048 Parameters 
    21049 --- 
    21050 Chain pairing | bb 
    21051 Alignment algorithm | Needleman-Wunsch 
    21052 Similarity matrix | BLOSUM-62 
    21053 SS fraction | 0.3 
    21054 Gap open (HH/SS/other) | 18/18/6 
    21055 Gap extend | 1 
    21056 SS matrix |  |  | H | S | O 
    21057 ---|---|---|--- 
    21058 H | 6 | -9 | -6 
    21059 S |  | 6 | -6 
    21060 O |  |  | 4 
    21061 Iteration cutoff | 2 
    21062  
    21063 Matchmaker 3j2w.pdb, chain I (#2) with EEEV AlphaFold.pdb, chain A (#46),
    21064 sequence alignment score = 506.1 
    21065 RMSD between 148 pruned atom pairs is 0.711 angstroms; (across all 149 pairs:
    21066 0.764) 
    21067  
    21068 
    21069 > hide #45 models
    21070 
    21071 > select add #45
    21072 
    21073 4153 atoms, 4213 bonds, 259 residues, 1 model selected 
    21074 
    21075 > select subtract #45
    21076 
    21077 Nothing selected 
    21078 
    21079 > color #46 black
    21080 
    21081 > color #46 #444444ff
    21082 
    21083 > color #46 #646464ff
    21084 
    21085 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    21086 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    21087 
    21088 > ui mousemode right select
    21089 
    21090 > select #2/I:126
    21091 
    21092 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21093 
    21094 > select #46/A:119
    21095 
    21096 14 atoms, 13 bonds, 1 residue, 1 model selected 
    21097 Alignment identifier is 46/A 
    21098 
    21099 > style sel stick
    21100 
    21101 Changed 14 atom styles 
    21102 
    21103 > show sel atoms
    21104 
    21105 > color sel orange
    21106 
    21107 > set bgColor black
    21108 
    21109 > set bgColor white
    21110 
    21111 > ui mousemode right translate
    21112 
    21113 > ui mousemode right rotate
    21114 
    21115 > ui mousemode right select
    21116 
    21117 > select #46/A:121
    21118 
    21119 17 atoms, 16 bonds, 1 residue, 1 model selected 
    21120 
    21121 > style sel stick
    21122 
    21123 Changed 17 atom styles 
    21124 
    21125 > show sel atoms
    21126 
    21127 > color sel orange
    21128 
    21129 > ui mousemode right translate
    21130 
    21131 > ui mousemode right select
    21132 
    21133 > select #2/I:240
    21134 
    21135 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21136 
    21137 > select #2/I:240
    21138 
    21139 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21140 
    21141 > select #46/A:233
    21142 
    21143 15 atoms, 14 bonds, 1 residue, 1 model selected 
    21144 
    21145 > style sel stick
    21146 
    21147 Changed 15 atom styles 
    21148 
    21149 > show sel atoms
    21150 
    21151 > color sel red
    21152 
    21153 > ui mousemode right translate
    21154 
    21155 > ui mousemode right select
    21156 
    21157 > select #2/I:190
    21158 
    21159 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21160 
    21161 > select #2/I:190
    21162 
    21163 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21164 
    21165 > select #46/A:183
    21166 
    21167 14 atoms, 14 bonds, 1 residue, 1 model selected 
    21168 
    21169 > style sel stick
    21170 
    21171 Changed 14 atom styles 
    21172 
    21173 > show sel atoms
    21174 
    21175 > color sel magenta
    21176 
    21177 > select #2/I:190
    21178 
    21179 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21180 
    21181 > select #46/A:183
    21182 
    21183 14 atoms, 14 bonds, 1 residue, 1 model selected 
    21184 
    21185 > ui mousemode right translate
    21186 
    21187 > ui mousemode right select
    21188 
    21189 > select #2/I:183
    21190 
    21191 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21192 
    21193 > select #46/A:176
    21194 
    21195 17 atoms, 16 bonds, 1 residue, 1 model selected 
    21196 
    21197 > select #46/A:176
    21198 
    21199 17 atoms, 16 bonds, 1 residue, 1 model selected 
    21200 
    21201 > ui mousemode right translate
    21202 
    21203 > style sel stick
    21204 
    21205 Changed 17 atom styles 
    21206 
    21207 > show sel atoms
    21208 
    21209 > color sel orange
    21210 
    21211 > style sel stick
    21212 
    21213 Changed 17 atom styles 
    21214 
    21215 > ui mousemode right select
    21216 
    21217 > select #2/I:178
    21218 
    21219 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21220 
    21221 > select #46/A:171
    21222 
    21223 22 atoms, 21 bonds, 1 residue, 1 model selected 
    21224 
    21225 > ui mousemode right translate
    21226 
    21227 > style sel stick
    21228 
    21229 Changed 22 atom styles 
    21230 
    21231 > show sel atoms
    21232 
    21233 > color sel blue
    21234 
    21235 > ui mousemode right select
    21236 
    21237 > select #2/I:157
    21238 
    21239 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21240 
    21241 > select clear
    21242 
    21243 > select #46/A:150
    21244 
    21245 10 atoms, 9 bonds, 1 residue, 1 model selected 
    21246 
    21247 > select #2/I:157
    21248 
    21249 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21250 
    21251 > select #46/A:150
    21252 
    21253 10 atoms, 9 bonds, 1 residue, 1 model selected 
    21254 
    21255 > select #46/A:150
    21256 
    21257 10 atoms, 9 bonds, 1 residue, 1 model selected 
    21258 
    21259 > style sel stick
    21260 
    21261 Changed 10 atom styles 
    21262 
    21263 > show sel atoms
    21264 
    21265 > color sel gray
    21266 
    21267 Drag select of 2 residues 
    21268 
    21269 > select #2/I:156
    21270 
    21271 5 atoms, 4 bonds, 1 residue, 1 model selected 
    21272 Drag select of 1 residues 
    21273 
    21274 > select clear
    21275 
    21276 [Repeated 1 time(s)]
    21277 
    21278 > ui mousemode right translate
    21279 
    21280 > ui mousemode right select
    21281 
    21282 > select #2/I:154
    21283 
    21284 8 atoms, 7 bonds, 1 residue, 1 model selected 
    21285 
    21286 > select #2/I:154
    21287 
    21288 8 atoms, 7 bonds, 1 residue, 1 model selected 
    21289 
    21290 > select #46/A:147
    21291 
    21292 17 atoms, 16 bonds, 1 residue, 1 model selected 
    21293 
    21294 > style sel stick
    21295 
    21296 Changed 17 atom styles 
    21297 
    21298 > show sel atoms
    21299 
    21300 > color sel orange
    21301 
    21302 > select clear
    21303 
    21304 [Repeated 1 time(s)]
    21305 
    21306 > ui mousemode right translate
    21307 
    21308 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    21309 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    21310 
    21311 ——— End of log from Wed Jul 5 13:32:58 2023 ———
    21312 
    21313 opened ChimeraX session 
    21314 
    21315 > color #46 #424242ff
    21316 
    21317 > color #46 #323232ff
    21318 
    21319 > color #46 #3a3a3aff
    21320 
    21321 > ui mousemode right select
    21322 
    21323 > select #46/A:147
    21324 
    21325 17 atoms, 16 bonds, 1 residue, 1 model selected 
    21326 
    21327 > select clear
    21328 
    21329 > ui mousemode right translate
    21330 
    21331 > ui mousemode right select
    21332 
    21333 > select #46/A:150
    21334 
    21335 10 atoms, 9 bonds, 1 residue, 1 model selected 
    21336 
    21337 > color sel gray
    21338 
    21339 > ui mousemode right translate
    21340 
    21341 > ui mousemode right select
    21342 
    21343 > select #46/A:171@CA
    21344 
    21345 1 atom, 1 residue, 1 model selected 
    21346 
    21347 > color #46 #28293aff
    21348 
    21349 > color #46 #aaaa7fff
    21350 
    21351 > color #46 #55007fff
    21352 
    21353 > color #46 magenta
    21354 
    21355 > color #46 #550000ff
    21356 
    21357 > color #46 #660000ff
    21358 
    21359 > color #46 #710000ff
    21360 
    21361 > color #46 #6f0000ff
    21362 
    21363 > select clear
    21364 
    21365 [Repeated 1 time(s)]
    21366 
    21367 > ui mousemode right translate
    21368 
    21369 > show #30 models
    21370 
    21371 > hide #30 models
    21372 
    21373 > ui mousemode right select
    21374 
    21375 > select clear
    21376 
    21377 [Repeated 1 time(s)]
    21378 
    21379 > select #46/A:150
    21380 
    21381 10 atoms, 9 bonds, 1 residue, 1 model selected 
    21382 
    21383 > color sel gray
    21384 
    21385 > ui mousemode right translate
    21386 
    21387 > ui mousemode right select
    21388 
    21389 > select #46/A:119
    21390 
    21391 14 atoms, 13 bonds, 1 residue, 1 model selected 
    21392 
    21393 > color sel orange
    21394 
    21395 > select #46/A:121
    21396 
    21397 17 atoms, 16 bonds, 1 residue, 1 model selected 
    21398 
    21399 > color sel orange
    21400 
    21401 > ui mousemode right translate
    21402 
    21403 > ui mousemode right select
    21404 
    21405 > select #46/A:233
    21406 
    21407 15 atoms, 14 bonds, 1 residue, 1 model selected 
    21408 
    21409 > color sel red
    21410 
    21411 > ui mousemode right translate
    21412 
    21413 > ui mousemode right select
    21414 
    21415 Drag select of 2 residues 
    21416 
    21417 > select #46/A:183
    21418 
    21419 14 atoms, 14 bonds, 1 residue, 1 model selected 
    21420 
    21421 > select #46/A:183
    21422 
    21423 14 atoms, 14 bonds, 1 residue, 1 model selected 
    21424 
    21425 > color sel magenta
    21426 
    21427 > ui mousemode right translate
    21428 
    21429 > ui mousemode right select
    21430 
    21431 > select #46/A:176
    21432 
    21433 17 atoms, 16 bonds, 1 residue, 1 model selected 
    21434 
    21435 > color sel orange
    21436 
    21437 > ui mousemode right translate
    21438 
    21439 > ui mousemode right select
    21440 
    21441 > select #46/A:171
    21442 
    21443 22 atoms, 21 bonds, 1 residue, 1 model selected 
    21444 
    21445 > color sel blue
    21446 
    21447 > ui mousemode right translate
    21448 
    21449 > ui mousemode right select
    21450 
    21451 > select #46/A:150
    21452 
    21453 10 atoms, 9 bonds, 1 residue, 1 model selected 
    21454 
    21455 > select #46/A:147
    21456 
    21457 17 atoms, 16 bonds, 1 residue, 1 model selected 
    21458 
    21459 > color sel orange
    21460 
    21461 > ui mousemode right translate
    21462 
    21463 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    21464 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    21465 
    21466 ——— End of log from Wed Jul 5 13:38:28 2023 ———
    21467 
    21468 opened ChimeraX session 
    21469 
    21470 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    21471 > UASLP/Lab Virología/AlphaFold/Getah virus AlphaFold.pdb"
    21472 
    21473 Chain information for Getah virus AlphaFold.pdb #47 
    21474 --- 
    21475 Chain | Description 
    21476 A | No description available 
    21477  
    21478 
    21479 > color #47 #aaaa7fff
    21480 
    21481 > color #47 #aa5500ff
    21482 
    21483 > color #47 #a15100ff
    21484 
    21485 > color #47 #8c4600ff
    21486 
    21487 > color #47 #8c4b0aff
    21488 
    21489 > color #47 #8c5512ff
    21490 
    21491 > color #47 #8c5d0cff
    21492 
    21493 > color #47 #9c680dff
    21494 
    21495 > color #47 #8c5d0cff
    21496 
    21497 > color #47 #aa5500ff
    21498 
    21499 > color #47 #a35200ff
    21500 
    21501 > color #47 #ad5700ff
    21502 
    21503 > hide #46 models
    21504 
    21505 > select add #46
    21506 
    21507 4167 atoms, 4228 bonds, 261 residues, 1 model selected 
    21508 
    21509 > select subtract #46
    21510 
    21511 Nothing selected 
    21512 
    21513 > ui tool show Matchmaker
    21514 
    21515 > matchmaker #47 to #2
    21516 
    21517 Parameters 
    21518 --- 
    21519 Chain pairing | bb 
    21520 Alignment algorithm | Needleman-Wunsch 
    21521 Similarity matrix | BLOSUM-62 
    21522 SS fraction | 0.3 
    21523 Gap open (HH/SS/other) | 18/18/6 
    21524 Gap extend | 1 
    21525 SS matrix |  |  | H | S | O 
    21526 ---|---|---|--- 
    21527 H | 6 | -9 | -6 
    21528 S |  | 6 | -6 
    21529 O |  |  | 4 
    21530 Iteration cutoff | 2 
    21531  
    21532 Matchmaker 3j2w.pdb, chain I (#2) with Getah virus AlphaFold.pdb, chain A
    21533 (#47), sequence alignment score = 673.5 
    21534 RMSD between 145 pruned atom pairs is 0.778 angstroms; (across all 149 pairs:
    21535 0.993) 
    21536  
    21537 
    21538 > ui mousemode right select
    21539 
    21540 > select #2/I:126
    21541 
    21542 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21543 
    21544 > select #47/A:127
    21545 
    21546 12 atoms, 11 bonds, 1 residue, 1 model selected 
    21547 Alignment identifier is 47/A 
    21548 
    21549 > style sel stick
    21550 
    21551 Changed 12 atom styles 
    21552 
    21553 > show sel atoms
    21554 
    21555 > color sel red
    21556 
    21557 > select #2/I:128
    21558 
    21559 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21560 
    21561 > select #2/I:126
    21562 
    21563 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21564 
    21565 > select #47/A:127
    21566 
    21567 12 atoms, 11 bonds, 1 residue, 1 model selected 
    21568 
    21569 > select #2/I:128
    21570 
    21571 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21572 
    21573 > select clear
    21574 
    21575 > select #47/A:129
    21576 
    21577 22 atoms, 21 bonds, 1 residue, 1 model selected 
    21578 
    21579 > style sel stick
    21580 
    21581 Changed 22 atom styles 
    21582 
    21583 > show sel atoms
    21584 
    21585 > color sel blue
    21586 
    21587 > ui mousemode right translate
    21588 
    21589 > ui mousemode right select
    21590 
    21591 > select #2/I:240
    21592 
    21593 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21594 
    21595 > select #47/A:241
    21596 
    21597 15 atoms, 14 bonds, 1 residue, 1 model selected 
    21598 
    21599 > style sel stick
    21600 
    21601 Changed 15 atom styles 
    21602 
    21603 > show sel atoms
    21604 
    21605 > color sel red
    21606 
    21607 > ui mousemode right translate
    21608 
    21609 > ui mousemode right select
    21610 
    21611 > select #2/I:190
    21612 
    21613 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21614 
    21615 > select #47/A:191
    21616 
    21617 15 atoms, 14 bonds, 1 residue, 1 model selected 
    21618 
    21619 > style sel stick
    21620 
    21621 Changed 15 atom styles 
    21622 
    21623 > show sel atoms
    21624 
    21625 > color sel red
    21626 
    21627 > ui mousemode right translate
    21628 
    21629 > ui mousemode right select
    21630 
    21631 > select #2/I:183
    21632 
    21633 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21634 
    21635 > select #47/A:184
    21636 
    21637 22 atoms, 21 bonds, 1 residue, 1 model selected 
    21638 
    21639 > style sel stick
    21640 
    21641 Changed 22 atom styles 
    21642 
    21643 > show sel atoms
    21644 
    21645 > color sel blue
    21646 
    21647 > ui mousemode right translate
    21648 
    21649 > ui mousemode right select
    21650 
    21651 > select #2/I:178
    21652 
    21653 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21654 
    21655 > select #47/A:179
    21656 
    21657 22 atoms, 21 bonds, 1 residue, 1 model selected 
    21658 
    21659 > style sel stick
    21660 
    21661 Changed 22 atom styles 
    21662 
    21663 > show sel atoms
    21664 
    21665 > color sel blue
    21666 
    21667 > ui mousemode right translate
    21668 
    21669 > ui mousemode right select
    21670 
    21671 > select #2/I:157
    21672 
    21673 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21674 
    21675 > select #47/A:158
    21676 
    21677 22 atoms, 21 bonds, 1 residue, 1 model selected 
    21678 
    21679 > style sel stick
    21680 
    21681 Changed 22 atom styles 
    21682 
    21683 > show sel atoms
    21684 
    21685 > color sel blue
    21686 
    21687 > select #2/I:154
    21688 
    21689 8 atoms, 7 bonds, 1 residue, 1 model selected 
    21690 
    21691 > select #47/A:155
    21692 
    21693 12 atoms, 11 bonds, 1 residue, 1 model selected 
    21694 
    21695 > style sel stick
    21696 
    21697 Changed 12 atom styles 
    21698 
    21699 > show sel atoms
    21700 
    21701 > color sel red
    21702 
    21703 > ui mousemode right translate
    21704 
    21705 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    21706 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    21707 
    21708 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    21709 > UASLP/Lab Virología/AlphaFold/Mayaro virus AlphaFold.pdb"
    21710 
    21711 Chain information for Mayaro virus AlphaFold.pdb #48 
    21712 --- 
    21713 Chain | Description 
    21714 A | No description available 
    21715  
    21716 
    21717 > hide #47 models
    21718 
    21719 > select add #47
    21720 
    21721 4298 atoms, 4353 bonds, 268 residues, 1 model selected 
    21722 
    21723 > select subtract #47
    21724 
    21725 Nothing selected 
    21726 
    21727 > color #48 #ffaa00ff
    21728 
    21729 > color #48 #55aa00ff
    21730 
    21731 > color #48 #51a200ff
    21732 
    21733 > ui tool show Matchmaker
    21734 
    21735 > matchmaker #48 to #2
    21736 
    21737 Parameters 
    21738 --- 
    21739 Chain pairing | bb 
    21740 Alignment algorithm | Needleman-Wunsch 
    21741 Similarity matrix | BLOSUM-62 
    21742 SS fraction | 0.3 
    21743 Gap open (HH/SS/other) | 18/18/6 
    21744 Gap extend | 1 
    21745 SS matrix |  |  | H | S | O 
    21746 ---|---|---|--- 
    21747 H | 6 | -9 | -6 
    21748 S |  | 6 | -6 
    21749 O |  |  | 4 
    21750 Iteration cutoff | 2 
    21751  
    21752 Matchmaker 3j2w.pdb, chain I (#2) with Mayaro virus AlphaFold.pdb, chain A
    21753 (#48), sequence alignment score = 674.3 
    21754 RMSD between 147 pruned atom pairs is 0.759 angstroms; (across all 149 pairs:
    21755 0.801) 
    21756  
    21757 
    21758 > color #48 #59b100ff
    21759 
    21760 > color #48 #5bb600ff
    21761 
    21762 [Repeated 1 time(s)]
    21763 
    21764 > color #48 #5bb500ff
    21765 
    21766 > color #48 #5ab300ff
    21767 
    21768 > color #48 #60ba00ff
    21769 
    21770 > ui mousemode right select
    21771 
    21772 > select #2/I:126
    21773 
    21774 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21775 
    21776 > select #48/A:117
    21777 
    21778 15 atoms, 14 bonds, 1 residue, 1 model selected 
    21779 Alignment identifier is 48/A 
    21780 
    21781 > style sel stick
    21782 
    21783 Changed 15 atom styles 
    21784 
    21785 > show sel atoms
    21786 
    21787 > color sel red
    21788 
    21789 > select #2/I:128
    21790 
    21791 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21792 
    21793 > select #48/A:119
    21794 
    21795 22 atoms, 21 bonds, 1 residue, 1 model selected 
    21796 
    21797 > style sel stick
    21798 
    21799 Changed 22 atom styles 
    21800 
    21801 > show sel atoms
    21802 
    21803 > color sel blue
    21804 
    21805 > ui mousemode right translate
    21806 
    21807 > ui mousemode right select
    21808 
    21809 > select #2/I:240
    21810 
    21811 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21812 
    21813 > select #48/A:231
    21814 
    21815 15 atoms, 14 bonds, 1 residue, 1 model selected 
    21816 
    21817 > style sel stick
    21818 
    21819 Changed 15 atom styles 
    21820 
    21821 > show sel atoms
    21822 
    21823 > color sel orange red
    21824 
    21825 > color sel red
    21826 
    21827 > ui mousemode right translate
    21828 
    21829 > ui mousemode right select
    21830 
    21831 > select #2/I:183
    21832 
    21833 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21834 
    21835 > ui mousemode right translate
    21836 
    21837 > ui mousemode right select
    21838 
    21839 > select #2/I:190
    21840 
    21841 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21842 
    21843 > select #48/A:181
    21844 
    21845 15 atoms, 14 bonds, 1 residue, 1 model selected 
    21846 
    21847 > style sel stick
    21848 
    21849 Changed 15 atom styles 
    21850 
    21851 > show sel atoms
    21852 
    21853 > color sel red
    21854 
    21855 > ui mousemode right translate
    21856 
    21857 > ui mousemode right select
    21858 
    21859 > select #2/I:183
    21860 
    21861 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21862 
    21863 > select #48/A:174
    21864 
    21865 22 atoms, 21 bonds, 1 residue, 1 model selected 
    21866 
    21867 > style sel stick
    21868 
    21869 Changed 22 atom styles 
    21870 
    21871 > show sel atoms
    21872 
    21873 > color sel blue
    21874 
    21875 > ui mousemode right translate
    21876 
    21877 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    21878 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    21879 
    21880 ——— End of log from Thu Jul 6 13:25:11 2023 ———
    21881 
    21882 opened ChimeraX session 
    21883 
    21884 > ui mousemode right select
    21885 
    21886 > select #48/A:117
    21887 
    21888 15 atoms, 14 bonds, 1 residue, 1 model selected 
    21889 
    21890 > select #48/A:119
    21891 
    21892 22 atoms, 21 bonds, 1 residue, 1 model selected 
    21893 
    21894 > ui mousemode right translate
    21895 
    21896 > ui mousemode right select
    21897 
    21898 > select #48/A:231
    21899 
    21900 15 atoms, 14 bonds, 1 residue, 1 model selected 
    21901 
    21902 > ui mousemode right translate
    21903 
    21904 > ui mousemode right select
    21905 
    21906 > select #48/A:181
    21907 
    21908 15 atoms, 14 bonds, 1 residue, 1 model selected 
    21909 
    21910 > select #2/I:190
    21911 
    21912 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21913 
    21914 > select #48/A:174
    21915 
    21916 22 atoms, 21 bonds, 1 residue, 1 model selected 
    21917 
    21918 > ui mousemode right translate
    21919 
    21920 > ui mousemode right select
    21921 
    21922 > select #2/I:178
    21923 
    21924 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21925 
    21926 > select #48/A:169
    21927 
    21928 22 atoms, 21 bonds, 1 residue, 1 model selected 
    21929 
    21930 > ui mousemode right translate
    21931 
    21932 > ui mousemode right select
    21933 
    21934 > style sel stick
    21935 
    21936 Changed 22 atom styles 
    21937 
    21938 > show sel atoms
    21939 
    21940 > color sel red
    21941 
    21942 > color sel blue
    21943 
    21944 > select #2/I:178
    21945 
    21946 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21947 
    21948 > ui mousemode right translate
    21949 
    21950 > ui mousemode right select
    21951 
    21952 > select #2/I:157
    21953 
    21954 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21955 
    21956 > select #48/A:148
    21957 
    21958 24 atoms, 23 bonds, 1 residue, 1 model selected 
    21959 
    21960 > ui mousemode right rotate
    21961 
    21962 > ui mousemode right translate
    21963 
    21964 > style sel stick
    21965 
    21966 Changed 24 atom styles 
    21967 
    21968 > show sel atoms
    21969 
    21970 > color sel red
    21971 
    21972 > color sel blue
    21973 
    21974 > ui mousemode right rotate
    21975 
    21976 > ui mousemode right select
    21977 
    21978 > select #2/I:154
    21979 
    21980 8 atoms, 7 bonds, 1 residue, 1 model selected 
    21981 
    21982 > select #48/A:145
    21983 
    21984 12 atoms, 11 bonds, 1 residue, 1 model selected 
    21985 
    21986 > select #2/I:154
    21987 
    21988 8 atoms, 7 bonds, 1 residue, 1 model selected 
    21989 
    21990 > select #48/A:145
    21991 
    21992 12 atoms, 11 bonds, 1 residue, 1 model selected 
    21993 
    21994 > select #2/I:154
    21995 
    21996 8 atoms, 7 bonds, 1 residue, 1 model selected 
    21997 
    21998 > select #48/A:145
    21999 
    22000 12 atoms, 11 bonds, 1 residue, 1 model selected 
    22001 
    22002 > ui mousemode right translate
    22003 
    22004 > style sel stick
    22005 
    22006 Changed 12 atom styles 
    22007 
    22008 > show sel atoms
    22009 
    22010 > color sel red
    22011 
    22012 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    22013 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    22014 
    22015 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    22016 > UASLP/Lab Virología/AlphaFold/SFV AlphaFold.pdb"
    22017 
    22018 Chain information for SFV AlphaFold.pdb #49 
    22019 --- 
    22020 Chain | Description 
    22021 A | No description available 
    22022  
    22023 
    22024 > color #49 #cd965eff
    22025 
    22026 > color #49 #ffaaffff
    22027 
    22028 > color #49 #ff007fff
    22029 
    22030 > color #49 #ff257cff
    22031 
    22032 > color #49 #ff478eff
    22033 
    22034 > color #49 #ff66b5ff
    22035 
    22036 > color #49 #ff8abfff
    22037 
    22038 > color #49 #ff74b3ff
    22039 
    22040 > color #49 #ff576dff
    22041 
    22042 > select add #48
    22043 
    22044 4180 atoms, 4234 bonds, 258 residues, 1 model selected 
    22045 
    22046 > select subtract #48
    22047 
    22048 Nothing selected 
    22049 
    22050 > ui tool show Matchmaker
    22051 
    22052 > matchmaker #49 to #2
    22053 
    22054 Parameters 
    22055 --- 
    22056 Chain pairing | bb 
    22057 Alignment algorithm | Needleman-Wunsch 
    22058 Similarity matrix | BLOSUM-62 
    22059 SS fraction | 0.3 
    22060 Gap open (HH/SS/other) | 18/18/6 
    22061 Gap extend | 1 
    22062 SS matrix |  |  | H | S | O 
    22063 ---|---|---|--- 
    22064 H | 6 | -9 | -6 
    22065 S |  | 6 | -6 
    22066 O |  |  | 4 
    22067 Iteration cutoff | 2 
    22068  
    22069 Matchmaker 3j2w.pdb, chain I (#2) with SFV AlphaFold.pdb, chain A (#49),
    22070 sequence alignment score = 688.6 
    22071 RMSD between 147 pruned atom pairs is 0.722 angstroms; (across all 149 pairs:
    22072 0.761) 
    22073  
    22074 
    22075 > hide #48 models
    22076 
    22077 > ui mousemode right select
    22078 
    22079 > select #2/I:126
    22080 
    22081 9 atoms, 8 bonds, 1 residue, 1 model selected 
    22082 
    22083 > select #2/I:126
    22084 
    22085 9 atoms, 8 bonds, 1 residue, 1 model selected 
    22086 
    22087 > select #49/A:126
    22088 
    22089 15 atoms, 14 bonds, 1 residue, 1 model selected 
    22090 
    22091 > select #49/A:126
    22092 
    22093 15 atoms, 14 bonds, 1 residue, 1 model selected 
    22094 
    22095 > select #2/I:126
    22096 
    22097 9 atoms, 8 bonds, 1 residue, 1 model selected 
    22098 
    22099 > select #49/A:126
    22100 
    22101 15 atoms, 14 bonds, 1 residue, 1 model selected 
    22102 Alignment identifier is 49/A 
    22103 
    22104 > ui mousemode right translate
    22105 
    22106 > style sel stick
    22107 
    22108 Changed 15 atom styles 
    22109 
    22110 > show sel atoms
    22111 
    22112 > color sel red
    22113 
    22114 > ui mousemode right select
    22115 
    22116 > select #49/A:128
    22117 
    22118 22 atoms, 21 bonds, 1 residue, 1 model selected 
    22119 
    22120 > style sel stick
    22121 
    22122 Changed 22 atom styles 
    22123 
    22124 > show sel atoms
    22125 
    22126 > color sel blue
    22127 
    22128 > ui mousemode right translate
    22129 
    22130 > ui mousemode right select
    22131 
    22132 > select #2/I:240
    22133 
    22134 9 atoms, 8 bonds, 1 residue, 1 model selected 
    22135 
    22136 > select clear
    22137 
    22138 > select #49/A:240
    22139 
    22140 15 atoms, 14 bonds, 1 residue, 1 model selected 
    22141 
    22142 > style sel stick
    22143 
    22144 Changed 15 atom styles 
    22145 
    22146 > show sel atoms
    22147 
    22148 > color sel red
    22149 
    22150 > show sel cartoons
    22151 
    22152 > select clear
    22153 
    22154 [Repeated 1 time(s)]
    22155 
    22156 > ui mousemode right translate
    22157 
    22158 > color #49 #ff6b75ff
    22159 
    22160 > color #49 #ff8c98ff
    22161 
    22162 > color #49 #ff878fff
    22163 
    22164 > color #49 #ff7d7fff
    22165 
    22166 > ui mousemode right rotate
    22167 
    22168 > ui mousemode right select
    22169 
    22170 > select #49/A:126
    22171 
    22172 15 atoms, 14 bonds, 1 residue, 1 model selected 
    22173 
    22174 > color sel red
    22175 
    22176 > select #49/A:128
    22177 
    22178 22 atoms, 21 bonds, 1 residue, 1 model selected 
    22179 
    22180 > color sel blue
    22181 
    22182 > ui mousemode right translate
    22183 
    22184 > ui mousemode right select
    22185 
    22186 > select #49/A:240
    22187 
    22188 15 atoms, 14 bonds, 1 residue, 1 model selected 
    22189 
    22190 > color sel red
    22191 
    22192 > ui mousemode right translate
    22193 
    22194 > ui mousemode right select
    22195 
    22196 > select #2/I:190
    22197 
    22198 9 atoms, 8 bonds, 1 residue, 1 model selected 
    22199 
    22200 > select #49/A:190
    22201 
    22202 15 atoms, 14 bonds, 1 residue, 1 model selected 
    22203 
    22204 > ui mousemode right translate
    22205 
    22206 > color sel red
    22207 
    22208 > style sel stick
    22209 
    22210 Changed 15 atom styles 
    22211 
    22212 > show sel atoms
    22213 
    22214 > ui mousemode right select
    22215 
    22216 Drag select of 1 residues 
    22217 
    22218 > select #2/I:183@CA
    22219 
    22220 1 atom, 1 residue, 1 model selected 
    22221 
    22222 > select #49/A:183
    22223 
    22224 22 atoms, 21 bonds, 1 residue, 1 model selected 
    22225 
    22226 > style sel stick
    22227 
    22228 Changed 22 atom styles 
    22229 
    22230 > show sel atoms
    22231 
    22232 > color sel blue
    22233 
    22234 > ui mousemode right zoom
    22235 
    22236 > ui mousemode right translate
    22237 
    22238 > ui mousemode right select
    22239 
    22240 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    22241 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    22242 
    22243 ——— End of log from Mon Jul 10 15:59:37 2023 ———
    22244 
    22245 opened ChimeraX session 
    22246 
    22247 > ui mousemode right select
    22248 
    22249 > select #2/I:178
    22250 
    22251 9 atoms, 8 bonds, 1 residue, 1 model selected 
    22252 
    22253 > select #49/A:178
    22254 
    22255 24 atoms, 23 bonds, 1 residue, 1 model selected 
    22256 
    22257 > select #49/A:178
    22258 
    22259 24 atoms, 23 bonds, 1 residue, 1 model selected 
    22260 
    22261 > select clear
    22262 
    22263 > select #2/I:178
    22264 
    22265 9 atoms, 8 bonds, 1 residue, 1 model selected 
    22266 
    22267 > select #49/A:178
    22268 
    22269 24 atoms, 23 bonds, 1 residue, 1 model selected 
    22270 
    22271 > select #49/A:178
    22272 
    22273 24 atoms, 23 bonds, 1 residue, 1 model selected 
    22274 
    22275 > ui mousemode right translate
    22276 
    22277 > style sel stick
    22278 
    22279 Changed 24 atom styles 
    22280 
    22281 > show sel atoms
    22282 
    22283 > color sel blue
    22284 
    22285 > ui mousemode right select
    22286 
    22287 > select #2/I:157
    22288 
    22289 9 atoms, 8 bonds, 1 residue, 1 model selected 
    22290 
    22291 > select #49/A:157
    22292 
    22293 22 atoms, 21 bonds, 1 residue, 1 model selected 
    22294 
    22295 > ui mousemode right translate
    22296 
    22297 > style sel stick
    22298 
    22299 Changed 22 atom styles 
    22300 
    22301 > show sel atoms
    22302 
    22303 > color sel blue
    22304 
    22305 > ui mousemode right select
    22306 
    22307 > select #2/I:154
    22308 
    22309 8 atoms, 7 bonds, 1 residue, 1 model selected 
    22310 
    22311 > select #2/I:154
    22312 
    22313 8 atoms, 7 bonds, 1 residue, 1 model selected 
    22314 
    22315 > select #49/A:154
    22316 
    22317 12 atoms, 11 bonds, 1 residue, 1 model selected 
    22318 
    22319 > ui mousemode right translate
    22320 
    22321 > style sel stick
    22322 
    22323 Changed 12 atom styles 
    22324 
    22325 > show sel atoms
    22326 
    22327 > color sel blue
    22328 
    22329 > color sel red
    22330 
    22331 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    22332 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    22333 
    22334 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    22335 > UASLP/Lab Virología/AlphaFold/Sindbis virus AlphaFold.pdb"
    22336 
    22337 Chain information for Sindbis virus AlphaFold.pdb #50 
    22338 --- 
    22339 Chain | Description 
    22340 A | No description available 
    22341  
    22342 
    22343 > color #50 white
    22344 
    22345 > color #50 #ccccccff
    22346 
    22347 > color #50 #c5c5c5ff
    22348 
    22349 > color #50 #b0b0b0ff
    22350 
    22351 > color #50 #b8b8b8ff
    22352 
    22353 > hide #49 models
    22354 
    22355 > select add #49
    22356 
    22357 4263 atoms, 4315 bonds, 267 residues, 1 model selected 
    22358 
    22359 > select subtract #49
    22360 
    22361 Nothing selected 
    22362 
    22363 > ui tool show Matchmaker
    22364 
    22365 > matchmaker #50 to #2
    22366 
    22367 Parameters 
    22368 --- 
    22369 Chain pairing | bb 
    22370 Alignment algorithm | Needleman-Wunsch 
    22371 Similarity matrix | BLOSUM-62 
    22372 SS fraction | 0.3 
    22373 Gap open (HH/SS/other) | 18/18/6 
    22374 Gap extend | 1 
    22375 SS matrix |  |  | H | S | O 
    22376 ---|---|---|--- 
    22377 H | 6 | -9 | -6 
    22378 S |  | 6 | -6 
    22379 O |  |  | 4 
    22380 Iteration cutoff | 2 
    22381  
    22382 Matchmaker 3j2w.pdb, chain I (#2) with Sindbis virus AlphaFold.pdb, chain A
    22383 (#50), sequence alignment score = 517.9 
    22384 RMSD between 146 pruned atom pairs is 0.676 angstroms; (across all 149 pairs:
    22385 0.789) 
    22386  
    22387 
    22388 > ui mousemode right rotate
    22389 
    22390 > ui mousemode right select
    22391 
    22392 > select #2/I:126
    22393 
    22394 9 atoms, 8 bonds, 1 residue, 1 model selected 
    22395 
    22396 > select #50/A:121
    22397 
    22398 15 atoms, 14 bonds, 1 residue, 1 model selected 
    22399 Alignment identifier is 50/A 
    22400 
    22401 > select #50/A:122
    22402 
    22403 12 atoms, 11 bonds, 1 residue, 1 model selected 
    22404 
    22405 > select #50/A:121
    22406 
    22407 15 atoms, 14 bonds, 1 residue, 1 model selected 
    22408 
    22409 > select #50/A:121
    22410 
    22411 15 atoms, 14 bonds, 1 residue, 1 model selected 
    22412 
    22413 > show #49 models
    22414 
    22415 Drag select of 2 residues 
    22416 
    22417 > select clear
    22418 
    22419 > hide #50 models
    22420 
    22421 > ui mousemode right translate
    22422 
    22423 > ui mousemode right select
    22424 
    22425 > select #49/A:183
    22426 
    22427 22 atoms, 21 bonds, 1 residue, 1 model selected 
    22428 
    22429 > select #49/A:178
    22430 
    22431 24 atoms, 23 bonds, 1 residue, 1 model selected 
    22432 
    22433 > select #2/I:178
    22434 
    22435 9 atoms, 8 bonds, 1 residue, 1 model selected 
    22436 
    22437 > select #2/I:178
    22438 
    22439 9 atoms, 8 bonds, 1 residue, 1 model selected 
    22440 
    22441 > select #49/A:178
    22442 
    22443 24 atoms, 23 bonds, 1 residue, 1 model selected 
    22444 Alignment identifier is 49/A 
    22445 
    22446 > show #50 models
    22447 
    22448 > select add #49
    22449 
    22450 4263 atoms, 4315 bonds, 267 residues, 1 model selected 
    22451 
    22452 > select subtract #49
    22453 
    22454 Nothing selected 
    22455 Drag select of 2 residues 
    22456 
    22457 > select #2/I:178
    22458 
    22459 9 atoms, 8 bonds, 1 residue, 1 model selected 
    22460 
    22461 > select #49/A:178
    22462 
    22463 24 atoms, 23 bonds, 1 residue, 1 model selected 
    22464 Alignment identifier is 49/A 
    22465 Drag select of 3 residues 
    22466 
    22467 > select #50/A:110
    22468 
    22469 19 atoms, 18 bonds, 1 residue, 1 model selected 
    22470 
    22471 > ui mousemode right translate
    22472 
    22473 > hide #50 models
    22474 
    22475 > select add #50
    22476 
    22477 4183 atoms, 4237 bonds, 264 residues, 1 model selected 
    22478 
    22479 > select subtract #50
    22480 
    22481 Nothing selected 
    22482 
    22483 > ui mousemode right select
    22484 
    22485 > select #49/A:183
    22486 
    22487 22 atoms, 21 bonds, 1 residue, 1 model selected 
    22488 
    22489 > ui mousemode right translate
    22490 
    22491 > ui mousemode right select
    22492 
    22493 > select #49/A:157
    22494 
    22495 22 atoms, 21 bonds, 1 residue, 1 model selected 
    22496 
    22497 > select #49/A:157
    22498 
    22499 22 atoms, 21 bonds, 1 residue, 1 model selected 
    22500 
    22501 > ui mousemode right translate
    22502 
    22503 > hide #49 models
    22504 
    22505 > select add #49
    22506 
    22507 4263 atoms, 4315 bonds, 267 residues, 1 model selected 
    22508 
    22509 > select subtract #49
    22510 
    22511 Nothing selected 
    22512 
    22513 > show #50 models
    22514 
    22515 > ui mousemode right select
    22516 
    22517 > select #50/A:122
    22518 
    22519 12 atoms, 11 bonds, 1 residue, 1 model selected 
    22520 Drag select of 8 residues 
    22521 
    22522 > select #50/A:122
    22523 
    22524 12 atoms, 11 bonds, 1 residue, 1 model selected 
    22525 
    22526 > style sel stick
    22527 
    22528 Changed 12 atom styles 
    22529 
    22530 > show sel atoms
    22531 
    22532 > color sel red
    22533 
    22534 Drag select of 2 residues 
    22535 
    22536 > select clear
    22537 
    22538 > ui mousemode right translate
    22539 
    22540 > ui mousemode right select
    22541 
    22542 > select #50/A:121
    22543 
    22544 15 atoms, 14 bonds, 1 residue, 1 model selected 
    22545 
    22546 > style sel stick
    22547 
    22548 Changed 15 atom styles 
    22549 
    22550 > show sel atoms
    22551 
    22552 > color sel orange red
    22553 
    22554 > ui mousemode right translate
    22555 
    22556 > ui mousemode right select
    22557 
    22558 > select #50/A:122
    22559 
    22560 12 atoms, 11 bonds, 1 residue, 1 model selected 
    22561 
    22562 > select #50/A:121
    22563 
    22564 15 atoms, 14 bonds, 1 residue, 1 model selected 
    22565 
    22566 > color sel light gray
    22567 
    22568 > hide sel cartoons
    22569 
    22570 [Repeated 1 time(s)]
    22571 
    22572 > show sel cartoons
    22573 
    22574 > hide sel atoms
    22575 
    22576 > color sel byhetero
    22577 
    22578 > color sel byelement
    22579 
    22580 > color #50 #bcbcbcff
    22581 
    22582 Drag select of 5 residues 
    22583 
    22584 > select clear
    22585 
    22586 > select #50/A:122
    22587 
    22588 12 atoms, 11 bonds, 1 residue, 1 model selected 
    22589 
    22590 > color sel red
    22591 
    22592 > ui mousemode right translate
    22593 
    22594 > ui mousemode right select
    22595 
    22596 > select #2/I:236
    22597 
    22598 4 atoms, 3 bonds, 1 residue, 1 model selected 
    22599 
    22600 > ui mousemode right translate
    22601 
    22602 > ui mousemode right select
    22603 
    22604 > select #50/A:122
    22605 
    22606 12 atoms, 11 bonds, 1 residue, 1 model selected 
    22607 
    22608 > select #50/A:122
    22609 
    22610 12 atoms, 11 bonds, 1 residue, 1 model selected 
    22611 
    22612 > select #50/A:124
    22613 
    22614 12 atoms, 11 bonds, 1 residue, 1 model selected 
    22615 
    22616 > select #2/I:128
    22617 
    22618 9 atoms, 8 bonds, 1 residue, 1 model selected 
    22619 
    22620 > select #50/A:124
    22621 
    22622 12 atoms, 11 bonds, 1 residue, 1 model selected 
    22623 
    22624 > select #2/I:128
    22625 
    22626 9 atoms, 8 bonds, 1 residue, 1 model selected 
    22627 
    22628 > select #50/A:124
    22629 
    22630 12 atoms, 11 bonds, 1 residue, 1 model selected 
    22631 
    22632 > ui mousemode right translate
    22633 
    22634 > style sel stick
    22635 
    22636 Changed 12 atom styles 
    22637 
    22638 > show sel atoms
    22639 
    22640 > color sel red
    22641 
    22642 > ui mousemode right select
    22643 
    22644 > select #50/A:236
    22645 
    22646 15 atoms, 14 bonds, 1 residue, 1 model selected 
    22647 
    22648 > select #2/I:240
    22649 
    22650 9 atoms, 8 bonds, 1 residue, 1 model selected 
    22651 
    22652 > select #50/A:236
    22653 
    22654 15 atoms, 14 bonds, 1 residue, 1 model selected 
    22655 
    22656 > ui mousemode right translate
    22657 
    22658 > ui mousemode right select
    22659 
    22660 > ui mousemode right translate
    22661 
    22662 > style sel stick
    22663 
    22664 Changed 15 atom styles 
    22665 
    22666 > show sel atoms
    22667 
    22668 > color sel red
    22669 
    22670 > ui mousemode right select
    22671 
    22672 > select #2/I:190
    22673 
    22674 9 atoms, 8 bonds, 1 residue, 1 model selected 
    22675 
    22676 > select #50/A:186
    22677 
    22678 15 atoms, 14 bonds, 1 residue, 1 model selected 
    22679 
    22680 > ui mousemode right translate
    22681 
    22682 > style sel stick
    22683 
    22684 Changed 15 atom styles 
    22685 
    22686 > show sel atoms
    22687 
    22688 > color sel red
    22689 
    22690 > ui mousemode right select
    22691 
    22692 > select #2/I:183
    22693 
    22694 9 atoms, 8 bonds, 1 residue, 1 model selected 
    22695 
    22696 > select #50/A:179
    22697 
    22698 14 atoms, 13 bonds, 1 residue, 1 model selected 
    22699 
    22700 > select #50/A:179
    22701 
    22702 14 atoms, 13 bonds, 1 residue, 1 model selected 
    22703 
    22704 > style sel stick
    22705 
    22706 Changed 14 atom styles 
    22707 
    22708 > show sel atoms
    22709 
    22710 > color sel orange
    22711 
    22712 > ui mousemode right translate
    22713 
    22714 > ui mousemode right select
    22715 
    22716 > select #2/I:178
    22717 
    22718 9 atoms, 8 bonds, 1 residue, 1 model selected 
    22719 
    22720 > select #50/A:174
    22721 
    22722 24 atoms, 23 bonds, 1 residue, 1 model selected 
    22723 
    22724 > ui mousemode right translate
    22725 
    22726 > style sel stick
    22727 
    22728 Changed 24 atom styles 
    22729 
    22730 > show sel atoms
    22731 
    22732 > color sel blue
    22733 
    22734 > ui mousemode right select
    22735 
    22736 > select #2/I:157
    22737 
    22738 9 atoms, 8 bonds, 1 residue, 1 model selected 
    22739 
    22740 > select #50/A:153
    22741 
    22742 22 atoms, 21 bonds, 1 residue, 1 model selected 
    22743 
    22744 > select #50/A:153
    22745 
    22746 22 atoms, 21 bonds, 1 residue, 1 model selected 
    22747 
    22748 > ui mousemode right translate
    22749 
    22750 > style sel stick
    22751 
    22752 Changed 22 atom styles 
    22753 
    22754 > show sel atoms
    22755 
    22756 > color sel blue
    22757 
    22758 > ui mousemode right select
    22759 
    22760 > select #2/I:154
    22761 
    22762 8 atoms, 7 bonds, 1 residue, 1 model selected 
    22763 
    22764 > select #50/A:150
    22765 
    22766 16 atoms, 15 bonds, 1 residue, 1 model selected 
    22767 
    22768 > style sel stick
    22769 
    22770 Changed 16 atom styles 
    22771 
    22772 > show sel atoms
    22773 
    22774 > color sel gray
    22775 
    22776 > ui mousemode right translate
    22777 
    22778 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    22779 > UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
    22780 
    22781 ——— End of log from Mon Jul 10 18:33:01 2023 ———
    22782 
    22783 opened ChimeraX session 
    22784 
    22785 > hide #2 models
    22786 
    22787 > ui tool show Matchmaker
    22788 
    22789 > matchmaker #43 to #50
    22790 
    22791 Parameters 
    22792 --- 
    22793 Chain pairing | bb 
    22794 Alignment algorithm | Needleman-Wunsch 
    22795 Similarity matrix | BLOSUM-62 
    22796 SS fraction | 0.3 
    22797 Gap open (HH/SS/other) | 18/18/6 
    22798 Gap extend | 1 
    22799 SS matrix |  |  | H | S | O 
    22800 ---|---|---|--- 
    22801 H | 6 | -9 | -6 
    22802 S |  | 6 | -6 
    22803 O |  |  | 4 
    22804 Iteration cutoff | 2 
    22805  
    22806 Matchmaker Sindbis virus AlphaFold.pdb, chain A (#50) with Aura virus
    22807 AlphaFold.pdb, chain A (#43), sequence alignment score = 980.1 
    22808 RMSD between 167 pruned atom pairs is 0.483 angstroms; (across all 262 pairs:
    22809 15.441) 
    22810  
    22811 
    22812 > ui tool show Matchmaker
    22813 
    22814 > matchmaker #43 to #50
    22815 
    22816 Parameters 
    22817 --- 
    22818 Chain pairing | bb 
    22819 Alignment algorithm | Needleman-Wunsch 
    22820 Similarity matrix | BLOSUM-62 
    22821 SS fraction | 0.3 
    22822 Gap open (HH/SS/other) | 18/18/6 
    22823 Gap extend | 1 
    22824 SS matrix |  |  | H | S | O 
    22825 ---|---|---|--- 
    22826 H | 6 | -9 | -6 
    22827 S |  | 6 | -6 
    22828 O |  |  | 4 
    22829 Iteration cutoff | 2 
    22830  
    22831 Matchmaker Sindbis virus AlphaFold.pdb, chain A (#50) with Aura virus
    22832 AlphaFold.pdb, chain A (#43), sequence alignment score = 980.1 
    22833 RMSD between 167 pruned atom pairs is 0.483 angstroms; (across all 262 pairs:
    22834 15.441) 
    22835  
    22836 
    22837 > show #43 models
    22838 
    22839 > ui mousemode right select
    22840 
    22841 > ui mousemode right translate
    22842 
    22843 > select #50/A:150
    22844 
    22845 16 atoms, 15 bonds, 1 residue, 1 model selected 
    22846 
    22847 > select #50/A:150
    22848 
    22849 16 atoms, 15 bonds, 1 residue, 1 model selected 
    22850 
    22851 > ui mousemode right select
    22852 
    22853 > select clear
    22854 
    22855 > select #50/A:179
    22856 
    22857 14 atoms, 13 bonds, 1 residue, 1 model selected 
    22858 
    22859 > select #50/A:180
    22860 
    22861 21 atoms, 21 bonds, 1 residue, 1 model selected 
    22862 
    22863 > style sel stick
    22864 
    22865 Changed 21 atom styles 
    22866 
    22867 > show sel atoms
    22868 
    22869 > select #50/A:179
    22870 
    22871 14 atoms, 13 bonds, 1 residue, 1 model selected 
    22872 
    22873 > select #50/A:179
    22874 
    22875 14 atoms, 13 bonds, 1 residue, 1 model selected 
    22876 
    22877 > hide sel atoms
    22878 
    22879 [Repeated 1 time(s)]
    22880 
    22881 > hide sel cartoons
    22882 
    22883 > show sel cartoons
    22884 
    22885 > color #50 #bfbfbfff
    22886 
    22887 > select #50/A:180
    22888 
    22889 21 atoms, 21 bonds, 1 residue, 1 model selected 
    22890 
    22891 > color sel magenta
    22892 
    22893 > color sel gray
    22894 
    22895 Drag select of 2 residues 
    22896 [Repeated 1 time(s)]
    22897 
    22898 > select #43/A:229
    22899 
    22900 16 atoms, 15 bonds, 1 residue, 1 model selected 
    22901 
    22902 > select clear
    22903 
    22904 [Repeated 1 time(s)]
    22905 
    22906 > ui mousemode right zoom
    22907 
    22908 > ui mousemode right translate
    22909 
    22910 > ui mousemode right select
    22911 
    22912 > select clear
    22913 
    22914 > select #43/A:127
    22915 
    22916 22 atoms, 21 bonds, 1 residue, 1 model selected 
    22917 
    22918 > style sel stick
    22919 
    22920 Changed 22 atom styles 
    22921 
    22922 > show sel cartoons
    22923 
    22924 > hide sel atoms
    22925 
    22926 > select #43/A:125
    22927 
    22928 12 atoms, 11 bonds, 1 residue, 1 model selected 
    22929 
    22930 > select #43/A:125
    22931 
    22932 12 atoms, 11 bonds, 1 residue, 1 model selected 
    22933 
    22934 > hide sel atoms
    22935 
    22936 > select #50/A:124
    22937 
    22938 12 atoms, 11 bonds, 1 residue, 1 model selected 
    22939 
    22940 > hide sel atoms
    22941 
    22942 > select #50/A:122
    22943 
    22944 12 atoms, 11 bonds, 1 residue, 1 model selected 
    22945 
    22946 > hide sel atoms
    22947 
    22948 > select #43/A:127
    22949 
    22950 22 atoms, 21 bonds, 1 residue, 1 model selected 
    22951 
    22952 > color #43 #c898f8ff
    22953 
    22954 > ui mousemode right translate
    22955 
    22956 > color #43 #c092eeff
    22957 
    22958 > ui mousemode right select
    22959 
    22960 > select #50/A:236
    22961 
    22962 15 atoms, 14 bonds, 1 residue, 1 model selected 
    22963 
    22964 > hide sel atoms
    22965 
    22966 > select #43/A:239
    22967 
    22968 15 atoms, 14 bonds, 1 residue, 1 model selected 
    22969 
    22970 > hide sel atoms
    22971 
    22972 > ui mousemode right translate
    22973 
    22974 > ui mousemode right select
    22975 
    22976 > select #50/A:186
    22977 
    22978 15 atoms, 14 bonds, 1 residue, 1 model selected 
    22979 
    22980 > hide sel atoms
    22981 
    22982 > select #50/A:186
    22983 
    22984 15 atoms, 14 bonds, 1 residue, 1 model selected 
    22985 
    22986 > select #43/A:189
    22987 
    22988 15 atoms, 14 bonds, 1 residue, 1 model selected 
    22989 
    22990 > hide sel atoms
    22991 
    22992 > ui mousemode right translate
    22993 
    22994 > ui mousemode right select
    22995 
    22996 > select #50/A:174
    22997 
    22998 24 atoms, 23 bonds, 1 residue, 1 model selected 
    22999 
    23000 > hide sel atoms
    23001 
    23002 > select #43/A:177
    23003 
    23004 22 atoms, 21 bonds, 1 residue, 1 model selected 
    23005 
    23006 > hide sel atoms
    23007 
    23008 Drag select of 8 residues 
    23009 
    23010 > select clear
    23011 
    23012 > ui mousemode right translate
    23013 
    23014 > ui mousemode right select
    23015 
    23016 > select #50/A:150
    23017 
    23018 16 atoms, 15 bonds, 1 residue, 1 model selected 
    23019 
    23020 > hide sel atoms
    23021 
    23022 > select #43/A:153@CA
    23023 
    23024 1 atom, 1 residue, 1 model selected 
    23025 
    23026 > hide sel atoms
    23027 
    23028 > hide sel cartoons
    23029 
    23030 > show sel cartoons
    23031 
    23032 > hide sel atoms
    23033 
    23034 > show sel atoms
    23035 
    23036 > select #43/A:153
    23037 
    23038 10 atoms, 9 bonds, 1 residue, 1 model selected 
    23039 
    23040 > hide sel atoms
    23041 
    23042 Drag select of 7 residues 
    23043 
    23044 > select #50/A:153
    23045 
    23046 22 atoms, 21 bonds, 1 residue, 1 model selected 
    23047 
    23048 > hide sel atoms
    23049 
    23050 > select #43/A:156
    23051 
    23052 22 atoms, 21 bonds, 1 residue, 1 model selected 
    23053 
    23054 > select #43/A:156
    23055 
    23056 22 atoms, 21 bonds, 1 residue, 1 model selected 
    23057 
    23058 > hide sel cartoons
    23059 
    23060 [Repeated 1 time(s)]
    23061 
    23062 > show sel cartoons
    23063 
    23064 > hide sel atoms
    23065 
    23066 > color #50 #d6d6d6ff
    23067 
    23068 > color #50 blue
    23069 
    23070 > color #50 #0055ffff
    23071 
    23072 > color #50 #55aaffff
    23073 
    23074 > color #50 #4e9debff
    23075 
    23076 > color #50 #61a4ebff
    23077 
    23078 > color #50 #5997d9ff
    23079 
    23080 > color #50 #5092d9ff
    23081 
    23082 > color #50 #579eebff
    23083 
    23084 > color #50 #549ae5ff
    23085 
    23086 Drag select of 4 residues 
    23087 
    23088 > select #43/A:228
    23089 
    23090 22 atoms, 21 bonds, 1 residue, 1 model selected 
    23091 
    23092 > ui mousemode right translate
    23093 
    23094 > ui mousemode right select
    23095 
    23096 > select #50/A:180
    23097 
    23098 21 atoms, 21 bonds, 1 residue, 1 model selected 
    23099 
    23100 > color sel gray
    23101 
    23102 > select #43/A:183
    23103 
    23104 21 atoms, 21 bonds, 1 residue, 1 model selected 
    23105 Alignment identifier is 43/A 
    23106 
    23107 > color sel gray
    23108 
    23109 > select #50/A:180
    23110 
    23111 21 atoms, 21 bonds, 1 residue, 1 model selected 
    23112 
    23113 > select #50/A:180
    23114 
    23115 21 atoms, 21 bonds, 1 residue, 1 model selected 
    23116 
    23117 > select #50/A:180
    23118 
    23119 21 atoms, 21 bonds, 1 residue, 1 model selected 
    23120 
    23121 > select #43/A:183
    23122 
    23123 21 atoms, 21 bonds, 1 residue, 1 model selected 
    23124 
    23125 > select #43/A:183
    23126 
    23127 21 atoms, 21 bonds, 1 residue, 1 model selected 
    23128 
    23129 > style sel stick
    23130 
    23131 Changed 21 atom styles 
    23132 
    23133 > show sel cartoons
    23134 
    23135 > show sel atoms
    23136 
    23137 > ui mousemode right translate
    23138 
    23139 > ui mousemode right select
    23140 
    23141 > select #50/A:183
    23142 
    23143 15 atoms, 14 bonds, 1 residue, 1 model selected 
    23144 
    23145 > select #50/A:183
    23146 
    23147 15 atoms, 14 bonds, 1 residue, 1 model selected 
    23148 
    23149 > style sel stick
    23150 
    23151 Changed 15 atom styles 
    23152 
    23153 > show sel atoms
    23154 
    23155 > color sel red
    23156 
    23157 > ui mousemode right translate
    23158 
    23159 > ui mousemode right select
    23160 
    23161 > select #50/A:183
    23162 
    23163 15 atoms, 14 bonds, 1 residue, 1 model selected 
    23164 
    23165 > select #50/A:183
    23166 
    23167 15 atoms, 14 bonds, 1 residue, 1 model selected 
    23168 
    23169 > select #43/A:186
    23170 
    23171 15 atoms, 14 bonds, 1 residue, 1 model selected 
    23172 
    23173 > style sel stick
    23174 
    23175 Changed 15 atom styles 
    23176 
    23177 > show sel atoms
    23178 
    23179 > color sel red
    23180 
    23181 Drag select of 2 residues 
    23182 
    23183 > select clear
    23184 
    23185 > ui mousemode right translate
    23186 
    23187 > ui mousemode right select
    23188 
    23189 > select #50/A:246
    23190 
    23191 14 atoms, 13 bonds, 1 residue, 1 model selected 
    23192 
    23193 > ui mousemode right translate
    23194 
    23195 > ui mousemode right select
    23196 
    23197 > select #50/A:245
    23198 
    23199 16 atoms, 15 bonds, 1 residue, 1 model selected 
    23200 
    23201 > select #50/A:246
    23202 
    23203 14 atoms, 13 bonds, 1 residue, 1 model selected 
    23204 
    23205 > select #50/A:247
    23206 
    23207 24 atoms, 25 bonds, 1 residue, 1 model selected 
    23208 
    23209 > select #43/A:249
    23210 
    23211 14 atoms, 13 bonds, 1 residue, 1 model selected 
    23212 
    23213 > select #50/A:246
    23214 
    23215 14 atoms, 13 bonds, 1 residue, 1 model selected 
    23216 
    23217 > select #50/A:247
    23218 
    23219 24 atoms, 25 bonds, 1 residue, 1 model selected 
    23220 
    23221 > style sel stick
    23222 
    23223 Changed 24 atom styles 
    23224 
    23225 > show sel atoms
    23226 
    23227 > color sel gray
    23228 
    23229 > select #43/A:250
    23230 
    23231 24 atoms, 25 bonds, 1 residue, 1 model selected 
    23232 
    23233 > style sel stick
    23234 
    23235 Changed 24 atom styles 
    23236 
    23237 > show sel atoms
    23238 
    23239 > style sel stick
    23240 
    23241 Changed 24 atom styles 
    23242 
    23243 > show sel atoms
    23244 
    23245 > style sel stick
    23246 
    23247 Changed 24 atom styles 
    23248 
    23249 > show sel atoms
    23250 
    23251 > color sel light gray
    23252 
    23253 > color sel gray
    23254 
    23255 > ui mousemode right translate
    23256 
    23257 > hide #43 models
    23258 
    23259 > show #43 models
    23260 
    23261 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    23262 > UASLP/Lab Virología/overlap of CP structures.cxs"
    23263 
    23264 ——— End of log from Tue Jul 18 20:54:16 2023 ———
    23265 
    23266 opened ChimeraX session 
    23267 
    23268 > hide #43 models
    23269 
    23270 > select add #43
    23271 
    23272 4223 atoms, 4279 bonds, 267 residues, 1 model selected 
    23273 
    23274 > select subtract #43
    23275 
    23276 Nothing selected 
    23277 
    23278 > show #44 models
    23279 
    23280 > color #44 #e19a60ff
    23281 
    23282 > set bgColor black
    23283 
    23284 > set bgColor white
    23285 
    23286 > ui mousemode right select
    23287 
    23288 > select #44/A:112
    23289 
    23290 12 atoms, 11 bonds, 1 residue, 1 model selected 
    23291 
    23292 > show sel atoms
    23293 
    23294 [Repeated 1 time(s)]
    23295 
    23296 > hide sel atoms
    23297 
    23298 > select #44/A:114
    23299 
    23300 22 atoms, 21 bonds, 1 residue, 1 model selected 
    23301 
    23302 > hide sel atoms
    23303 
    23304 > ui mousemode right rotate
    23305 
    23306 > ui mousemode right translate
    23307 
    23308 > ui mousemode right select
    23309 
    23310 > select #50/A:236
    23311 
    23312 15 atoms, 14 bonds, 1 residue, 1 model selected 
    23313 
    23314 > ui mousemode right translate
    23315 
    23316 > hide sel atoms
    23317 
    23318 [Repeated 1 time(s)]
    23319 
    23320 > ui mousemode right rotate
    23321 
    23322 > ui mousemode right select
    23323 
    23324 > select #44/A:226
    23325 
    23326 15 atoms, 14 bonds, 1 residue, 1 model selected 
    23327 
    23328 > hide sel atoms
    23329 
    23330 > ui mousemode right translate
    23331 
    23332 > ui mousemode right select
    23333 
    23334 > select #44/A:176
    23335 
    23336 15 atoms, 14 bonds, 1 residue, 1 model selected 
    23337 
    23338 > ui mousemode right translate
    23339 
    23340 > hide sel atoms
    23341 
    23342 > ui mousemode right select
    23343 
    23344 > select #44/A:173
    23345 
    23346 15 atoms, 14 bonds, 1 residue, 1 model selected 
    23347 
    23348 > select #50/A:183
    23349 
    23350 15 atoms, 14 bonds, 1 residue, 1 model selected 
    23351 
    23352 > select #44/A:174
    23353 
    23354 22 atoms, 21 bonds, 1 residue, 1 model selected 
    23355 
    23356 > select #44/A:173
    23357 
    23358 15 atoms, 14 bonds, 1 residue, 1 model selected 
    23359 Alignment identifier is 44/A 
    23360 
    23361 > select #50/A:183
    23362 
    23363 15 atoms, 14 bonds, 1 residue, 1 model selected 
    23364 
    23365 > select #44/A:173
    23366 
    23367 15 atoms, 14 bonds, 1 residue, 1 model selected 
    23368 
    23369 > style sel stick
    23370 
    23371 Changed 15 atom styles 
    23372 
    23373 > show sel atoms
    23374 
    23375 > color sel red
    23376 
    23377 > ui mousemode right translate
    23378 
    23379 > ui mousemode right select
    23380 
    23381 > select #44/A:169
    23382 
    23383 22 atoms, 21 bonds, 1 residue, 1 model selected 
    23384 
    23385 > hide sel atoms
    23386 
    23387 > ui mousemode right translate
    23388 
    23389 > ui mousemode right select
    23390 
    23391 > select #44/A:237
    23392 
    23393 24 atoms, 25 bonds, 1 residue, 1 model selected 
    23394 
    23395 > style sel stick
    23396 
    23397 Changed 24 atom styles 
    23398 
    23399 > show sel atoms
    23400 
    23401 > color sel gray
    23402 
    23403 > select #44/A:170
    23404 
    23405 20 atoms, 20 bonds, 1 residue, 1 model selected 
    23406 
    23407 > style sel stick
    23408 
    23409 Changed 20 atom styles 
    23410 
    23411 > show sel atoms
    23412 
    23413 > color sel gray
    23414 
    23415 > ui mousemode right translate
    23416 
    23417 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    23418 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    23419 
    23420 > ui mousemode right select
    23421 
    23422 > select #44/A:164
    23423 
    23424 22 atoms, 21 bonds, 1 residue, 1 model selected 
    23425 
    23426 > ui mousemode right translate
    23427 
    23428 > hide sel atoms
    23429 
    23430 > ui mousemode right select
    23431 
    23432 > select #44/A:143
    23433 
    23434 22 atoms, 21 bonds, 1 residue, 1 model selected 
    23435 
    23436 > ui mousemode right translate
    23437 
    23438 > hide sel atoms
    23439 
    23440 > show sel atoms
    23441 
    23442 > hide sel atoms
    23443 
    23444 > ui mousemode right rotate
    23445 
    23446 > ui mousemode right select
    23447 
    23448 > select #44/A:140
    23449 
    23450 15 atoms, 14 bonds, 1 residue, 1 model selected 
    23451 
    23452 > ui mousemode right translate
    23453 
    23454 > hide sel atoms
    23455 
    23456 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    23457 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    23458 
    23459 ——— End of log from Tue Jul 18 21:16:37 2023 ———
    23460 
    23461 opened ChimeraX session 
    23462 
    23463 > show #17 models
    23464 
    23465 > hide #44 models
    23466 
    23467 > select add #44
    23468 
    23469 4047 atoms, 4099 bonds, 253 residues, 1 model selected 
    23470 
    23471 > select subtract #44
    23472 
    23473 Nothing selected 
    23474 
    23475 > color #17 #007f5dff
    23476 
    23477 > ui mousemode right select
    23478 
    23479 > select #17/A:124
    23480 
    23481 22 atoms, 21 bonds, 1 residue, 1 model selected 
    23482 
    23483 > hide sel atoms
    23484 
    23485 > select clear
    23486 
    23487 > select #17/A:122
    23488 
    23489 12 atoms, 11 bonds, 1 residue, 1 model selected 
    23490 
    23491 > hide sel atoms
    23492 
    23493 > select clear
    23494 
    23495 > ui mousemode right translate
    23496 
    23497 > ui mousemode right select
    23498 
    23499 > select #50/A:236
    23500 
    23501 15 atoms, 14 bonds, 1 residue, 1 model selected 
    23502 
    23503 > select #17/A:236
    23504 
    23505 15 atoms, 14 bonds, 1 residue, 1 model selected 
    23506 
    23507 > ui mousemode right translate
    23508 
    23509 > hide sel atoms
    23510 
    23511 > ui mousemode right select
    23512 
    23513 > select #50/A:186
    23514 
    23515 15 atoms, 14 bonds, 1 residue, 1 model selected 
    23516 
    23517 > select #17/A:186
    23518 
    23519 15 atoms, 14 bonds, 1 residue, 1 model selected 
    23520 
    23521 > ui mousemode right translate
    23522 
    23523 Alignment identifier is 17/A 
    23524 
    23525 > show sel atoms
    23526 
    23527 > hide sel atoms
    23528 
    23529 > ui mousemode right rotate
    23530 
    23531 > ui mousemode right select
    23532 
    23533 > select #50/A:183
    23534 
    23535 15 atoms, 14 bonds, 1 residue, 1 model selected 
    23536 
    23537 > select #17/A:183
    23538 
    23539 15 atoms, 14 bonds, 1 residue, 1 model selected 
    23540 
    23541 > ui mousemode right rotate
    23542 
    23543 > ui mousemode right translate
    23544 
    23545 > style sel stick
    23546 
    23547 Changed 15 atom styles 
    23548 
    23549 > show sel atoms
    23550 
    23551 > color sel red
    23552 
    23553 > ui mousemode right select
    23554 
    23555 > select #17/A:179
    23556 
    23557 22 atoms, 21 bonds, 1 residue, 1 model selected 
    23558 
    23559 > ui mousemode right translate
    23560 
    23561 > show sel atoms
    23562 
    23563 > hide sel atoms
    23564 
    23565 > ui mousemode right select
    23566 
    23567 > select #50/A:247
    23568 
    23569 24 atoms, 25 bonds, 1 residue, 1 model selected 
    23570 
    23571 > select #17/A:247
    23572 
    23573 24 atoms, 25 bonds, 1 residue, 1 model selected 
    23574 
    23575 > ui mousemode right translate
    23576 
    23577 > style sel stick
    23578 
    23579 Changed 24 atom styles 
    23580 
    23581 > show sel atoms
    23582 
    23583 > color sel gray
    23584 
    23585 > ui mousemode right select
    23586 
    23587 > select #50/A:180
    23588 
    23589 21 atoms, 21 bonds, 1 residue, 1 model selected 
    23590 
    23591 > select #17/A:180
    23592 
    23593 21 atoms, 21 bonds, 1 residue, 1 model selected 
    23594 
    23595 > style sel stick
    23596 
    23597 Changed 21 atom styles 
    23598 
    23599 > show sel atoms
    23600 
    23601 > color sel gray
    23602 
    23603 > ui mousemode right translate
    23604 
    23605 > ui mousemode right select
    23606 
    23607 > select #17/A:183
    23608 
    23609 15 atoms, 14 bonds, 1 residue, 1 model selected 
    23610 
    23611 > ui mousemode right translate
    23612 
    23613 > ui mousemode right select
    23614 
    23615 > select #17/A:174
    23616 
    23617 24 atoms, 23 bonds, 1 residue, 1 model selected 
    23618 
    23619 > ui mousemode right translate
    23620 
    23621 > hide sel atoms
    23622 
    23623 > ui mousemode right rotate
    23624 
    23625 > ui mousemode right select
    23626 
    23627 > select #17/A:153
    23628 
    23629 22 atoms, 21 bonds, 1 residue, 1 model selected 
    23630 
    23631 > ui mousemode right translate
    23632 
    23633 > hide sel atoms
    23634 
    23635 > ui mousemode right select
    23636 
    23637 > select #17/A:150
    23638 
    23639 12 atoms, 11 bonds, 1 residue, 1 model selected 
    23640 
    23641 > select #17/A:150
    23642 
    23643 12 atoms, 11 bonds, 1 residue, 1 model selected 
    23644 
    23645 > ui mousemode right translate
    23646 
    23647 > hide sel atoms
    23648 
    23649 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    23650 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    23651 
    23652 > show #18 models
    23653 
    23654 > hide #17 models
    23655 
    23656 > select add #17
    23657 
    23658 4212 atoms, 4263 bonds, 263 residues, 1 model selected 
    23659 
    23660 > select subtract #17
    23661 
    23662 Nothing selected 
    23663 
    23664 > color #18 #f07d09ff
    23665 
    23666 > color #18 #ef7c09ff
    23667 
    23668 > ui mousemode right rotate
    23669 
    23670 > ui mousemode right select
    23671 
    23672 > select #18/A:125
    23673 
    23674 22 atoms, 21 bonds, 1 residue, 1 model selected 
    23675 
    23676 > ui mousemode right translate
    23677 
    23678 > hide sel atoms
    23679 
    23680 > ui mousemode right select
    23681 
    23682 > select #18/A:123
    23683 
    23684 12 atoms, 11 bonds, 1 residue, 1 model selected 
    23685 
    23686 > ui mousemode right translate
    23687 
    23688 > hide sel atoms
    23689 
    23690 > ui mousemode right select
    23691 
    23692 > select #18/A:241
    23693 
    23694 15 atoms, 14 bonds, 1 residue, 1 model selected 
    23695 
    23696 > ui mousemode right translate
    23697 
    23698 > hide sel atoms
    23699 
    23700 > ui mousemode right rotate
    23701 
    23702 > ui mousemode right select
    23703 
    23704 > select #18/A:190
    23705 
    23706 17 atoms, 16 bonds, 1 residue, 1 model selected 
    23707 
    23708 > ui mousemode right translate
    23709 
    23710 > hide sel atoms
    23711 
    23712 > ui mousemode right select
    23713 
    23714 > select #18/A:185
    23715 
    23716 24 atoms, 23 bonds, 1 residue, 1 model selected 
    23717 Alignment identifier is 18/A 
    23718 
    23719 > select #18/A:186
    23720 
    23721 14 atoms, 14 bonds, 1 residue, 1 model selected 
    23722 
    23723 > select #18/A:186
    23724 
    23725 14 atoms, 14 bonds, 1 residue, 1 model selected 
    23726 
    23727 > select #18/A:185
    23728 
    23729 24 atoms, 23 bonds, 1 residue, 1 model selected 
    23730 
    23731 > select #50/A:183
    23732 
    23733 15 atoms, 14 bonds, 1 residue, 1 model selected 
    23734 
    23735 > select #50/A:183
    23736 
    23737 15 atoms, 14 bonds, 1 residue, 1 model selected 
    23738 
    23739 > select #18/A:185
    23740 
    23741 24 atoms, 23 bonds, 1 residue, 1 model selected 
    23742 
    23743 > ui mousemode right rotate
    23744 
    23745 > ui mousemode right translate
    23746 
    23747 > style sel stick
    23748 
    23749 Changed 24 atom styles 
    23750 
    23751 > show sel atoms
    23752 
    23753 > color sel blue
    23754 
    23755 > ui mousemode right select
    23756 
    23757 > select #50/A:247
    23758 
    23759 24 atoms, 25 bonds, 1 residue, 1 model selected 
    23760 
    23761 > select #18/A:252
    23762 
    23763 24 atoms, 25 bonds, 1 residue, 1 model selected 
    23764 
    23765 > style sel stick
    23766 
    23767 Changed 24 atom styles 
    23768 
    23769 > show sel atoms
    23770 
    23771 > color sel gray
    23772 
    23773 > select #18/A:183
    23774 
    23775 16 atoms, 15 bonds, 1 residue, 1 model selected 
    23776 
    23777 > select #50/A:180
    23778 
    23779 21 atoms, 21 bonds, 1 residue, 1 model selected 
    23780 
    23781 > select #18/A:183
    23782 
    23783 16 atoms, 15 bonds, 1 residue, 1 model selected 
    23784 
    23785 > select #18/A:183
    23786 
    23787 16 atoms, 15 bonds, 1 residue, 1 model selected 
    23788 
    23789 > ui mousemode right translate
    23790 
    23791 > style sel stick
    23792 
    23793 Changed 16 atom styles 
    23794 
    23795 > show sel atoms
    23796 
    23797 > color sel gray
    23798 
    23799 > ui mousemode right select
    23800 
    23801 > select clear
    23802 
    23803 Drag select of 1 residues 
    23804 
    23805 > ui mousemode right translate
    23806 
    23807 > hide sel atoms
    23808 
    23809 > ui mousemode right select
    23810 
    23811 > select #18/A:175
    23812 
    23813 19 atoms, 18 bonds, 1 residue, 1 model selected 
    23814 
    23815 > ui mousemode right translate
    23816 
    23817 > hide sel atoms
    23818 
    23819 > ui mousemode right select
    23820 
    23821 > select #18/A:151
    23822 
    23823 15 atoms, 14 bonds, 1 residue, 1 model selected 
    23824 
    23825 > ui mousemode right translate
    23826 
    23827 > hide sel atoms
    23828 
    23829 > ui mousemode right select
    23830 
    23831 > select #18/A:154
    23832 
    23833 14 atoms, 13 bonds, 1 residue, 1 model selected 
    23834 
    23835 > ui mousemode right translate
    23836 
    23837 > hide sel atoms
    23838 
    23839 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    23840 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    23841 
    23842 ——— End of log from Wed Jul 19 11:49:32 2023 ———
    23843 
    23844 opened ChimeraX session 
    23845 
    23846 > hide #18 models
    23847 
    23848 > select add #18
    23849 
    23850 4336 atoms, 4396 bonds, 269 residues, 1 model selected 
    23851 
    23852 > select subtract #18
    23853 
    23854 Nothing selected 
    23855 
    23856 > show #19 models
    23857 
    23858 > ui tool show Matchmaker
    23859 
    23860 > matchmaker #19 to #50
    23861 
    23862 Parameters 
    23863 --- 
    23864 Chain pairing | bb 
    23865 Alignment algorithm | Needleman-Wunsch 
    23866 Similarity matrix | BLOSUM-62 
    23867 SS fraction | 0.3 
    23868 Gap open (HH/SS/other) | 18/18/6 
    23869 Gap extend | 1 
    23870 SS matrix |  |  | H | S | O 
    23871 ---|---|---|--- 
    23872 H | 6 | -9 | -6 
    23873 S |  | 6 | -6 
    23874 O |  |  | 4 
    23875 Iteration cutoff | 2 
    23876  
    23877 Matchmaker Sindbis virus AlphaFold.pdb, chain A (#50) with Cabassou virus
    23878 Alphafold.pdb, chain A (#19), sequence alignment score = 773.2 
    23879 RMSD between 10 pruned atom pairs is 1.228 angstroms; (across all 254 pairs:
    23880 35.143) 
    23881  
    23882 
    23883 > hide #19 models
    23884 
    23885 > show #19 models
    23886 
    23887 > hide #19 models
    23888 
    23889 > ui tool show Matchmaker
    23890 
    23891 > matchmaker #19 to #50
    23892 
    23893 Parameters 
    23894 --- 
    23895 Chain pairing | bb 
    23896 Alignment algorithm | Needleman-Wunsch 
    23897 Similarity matrix | BLOSUM-62 
    23898 SS fraction | 0.3 
    23899 Gap open (HH/SS/other) | 18/18/6 
    23900 Gap extend | 1 
    23901 SS matrix |  |  | H | S | O 
    23902 ---|---|---|--- 
    23903 H | 6 | -9 | -6 
    23904 S |  | 6 | -6 
    23905 O |  |  | 4 
    23906 Iteration cutoff | 2 
    23907  
    23908 Matchmaker Sindbis virus AlphaFold.pdb, chain A (#50) with Cabassou virus
    23909 Alphafold.pdb, chain A (#19), sequence alignment score = 773.2 
    23910 RMSD between 10 pruned atom pairs is 1.228 angstroms; (across all 254 pairs:
    23911 35.143) 
    23912  
    23913 
    23914 > show #19 models
    23915 
    23916 > show #18 models
    23917 
    23918 > hide #19 models
    23919 
    23920 > hide #18 models
    23921 
    23922 > show #18 models
    23923 
    23924 > hide #18 models
    23925 
    23926 > show #19 models
    23927 
    23928 > ui tool show Matchmaker
    23929 
    23930 > matchmaker #19 to #2
    23931 
    23932 Parameters 
    23933 --- 
    23934 Chain pairing | bb 
    23935 Alignment algorithm | Needleman-Wunsch 
    23936 Similarity matrix | BLOSUM-62 
    23937 SS fraction | 0.3 
    23938 Gap open (HH/SS/other) | 18/18/6 
    23939 Gap extend | 1 
    23940 SS matrix |  |  | H | S | O 
    23941 ---|---|---|--- 
    23942 H | 6 | -9 | -6 
    23943 S |  | 6 | -6 
    23944 O |  |  | 4 
    23945 Iteration cutoff | 2 
    23946  
    23947 Matchmaker 3j2w.pdb, chain I (#2) with Cabassou virus Alphafold.pdb, chain A
    23948 (#19), sequence alignment score = 523.2 
    23949 RMSD between 146 pruned atom pairs is 0.713 angstroms; (across all 149 pairs:
    23950 0.884) 
    23951  
    23952 
    23953 > color #19 #90d66bff
    23954 
    23955 > color #19 #92d86cff
    23956 
    23957 > color #19 #90d66bff
    23958 
    23959 > ui mousemode right select
    23960 
    23961 > select #19/A:135
    23962 
    23963 22 atoms, 21 bonds, 1 residue, 1 model selected 
    23964 
    23965 > hide sel cartoons
    23966 
    23967 > show sel cartoons
    23968 
    23969 > hide sel atoms
    23970 
    23971 > select #19/A:133
    23972 
    23973 12 atoms, 11 bonds, 1 residue, 1 model selected 
    23974 
    23975 > hide sel atoms
    23976 
    23977 > ui mousemode right translate
    23978 
    23979 > ui mousemode right select
    23980 
    23981 > select #19/A:247
    23982 
    23983 15 atoms, 14 bonds, 1 residue, 1 model selected 
    23984 
    23985 > ui mousemode right translate
    23986 
    23987 > hide sel atoms
    23988 
    23989 > ui mousemode right select
    23990 
    23991 > select #19/A:197
    23992 
    23993 17 atoms, 16 bonds, 1 residue, 1 model selected 
    23994 
    23995 > hide sel atoms
    23996 
    23997 Drag select of 1 residues 
    23998 
    23999 > select #50/A:185
    24000 
    24001 14 atoms, 14 bonds, 1 residue, 1 model selected 
    24002 
    24003 > ui mousemode right translate
    24004 
    24005 > ui mousemode right select
    24006 
    24007 > select #50/A:183
    24008 
    24009 15 atoms, 14 bonds, 1 residue, 1 model selected 
    24010 
    24011 > select #19/A:194
    24012 
    24013 15 atoms, 14 bonds, 1 residue, 1 model selected 
    24014 Alignment identifier is 19/A 
    24015 
    24016 > select #50/A:183
    24017 
    24018 15 atoms, 14 bonds, 1 residue, 1 model selected 
    24019 
    24020 > select #19/A:194
    24021 
    24022 15 atoms, 14 bonds, 1 residue, 1 model selected 
    24023 
    24024 > ui mousemode right translate
    24025 
    24026 > style sel stick
    24027 
    24028 Changed 15 atom styles 
    24029 
    24030 > show sel atoms
    24031 
    24032 > color sel red
    24033 
    24034 > ui mousemode right select
    24035 
    24036 > select #19/A:190
    24037 
    24038 24 atoms, 23 bonds, 1 residue, 1 model selected 
    24039 
    24040 > hide sel atoms
    24041 
    24042 > ui mousemode right translate
    24043 
    24044 > ui mousemode right select
    24045 
    24046 > select #50/A:247
    24047 
    24048 24 atoms, 25 bonds, 1 residue, 1 model selected 
    24049 
    24050 > select #19/A:258
    24051 
    24052 24 atoms, 25 bonds, 1 residue, 1 model selected 
    24053 
    24054 > ui mousemode right translate
    24055 
    24056 > style sel stick
    24057 
    24058 Changed 24 atom styles 
    24059 
    24060 > show sel atoms
    24061 
    24062 > color sel gray
    24063 
    24064 > ui mousemode right select
    24065 
    24066 > select #50/A:180
    24067 
    24068 21 atoms, 21 bonds, 1 residue, 1 model selected 
    24069 
    24070 > select #50/A:180
    24071 
    24072 21 atoms, 21 bonds, 1 residue, 1 model selected 
    24073 
    24074 > select #19/A:191
    24075 
    24076 21 atoms, 21 bonds, 1 residue, 1 model selected 
    24077 
    24078 > ui mousemode right translate
    24079 
    24080 > style sel stick
    24081 
    24082 Changed 21 atom styles 
    24083 
    24084 > show sel atoms
    24085 
    24086 > color sel gray
    24087 
    24088 > ui mousemode right select
    24089 
    24090 > select #19/A:185
    24091 
    24092 24 atoms, 23 bonds, 1 residue, 1 model selected 
    24093 
    24094 > hide sel atoms
    24095 
    24096 > select clear
    24097 
    24098 > select #19/A:206
    24099 
    24100 10 atoms, 9 bonds, 1 residue, 1 model selected 
    24101 
    24102 > select #19/A:161
    24103 
    24104 14 atoms, 13 bonds, 1 residue, 1 model selected 
    24105 
    24106 > hide sel atoms
    24107 
    24108 > select #19/A:163
    24109 
    24110 10 atoms, 9 bonds, 1 residue, 1 model selected 
    24111 
    24112 > select #19/A:164
    24113 
    24114 10 atoms, 9 bonds, 1 residue, 1 model selected 
    24115 
    24116 > hide sel atoms
    24117 
    24118 > ui mousemode right translate
    24119 
    24120 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    24121 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    24122 
    24123 > select add #19
    24124 
    24125 4422 atoms, 4482 bonds, 275 residues, 1 model selected 
    24126 
    24127 > select subtract #19
    24128 
    24129 Nothing selected 
    24130 
    24131 > hide #19 models
    24132 
    24133 > show #19 models
    24134 
    24135 > hide #19 models
    24136 
    24137 > show #18 models
    24138 
    24139 > ui mousemode right select
    24140 
    24141 > select #18/A:252
    24142 
    24143 24 atoms, 25 bonds, 1 residue, 1 model selected 
    24144 
    24145 > select #18/A:183
    24146 
    24147 16 atoms, 15 bonds, 1 residue, 1 model selected 
    24148 
    24149 > select add #18
    24150 
    24151 4336 atoms, 4396 bonds, 269 residues, 1 model selected 
    24152 
    24153 > select subtract #18
    24154 
    24155 Nothing selected 
    24156 
    24157 > hide #18 models
    24158 
    24159 > show #20 models
    24160 
    24161 > hide #20 models
    24162 
    24163 > show #2 models
    24164 
    24165 > ui mousemode right translate
    24166 
    24167 > ui mousemode right select
    24168 
    24169 > ui mousemode right translate
    24170 
    24171 > ui mousemode right select
    24172 
    24173 > select #2/I:126
    24174 
    24175 9 atoms, 8 bonds, 1 residue, 1 model selected 
    24176 
    24177 > hide sel cartoons
    24178 
    24179 [Repeated 1 time(s)]
    24180 
    24181 > show sel cartoons
    24182 
    24183 > hide sel atoms
    24184 
    24185 > color #2 #20e0eeff
    24186 
    24187 > select #2/I:128
    24188 
    24189 9 atoms, 8 bonds, 1 residue, 1 model selected 
    24190 
    24191 > hide sel atoms
    24192 
    24193 > ui mousemode right translate
    24194 
    24195 > ui mousemode right select
    24196 
    24197 > select #2/I:240
    24198 
    24199 9 atoms, 8 bonds, 1 residue, 1 model selected 
    24200 
    24201 > hide sel atoms
    24202 
    24203 > ui mousemode right translate
    24204 
    24205 > ui mousemode right select
    24206 
    24207 > select #2/I:190
    24208 
    24209 9 atoms, 8 bonds, 1 residue, 1 model selected 
    24210 
    24211 > ui mousemode right translate
    24212 
    24213 > hide sel atoms
    24214 
    24215 > ui mousemode right select
    24216 
    24217 > select #50/A:183
    24218 
    24219 15 atoms, 14 bonds, 1 residue, 1 model selected 
    24220 
    24221 > select #50/A:183
    24222 
    24223 15 atoms, 14 bonds, 1 residue, 1 model selected 
    24224 
    24225 > select #2/I:187
    24226 
    24227 9 atoms, 8 bonds, 1 residue, 1 model selected 
    24228 
    24229 > select #2/I:187
    24230 
    24231 9 atoms, 8 bonds, 1 residue, 1 model selected 
    24232 Alignment identifier is 2/I 
    24233 
    24234 > style sel stick
    24235 
    24236 Changed 9 atom styles 
    24237 
    24238 > show sel atoms
    24239 
    24240 > color sel red
    24241 
    24242 > select clear
    24243 
    24244 [Repeated 1 time(s)]
    24245 
    24246 > select #2/I:187
    24247 
    24248 9 atoms, 8 bonds, 1 residue, 1 model selected 
    24249 
    24250 > select #2/I:187
    24251 
    24252 9 atoms, 8 bonds, 1 residue, 1 model selected 
    24253 
    24254 > ui mousemode right translate
    24255 
    24256 > ui mousemode right rotate
    24257 
    24258 > ui mousemode right select
    24259 
    24260 > select #2/I:183
    24261 
    24262 9 atoms, 8 bonds, 1 residue, 1 model selected 
    24263 
    24264 > hide sel atoms
    24265 
    24266 > ui mousemode right translate
    24267 
    24268 > ui mousemode right select
    24269 
    24270 > select #2/I:178
    24271 
    24272 9 atoms, 8 bonds, 1 residue, 1 model selected 
    24273 
    24274 > ui mousemode right translate
    24275 
    24276 > hide sel atoms
    24277 
    24278 > ui mousemode right select
    24279 
    24280 > select #2/I:157
    24281 
    24282 9 atoms, 8 bonds, 1 residue, 1 model selected 
    24283 
    24284 > ui mousemode right translate
    24285 
    24286 > hide sel atoms
    24287 
    24288 > ui mousemode right select
    24289 
    24290 > select #2/I:154
    24291 
    24292 8 atoms, 7 bonds, 1 residue, 1 model selected 
    24293 
    24294 > ui mousemode right translate
    24295 
    24296 > show sel atoms
    24297 
    24298 > hide sel atoms
    24299 
    24300 > ui mousemode right select
    24301 
    24302 > select #2/I:251
    24303 
    24304 14 atoms, 15 bonds, 1 residue, 1 model selected 
    24305 
    24306 > select #50/A:247
    24307 
    24308 24 atoms, 25 bonds, 1 residue, 1 model selected 
    24309 
    24310 > select #2/I:251
    24311 
    24312 14 atoms, 15 bonds, 1 residue, 1 model selected 
    24313 
    24314 > select #50/A:247
    24315 
    24316 24 atoms, 25 bonds, 1 residue, 1 model selected 
    24317 
    24318 > select #2/I:251
    24319 
    24320 14 atoms, 15 bonds, 1 residue, 1 model selected 
    24321 
    24322 > select #2/I:251
    24323 
    24324 14 atoms, 15 bonds, 1 residue, 1 model selected 
    24325 
    24326 > select #50/A:247
    24327 
    24328 24 atoms, 25 bonds, 1 residue, 1 model selected 
    24329 
    24330 > select #2/I:251
    24331 
    24332 14 atoms, 15 bonds, 1 residue, 1 model selected 
    24333 
    24334 > ui mousemode right translate
    24335 
    24336 > style sel stick
    24337 
    24338 Changed 14 atom styles 
    24339 
    24340 > show sel atoms
    24341 
    24342 > color sel gray
    24343 
    24344 > ui mousemode right select
    24345 
    24346 > select #50/A:180
    24347 
    24348 21 atoms, 21 bonds, 1 residue, 1 model selected 
    24349 
    24350 > select #2/I:184
    24351 
    24352 11 atoms, 11 bonds, 1 residue, 1 model selected 
    24353 
    24354 > ui mousemode right translate
    24355 
    24356 > ui mousemode right select
    24357 
    24358 > ui mousemode right translate
    24359 
    24360 > style sel stick
    24361 
    24362 Changed 11 atom styles 
    24363 
    24364 > show sel atoms
    24365 
    24366 > color sel gray
    24367 
    24368 > hide sel atoms
    24369 
    24370 > show sel atoms
    24371 
    24372 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    24373 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    24374 
    24375 > hide #2 models
    24376 
    24377 > select add #2
    24378 
    24379 30928 atoms, 31759 bonds, 4020 residues, 1 model selected 
    24380 
    24381 > select subtract #2
    24382 
    24383 Nothing selected 
    24384 
    24385 > show #20 models
    24386 
    24387 > hide #20 models
    24388 
    24389 > show #46 models
    24390 
    24391 > hide #46 models
    24392 
    24393 > show #46 models
    24394 
    24395 > color #46 #750000ff
    24396 
    24397 > ui mousemode right select
    24398 
    24399 > select #46/A:119
    24400 
    24401 14 atoms, 13 bonds, 1 residue, 1 model selected 
    24402 
    24403 > ui mousemode right translate
    24404 
    24405 > hide sel atoms
    24406 
    24407 > ui mousemode right select
    24408 
    24409 > select #46/A:121
    24410 
    24411 17 atoms, 16 bonds, 1 residue, 1 model selected 
    24412 
    24413 > ui mousemode right translate
    24414 
    24415 > hide sel atoms
    24416 
    24417 > ui mousemode right select
    24418 
    24419 > select #46/A:233
    24420 
    24421 15 atoms, 14 bonds, 1 residue, 1 model selected 
    24422 
    24423 > ui mousemode right translate
    24424 
    24425 > hide sel atoms
    24426 
    24427 > ui mousemode right select
    24428 
    24429 > select #46/A:183
    24430 
    24431 14 atoms, 14 bonds, 1 residue, 1 model selected 
    24432 
    24433 > select #46/A:183
    24434 
    24435 14 atoms, 14 bonds, 1 residue, 1 model selected 
    24436 
    24437 > ui mousemode right translate
    24438 
    24439 > hide sel atoms
    24440 
    24441 > ui mousemode right select
    24442 
    24443 > select #50/A:183
    24444 
    24445 15 atoms, 14 bonds, 1 residue, 1 model selected 
    24446 
    24447 > select #50/A:183
    24448 
    24449 15 atoms, 14 bonds, 1 residue, 1 model selected 
    24450 
    24451 > select #50/A:183
    24452 
    24453 15 atoms, 14 bonds, 1 residue, 1 model selected 
    24454 
    24455 > select #46/A:180
    24456 
    24457 12 atoms, 11 bonds, 1 residue, 1 model selected 
    24458 Alignment identifier is 46/A 
    24459 
    24460 > select #50/A:183
    24461 
    24462 15 atoms, 14 bonds, 1 residue, 1 model selected 
    24463 
    24464 > select #46/A:180
    24465 
    24466 12 atoms, 11 bonds, 1 residue, 1 model selected 
    24467 
    24468 > select #50/A:183
    24469 
    24470 15 atoms, 14 bonds, 1 residue, 1 model selected 
    24471 
    24472 > select #46/A:180
    24473 
    24474 12 atoms, 11 bonds, 1 residue, 1 model selected 
    24475 
    24476 > ui mousemode right translate
    24477 
    24478 > style sel stick
    24479 
    24480 Changed 12 atom styles 
    24481 
    24482 > show sel atoms
    24483 
    24484 > color sel red
    24485 
    24486 > select add #46
    24487 
    24488 4167 atoms, 4228 bonds, 261 residues, 1 model selected 
    24489 
    24490 > select subtract #46
    24491 
    24492 Nothing selected 
    24493 
    24494 > ui mousemode right select
    24495 
    24496 > select #50/A:179
    24497 
    24498 14 atoms, 13 bonds, 1 residue, 1 model selected 
    24499 
    24500 > select #46/A:176
    24501 
    24502 17 atoms, 16 bonds, 1 residue, 1 model selected 
    24503 
    24504 > ui mousemode right translate
    24505 
    24506 > hide sel atoms
    24507 
    24508 > style sel ball
    24509 
    24510 Changed 17 atom styles 
    24511 
    24512 > ui mousemode right select
    24513 
    24514 > select #46/A:150
    24515 
    24516 10 atoms, 9 bonds, 1 residue, 1 model selected 
    24517 
    24518 > ui mousemode right translate
    24519 
    24520 > hide sel atoms
    24521 
    24522 > ui mousemode right select
    24523 
    24524 > select #46/A:147
    24525 
    24526 17 atoms, 16 bonds, 1 residue, 1 model selected 
    24527 
    24528 > ui mousemode right translate
    24529 
    24530 > hide sel atoms
    24531 
    24532 > ui mousemode right select
    24533 
    24534 > select #46/A:171
    24535 
    24536 22 atoms, 21 bonds, 1 residue, 1 model selected 
    24537 
    24538 > ui mousemode right translate
    24539 
    24540 > hide sel atoms
    24541 
    24542 > ui mousemode right select
    24543 
    24544 > select #50/A:247
    24545 
    24546 24 atoms, 25 bonds, 1 residue, 1 model selected 
    24547 
    24548 > select #46/A:244
    24549 
    24550 24 atoms, 25 bonds, 1 residue, 1 model selected 
    24551 
    24552 > ui mousemode right translate
    24553 
    24554 > style sel stick
    24555 
    24556 Changed 24 atom styles 
    24557 
    24558 > show sel atoms
    24559 
    24560 > color sel gray
    24561 
    24562 > ui mousemode right select
    24563 
    24564 > select #50/A:180@CA
    24565 
    24566 1 atom, 1 residue, 1 model selected 
    24567 
    24568 > select #46/A:177
    24569 
    24570 21 atoms, 21 bonds, 1 residue, 1 model selected 
    24571 
    24572 > ui mousemode right translate
    24573 
    24574 > style sel stick
    24575 
    24576 Changed 21 atom styles 
    24577 
    24578 > show sel atoms
    24579 
    24580 > color sel gray
    24581 
    24582 > select add #46
    24583 
    24584 4167 atoms, 4228 bonds, 261 residues, 1 model selected 
    24585 
    24586 > select subtract #46
    24587 
    24588 Nothing selected 
    24589 
    24590 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    24591 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    24592 
    24593 > hide #46 models
    24594 
    24595 > show #20 models
    24596 
    24597 > ui tool show Matchmaker
    24598 
    24599 > matchmaker #20 to #50
    24600 
    24601 Parameters 
    24602 --- 
    24603 Chain pairing | bb 
    24604 Alignment algorithm | Needleman-Wunsch 
    24605 Similarity matrix | BLOSUM-62 
    24606 SS fraction | 0.3 
    24607 Gap open (HH/SS/other) | 18/18/6 
    24608 Gap extend | 1 
    24609 SS matrix |  |  | H | S | O 
    24610 ---|---|---|--- 
    24611 H | 6 | -9 | -6 
    24612 S |  | 6 | -6 
    24613 O |  |  | 4 
    24614 Iteration cutoff | 2 
    24615  
    24616 Matchmaker Sindbis virus AlphaFold.pdb, chain A (#50) with Eilat virus
    24617 Alphafold.pdb, chain A (#20), sequence alignment score = 850 
    24618 RMSD between 154 pruned atom pairs is 0.618 angstroms; (across all 248 pairs:
    24619 35.914) 
    24620  
    24621 
    24622 > color #20 #00b383ff
    24623 
    24624 > ui mousemode right select
    24625 
    24626 > select #20/A:113
    24627 
    24628 22 atoms, 21 bonds, 1 residue, 1 model selected 
    24629 
    24630 > ui mousemode right translate
    24631 
    24632 > hide sel atoms
    24633 
    24634 > ui mousemode right select
    24635 
    24636 > select #20/A:115
    24637 
    24638 16 atoms, 15 bonds, 1 residue, 1 model selected 
    24639 
    24640 > hide sel cartoons
    24641 
    24642 > show sel cartoons
    24643 
    24644 > show sel atoms
    24645 
    24646 > hide sel atoms
    24647 
    24648 > ui mousemode right translate
    24649 
    24650 > ui mousemode right select
    24651 
    24652 > select #20/A:227
    24653 
    24654 15 atoms, 14 bonds, 1 residue, 1 model selected 
    24655 
    24656 > ui mousemode right translate
    24657 
    24658 > hide sel atoms
    24659 
    24660 > ui mousemode right select
    24661 
    24662 > select #20/A:177
    24663 
    24664 12 atoms, 11 bonds, 1 residue, 1 model selected 
    24665 
    24666 > ui mousemode right translate
    24667 
    24668 > hide sel atoms
    24669 
    24670 > ui mousemode right select
    24671 
    24672 > select #50/A:183
    24673 
    24674 15 atoms, 14 bonds, 1 residue, 1 model selected 
    24675 
    24676 > select #20/A:174
    24677 
    24678 15 atoms, 14 bonds, 1 residue, 1 model selected 
    24679 Alignment identifier is 20/A 
    24680 
    24681 > ui mousemode right translate
    24682 
    24683 > style sel stick
    24684 
    24685 Changed 15 atom styles 
    24686 
    24687 > hide sel atoms
    24688 
    24689 > show sel atoms
    24690 
    24691 > color sel red
    24692 
    24693 > ui mousemode right select
    24694 
    24695 > select #50/A:247
    24696 
    24697 24 atoms, 25 bonds, 1 residue, 1 model selected 
    24698 
    24699 > select #20/A:238
    24700 
    24701 24 atoms, 25 bonds, 1 residue, 1 model selected 
    24702 
    24703 > select #20/A:238
    24704 
    24705 24 atoms, 25 bonds, 1 residue, 1 model selected 
    24706 
    24707 > select #50/A:247
    24708 
    24709 24 atoms, 25 bonds, 1 residue, 1 model selected 
    24710 
    24711 > select #20/A:238
    24712 
    24713 24 atoms, 25 bonds, 1 residue, 1 model selected 
    24714 
    24715 > ui mousemode right translate
    24716 
    24717 > show sel atoms
    24718 
    24719 > color sel gray
    24720 
    24721 > ui mousemode right select
    24722 
    24723 > select #50/A:180
    24724 
    24725 21 atoms, 21 bonds, 1 residue, 1 model selected 
    24726 
    24727 > select #20/A:171
    24728 
    24729 21 atoms, 21 bonds, 1 residue, 1 model selected 
    24730 
    24731 > ui mousemode right translate
    24732 
    24733 > style sel stick
    24734 
    24735 Changed 21 atom styles 
    24736 
    24737 > show sel atoms
    24738 
    24739 > color sel gray
    24740 
    24741 > ui mousemode right select
    24742 
    24743 > select #20/A:165
    24744 
    24745 24 atoms, 23 bonds, 1 residue, 1 model selected 
    24746 
    24747 > ui mousemode right translate
    24748 
    24749 > hide sel atoms
    24750 
    24751 > ui mousemode right select
    24752 
    24753 > select #20/A:141@CA
    24754 
    24755 1 atom, 1 residue, 1 model selected 
    24756 
    24757 > ui mousemode right translate
    24758 
    24759 > hide sel atoms
    24760 
    24761 > show sel atoms
    24762 
    24763 > ui mousemode right select
    24764 
    24765 > select #20/A:141
    24766 
    24767 19 atoms, 18 bonds, 1 residue, 1 model selected 
    24768 
    24769 > select #20/A:141@CA
    24770 
    24771 1 atom, 1 residue, 1 model selected 
    24772 
    24773 > ui mousemode right translate
    24774 
    24775 > hide sel atoms
    24776 
    24777 > hide sel cartoons
    24778 
    24779 > show sel cartoons
    24780 
    24781 > show sel atoms
    24782 
    24783 > ui mousemode right select
    24784 
    24785 > select #20/A:141
    24786 
    24787 19 atoms, 18 bonds, 1 residue, 1 model selected 
    24788 
    24789 > hide sel atoms
    24790 
    24791 > select clear
    24792 
    24793 > ui mousemode right translate
    24794 
    24795 > ui mousemode right rotate
    24796 
    24797 > ui mousemode right select
    24798 
    24799 > select #20/A:144
    24800 
    24801 11 atoms, 10 bonds, 1 residue, 1 model selected 
    24802 
    24803 > ui mousemode right translate
    24804 
    24805 > hide sel atoms
    24806 
    24807 > ui mousemode right select
    24808 
    24809 > select #20/A:238
    24810 
    24811 24 atoms, 25 bonds, 1 residue, 1 model selected 
    24812 
    24813 > select #20/A:171
    24814 
    24815 21 atoms, 21 bonds, 1 residue, 1 model selected 
    24816 
    24817 > ui mousemode right translate
    24818 
    24819 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    24820 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    24821 
    24822 > hide #20 models
    24823 
    24824 > select add #20
    24825 
    24826 3966 atoms, 4011 bonds, 255 residues, 1 model selected 
    24827 
    24828 > select subtract #20
    24829 
    24830 Nothing selected 
    24831 
    24832 > show #15 models
    24833 
    24834 > hide #15 models
    24835 
    24836 > show #16 models
    24837 
    24838 > color #16 #fe00feff
    24839 
    24840 > ui mousemode right select
    24841 
    24842 > select #16/A:134
    24843 
    24844 22 atoms, 21 bonds, 1 residue, 1 model selected 
    24845 
    24846 > hide sel atoms
    24847 
    24848 > select #16/A:132
    24849 
    24850 15 atoms, 14 bonds, 1 residue, 1 model selected 
    24851 
    24852 > hide sel atoms
    24853 
    24854 > ui mousemode right rotate
    24855 
    24856 > ui mousemode right translate
    24857 
    24858 > ui mousemode right select
    24859 
    24860 > select #16/A:246
    24861 
    24862 15 atoms, 14 bonds, 1 residue, 1 model selected 
    24863 
    24864 > select #16/A:246
    24865 
    24866 15 atoms, 14 bonds, 1 residue, 1 model selected 
    24867 
    24868 > ui mousemode right translate
    24869 
    24870 > hide sel atoms
    24871 
    24872 > ui mousemode right select
    24873 
    24874 > select #50/A:186
    24875 
    24876 15 atoms, 14 bonds, 1 residue, 1 model selected 
    24877 
    24878 > select #16/A:196
    24879 
    24880 17 atoms, 16 bonds, 1 residue, 1 model selected 
    24881 
    24882 > ui mousemode right translate
    24883 
    24884 > hide sel atoms
    24885 
    24886 > ui mousemode right select
    24887 
    24888 > select clear
    24889 
    24890 > select #50/A:183
    24891 
    24892 15 atoms, 14 bonds, 1 residue, 1 model selected 
    24893 
    24894 > select #16/A:193
    24895 
    24896 15 atoms, 14 bonds, 1 residue, 1 model selected 
    24897 
    24898 > interfaces select & ~solvent
    24899 
    24900 Missing or invalid "atoms" argument: invalid atoms specifier 
    24901 Alignment identifier is 16/A 
    24902 
    24903 > ui mousemode right translate
    24904 
    24905 > style sel stick
    24906 
    24907 Changed 15 atom styles 
    24908 
    24909 > show sel atoms
    24910 
    24911 > color sel red
    24912 
    24913 > ui mousemode right select
    24914 
    24915 > select #50/A:247
    24916 
    24917 24 atoms, 25 bonds, 1 residue, 1 model selected 
    24918 
    24919 > select #16/A:257
    24920 
    24921 24 atoms, 25 bonds, 1 residue, 1 model selected 
    24922 
    24923 > ui mousemode right translate
    24924 
    24925 > style sel stick
    24926 
    24927 Changed 24 atom styles 
    24928 
    24929 > show sel atoms
    24930 
    24931 > color sel gray
    24932 
    24933 > ui mousemode right select
    24934 
    24935 > select #50/A:180
    24936 
    24937 21 atoms, 21 bonds, 1 residue, 1 model selected 
    24938 
    24939 > select #16/A:190
    24940 
    24941 21 atoms, 21 bonds, 1 residue, 1 model selected 
    24942 
    24943 > ui mousemode right translate
    24944 
    24945 > style sel stick
    24946 
    24947 Changed 21 atom styles 
    24948 
    24949 > show sel atoms
    24950 
    24951 > color sel gray
    24952 
    24953 > ui mousemode right select
    24954 
    24955 > select #16/A:189@CA
    24956 
    24957 1 atom, 1 residue, 1 model selected 
    24958 
    24959 > select #16/A:189
    24960 
    24961 22 atoms, 21 bonds, 1 residue, 1 model selected 
    24962 
    24963 > ui mousemode right translate
    24964 
    24965 > hide sel atoms
    24966 
    24967 > ui mousemode right select
    24968 
    24969 > select #16/A:184
    24970 
    24971 24 atoms, 23 bonds, 1 residue, 1 model selected 
    24972 
    24973 > select #16/A:184
    24974 
    24975 24 atoms, 23 bonds, 1 residue, 1 model selected 
    24976 
    24977 > hide sel atoms
    24978 
    24979 > ui mousemode right rotate
    24980 
    24981 > ui mousemode right translate
    24982 
    24983 > ui mousemode right select
    24984 
    24985 > select #16/A:163
    24986 
    24987 10 atoms, 9 bonds, 1 residue, 1 model selected 
    24988 
    24989 > ui mousemode right translate
    24990 
    24991 > show sel cartoons
    24992 
    24993 > hide sel atoms
    24994 
    24995 > ui mousemode right select
    24996 
    24997 > select #16/A:160
    24998 
    24999 16 atoms, 15 bonds, 1 residue, 1 model selected 
    25000 
    25001 > ui mousemode right translate
    25002 
    25003 > hide sel atoms
    25004 
    25005 > ui mousemode right select
    25006 
    25007 > select #16/A:193
    25008 
    25009 15 atoms, 14 bonds, 1 residue, 1 model selected 
    25010 
    25011 > select #16/A:257
    25012 
    25013 24 atoms, 25 bonds, 1 residue, 1 model selected 
    25014 
    25015 > select #16/A:190
    25016 
    25017 21 atoms, 21 bonds, 1 residue, 1 model selected 
    25018 
    25019 > select #16/A:190
    25020 
    25021 21 atoms, 21 bonds, 1 residue, 1 model selected 
    25022 
    25023 > ui mousemode right translate
    25024 
    25025 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    25026 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    25027 
    25028 ——— End of log from Mon Jul 31 10:36:12 2023 ———
    25029 
    25030 opened ChimeraX session 
    25031 
    25032 > show #47 models
    25033 
    25034 > hide #16 models
    25035 
    25036 > select add #16
    25037 
    25038 4411 atoms, 4467 bonds, 274 residues, 1 model selected 
    25039 
    25040 > select subtract #16
    25041 
    25042 Nothing selected 
    25043 
    25044 > color #47 #b05800ff
    25045 
    25046 > color #47 #ad5700ff
    25047 
    25048 > ui mousemode right select
    25049 
    25050 > select #47/A:127
    25051 
    25052 12 atoms, 11 bonds, 1 residue, 1 model selected 
    25053 
    25054 > ui mousemode right translate
    25055 
    25056 > hide sel atoms
    25057 
    25058 > ui mousemode right select
    25059 
    25060 > select #47/A:129
    25061 
    25062 22 atoms, 21 bonds, 1 residue, 1 model selected 
    25063 
    25064 > ui mousemode right translate
    25065 
    25066 > hide sel cartoons
    25067 
    25068 [Repeated 1 time(s)]
    25069 
    25070 > show sel cartoons
    25071 
    25072 > hide sel atoms
    25073 
    25074 > ui mousemode right select
    25075 
    25076 > select #47/A:241
    25077 
    25078 15 atoms, 14 bonds, 1 residue, 1 model selected 
    25079 
    25080 > ui mousemode right translate
    25081 
    25082 > hide sel atoms
    25083 
    25084 > ui mousemode right select
    25085 
    25086 > select #47/A:191@CA
    25087 
    25088 1 atom, 1 residue, 1 model selected 
    25089 
    25090 > select #47/A:191
    25091 
    25092 15 atoms, 14 bonds, 1 residue, 1 model selected 
    25093 
    25094 > ui mousemode right translate
    25095 
    25096 > hide sel atoms
    25097 
    25098 > ui mousemode right select
    25099 
    25100 > select #50/A:183
    25101 
    25102 15 atoms, 14 bonds, 1 residue, 1 model selected 
    25103 Destroying pre-existing alignment with identifier 50/A 
    25104 Alignment identifier is 50/A 
    25105 
    25106 > select #47/A:188
    25107 
    25108 15 atoms, 14 bonds, 1 residue, 1 model selected 
    25109 Alignment identifier is 47/A 
    25110 
    25111 > style sel stick
    25112 
    25113 Changed 15 atom styles 
    25114 
    25115 > show sel atoms
    25116 
    25117 > color sel red
    25118 
    25119 > ui mousemode right translate
    25120 
    25121 > ui mousemode right select
    25122 
    25123 > select #50/A:179
    25124 
    25125 14 atoms, 13 bonds, 1 residue, 1 model selected 
    25126 
    25127 > select #47/A:184
    25128 
    25129 22 atoms, 21 bonds, 1 residue, 1 model selected 
    25130 
    25131 > ui mousemode right rotate
    25132 
    25133 > ui mousemode right translate
    25134 
    25135 > hide sel atoms
    25136 
    25137 > ui mousemode right select
    25138 
    25139 > select #47/A:179@CA
    25140 
    25141 1 atom, 1 residue, 1 model selected 
    25142 
    25143 > select #47/A:179@CA
    25144 
    25145 1 atom, 1 residue, 1 model selected 
    25146 Drag select of 4 residues 
    25147 
    25148 > select #47/A:177
    25149 
    25150 17 atoms, 17 bonds, 1 residue, 1 model selected 
    25151 
    25152 > select #47/A:179
    25153 
    25154 22 atoms, 21 bonds, 1 residue, 1 model selected 
    25155 
    25156 > ui mousemode right translate
    25157 
    25158 > hide sel atoms
    25159 
    25160 > ui mousemode right select
    25161 
    25162 > select #47/A:158
    25163 
    25164 22 atoms, 21 bonds, 1 residue, 1 model selected 
    25165 
    25166 > ui mousemode right translate
    25167 
    25168 > hide sel atoms
    25169 
    25170 > ui mousemode right select
    25171 
    25172 > select #47/A:155
    25173 
    25174 12 atoms, 11 bonds, 1 residue, 1 model selected 
    25175 
    25176 > select #47/A:155
    25177 
    25178 12 atoms, 11 bonds, 1 residue, 1 model selected 
    25179 
    25180 > ui mousemode right translate
    25181 
    25182 > hide sel atoms
    25183 
    25184 > ui mousemode right select
    25185 
    25186 > select #50/A:247
    25187 
    25188 24 atoms, 25 bonds, 1 residue, 1 model selected 
    25189 
    25190 > select #47/A:252
    25191 
    25192 24 atoms, 25 bonds, 1 residue, 1 model selected 
    25193 
    25194 > select #50/A:247
    25195 
    25196 24 atoms, 25 bonds, 1 residue, 1 model selected 
    25197 
    25198 > select #47/A:252
    25199 
    25200 24 atoms, 25 bonds, 1 residue, 1 model selected 
    25201 Drag select of 2 residues 
    25202 [Repeated 1 time(s)]
    25203 
    25204 > ui mousemode right translate
    25205 
    25206 > ui mousemode right select
    25207 
    25208 > select #50/A:247
    25209 
    25210 24 atoms, 25 bonds, 1 residue, 1 model selected 
    25211 
    25212 > select #47/A:252
    25213 
    25214 24 atoms, 25 bonds, 1 residue, 1 model selected 
    25215 
    25216 > select #47/A:252
    25217 
    25218 24 atoms, 25 bonds, 1 residue, 1 model selected 
    25219 
    25220 > ui mousemode right translate
    25221 
    25222 > hide sel atoms
    25223 
    25224 > show sel atoms
    25225 
    25226 > color sel gray
    25227 
    25228 > ui mousemode right select
    25229 
    25230 > select #47/A:185
    25231 
    25232 21 atoms, 21 bonds, 1 residue, 1 model selected 
    25233 
    25234 > ui mousemode right translate
    25235 
    25236 > show sel atoms
    25237 
    25238 > color sel dark gray
    25239 
    25240 > color sel gray
    25241 
    25242 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    25243 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    25244 
    25245 > open "C:/Users/Carolina/Downloads/Fort Morgan virus AlphaFold.pdb"
    25246 
    25247 Chain information for Fort Morgan virus AlphaFold.pdb #51 
    25248 --- 
    25249 Chain | Description 
    25250 A | No description available 
    25251  
    25252 
    25253 > color #51 #55557fff
    25254 
    25255 > color #51 #00aa7fff
    25256 
    25257 > color #51 #aaff7fff
    25258 
    25259 > color #51 #00557fff
    25260 
    25261 > color #51 #006999ff
    25262 
    25263 > color #51 #1d5999ff
    25264 
    25265 > color #51 #2f7999ff
    25266 
    25267 > color #51 #3a6899ff
    25268 
    25269 > color #51 #4276adff
    25270 
    25271 > color #51 #4f81adff
    25272 
    25273 > hide #47 models
    25274 
    25275 > select add #47
    25276 
    25277 4298 atoms, 4353 bonds, 268 residues, 1 model selected 
    25278 
    25279 > select subtract #47
    25280 
    25281 Nothing selected 
    25282 
    25283 > ui tool show Matchmaker
    25284 
    25285 > matchmaker #51 to #50
    25286 
    25287 Parameters 
    25288 --- 
    25289 Chain pairing | bb 
    25290 Alignment algorithm | Needleman-Wunsch 
    25291 Similarity matrix | BLOSUM-62 
    25292 SS fraction | 0.3 
    25293 Gap open (HH/SS/other) | 18/18/6 
    25294 Gap extend | 1 
    25295 SS matrix |  |  | H | S | O 
    25296 ---|---|---|--- 
    25297 H | 6 | -9 | -6 
    25298 S |  | 6 | -6 
    25299 O |  |  | 4 
    25300 Iteration cutoff | 2 
    25301  
    25302 Matchmaker Sindbis virus AlphaFold.pdb, chain A (#50) with Fort Morgan virus
    25303 AlphaFold.pdb, chain A (#51), sequence alignment score = 836.3 
    25304 RMSD between 167 pruned atom pairs is 0.504 angstroms; (across all 260 pairs:
    25305 13.821) 
    25306  
    25307 
    25308 > color #51 #00557fff
    25309 
    25310 > color #51 #006c9eff
    25311 
    25312 > color #51 #00608cff
    25313 
    25314 > color #51 #17448cff
    25315 
    25316 > color #51 #311f8cff
    25317 
    25318 > color #51 #00007fff
    25319 
    25320 > color #51 blue
    25321 
    25322 > color #51 #0000d6ff
    25323 
    25324 > color #51 #00007fff
    25325 
    25326 > color #51 #0000a8ff
    25327 
    25328 > color #51 #0000c5ff
    25329 
    25330 > color #51 #0000b4ff
    25331 
    25332 > color #51 #0e27b4ff
    25333 
    25334 > color #51 #171eb4ff
    25335 
    25336 > color #51 #2129b4ff
    25337 
    25338 > color #51 #2836b4ff
    25339 
    25340 > color #51 #272eb4ff
    25341 
    25342 > ui mousemode right rotate
    25343 
    25344 > ui mousemode right select
    25345 
    25346 > select #50/A:183
    25347 
    25348 15 atoms, 14 bonds, 1 residue, 1 model selected 
    25349 
    25350 > select #51/A:180
    25351 
    25352 15 atoms, 14 bonds, 1 residue, 1 model selected 
    25353 Alignment identifier is 51/A 
    25354 
    25355 > ui mousemode right translate
    25356 
    25357 > style sel stick
    25358 
    25359 Changed 15 atom styles 
    25360 
    25361 > show sel atoms
    25362 
    25363 > color sel red
    25364 
    25365 > ui mousemode right select
    25366 
    25367 [Repeated 1 time(s)]
    25368 
    25369 > select #51/A:244
    25370 
    25371 24 atoms, 25 bonds, 1 residue, 1 model selected 
    25372 
    25373 > select #50/A:247
    25374 
    25375 24 atoms, 25 bonds, 1 residue, 1 model selected 
    25376 
    25377 > select #51/A:244
    25378 
    25379 24 atoms, 25 bonds, 1 residue, 1 model selected 
    25380 
    25381 > ui mousemode right translate
    25382 
    25383 > style sel stick
    25384 
    25385 Changed 24 atom styles 
    25386 
    25387 > hide sel atoms
    25388 
    25389 > show sel atoms
    25390 
    25391 > color sel gray
    25392 
    25393 > ui mousemode right select
    25394 
    25395 > select #50/A:180
    25396 
    25397 21 atoms, 21 bonds, 1 residue, 1 model selected 
    25398 
    25399 > select #51/A:177
    25400 
    25401 21 atoms, 21 bonds, 1 residue, 1 model selected 
    25402 
    25403 > ui mousemode right translate
    25404 
    25405 > style sel stick
    25406 
    25407 Changed 21 atom styles 
    25408 
    25409 > show sel atoms
    25410 
    25411 > color sel gray
    25412 
    25413 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    25414 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    25415 
    25416 > hide #51 models
    25417 
    25418 > select add #51
    25419 
    25420 4193 atoms, 4251 bonds, 261 residues, 1 model selected 
    25421 
    25422 > select subtract #51
    25423 
    25424 Nothing selected 
    25425 
    25426 > show #47 models
    25427 
    25428 > hide #47 models
    25429 
    25430 > show #21 models
    25431 
    25432 > color #21 #0077b3ff
    25433 
    25434 > color #21 #006ea5ff
    25435 
    25436 > color #21 #0073adff
    25437 
    25438 > color #21 #006fa6ff
    25439 
    25440 > ui mousemode right select
    25441 
    25442 > select #21/A:117
    25443 
    25444 14 atoms, 13 bonds, 1 residue, 1 model selected 
    25445 
    25446 > ui mousemode right translate
    25447 
    25448 > hide sel atoms
    25449 
    25450 > ui mousemode right select
    25451 
    25452 > select #21/A:119
    25453 
    25454 17 atoms, 16 bonds, 1 residue, 1 model selected 
    25455 
    25456 > ui mousemode right select
    25457 
    25458 > hide sel atoms
    25459 
    25460 > ui mousemode right translate
    25461 
    25462 > ui mousemode right select
    25463 
    25464 > select #21/A:231
    25465 
    25466 15 atoms, 14 bonds, 1 residue, 1 model selected 
    25467 
    25468 > ui mousemode right translate
    25469 
    25470 > hide sel atoms
    25471 
    25472 > ui mousemode right select
    25473 
    25474 > select #21/A:181@N
    25475 
    25476 1 atom, 1 residue, 1 model selected 
    25477 
    25478 > select #21/A:181
    25479 
    25480 14 atoms, 14 bonds, 1 residue, 1 model selected 
    25481 
    25482 > hide sel atoms
    25483 
    25484 > ui mousemode right translate
    25485 
    25486 > ui mousemode right select
    25487 
    25488 > select #50/A:183
    25489 
    25490 15 atoms, 14 bonds, 1 residue, 1 model selected 
    25491 
    25492 > select #21/A:178
    25493 
    25494 15 atoms, 14 bonds, 1 residue, 1 model selected 
    25495 
    25496 > ui mousemode right translate
    25497 
    25498 > style sel stick
    25499 
    25500 Changed 15 atom styles 
    25501 
    25502 > show sel atoms
    25503 
    25504 > color sel red
    25505 
    25506 > ui mousemode right select
    25507 
    25508 > select #50/A:247
    25509 
    25510 24 atoms, 25 bonds, 1 residue, 1 model selected 
    25511 
    25512 > select #21/A:242
    25513 
    25514 24 atoms, 25 bonds, 1 residue, 1 model selected 
    25515 Alignment identifier is 21/A 
    25516 
    25517 > style sel stick
    25518 
    25519 Changed 24 atom styles 
    25520 
    25521 > show sel atoms
    25522 
    25523 > color sel gray
    25524 
    25525 > select #50/A:247
    25526 
    25527 24 atoms, 25 bonds, 1 residue, 1 model selected 
    25528 
    25529 > select clear
    25530 
    25531 [Repeated 2 time(s)]
    25532 
    25533 > ui mousemode right translate
    25534 
    25535 > ui mousemode right select
    25536 
    25537 > select #21/A:175
    25538 
    25539 21 atoms, 21 bonds, 1 residue, 1 model selected 
    25540 
    25541 > select #50/A:180
    25542 
    25543 21 atoms, 21 bonds, 1 residue, 1 model selected 
    25544 
    25545 > select #21/A:175
    25546 
    25547 21 atoms, 21 bonds, 1 residue, 1 model selected 
    25548 
    25549 > ui mousemode right translate
    25550 
    25551 > style sel stick
    25552 
    25553 Changed 21 atom styles 
    25554 
    25555 > show sel atoms
    25556 
    25557 > color sel gray
    25558 
    25559 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    25560 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    25561 
    25562 ——— End of log from Mon Jul 31 12:55:07 2023 ———
    25563 
    25564 opened ChimeraX session 
    25565 
    25566 > show #22 models
    25567 
    25568 > hide #21 models
    25569 
    25570 > select add #21
    25571 
    25572 4166 atoms, 4222 bonds, 259 residues, 1 model selected 
    25573 
    25574 > select subtract #21
    25575 
    25576 Nothing selected 
    25577 
    25578 > color #22 #fa5300ff
    25579 
    25580 > color #22 #ff5500ff
    25581 
    25582 > color #22 #ff7a0eff
    25583 
    25584 > ui mousemode right rotate
    25585 
    25586 > ui mousemode right select
    25587 
    25588 > select #22/A:121
    25589 
    25590 17 atoms, 16 bonds, 1 residue, 1 model selected 
    25591 
    25592 > hide sel atoms
    25593 
    25594 > select #22/A:119
    25595 
    25596 14 atoms, 13 bonds, 1 residue, 1 model selected 
    25597 
    25598 > hide sel atoms
    25599 
    25600 > select #22/A:147@CB
    25601 
    25602 1 atom, 1 residue, 1 model selected 
    25603 
    25604 > ui mousemode right translate
    25605 
    25606 > ui mousemode right select
    25607 
    25608 > select #50/A:236
    25609 
    25610 15 atoms, 14 bonds, 1 residue, 1 model selected 
    25611 
    25612 > select #22/A:233
    25613 
    25614 15 atoms, 14 bonds, 1 residue, 1 model selected 
    25615 
    25616 > hide sel atoms
    25617 
    25618 > ui mousemode right translate
    25619 
    25620 > ui mousemode right select
    25621 
    25622 > select #22/A:171
    25623 
    25624 22 atoms, 21 bonds, 1 residue, 1 model selected 
    25625 
    25626 > hide sel atoms
    25627 
    25628 > select #22/A:150
    25629 
    25630 10 atoms, 9 bonds, 1 residue, 1 model selected 
    25631 
    25632 > hide sel atoms
    25633 
    25634 > select #22/A:147
    25635 
    25636 17 atoms, 16 bonds, 1 residue, 1 model selected 
    25637 
    25638 > hide sel atoms
    25639 
    25640 > ui mousemode right translate
    25641 
    25642 > ui mousemode right select
    25643 
    25644 > select #22/A:176
    25645 
    25646 17 atoms, 16 bonds, 1 residue, 1 model selected 
    25647 
    25648 > hide sel atoms
    25649 
    25650 > ui mousemode right translate
    25651 
    25652 > ui mousemode right select
    25653 
    25654 > select #22/A:183
    25655 
    25656 14 atoms, 14 bonds, 1 residue, 1 model selected 
    25657 
    25658 > hide sel atoms
    25659 
    25660 > ui mousemode right translate
    25661 
    25662 > ui mousemode right select
    25663 
    25664 > select #22/A:180
    25665 
    25666 15 atoms, 14 bonds, 1 residue, 1 model selected 
    25667 
    25668 > style sel stick
    25669 
    25670 Changed 15 atom styles 
    25671 
    25672 > show sel atoms
    25673 
    25674 > select #50/A:183
    25675 
    25676 15 atoms, 14 bonds, 1 residue, 1 model selected 
    25677 
    25678 > select #50/A:183
    25679 
    25680 15 atoms, 14 bonds, 1 residue, 1 model selected 
    25681 
    25682 > select #22/A:180
    25683 
    25684 15 atoms, 14 bonds, 1 residue, 1 model selected 
    25685 
    25686 > select #22/A:180
    25687 
    25688 15 atoms, 14 bonds, 1 residue, 1 model selected 
    25689 Alignment identifier is 22/A 
    25690 
    25691 > color sel red
    25692 
    25693 > ui mousemode right translate
    25694 
    25695 > ui mousemode right rotate
    25696 
    25697 > ui mousemode right select
    25698 
    25699 > select #50/A:247
    25700 
    25701 24 atoms, 25 bonds, 1 residue, 1 model selected 
    25702 
    25703 > select #22/A:244
    25704 
    25705 24 atoms, 25 bonds, 1 residue, 1 model selected 
    25706 
    25707 > ui mousemode right translate
    25708 
    25709 > style sel stick
    25710 
    25711 Changed 24 atom styles 
    25712 
    25713 > show sel atoms
    25714 
    25715 > color sel gray
    25716 
    25717 > ui mousemode right select
    25718 
    25719 > select #50/A:180
    25720 
    25721 21 atoms, 21 bonds, 1 residue, 1 model selected 
    25722 
    25723 > select #22/A:177
    25724 
    25725 21 atoms, 21 bonds, 1 residue, 1 model selected 
    25726 
    25727 > ui mousemode right translate
    25728 
    25729 > style sel stick
    25730 
    25731 Changed 21 atom styles 
    25732 
    25733 > show sel atoms
    25734 
    25735 > color sel gray
    25736 
    25737 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    25738 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    25739 
    25740 > show #48 models
    25741 
    25742 > select add #22
    25743 
    25744 4167 atoms, 4228 bonds, 261 residues, 1 model selected 
    25745 
    25746 > select subtract #22
    25747 
    25748 Nothing selected 
    25749 
    25750 > hide #22 models
    25751 
    25752 > ui mousemode right select
    25753 
    25754 > select #48/A:238
    25755 
    25756 11 atoms, 10 bonds, 1 residue, 1 model selected 
    25757 
    25758 > select #48/A:238
    25759 
    25760 11 atoms, 10 bonds, 1 residue, 1 model selected 
    25761 Alignment identifier is 48/A 
    25762 
    25763 > ui mousemode right translate
    25764 
    25765 > color #48 #62bd00ff
    25766 
    25767 > color #48 #60ba00ff
    25768 
    25769 > ui mousemode right select
    25770 
    25771 > select #48/A:119
    25772 
    25773 22 atoms, 21 bonds, 1 residue, 1 model selected 
    25774 
    25775 > hide sel atoms
    25776 
    25777 > select #48/A:117
    25778 
    25779 15 atoms, 14 bonds, 1 residue, 1 model selected 
    25780 
    25781 > hide sel atoms
    25782 
    25783 > ui mousemode right translate
    25784 
    25785 > ui mousemode right select
    25786 
    25787 > select #48/A:231
    25788 
    25789 15 atoms, 14 bonds, 1 residue, 1 model selected 
    25790 
    25791 > ui mousemode right translate
    25792 
    25793 > hide sel atoms
    25794 
    25795 > ui mousemode right select
    25796 
    25797 > select #48/A:181
    25798 
    25799 15 atoms, 14 bonds, 1 residue, 1 model selected 
    25800 
    25801 > ui mousemode right translate
    25802 
    25803 > hide sel atoms
    25804 
    25805 > ui mousemode right select
    25806 
    25807 > select #50/A:183
    25808 
    25809 15 atoms, 14 bonds, 1 residue, 1 model selected 
    25810 
    25811 > select #50/A:183
    25812 
    25813 15 atoms, 14 bonds, 1 residue, 1 model selected 
    25814 
    25815 > select #48/A:178
    25816 
    25817 15 atoms, 14 bonds, 1 residue, 1 model selected 
    25818 
    25819 > select #48/A:178
    25820 
    25821 15 atoms, 14 bonds, 1 residue, 1 model selected 
    25822 
    25823 > ui mousemode right translate
    25824 
    25825 > style sel stick
    25826 
    25827 Changed 15 atom styles 
    25828 
    25829 > show sel atoms
    25830 
    25831 > color sel red
    25832 
    25833 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    25834 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    25835 
    25836 ——— End of log from Tue Aug 1 09:36:23 2023 ———
    25837 
    25838 opened ChimeraX session 
    25839 
    25840 > ui mousemode right select
    25841 
    25842 > select #50/A:247
    25843 
    25844 24 atoms, 25 bonds, 1 residue, 1 model selected 
    25845 
    25846 > select #48/A:242
    25847 
    25848 24 atoms, 25 bonds, 1 residue, 1 model selected 
    25849 
    25850 > ui mousemode right translate
    25851 
    25852 > style sel stick
    25853 
    25854 Changed 24 atom styles 
    25855 
    25856 > show sel atoms
    25857 
    25858 > color sel gray
    25859 
    25860 > set bgColor white
    25861 
    25862 > ui mousemode right rotate
    25863 
    25864 > ui mousemode right select
    25865 
    25866 > select #50/A:180
    25867 
    25868 21 atoms, 21 bonds, 1 residue, 1 model selected 
    25869 
    25870 > select #48/A:175
    25871 
    25872 21 atoms, 21 bonds, 1 residue, 1 model selected 
    25873 
    25874 > ui mousemode right translate
    25875 
    25876 > style sel stick
    25877 
    25878 Changed 21 atom styles 
    25879 
    25880 > show sel atoms
    25881 
    25882 > color sel gray
    25883 
    25884 > ui mousemode right select
    25885 
    25886 > select #48/A:174@CA
    25887 
    25888 1 atom, 1 residue, 1 model selected 
    25889 
    25890 > select #48/A:174@CA
    25891 
    25892 1 atom, 1 residue, 1 model selected 
    25893 
    25894 > select clear
    25895 
    25896 > select #48/A:174
    25897 
    25898 22 atoms, 21 bonds, 1 residue, 1 model selected 
    25899 
    25900 > select #48/A:174
    25901 
    25902 22 atoms, 21 bonds, 1 residue, 1 model selected 
    25903 
    25904 > ui mousemode right translate
    25905 
    25906 > hide sel atoms
    25907 
    25908 > ui mousemode right select
    25909 
    25910 > select #48/A:169
    25911 
    25912 22 atoms, 21 bonds, 1 residue, 1 model selected 
    25913 
    25914 > select #48/A:169
    25915 
    25916 22 atoms, 21 bonds, 1 residue, 1 model selected 
    25917 
    25918 > hide sel atoms
    25919 
    25920 > ui mousemode right translate
    25921 
    25922 > ui mousemode right select
    25923 
    25924 > select #48/A:145
    25925 
    25926 12 atoms, 11 bonds, 1 residue, 1 model selected 
    25927 
    25928 > hide sel atoms
    25929 
    25930 > select #48/A:147
    25931 
    25932 10 atoms, 9 bonds, 1 residue, 1 model selected 
    25933 
    25934 > hide sel atoms
    25935 
    25936 [Repeated 1 time(s)]
    25937 
    25938 > show sel atoms
    25939 
    25940 > hide sel atoms
    25941 
    25942 > select #48/A:147
    25943 
    25944 10 atoms, 9 bonds, 1 residue, 1 model selected 
    25945 
    25946 > select #48/A:148
    25947 
    25948 24 atoms, 23 bonds, 1 residue, 1 model selected 
    25949 
    25950 > hide sel atoms
    25951 
    25952 > ui mousemode right translate
    25953 
    25954 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    25955 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    25956 
    25957 > select add #48
    25958 
    25959 4180 atoms, 4234 bonds, 258 residues, 1 model selected 
    25960 
    25961 > select subtract #48
    25962 
    25963 Nothing selected 
    25964 
    25965 > hide #48 models
    25966 
    25967 > show #43 models
    25968 
    25969 > hide #43 models
    25970 
    25971 > show #44 models
    25972 
    25973 > hide #44 models
    25974 
    25975 > show #17 models
    25976 
    25977 > hide #17 models
    25978 
    25979 > show #18 models
    25980 
    25981 > hide #18 models
    25982 
    25983 > show #19 models
    25984 
    25985 > hide #19 models
    25986 
    25987 > show #2 models
    25988 
    25989 > hide #2 models
    25990 
    25991 > show #46 models
    25992 
    25993 > hide #46 models
    25994 
    25995 > show #20 models
    25996 
    25997 > ui mousemode right select
    25998 
    25999 > select #20/A:170
    26000 
    26001 10 atoms, 9 bonds, 1 residue, 1 model selected 
    26002 
    26003 > hide sel atoms
    26004 
    26005 > ui mousemode right translate
    26006 
    26007 > hide #20 models
    26008 
    26009 > select add #20
    26010 
    26011 3966 atoms, 4011 bonds, 255 residues, 1 model selected 
    26012 
    26013 > show #21 models
    26014 
    26015 > select subtract #20
    26016 
    26017 Nothing selected 
    26018 
    26019 > select add #20
    26020 
    26021 3966 atoms, 4011 bonds, 255 residues, 1 model selected 
    26022 
    26023 > select subtract #20
    26024 
    26025 Nothing selected 
    26026 
    26027 > hide #21 models
    26028 
    26029 > show #16 models
    26030 
    26031 > hide #50 models
    26032 
    26033 > show #51 models
    26034 
    26035 > hide #51 models
    26036 
    26037 > show #47 models
    26038 
    26039 > hide #47 models
    26040 
    26041 > show #21 models
    26042 
    26043 > ui mousemode right select
    26044 
    26045 > select #16/A:193
    26046 
    26047 15 atoms, 14 bonds, 1 residue, 1 model selected 
    26048 
    26049 > hide #16 models
    26050 
    26051 > show #50 models
    26052 
    26053 Drag select of 2 residues 
    26054 
    26055 > select #21/A:178
    26056 
    26057 15 atoms, 14 bonds, 1 residue, 1 model selected 
    26058 
    26059 > ui mousemode right translate
    26060 
    26061 > ui mousemode right select
    26062 
    26063 > select #21/A:242
    26064 
    26065 24 atoms, 25 bonds, 1 residue, 1 model selected 
    26066 
    26067 > select #21/A:175
    26068 
    26069 21 atoms, 21 bonds, 1 residue, 1 model selected 
    26070 
    26071 > ui mousemode right translate
    26072 
    26073 > ui mousemode right select
    26074 
    26075 > select #21/A:174
    26076 
    26077 17 atoms, 16 bonds, 1 residue, 1 model selected 
    26078 
    26079 > select #21/A:174
    26080 
    26081 17 atoms, 16 bonds, 1 residue, 1 model selected 
    26082 
    26083 > hide sel atoms
    26084 
    26085 > ui mousemode right translate
    26086 
    26087 > ui mousemode right select
    26088 
    26089 > select #21/A:169
    26090 
    26091 22 atoms, 21 bonds, 1 residue, 1 model selected 
    26092 
    26093 > select #21/A:169
    26094 
    26095 22 atoms, 21 bonds, 1 residue, 1 model selected 
    26096 
    26097 > ui mousemode right translate
    26098 
    26099 > hide sel atoms
    26100 
    26101 > ui mousemode right select
    26102 
    26103 > select #21/A:145
    26104 
    26105 17 atoms, 16 bonds, 1 residue, 1 model selected 
    26106 
    26107 > hide sel atoms
    26108 
    26109 > select #21/A:148
    26110 
    26111 10 atoms, 9 bonds, 1 residue, 1 model selected 
    26112 
    26113 > hide sel atoms
    26114 
    26115 > ui mousemode right translate
    26116 
    26117 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    26118 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    26119 
    26120 > show #51 models
    26121 
    26122 > hide #51 models
    26123 
    26124 > hide #50 models
    26125 
    26126 > show #50 models
    26127 
    26128 > hide #50 models
    26129 
    26130 > show #50 models
    26131 
    26132 > select add #21
    26133 
    26134 4166 atoms, 4222 bonds, 259 residues, 1 model selected 
    26135 
    26136 > select subtract #21
    26137 
    26138 Nothing selected 
    26139 
    26140 > hide #21 models
    26141 
    26142 > show #21 models
    26143 
    26144 > show #43 models
    26145 
    26146 > hide #43 models
    26147 
    26148 > hide #21 models
    26149 
    26150 > show #22 models
    26151 
    26152 > hide #22 models
    26153 
    26154 > show #48 models
    26155 
    26156 > hide #48 models
    26157 
    26158 > show #11 models
    26159 
    26160 > color #11 #5a43cfff
    26161 
    26162 > ui mousemode right select
    26163 
    26164 > select #11/A:132
    26165 
    26166 22 atoms, 21 bonds, 1 residue, 1 model selected 
    26167 
    26168 > hide sel atoms
    26169 
    26170 > select #11/A:130
    26171 
    26172 15 atoms, 14 bonds, 1 residue, 1 model selected 
    26173 
    26174 > hide sel atoms
    26175 
    26176 > ui mousemode right translate
    26177 
    26178 > ui mousemode right select
    26179 
    26180 > select #11/A:244
    26181 
    26182 15 atoms, 14 bonds, 1 residue, 1 model selected 
    26183 
    26184 > hide sel atoms
    26185 
    26186 > ui mousemode right translate
    26187 
    26188 > ui mousemode right select
    26189 
    26190 > select #11/A:194
    26191 
    26192 15 atoms, 14 bonds, 1 residue, 1 model selected 
    26193 
    26194 > ui mousemode right translate
    26195 
    26196 > hide sel atoms
    26197 
    26198 > ui mousemode right select
    26199 
    26200 > select #11/A:192
    26201 
    26202 22 atoms, 21 bonds, 1 residue, 1 model selected 
    26203 
    26204 > select #11/A:191
    26205 
    26206 15 atoms, 14 bonds, 1 residue, 1 model selected 
    26207 Alignment identifier is 11/A 
    26208 
    26209 > show sel atoms
    26210 
    26211 > ui mousemode right translate
    26212 
    26213 > color sel red
    26214 
    26215 > ui mousemode right select
    26216 
    26217 > select #50/A:247
    26218 
    26219 24 atoms, 25 bonds, 1 residue, 1 model selected 
    26220 
    26221 > select #11/A:255
    26222 
    26223 24 atoms, 25 bonds, 1 residue, 1 model selected 
    26224 
    26225 > ui mousemode right translate
    26226 
    26227 > show sel atoms
    26228 
    26229 > color sel gray
    26230 
    26231 > ui mousemode right select
    26232 
    26233 > select #50/A:180
    26234 
    26235 21 atoms, 21 bonds, 1 residue, 1 model selected 
    26236 
    26237 > select #11/A:188
    26238 
    26239 20 atoms, 20 bonds, 1 residue, 1 model selected 
    26240 
    26241 > ui mousemode right translate
    26242 
    26243 > show sel atoms
    26244 
    26245 > color sel gray
    26246 
    26247 > ui mousemode right select
    26248 
    26249 > select #11/A:187@CA
    26250 
    26251 1 atom, 1 residue, 1 model selected 
    26252 
    26253 > select #11/A:187@CA
    26254 
    26255 1 atom, 1 residue, 1 model selected 
    26256 
    26257 > hide sel atoms
    26258 
    26259 > show sel atoms
    26260 
    26261 > select #11/A:187
    26262 
    26263 17 atoms, 16 bonds, 1 residue, 1 model selected 
    26264 
    26265 > show sel atoms
    26266 
    26267 > hide sel atoms
    26268 
    26269 > select #11/A:182
    26270 
    26271 22 atoms, 21 bonds, 1 residue, 1 model selected 
    26272 
    26273 > hide sel atoms
    26274 
    26275 > select #11/A:161
    26276 
    26277 22 atoms, 21 bonds, 1 residue, 1 model selected 
    26278 
    26279 > hide sel atoms
    26280 
    26281 > select #11/A:158
    26282 
    26283 12 atoms, 11 bonds, 1 residue, 1 model selected 
    26284 
    26285 > hide sel atoms
    26286 
    26287 > ui mousemode right translate
    26288 
    26289 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    26290 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    26291 
    26292 > show #44 models
    26293 
    26294 > hide #11 models
    26295 
    26296 > select add #11
    26297 
    26298 4348 atoms, 4410 bonds, 271 residues, 1 model selected 
    26299 
    26300 > select subtract #11
    26301 
    26302 Nothing selected 
    26303 
    26304 > ui mousemode right select
    26305 
    26306 > select #44/A:173
    26307 
    26308 15 atoms, 14 bonds, 1 residue, 1 model selected 
    26309 
    26310 > select #44/A:237
    26311 
    26312 24 atoms, 25 bonds, 1 residue, 1 model selected 
    26313 
    26314 > select #44/A:170
    26315 
    26316 20 atoms, 20 bonds, 1 residue, 1 model selected 
    26317 Alignment identifier is 44/A 
    26318 
    26319 > hide #44 models
    26320 
    26321 > select add #44
    26322 
    26323 4047 atoms, 4099 bonds, 253 residues, 1 model selected 
    26324 
    26325 > select subtract #44
    26326 
    26327 Nothing selected 
    26328 
    26329 > show #18 models
    26330 
    26331 > show #23 models
    26332 
    26333 > hide #18 models
    26334 
    26335 > hide #23 models
    26336 
    26337 > show #23 models
    26338 
    26339 > ui tool show Matchmaker
    26340 
    26341 > matchmaker #23 to #50
    26342 
    26343 Parameters 
    26344 --- 
    26345 Chain pairing | bb 
    26346 Alignment algorithm | Needleman-Wunsch 
    26347 Similarity matrix | BLOSUM-62 
    26348 SS fraction | 0.3 
    26349 Gap open (HH/SS/other) | 18/18/6 
    26350 Gap extend | 1 
    26351 SS matrix |  |  | H | S | O 
    26352 ---|---|---|--- 
    26353 H | 6 | -9 | -6 
    26354 S |  | 6 | -6 
    26355 O |  |  | 4 
    26356 Iteration cutoff | 2 
    26357  
    26358 Matchmaker Sindbis virus AlphaFold.pdb, chain A (#50) with Mosso das Pedras
    26359 virus AlphaFold.pdb, chain A (#23), sequence alignment score = 753.4 
    26360 RMSD between 159 pruned atom pairs is 0.501 angstroms; (across all 252 pairs:
    26361 36.942) 
    26362  
    26363 Drag select of 1 residues 
    26364 
    26365 > select #50/A:135
    26366 
    26367 22 atoms, 21 bonds, 1 residue, 1 model selected 
    26368 
    26369 > color #23 #a2a279ff
    26370 
    26371 Drag select of 79 residues 
    26372 
    26373 > select clear
    26374 
    26375 [Repeated 1 time(s)]
    26376 
    26377 > ui mousemode right translate
    26378 
    26379 > ui mousemode right select
    26380 
    26381 > select #23/A:139
    26382 
    26383 22 atoms, 21 bonds, 1 residue, 1 model selected 
    26384 
    26385 > ui mousemode right translate
    26386 
    26387 > hide sel atoms
    26388 
    26389 > ui mousemode right select
    26390 
    26391 > select #23/A:137
    26392 
    26393 12 atoms, 11 bonds, 1 residue, 1 model selected 
    26394 
    26395 > ui mousemode right translate
    26396 
    26397 > hide sel atoms
    26398 
    26399 > ui mousemode right select
    26400 
    26401 > select #50/A:236
    26402 
    26403 15 atoms, 14 bonds, 1 residue, 1 model selected 
    26404 
    26405 > select #23/A:251
    26406 
    26407 15 atoms, 14 bonds, 1 residue, 1 model selected 
    26408 
    26409 > ui mousemode right translate
    26410 
    26411 > hide sel atoms
    26412 
    26413 > ui mousemode right select
    26414 
    26415 > select #23/A:201
    26416 
    26417 24 atoms, 23 bonds, 1 residue, 1 model selected 
    26418 
    26419 > ui mousemode right translate
    26420 
    26421 > hide sel atoms
    26422 
    26423 > ui mousemode right rotate
    26424 
    26425 > ui mousemode right select
    26426 
    26427 > select #23/A:198
    26428 
    26429 15 atoms, 14 bonds, 1 residue, 1 model selected 
    26430 
    26431 > select #50/A:183
    26432 
    26433 15 atoms, 14 bonds, 1 residue, 1 model selected 
    26434 
    26435 > select #23/A:198
    26436 
    26437 15 atoms, 14 bonds, 1 residue, 1 model selected 
    26438 Alignment identifier is 23/A 
    26439 
    26440 > color sel red
    26441 
    26442 > select clear
    26443 
    26444 > ui mousemode right rotate
    26445 
    26446 > ui mousemode right translate
    26447 
    26448 > ui mousemode right select
    26449 
    26450 > select #23/A:262
    26451 
    26452 24 atoms, 25 bonds, 1 residue, 1 model selected 
    26453 
    26454 > select #23/A:262
    26455 
    26456 24 atoms, 25 bonds, 1 residue, 1 model selected 
    26457 
    26458 > ui mousemode right rotate
    26459 
    26460 > ui mousemode right select
    26461 
    26462 > show sel atoms
    26463 
    26464 > color sel gray
    26465 
    26466 > ui mousemode right translate
    26467 
    26468 > ui mousemode right select
    26469 
    26470 > select #50/A:180
    26471 
    26472 21 atoms, 21 bonds, 1 residue, 1 model selected 
    26473 
    26474 > select #50/A:180
    26475 
    26476 21 atoms, 21 bonds, 1 residue, 1 model selected 
    26477 
    26478 > select #23/A:195
    26479 
    26480 21 atoms, 21 bonds, 1 residue, 1 model selected 
    26481 
    26482 > ui mousemode right translate
    26483 
    26484 > show sel atoms
    26485 
    26486 > color sel gray
    26487 
    26488 > ui mousemode right select
    26489 
    26490 Drag select of 2 residues 
    26491 
    26492 > ui mousemode right translate
    26493 
    26494 > ui mousemode right select
    26495 
    26496 > select #23/A:194@CA
    26497 
    26498 1 atom, 1 residue, 1 model selected 
    26499 
    26500 > select #23/A:194
    26501 
    26502 22 atoms, 21 bonds, 1 residue, 1 model selected 
    26503 
    26504 > show sel cartoons
    26505 
    26506 > hide sel atoms
    26507 
    26508 > select #23/A:189
    26509 
    26510 24 atoms, 23 bonds, 1 residue, 1 model selected 
    26511 
    26512 > hide sel atoms
    26513 
    26514 > select #23/A:165
    26515 
    26516 19 atoms, 18 bonds, 1 residue, 1 model selected 
    26517 
    26518 > hide sel atoms
    26519 
    26520 > select #23/A:168
    26521 
    26522 10 atoms, 9 bonds, 1 residue, 1 model selected 
    26523 
    26524 > hide sel atoms
    26525 
    26526 > ui mousemode right translate
    26527 
    26528 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    26529 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    26530 
    26531 > hide #23 models
    26532 
    26533 > select add #23
    26534 
    26535 4449 atoms, 4504 bonds, 279 residues, 1 model selected 
    26536 
    26537 > select subtract #23
    26538 
    26539 Nothing selected 
    26540 
    26541 > show #25 models
    26542 
    26543 > color #25 #fd7ac9ff
    26544 
    26545 > color #25 #ff7bcaff
    26546 
    26547 > ui mousemode right select
    26548 
    26549 Drag select of 4 residues 
    26550 
    26551 > select clear
    26552 
    26553 > ui mousemode right translate
    26554 
    26555 > ui mousemode right select
    26556 
    26557 > select #25/A:135
    26558 
    26559 22 atoms, 21 bonds, 1 residue, 1 model selected 
    26560 
    26561 > hide sel atoms
    26562 
    26563 > select #25/A:133
    26564 
    26565 12 atoms, 11 bonds, 1 residue, 1 model selected 
    26566 
    26567 > hide sel atoms
    26568 
    26569 > ui mousemode right translate
    26570 
    26571 > ui mousemode right rotate
    26572 
    26573 > ui mousemode right select
    26574 
    26575 > select #25/A:247
    26576 
    26577 15 atoms, 14 bonds, 1 residue, 1 model selected 
    26578 
    26579 > hide sel atoms
    26580 
    26581 > ui mousemode right translate
    26582 
    26583 > ui mousemode right select
    26584 
    26585 > select #50/A:183
    26586 
    26587 15 atoms, 14 bonds, 1 residue, 1 model selected 
    26588 
    26589 > select clear
    26590 
    26591 > select #25/A:194
    26592 
    26593 12 atoms, 11 bonds, 1 residue, 1 model selected 
    26594 
    26595 > select #25/A:194
    26596 
    26597 12 atoms, 11 bonds, 1 residue, 1 model selected 
    26598 Alignment identifier is 25/A 
    26599 
    26600 > show sel atoms
    26601 
    26602 > color sel red
    26603 
    26604 > ui mousemode right translate
    26605 
    26606 > ui mousemode right select
    26607 
    26608 > select #50/A:247
    26609 
    26610 24 atoms, 25 bonds, 1 residue, 1 model selected 
    26611 
    26612 > select #50/A:247
    26613 
    26614 24 atoms, 25 bonds, 1 residue, 1 model selected 
    26615 
    26616 > select #25/A:258
    26617 
    26618 24 atoms, 25 bonds, 1 residue, 1 model selected 
    26619 
    26620 > ui mousemode right translate
    26621 
    26622 > show sel atoms
    26623 
    26624 > color sel gray
    26625 
    26626 > ui mousemode right select
    26627 
    26628 > select #25/A:191
    26629 
    26630 21 atoms, 21 bonds, 1 residue, 1 model selected 
    26631 
    26632 > select #25/A:191
    26633 
    26634 21 atoms, 21 bonds, 1 residue, 1 model selected 
    26635 
    26636 > ui mousemode right translate
    26637 
    26638 > show sel atoms
    26639 
    26640 > color sel gray
    26641 
    26642 > ui mousemode right select
    26643 
    26644 > select #25/A:197
    26645 
    26646 17 atoms, 16 bonds, 1 residue, 1 model selected 
    26647 
    26648 > hide sel atoms
    26649 
    26650 > ui mousemode right translate
    26651 
    26652 > ui mousemode right select
    26653 
    26654 > select #25/A:190@CA
    26655 
    26656 1 atom, 1 residue, 1 model selected 
    26657 
    26658 > select #25/A:190
    26659 
    26660 22 atoms, 21 bonds, 1 residue, 1 model selected 
    26661 
    26662 > ui mousemode right translate
    26663 
    26664 > hide sel atoms
    26665 
    26666 > ui mousemode right select
    26667 
    26668 > select #25/A:185
    26669 
    26670 24 atoms, 23 bonds, 1 residue, 1 model selected 
    26671 
    26672 > select #25/A:185
    26673 
    26674 24 atoms, 23 bonds, 1 residue, 1 model selected 
    26675 
    26676 > hide sel atoms
    26677 
    26678 [Repeated 2 time(s)]
    26679 
    26680 > select #25/A:161
    26681 
    26682 14 atoms, 13 bonds, 1 residue, 1 model selected 
    26683 
    26684 > select #25/A:161
    26685 
    26686 14 atoms, 13 bonds, 1 residue, 1 model selected 
    26687 
    26688 > hide sel atoms
    26689 
    26690 > select #25/A:164@CA
    26691 
    26692 1 atom, 1 residue, 1 model selected 
    26693 
    26694 > hide sel atoms
    26695 
    26696 > ui mousemode right translate
    26697 
    26698 > ui mousemode right select
    26699 
    26700 > select #25/A:164@CA
    26701 
    26702 1 atom, 1 residue, 1 model selected 
    26703 
    26704 > select #25/A:164
    26705 
    26706 11 atoms, 10 bonds, 1 residue, 1 model selected 
    26707 
    26708 > show sel atoms
    26709 
    26710 > hide sel atoms
    26711 
    26712 > ui mousemode right translate
    26713 
    26714 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    26715 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    26716 
    26717 > show #23 models
    26718 
    26719 > show #24 models
    26720 
    26721 > hide #24 models
    26722 
    26723 > hide #23 models
    26724 
    26725 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    26726 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    26727 
    26728 ——— End of log from Tue Aug 1 14:51:39 2023 ———
    26729 
    26730 opened ChimeraX session 
    26731 
    26732 > hide #25 models
    26733 
    26734 > show #25 models
    26735 
    26736 > select add #25
    26737 
    26738 4421 atoms, 4479 bonds, 275 residues, 1 model selected 
    26739 
    26740 > hide #25 models
    26741 
    26742 > select subtract #25
    26743 
    26744 Nothing selected 
    26745 
    26746 > show #15 models
    26747 
    26748 > color #15 #fa9765ff
    26749 
    26750 > color #15 #ff9a67ff
    26751 
    26752 > ui mousemode right select
    26753 
    26754 > select #15/A:130
    26755 
    26756 15 atoms, 14 bonds, 1 residue, 1 model selected 
    26757 
    26758 > hide sel atoms
    26759 
    26760 Drag select of 1 residues 
    26761 
    26762 > select #15/A:128
    26763 
    26764 12 atoms, 11 bonds, 1 residue, 1 model selected 
    26765 
    26766 > hide sel atoms
    26767 
    26768 > ui mousemode right translate
    26769 
    26770 > ui mousemode right select
    26771 
    26772 > select clear
    26773 
    26774 > select #15/A:242
    26775 
    26776 15 atoms, 14 bonds, 1 residue, 1 model selected 
    26777 
    26778 > ui mousemode right translate
    26779 
    26780 > hide sel atoms
    26781 
    26782 > ui mousemode right select
    26783 
    26784 > select #15/A:192
    26785 
    26786 15 atoms, 14 bonds, 1 residue, 1 model selected 
    26787 
    26788 > ui mousemode right translate
    26789 
    26790 > hide sel atoms
    26791 
    26792 > ui mousemode right select
    26793 
    26794 > select #50/A:183
    26795 
    26796 15 atoms, 14 bonds, 1 residue, 1 model selected 
    26797 
    26798 > select #15/A:189
    26799 
    26800 15 atoms, 14 bonds, 1 residue, 1 model selected 
    26801 
    26802 > ~hbonds
    26803 
    26804 Alignment identifier is 15/A 
    26805 
    26806 > ui mousemode right translate
    26807 
    26808 > show sel atoms
    26809 
    26810 > color sel red
    26811 
    26812 > ui mousemode right select
    26813 
    26814 > select #50/A:247
    26815 
    26816 24 atoms, 25 bonds, 1 residue, 1 model selected 
    26817 
    26818 > select #15/A:253
    26819 
    26820 24 atoms, 25 bonds, 1 residue, 1 model selected 
    26821 
    26822 > ui mousemode right translate
    26823 
    26824 > show sel atoms
    26825 
    26826 > color sel gray
    26827 
    26828 > ui mousemode right select
    26829 
    26830 > select clear
    26831 
    26832 > select #15/A:186
    26833 
    26834 21 atoms, 21 bonds, 1 residue, 1 model selected 
    26835 
    26836 > select #15/A:186
    26837 
    26838 21 atoms, 21 bonds, 1 residue, 1 model selected 
    26839 
    26840 > select clear
    26841 
    26842 > ui mousemode right translate
    26843 
    26844 > ui mousemode right select
    26845 
    26846 > select #15/A:186
    26847 
    26848 21 atoms, 21 bonds, 1 residue, 1 model selected 
    26849 
    26850 > select #50/A:180
    26851 
    26852 21 atoms, 21 bonds, 1 residue, 1 model selected 
    26853 
    26854 > select #15/A:186
    26855 
    26856 21 atoms, 21 bonds, 1 residue, 1 model selected 
    26857 
    26858 > ui mousemode right translate
    26859 
    26860 > show sel atoms
    26861 
    26862 > color sel gray
    26863 
    26864 > ui mousemode right select
    26865 
    26866 > select #15/A:185
    26867 
    26868 22 atoms, 21 bonds, 1 residue, 1 model selected 
    26869 
    26870 > show sel atoms
    26871 
    26872 > hide sel atoms
    26873 
    26874 > select #15/A:180
    26875 
    26876 24 atoms, 23 bonds, 1 residue, 1 model selected 
    26877 
    26878 > hide sel atoms
    26879 
    26880 > select #15/A:159
    26881 
    26882 22 atoms, 21 bonds, 1 residue, 1 model selected 
    26883 
    26884 > hide sel atoms
    26885 
    26886 > select #15/A:156
    26887 
    26888 15 atoms, 14 bonds, 1 residue, 1 model selected 
    26889 
    26890 > hide sel atoms
    26891 
    26892 > ui mousemode right translate
    26893 
    26894 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    26895 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    26896 
    26897 > select add #15
    26898 
    26899 4293 atoms, 4344 bonds, 269 residues, 1 model selected 
    26900 
    26901 > select subtract #15
    26902 
    26903 Nothing selected 
    26904 
    26905 > hide #15 models
    26906 
    26907 > show #26 models
    26908 
    26909 > color #26 #69699cff
    26910 
    26911 > color #26 #7171a8ff
    26912 
    26913 > color #26 #8686c8ff
    26914 
    26915 > color #26 #7979b4ff
    26916 
    26917 > color #26 #5d5d8aff
    26918 
    26919 > color #26 #646495ff
    26920 
    26921 > color #26 #7676b0ff
    26922 
    26923 > ui mousemode right rotate
    26924 
    26925 > ui mousemode right select
    26926 
    26927 > select #26/A:121
    26928 
    26929 22 atoms, 21 bonds, 1 residue, 1 model selected 
    26930 
    26931 > hide sel atoms
    26932 
    26933 > select #26/A:120
    26934 
    26935 7 atoms, 6 bonds, 1 residue, 1 model selected 
    26936 
    26937 > select #26/A:119
    26938 
    26939 15 atoms, 14 bonds, 1 residue, 1 model selected 
    26940 
    26941 > hide sel atoms
    26942 
    26943 > ui mousemode right translate
    26944 
    26945 > ui mousemode right select
    26946 
    26947 > select #50/A:236
    26948 
    26949 15 atoms, 14 bonds, 1 residue, 1 model selected 
    26950 
    26951 > select #26/A:233
    26952 
    26953 15 atoms, 14 bonds, 1 residue, 1 model selected 
    26954 
    26955 > hide sel atoms
    26956 
    26957 > ui mousemode right translate
    26958 
    26959 > ui mousemode right select
    26960 
    26961 > select #26/A:183
    26962 
    26963 15 atoms, 14 bonds, 1 residue, 1 model selected 
    26964 
    26965 > ui mousemode right translate
    26966 
    26967 > hide sel atoms
    26968 
    26969 > ui mousemode right select
    26970 
    26971 > select #26/A:180
    26972 
    26973 15 atoms, 14 bonds, 1 residue, 1 model selected 
    26974 Alignment identifier is 26/A 
    26975 
    26976 > ui mousemode right translate
    26977 
    26978 > show sel atoms
    26979 
    26980 > color sel red
    26981 
    26982 > ui mousemode right select
    26983 
    26984 > select #26/A:244
    26985 
    26986 24 atoms, 25 bonds, 1 residue, 1 model selected 
    26987 
    26988 > ui mousemode right translate
    26989 
    26990 > show sel atoms
    26991 
    26992 > color sel light gray
    26993 
    26994 > color sel gray
    26995 
    26996 > ui mousemode right select
    26997 
    26998 > select clear
    26999 
    27000 > select #26/A:177
    27001 
    27002 20 atoms, 20 bonds, 1 residue, 1 model selected 
    27003 
    27004 > ui mousemode right translate
    27005 
    27006 > show sel atoms
    27007 
    27008 > color sel gray
    27009 
    27010 > ui mousemode right select
    27011 
    27012 > select #26/A:176
    27013 
    27014 22 atoms, 21 bonds, 1 residue, 1 model selected 
    27015 
    27016 > hide sel atoms
    27017 
    27018 > select #26/A:171
    27019 
    27020 22 atoms, 21 bonds, 1 residue, 1 model selected 
    27021 
    27022 > hide sel atoms
    27023 
    27024 > select #26/A:150
    27025 
    27026 22 atoms, 21 bonds, 1 residue, 1 model selected 
    27027 
    27028 > hide sel atoms
    27029 
    27030 > select #26/A:147
    27031 
    27032 12 atoms, 11 bonds, 1 residue, 1 model selected 
    27033 
    27034 > hide sel atoms
    27035 
    27036 > ui mousemode right translate
    27037 
    27038 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    27039 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    27040 
    27041 > select add #26
    27042 
    27043 4242 atoms, 4287 bonds, 260 residues, 1 model selected 
    27044 
    27045 > select subtract #26
    27046 
    27047 Nothing selected 
    27048 
    27049 > hide #26 models
    27050 
    27051 > show #27 models
    27052 
    27053 > color #27 #a3007dff
    27054 
    27055 > color #27 #a2007cff
    27056 
    27057 > ui mousemode right select
    27058 
    27059 > select #27/A:135
    27060 
    27061 24 atoms, 23 bonds, 1 residue, 1 model selected 
    27062 
    27063 > hide sel atoms
    27064 
    27065 > select #27/A:133
    27066 
    27067 15 atoms, 14 bonds, 1 residue, 1 model selected 
    27068 
    27069 > hide sel atoms
    27070 
    27071 > ui mousemode right translate
    27072 
    27073 > ui mousemode right select
    27074 
    27075 > select #27/A:247
    27076 
    27077 15 atoms, 14 bonds, 1 residue, 1 model selected 
    27078 
    27079 > ui mousemode right translate
    27080 
    27081 > hide sel atoms
    27082 
    27083 > ui mousemode right select
    27084 
    27085 > select #27/A:197
    27086 
    27087 17 atoms, 16 bonds, 1 residue, 1 model selected 
    27088 
    27089 > ui mousemode right translate
    27090 
    27091 > hide sel atoms
    27092 
    27093 > ui mousemode right select
    27094 
    27095 > select #27/A:194
    27096 
    27097 15 atoms, 14 bonds, 1 residue, 1 model selected 
    27098 Alignment identifier is 27/A 
    27099 
    27100 > ui mousemode right translate
    27101 
    27102 > show sel atoms
    27103 
    27104 > color sel red
    27105 
    27106 > ui mousemode right select
    27107 
    27108 > select #27/A:258
    27109 
    27110 24 atoms, 25 bonds, 1 residue, 1 model selected 
    27111 
    27112 > ui mousemode right translate
    27113 
    27114 > show sel atoms
    27115 
    27116 > color sel gray
    27117 
    27118 > ui mousemode right select
    27119 
    27120 > select #27/A:191
    27121 
    27122 21 atoms, 21 bonds, 1 residue, 1 model selected 
    27123 
    27124 > ui mousemode right translate
    27125 
    27126 > show sel atoms
    27127 
    27128 > color sel gray
    27129 
    27130 > ui mousemode right select
    27131 
    27132 > select #27/A:190
    27133 
    27134 22 atoms, 21 bonds, 1 residue, 1 model selected 
    27135 
    27136 > hide sel atoms
    27137 
    27138 > select #27/A:185
    27139 
    27140 24 atoms, 23 bonds, 1 residue, 1 model selected 
    27141 
    27142 > hide sel atoms
    27143 
    27144 > select #27/A:164
    27145 
    27146 10 atoms, 9 bonds, 1 residue, 1 model selected 
    27147 
    27148 > hide sel atoms
    27149 
    27150 > select #27/A:161
    27151 
    27152 10 atoms, 9 bonds, 1 residue, 1 model selected 
    27153 
    27154 > hide sel atoms
    27155 
    27156 > ui mousemode right translate
    27157 
    27158 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    27159 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    27160 
    27161 > select add #27
    27162 
    27163 4429 atoms, 4485 bonds, 275 residues, 1 model selected 
    27164 
    27165 > select subtract #27
    27166 
    27167 Nothing selected 
    27168 
    27169 > hide #27 models
    27170 
    27171 > show #28 models
    27172 
    27173 > color #28 #4b4b4bff
    27174 
    27175 > color #28 #464646ff
    27176 
    27177 > color #28 #3a3a3aff
    27178 
    27179 > ui mousemode right select
    27180 
    27181 > select #28/A:138
    27182 
    27183 24 atoms, 23 bonds, 1 residue, 1 model selected 
    27184 
    27185 > hide sel atoms
    27186 
    27187 > select #28/A:136
    27188 
    27189 12 atoms, 11 bonds, 1 residue, 1 model selected 
    27190 
    27191 > hide sel atoms
    27192 
    27193 > select clear
    27194 
    27195 [Repeated 1 time(s)]
    27196 
    27197 > ui mousemode right translate
    27198 
    27199 > ui mousemode right select
    27200 
    27201 > select #28/A:250
    27202 
    27203 15 atoms, 14 bonds, 1 residue, 1 model selected 
    27204 
    27205 > select #28/A:250
    27206 
    27207 15 atoms, 14 bonds, 1 residue, 1 model selected 
    27208 
    27209 > select #28/A:250
    27210 
    27211 15 atoms, 14 bonds, 1 residue, 1 model selected 
    27212 
    27213 > ui mousemode right translate
    27214 
    27215 > hide sel atoms
    27216 
    27217 > ui mousemode right select
    27218 
    27219 > select #28/A:200
    27220 
    27221 17 atoms, 16 bonds, 1 residue, 1 model selected 
    27222 
    27223 > hide sel atoms
    27224 
    27225 > select #28/A:197
    27226 
    27227 15 atoms, 14 bonds, 1 residue, 1 model selected 
    27228 Alignment identifier is 28/A 
    27229 
    27230 > ui mousemode right translate
    27231 
    27232 > show sel atoms
    27233 
    27234 > color sel red
    27235 
    27236 > ui mousemode right select
    27237 
    27238 > select #28/A:261
    27239 
    27240 24 atoms, 25 bonds, 1 residue, 1 model selected 
    27241 
    27242 > ui mousemode right translate
    27243 
    27244 > show sel atoms
    27245 
    27246 > color sel gray
    27247 
    27248 > ui mousemode right select
    27249 
    27250 > select #28/A:194
    27251 
    27252 21 atoms, 21 bonds, 1 residue, 1 model selected 
    27253 
    27254 > ui mousemode right translate
    27255 
    27256 > show sel atoms
    27257 
    27258 > color sel gray
    27259 
    27260 > ui mousemode right select
    27261 
    27262 > select #28/A:193
    27263 
    27264 22 atoms, 21 bonds, 1 residue, 1 model selected 
    27265 
    27266 > hide sel atoms
    27267 
    27268 > ui mousemode right translate
    27269 
    27270 > ui mousemode right select
    27271 
    27272 > select #28/A:188
    27273 
    27274 24 atoms, 23 bonds, 1 residue, 1 model selected 
    27275 
    27276 > ui mousemode right translate
    27277 
    27278 > hide sel atoms
    27279 
    27280 > ui mousemode right select
    27281 
    27282 > select #28/A:164
    27283 
    27284 16 atoms, 15 bonds, 1 residue, 1 model selected 
    27285 
    27286 > hide sel atoms
    27287 
    27288 > select #28/A:167
    27289 
    27290 14 atoms, 13 bonds, 1 residue, 1 model selected 
    27291 
    27292 > hide sel atoms
    27293 
    27294 > ui mousemode right translate
    27295 
    27296 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    27297 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    27298 
    27299 > select add #28
    27300 
    27301 4421 atoms, 4477 bonds, 278 residues, 1 model selected 
    27302 
    27303 > select subtract #28
    27304 
    27305 Nothing selected 
    27306 
    27307 > show #10 models
    27308 
    27309 > hide #28 models
    27310 
    27311 > color #10 #810081ff
    27312 
    27313 > ui mousemode right select
    27314 
    27315 > select #10/A:131
    27316 
    27317 22 atoms, 21 bonds, 1 residue, 1 model selected 
    27318 
    27319 > hide sel atoms
    27320 
    27321 > select #10/A:129
    27322 
    27323 12 atoms, 11 bonds, 1 residue, 1 model selected 
    27324 
    27325 > hide sel atoms
    27326 
    27327 > ui mousemode right translate
    27328 
    27329 > ui mousemode right select
    27330 
    27331 > select #10/A:243
    27332 
    27333 15 atoms, 14 bonds, 1 residue, 1 model selected 
    27334 
    27335 > hide sel atoms
    27336 
    27337 > ui mousemode right translate
    27338 
    27339 > ui mousemode right select
    27340 
    27341 > select #10/A:193
    27342 
    27343 15 atoms, 14 bonds, 1 residue, 1 model selected 
    27344 
    27345 > hide sel atoms
    27346 
    27347 > ui mousemode right translate
    27348 
    27349 > ui mousemode right select
    27350 
    27351 > select #10/A:190
    27352 
    27353 15 atoms, 14 bonds, 1 residue, 1 model selected 
    27354 Alignment identifier is 10/A 
    27355 
    27356 > ui mousemode right translate
    27357 
    27358 > show sel atoms
    27359 
    27360 > color sel red
    27361 
    27362 > ui mousemode right select
    27363 
    27364 > select #10/A:254
    27365 
    27366 24 atoms, 25 bonds, 1 residue, 1 model selected 
    27367 
    27368 > ui mousemode right translate
    27369 
    27370 > show sel atoms
    27371 
    27372 > color sel gray
    27373 
    27374 > ui mousemode right select
    27375 
    27376 > select #10/A:187
    27377 
    27378 21 atoms, 21 bonds, 1 residue, 1 model selected 
    27379 
    27380 > ui mousemode right translate
    27381 
    27382 > show sel atoms
    27383 
    27384 > color sel gray
    27385 
    27386 > ui mousemode right select
    27387 
    27388 > select #10/A:186
    27389 
    27390 22 atoms, 21 bonds, 1 residue, 1 model selected 
    27391 
    27392 > select #10/A:186
    27393 
    27394 22 atoms, 21 bonds, 1 residue, 1 model selected 
    27395 
    27396 > hide sel atoms
    27397 
    27398 > select #10/A:181
    27399 
    27400 22 atoms, 21 bonds, 1 residue, 1 model selected 
    27401 
    27402 > hide sel atoms
    27403 
    27404 > select #10/A:157
    27405 
    27406 12 atoms, 11 bonds, 1 residue, 1 model selected 
    27407 
    27408 > hide sel atoms
    27409 
    27410 > select #10/A:156
    27411 
    27412 14 atoms, 14 bonds, 1 residue, 1 model selected 
    27413 
    27414 > hide sel atoms
    27415 
    27416 > select #10/A:156
    27417 
    27418 14 atoms, 14 bonds, 1 residue, 1 model selected 
    27419 
    27420 > select #10/A:157
    27421 
    27422 12 atoms, 11 bonds, 1 residue, 1 model selected 
    27423 
    27424 > hide sel atoms
    27425 
    27426 > show sel atoms
    27427 
    27428 > hide sel atoms
    27429 
    27430 > select #10/A:160
    27431 
    27432 22 atoms, 21 bonds, 1 residue, 1 model selected 
    27433 
    27434 > hide sel atoms
    27435 
    27436 > ui mousemode right translate
    27437 
    27438 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    27439 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    27440 
    27441 > select add #10
    27442 
    27443 4349 atoms, 4399 bonds, 270 residues, 1 model selected 
    27444 
    27445 > select subtract #10
    27446 
    27447 Nothing selected 
    27448 
    27449 > show #13 models
    27450 
    27451 > hide #10 models
    27452 
    27453 > color #13 #5e45d8ff
    27454 
    27455 > color #13 #6248e1ff
    27456 
    27457 > ui mousemode right select
    27458 
    27459 > select #13/A:143
    27460 
    27461 10 atoms, 9 bonds, 1 residue, 1 model selected 
    27462 
    27463 > hide sel atoms
    27464 
    27465 > select #13/A:141
    27466 
    27467 12 atoms, 11 bonds, 1 residue, 1 model selected 
    27468 
    27469 > hide sel atoms
    27470 
    27471 > select #13/A:254
    27472 
    27473 12 atoms, 11 bonds, 1 residue, 1 model selected 
    27474 
    27475 > hide sel atoms
    27476 
    27477 > ui mousemode right translate
    27478 
    27479 > ui mousemode right select
    27480 
    27481 > select clear
    27482 
    27483 > select #13/A:204
    27484 
    27485 12 atoms, 11 bonds, 1 residue, 1 model selected 
    27486 
    27487 > ui mousemode right translate
    27488 
    27489 > hide sel atoms
    27490 
    27491 > ui mousemode right select
    27492 
    27493 > select #13/A:202
    27494 
    27495 17 atoms, 16 bonds, 1 residue, 1 model selected 
    27496 
    27497 > select #13/A:201
    27498 
    27499 14 atoms, 13 bonds, 1 residue, 1 model selected 
    27500 Alignment identifier is 13/A 
    27501 
    27502 > select #13/A:202
    27503 
    27504 17 atoms, 16 bonds, 1 residue, 1 model selected 
    27505 
    27506 > ui mousemode right translate
    27507 
    27508 > show sel atoms
    27509 
    27510 > color sel gray
    27511 
    27512 > ui mousemode right select
    27513 
    27514 > select #50/A:247
    27515 
    27516 24 atoms, 25 bonds, 1 residue, 1 model selected 
    27517 
    27518 > select #13/A:265
    27519 
    27520 20 atoms, 20 bonds, 1 residue, 1 model selected 
    27521 
    27522 > select #50/A:247
    27523 
    27524 24 atoms, 25 bonds, 1 residue, 1 model selected 
    27525 
    27526 > select #13/A:265
    27527 
    27528 20 atoms, 20 bonds, 1 residue, 1 model selected 
    27529 
    27530 > select #50/A:247
    27531 
    27532 24 atoms, 25 bonds, 1 residue, 1 model selected 
    27533 
    27534 > select #13/A:265
    27535 
    27536 20 atoms, 20 bonds, 1 residue, 1 model selected 
    27537 
    27538 > ui mousemode right translate
    27539 
    27540 > show sel atoms
    27541 
    27542 > color sel gray
    27543 
    27544 > ui mousemode right select
    27545 
    27546 > select #13/A:199
    27547 
    27548 14 atoms, 14 bonds, 1 residue, 1 model selected 
    27549 
    27550 > ui mousemode right translate
    27551 
    27552 > show sel atoms
    27553 
    27554 > color sel magenta
    27555 
    27556 > ui mousemode right select
    27557 
    27558 > select #13/A:172
    27559 
    27560 12 atoms, 11 bonds, 1 residue, 1 model selected 
    27561 
    27562 > hide sel atoms
    27563 
    27564 > select #13/A:169
    27565 
    27566 15 atoms, 14 bonds, 1 residue, 1 model selected 
    27567 
    27568 > hide sel atoms
    27569 
    27570 > ui mousemode right translate
    27571 
    27572 > ui mousemode right select
    27573 
    27574 > select #13/A:198
    27575 
    27576 15 atoms, 14 bonds, 1 residue, 1 model selected 
    27577 
    27578 > hide sel atoms
    27579 
    27580 > ui mousemode right translate
    27581 
    27582 > ui mousemode right select
    27583 
    27584 > select #13/A:193
    27585 
    27586 24 atoms, 23 bonds, 1 residue, 1 model selected 
    27587 
    27588 > ui mousemode right translate
    27589 
    27590 > hide sel atoms
    27591 
    27592 > color #13 #7757e1ff
    27593 
    27594 > color #13 #886de1ff
    27595 
    27596 > color #13 #7865e1ff
    27597 
    27598 > color #13 #8956e1ff
    27599 
    27600 > color #13 #7856e1ff
    27601 
    27602 > color #13 #7865e1ff
    27603 
    27604 > color #13 #7461e1ff
    27605 
    27606 > color #13 #7763e6ff
    27607 
    27608 > color #13 #5446a3ff
    27609 
    27610 > color #13 #6b59cfff
    27611 
    27612 > color #13 #795fcfff
    27613 
    27614 > color #13 #8a62cfff
    27615 
    27616 > color #13 #6d59cfff
    27617 
    27618 > color #13 #6b57cfff
    27619 
    27620 > color #13 #675dcfff
    27621 
    27622 > color #13 #6c62d9ff
    27623 
    27624 > color #13 #6960d4ff
    27625 
    27626 > set bgColor white
    27627 
    27628 > ui mousemode right select
    27629 
    27630 > select #13/A:202
    27631 
    27632 17 atoms, 16 bonds, 1 residue, 1 model selected 
    27633 
    27634 > color sel gray
    27635 
    27636 > ui mousemode right translate
    27637 
    27638 > ui mousemode right select
    27639 
    27640 > select #13/A:265
    27641 
    27642 20 atoms, 20 bonds, 1 residue, 1 model selected 
    27643 
    27644 > color sel gray
    27645 
    27646 > select #13/A:199
    27647 
    27648 14 atoms, 14 bonds, 1 residue, 1 model selected 
    27649 
    27650 > color sel magenta
    27651 
    27652 > ui mousemode right translate
    27653 
    27654 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    27655 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    27656 
    27657 ——— End of log from Wed Aug 2 11:23:08 2023 ———
    27658 
    27659 opened ChimeraX session 
    27660 
    27661 > select add #13
    27662 
    27663 4435 atoms, 4474 bonds, 282 residues, 1 model selected 
    27664 
    27665 > select subtract #13
    27666 
    27667 Nothing selected 
    27668 
    27669 > hide #13 models
    27670 
    27671 > show #!7 models
    27672 
    27673 > hide #!7 models
    27674 
    27675 > show #!7 models
    27676 
    27677 > hide #!7 models
    27678 
    27679 > show #49 models
    27680 
    27681 > color #49 #fe7d7fff
    27682 
    27683 > color #49 #ff7d7fff
    27684 
    27685 > ui mousemode right select
    27686 
    27687 > select #49/A:129
    27688 
    27689 16 atoms, 15 bonds, 1 residue, 1 model selected 
    27690 
    27691 > select #49/A:128
    27692 
    27693 22 atoms, 21 bonds, 1 residue, 1 model selected 
    27694 
    27695 > hide sel atoms
    27696 
    27697 > select #49/A:126
    27698 
    27699 15 atoms, 14 bonds, 1 residue, 1 model selected 
    27700 
    27701 > hide sel atoms
    27702 
    27703 > select #49/A:157
    27704 
    27705 22 atoms, 21 bonds, 1 residue, 1 model selected 
    27706 
    27707 > show sel atoms
    27708 
    27709 > hide sel atoms
    27710 
    27711 > select #49/A:154
    27712 
    27713 12 atoms, 11 bonds, 1 residue, 1 model selected 
    27714 
    27715 > hide sel atoms
    27716 
    27717 > ui mousemode right translate
    27718 
    27719 > ui mousemode right select
    27720 
    27721 > select #49/A:240
    27722 
    27723 15 atoms, 14 bonds, 1 residue, 1 model selected 
    27724 
    27725 > hide sel atoms
    27726 
    27727 > select #49/A:190
    27728 
    27729 15 atoms, 14 bonds, 1 residue, 1 model selected 
    27730 
    27731 > hide sel atoms
    27732 
    27733 > ui mousemode right translate
    27734 
    27735 > ui mousemode right select
    27736 
    27737 > select #49/A:187
    27738 
    27739 15 atoms, 14 bonds, 1 residue, 1 model selected 
    27740 
    27741 > ui mousemode right translate
    27742 
    27743 > show sel atoms
    27744 
    27745 > color sel red
    27746 
    27747 Alignment identifier is 49/A 
    27748 
    27749 > ui mousemode right select
    27750 
    27751 > select #49/A:251
    27752 
    27753 24 atoms, 25 bonds, 1 residue, 1 model selected 
    27754 
    27755 > show sel atoms
    27756 
    27757 > color sel gray
    27758 
    27759 > select #49/A:184
    27760 
    27761 21 atoms, 21 bonds, 1 residue, 1 model selected 
    27762 
    27763 > show sel atoms
    27764 
    27765 > color sel gray
    27766 
    27767 > select #49/A:183
    27768 
    27769 22 atoms, 21 bonds, 1 residue, 1 model selected 
    27770 
    27771 > ui mousemode right translate
    27772 
    27773 > ui mousemode right select
    27774 
    27775 > hide sel atoms
    27776 
    27777 > ui mousemode right translate
    27778 
    27779 > ui mousemode right select
    27780 
    27781 > select #49/A:178
    27782 
    27783 24 atoms, 23 bonds, 1 residue, 1 model selected 
    27784 
    27785 > ui mousemode right translate
    27786 
    27787 > hide sel atoms
    27788 
    27789 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    27790 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    27791 
    27792 > select add #49
    27793 
    27794 4263 atoms, 4315 bonds, 267 residues, 1 model selected 
    27795 
    27796 > select subtract #49
    27797 
    27798 Nothing selected 
    27799 
    27800 > hide #49 models
    27801 
    27802 > show #24 models
    27803 
    27804 > color #24 #6b6b4fff
    27805 
    27806 > color #24 #6c6c50ff
    27807 
    27808 > color #24 #828260ff
    27809 
    27810 > color #24 #5b5b43ff
    27811 
    27812 > color #24 #636349ff
    27813 
    27814 > color #24 #707053ff
    27815 
    27816 > ui mousemode right select
    27817 
    27818 > select #24/A:129
    27819 
    27820 19 atoms, 18 bonds, 1 residue, 1 model selected 
    27821 
    27822 > hide sel atoms
    27823 
    27824 > select #24/A:127
    27825 
    27826 12 atoms, 11 bonds, 1 residue, 1 model selected 
    27827 
    27828 > hide sel atoms
    27829 
    27830 > select #24/A:158
    27831 
    27832 22 atoms, 21 bonds, 1 residue, 1 model selected 
    27833 
    27834 > hide sel atoms
    27835 
    27836 > select #24/A:155
    27837 
    27838 19 atoms, 18 bonds, 1 residue, 1 model selected 
    27839 
    27840 > hide sel atoms
    27841 
    27842 > select #24/A:241
    27843 
    27844 15 atoms, 14 bonds, 1 residue, 1 model selected 
    27845 
    27846 > select #24/A:241
    27847 
    27848 15 atoms, 14 bonds, 1 residue, 1 model selected 
    27849 
    27850 > hide sel atoms
    27851 
    27852 > ui mousemode right translate
    27853 
    27854 > ui mousemode right select
    27855 
    27856 > select #24/A:191
    27857 
    27858 15 atoms, 14 bonds, 1 residue, 1 model selected 
    27859 
    27860 > ui mousemode right translate
    27861 
    27862 > hide sel atoms
    27863 
    27864 > ui mousemode right select
    27865 
    27866 > select #24/A:188
    27867 
    27868 15 atoms, 14 bonds, 1 residue, 1 model selected 
    27869 
    27870 > show sel atoms
    27871 
    27872 Alignment identifier is 24/A 
    27873 
    27874 > color sel red
    27875 
    27876 > select #24/A:252
    27877 
    27878 24 atoms, 25 bonds, 1 residue, 1 model selected 
    27879 
    27880 > select #24/A:252
    27881 
    27882 24 atoms, 25 bonds, 1 residue, 1 model selected 
    27883 
    27884 > show sel atoms
    27885 
    27886 > color sel gray
    27887 
    27888 > select #24/A:185
    27889 
    27890 20 atoms, 20 bonds, 1 residue, 1 model selected 
    27891 
    27892 > show sel atoms
    27893 
    27894 > color sel dark gray
    27895 
    27896 > color sel gray
    27897 
    27898 > ui mousemode right translate
    27899 
    27900 > color #24 #6a7045ff
    27901 
    27902 > color #24 #54704cff
    27903 
    27904 > color #24 #567045ff
    27905 
    27906 > color #24 #6e7057ff
    27907 
    27908 > color #24 #706d5aff
    27909 
    27910 > color #24 #6f704fff
    27911 
    27912 > color #24 #a5a676ff
    27913 
    27914 > color #24 #c9ca8fff
    27915 
    27916 > ui mousemode right rotate
    27917 
    27918 > ui mousemode right select
    27919 
    27920 > select #50/A:183
    27921 
    27922 15 atoms, 14 bonds, 1 residue, 1 model selected 
    27923 
    27924 > select #24/A:188
    27925 
    27926 15 atoms, 14 bonds, 1 residue, 1 model selected 
    27927 
    27928 > color sel red
    27929 
    27930 > select #24/A:252
    27931 
    27932 24 atoms, 25 bonds, 1 residue, 1 model selected 
    27933 
    27934 > color sel gray
    27935 
    27936 > select #24/A:185
    27937 
    27938 20 atoms, 20 bonds, 1 residue, 1 model selected 
    27939 
    27940 > color sel light gray
    27941 
    27942 > color sel gray
    27943 
    27944 > ui mousemode right translate
    27945 
    27946 > ui mousemode right select
    27947 
    27948 > select #24/A:184
    27949 
    27950 22 atoms, 21 bonds, 1 residue, 1 model selected 
    27951 
    27952 > hide sel atoms
    27953 
    27954 > ui mousemode right translate
    27955 
    27956 > ui mousemode right select
    27957 
    27958 > select #24/A:179
    27959 
    27960 24 atoms, 23 bonds, 1 residue, 1 model selected 
    27961 
    27962 > hide sel atoms
    27963 
    27964 > ui mousemode right translate
    27965 
    27966 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    27967 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    27968 
    27969 > show #29 models
    27970 
    27971 > color #29 #373e7fff
    27972 
    27973 > color #29 #363d7dff
    27974 
    27975 > select add #24
    27976 
    27977 4246 atoms, 4299 bonds, 268 residues, 1 model selected 
    27978 
    27979 > select subtract #24
    27980 
    27981 Nothing selected 
    27982 
    27983 > hide #24 models
    27984 
    27985 > ui mousemode right select
    27986 
    27987 > select #29/A:135
    27988 
    27989 22 atoms, 21 bonds, 1 residue, 1 model selected 
    27990 
    27991 > hide sel atoms
    27992 
    27993 > select #29/A:133
    27994 
    27995 12 atoms, 11 bonds, 1 residue, 1 model selected 
    27996 
    27997 > hide sel atoms
    27998 
    27999 > ui mousemode right translate
    28000 
    28001 > ui mousemode right select
    28002 
    28003 > select clear
    28004 
    28005 > ui mousemode right translate
    28006 
    28007 > ui mousemode right select
    28008 
    28009 > select #29/A:247
    28010 
    28011 15 atoms, 14 bonds, 1 residue, 1 model selected 
    28012 
    28013 > hide sel atoms
    28014 
    28015 > ui mousemode right translate
    28016 
    28017 > ui mousemode right select
    28018 
    28019 > select #29/A:197
    28020 
    28021 17 atoms, 16 bonds, 1 residue, 1 model selected 
    28022 
    28023 > hide sel atoms
    28024 
    28025 > select #29/A:194
    28026 
    28027 15 atoms, 14 bonds, 1 residue, 1 model selected 
    28028 Alignment identifier is 29/A 
    28029 
    28030 > ui mousemode right translate
    28031 
    28032 > show sel atoms
    28033 
    28034 > color sel red
    28035 
    28036 > ui mousemode right select
    28037 
    28038 > select #29/A:258
    28039 
    28040 24 atoms, 25 bonds, 1 residue, 1 model selected 
    28041 
    28042 > show sel atoms
    28043 
    28044 > color sel gray
    28045 
    28046 > select clear
    28047 
    28048 > ui mousemode right translate
    28049 
    28050 > ui mousemode right select
    28051 
    28052 > select #29/A:191
    28053 
    28054 21 atoms, 21 bonds, 1 residue, 1 model selected 
    28055 
    28056 > ui mousemode right translate
    28057 
    28058 > show sel atoms
    28059 
    28060 > color sel gray
    28061 
    28062 > ui mousemode right select
    28063 
    28064 > select #29/A:190
    28065 
    28066 22 atoms, 21 bonds, 1 residue, 1 model selected 
    28067 
    28068 > hide sel atoms
    28069 
    28070 > select #29/A:161
    28071 
    28072 14 atoms, 13 bonds, 1 residue, 1 model selected 
    28073 
    28074 > hide sel atoms
    28075 
    28076 > select #50/A:153
    28077 
    28078 22 atoms, 21 bonds, 1 residue, 1 model selected 
    28079 
    28080 > ui mousemode right translate
    28081 
    28082 > ui mousemode right select
    28083 
    28084 > select #29/A:185
    28085 
    28086 24 atoms, 23 bonds, 1 residue, 1 model selected 
    28087 
    28088 > hide sel atoms
    28089 
    28090 Drag select of 17 residues 
    28091 
    28092 > select clear
    28093 
    28094 [Repeated 1 time(s)]
    28095 
    28096 > ui mousemode right translate
    28097 
    28098 > ui mousemode right select
    28099 
    28100 > select #29/A:164
    28101 
    28102 10 atoms, 9 bonds, 1 residue, 1 model selected 
    28103 
    28104 > hide sel atoms
    28105 
    28106 Drag select of 8 residues 
    28107 
    28108 > select #29/A:163
    28109 
    28110 10 atoms, 9 bonds, 1 residue, 1 model selected 
    28111 
    28112 > ui mousemode right translate
    28113 
    28114 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    28115 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    28116 
    28117 > show #30 models
    28118 
    28119 > select add #29
    28120 
    28121 4432 atoms, 4487 bonds, 275 residues, 1 model selected 
    28122 
    28123 > select subtract #29
    28124 
    28125 Nothing selected 
    28126 
    28127 > hide #29 models
    28128 
    28129 > color #30 #910e0eff
    28130 
    28131 > show #46 models
    28132 
    28133 > hide #46 models
    28134 
    28135 > color #30 #9c0f0fff
    28136 
    28137 > ui mousemode right select
    28138 
    28139 > select #30/A:121
    28140 
    28141 15 atoms, 14 bonds, 1 residue, 1 model selected 
    28142 
    28143 > hide sel atoms
    28144 
    28145 > select #30/A:124
    28146 
    28147 22 atoms, 21 bonds, 1 residue, 1 model selected 
    28148 
    28149 > hide sel atoms
    28150 
    28151 > ui mousemode right translate
    28152 
    28153 > ui mousemode right select
    28154 
    28155 > select #30/A:236
    28156 
    28157 17 atoms, 16 bonds, 1 residue, 1 model selected 
    28158 
    28159 > hide sel atoms
    28160 
    28161 > ui mousemode right translate
    28162 
    28163 > ui mousemode right select
    28164 
    28165 > select #30/A:186@CA
    28166 
    28167 1 atom, 1 residue, 1 model selected 
    28168 
    28169 > select #30/A:186@CA
    28170 
    28171 1 atom, 1 residue, 1 model selected 
    28172 
    28173 > select #50/A:186
    28174 
    28175 15 atoms, 14 bonds, 1 residue, 1 model selected 
    28176 
    28177 > select #30/A:186
    28178 
    28179 15 atoms, 14 bonds, 1 residue, 1 model selected 
    28180 
    28181 > hide sel atoms
    28182 
    28183 > ui mousemode right translate
    28184 
    28185 > ui mousemode right select
    28186 
    28187 > select #30/A:183
    28188 
    28189 15 atoms, 14 bonds, 1 residue, 1 model selected 
    28190 
    28191 > ui mousemode right translate
    28192 
    28193 > show sel atoms
    28194 
    28195 > color sel red
    28196 
    28197 > color #30 #960f0fff
    28198 
    28199 > color #30 #930e0eff
    28200 
    28201 > show #46 models
    28202 
    28203 > hide #46 models
    28204 
    28205 > color sel red
    28206 
    28207 > ui mousemode right select
    28208 
    28209 > select #30/A:247
    28210 
    28211 24 atoms, 25 bonds, 1 residue, 1 model selected 
    28212 Alignment identifier is 30/A 
    28213 
    28214 > show sel atoms
    28215 
    28216 > color sel gray
    28217 
    28218 > select #30/A:180
    28219 
    28220 21 atoms, 21 bonds, 1 residue, 1 model selected 
    28221 
    28222 > select #30/A:180
    28223 
    28224 21 atoms, 21 bonds, 1 residue, 1 model selected 
    28225 
    28226 > show sel atoms
    28227 
    28228 > color sel gray
    28229 
    28230 > select #30/A:179
    28231 
    28232 22 atoms, 21 bonds, 1 residue, 1 model selected 
    28233 
    28234 > hide sel atoms
    28235 
    28236 > select #30/A:174
    28237 
    28238 24 atoms, 23 bonds, 1 residue, 1 model selected 
    28239 
    28240 > hide sel atoms
    28241 
    28242 > ui mousemode right translate
    28243 
    28244 > ui mousemode right select
    28245 
    28246 > select #30/A:153
    28247 
    28248 22 atoms, 21 bonds, 1 residue, 1 model selected 
    28249 
    28250 > hide sel atoms
    28251 
    28252 > select #30/A:150
    28253 
    28254 10 atoms, 9 bonds, 1 residue, 1 model selected 
    28255 
    28256 > hide sel atoms
    28257 
    28258 > ui mousemode right translate
    28259 
    28260 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    28261 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    28262 
    28263 > select add #30
    28264 
    28265 4192 atoms, 4243 bonds, 264 residues, 1 model selected 
    28266 
    28267 > select subtract #30
    28268 
    28269 Nothing selected 
    28270 
    28271 > show #31 models
    28272 
    28273 > hide #30 models
    28274 
    28275 > color #31 #ff54a4ff
    28276 
    28277 > ui mousemode right select
    28278 
    28279 > select #31/A:124
    28280 
    28281 22 atoms, 21 bonds, 1 residue, 1 model selected 
    28282 
    28283 > hide sel atoms
    28284 
    28285 > select #31/A:122
    28286 
    28287 12 atoms, 11 bonds, 1 residue, 1 model selected 
    28288 
    28289 > hide sel atoms
    28290 
    28291 > ui mousemode right translate
    28292 
    28293 > ui mousemode right select
    28294 
    28295 > select #31/A:236
    28296 
    28297 15 atoms, 14 bonds, 1 residue, 1 model selected 
    28298 
    28299 > hide sel atoms
    28300 
    28301 > ui mousemode right translate
    28302 
    28303 > ui mousemode right select
    28304 
    28305 > select #31/A:186
    28306 
    28307 15 atoms, 14 bonds, 1 residue, 1 model selected 
    28308 
    28309 > hide sel atoms
    28310 
    28311 > select #31/A:183
    28312 
    28313 15 atoms, 14 bonds, 1 residue, 1 model selected 
    28314 
    28315 > hide sel atoms
    28316 
    28317 > show sel atoms
    28318 
    28319 > color sel red
    28320 
    28321 > ui mousemode right translate
    28322 
    28323 > ui mousemode right select
    28324 
    28325 > select #31/A:179
    28326 
    28327 22 atoms, 21 bonds, 1 residue, 1 model selected 
    28328 
    28329 > hide sel atoms
    28330 
    28331 > select #31/A:247
    28332 
    28333 24 atoms, 25 bonds, 1 residue, 1 model selected 
    28334 Alignment identifier is 31/A 
    28335 
    28336 > select #31/A:180
    28337 
    28338 20 atoms, 20 bonds, 1 residue, 1 model selected 
    28339 
    28340 > show sel atoms
    28341 
    28342 > color sel gray
    28343 
    28344 > show #30 models
    28345 
    28346 > hide #30 models
    28347 
    28348 > select add #31
    28349 
    28350 4258 atoms, 4310 bonds, 263 residues, 1 model selected 
    28351 
    28352 > select subtract #31
    28353 
    28354 Nothing selected 
    28355 
    28356 > select #31/A:174
    28357 
    28358 24 atoms, 23 bonds, 1 residue, 1 model selected 
    28359 
    28360 > hide sel atoms
    28361 
    28362 > select #31/A:153
    28363 
    28364 22 atoms, 21 bonds, 1 residue, 1 model selected 
    28365 
    28366 > hide sel atoms
    28367 
    28368 > ui mousemode right translate
    28369 
    28370 > ui mousemode right rotate
    28371 
    28372 > ui mousemode right select
    28373 
    28374 > select #31/A:247
    28375 
    28376 24 atoms, 25 bonds, 1 residue, 1 model selected 
    28377 
    28378 > show sel atoms
    28379 
    28380 > color sel gray
    28381 
    28382 > ui mousemode right translate
    28383 
    28384 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    28385 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    28386 
    28387 ——— End of log from Wed Aug 2 11:55:29 2023 ———
    28388 
    28389 opened ChimeraX session 
    28390 
    28391 > select add #31
    28392 
    28393 4258 atoms, 4310 bonds, 263 residues, 1 model selected 
    28394 
    28395 > select subtract #31
    28396 
    28397 Nothing selected 
    28398 
    28399 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    28400 > UASLP/Lab Virología/AlphaFold/VEEV AlphaFold.pdb"
    28401 
    28402 Chain information for VEEV AlphaFold.pdb #52 
    28403 --- 
    28404 Chain | Description 
    28405 A | No description available 
    28406  
    28407 
    28408 > ui tool show Matchmaker
    28409 
    28410 > matchmaker #52 to #50
    28411 
    28412 Parameters 
    28413 --- 
    28414 Chain pairing | bb 
    28415 Alignment algorithm | Needleman-Wunsch 
    28416 Similarity matrix | BLOSUM-62 
    28417 SS fraction | 0.3 
    28418 Gap open (HH/SS/other) | 18/18/6 
    28419 Gap extend | 1 
    28420 SS matrix |  |  | H | S | O 
    28421 ---|---|---|--- 
    28422 H | 6 | -9 | -6 
    28423 S |  | 6 | -6 
    28424 O |  |  | 4 
    28425 Iteration cutoff | 2 
    28426  
    28427 Matchmaker Sindbis virus AlphaFold.pdb, chain A (#50) with VEEV AlphaFold.pdb,
    28428 chain A (#52), sequence alignment score = 780 
    28429 RMSD between 162 pruned atom pairs is 0.545 angstroms; (across all 256 pairs:
    28430 21.851) 
    28431  
    28432 
    28433 > color #52 yellow
    28434 
    28435 > color #52 #e6e600ff
    28436 
    28437 > hide #31 models
    28438 
    28439 > ui mousemode right select
    28440 
    28441 > select #52/A:194
    28442 
    28443 15 atoms, 14 bonds, 1 residue, 1 model selected 
    28444 
    28445 > show sel atoms
    28446 
    28447 > color sel red
    28448 
    28449 > select #52/A:258
    28450 
    28451 24 atoms, 25 bonds, 1 residue, 1 model selected 
    28452 
    28453 > show sel atoms
    28454 
    28455 > color sel gray
    28456 
    28457 > ui mousemode right translate
    28458 
    28459 > ui mousemode right rotate
    28460 
    28461 > ui mousemode right select
    28462 
    28463 > select #52/A:191
    28464 
    28465 21 atoms, 21 bonds, 1 residue, 1 model selected 
    28466 
    28467 > ui mousemode right translate
    28468 
    28469 > show sel atoms
    28470 
    28471 > color sel gray
    28472 
    28473 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    28474 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    28475 
    28476 > show #45 models
    28477 
    28478 > hide #52 models
    28479 
    28480 > color #45 #678ebfff
    28481 
    28482 > ui mousemode right select
    28483 
    28484 > select #45/A:119
    28485 
    28486 17 atoms, 16 bonds, 1 residue, 1 model selected 
    28487 
    28488 > hide sel atoms
    28489 
    28490 > select #45/A:117
    28491 
    28492 14 atoms, 13 bonds, 1 residue, 1 model selected 
    28493 
    28494 > hide sel atoms
    28495 
    28496 > ui mousemode right translate
    28497 
    28498 > ui mousemode right select
    28499 
    28500 > select #45/A:231
    28501 
    28502 15 atoms, 14 bonds, 1 residue, 1 model selected 
    28503 
    28504 > hide sel atoms
    28505 
    28506 > set bgColor black
    28507 
    28508 > set bgColor transparent
    28509 
    28510 > set bgColor white
    28511 
    28512 > set bgColor #ffffff00
    28513 
    28514 > ui mousemode right translate
    28515 
    28516 > ui mousemode right select
    28517 
    28518 > select #45/A:181
    28519 
    28520 14 atoms, 14 bonds, 1 residue, 1 model selected 
    28521 
    28522 > select #45/A:181
    28523 
    28524 14 atoms, 14 bonds, 1 residue, 1 model selected 
    28525 
    28526 > hide sel atoms
    28527 
    28528 > ui mousemode right translate
    28529 
    28530 > ui mousemode right select
    28531 
    28532 > select #45/A:178
    28533 
    28534 12 atoms, 11 bonds, 1 residue, 1 model selected 
    28535 
    28536 > show sel atoms
    28537 
    28538 Alignment identifier is 45/A 
    28539 
    28540 > show sel atoms
    28541 
    28542 > color sel red
    28543 
    28544 > ui mousemode right translate
    28545 
    28546 > ui mousemode right select
    28547 
    28548 > select #50/A:247
    28549 
    28550 24 atoms, 25 bonds, 1 residue, 1 model selected 
    28551 
    28552 > select #50/A:247
    28553 
    28554 24 atoms, 25 bonds, 1 residue, 1 model selected 
    28555 
    28556 > select #50/A:247
    28557 
    28558 24 atoms, 25 bonds, 1 residue, 1 model selected 
    28559 
    28560 > select #45/A:242
    28561 
    28562 24 atoms, 25 bonds, 1 residue, 1 model selected 
    28563 
    28564 > ui mousemode right translate
    28565 
    28566 > show sel atoms
    28567 
    28568 > color sel gray
    28569 
    28570 > ui mousemode right select
    28571 
    28572 > select #50/A:180
    28573 
    28574 21 atoms, 21 bonds, 1 residue, 1 model selected 
    28575 
    28576 > select #45/A:175
    28577 
    28578 21 atoms, 21 bonds, 1 residue, 1 model selected 
    28579 
    28580 > ui mousemode right translate
    28581 
    28582 > show sel atoms
    28583 
    28584 > color sel gray
    28585 
    28586 > ui mousemode right select
    28587 
    28588 > select #50/A:247
    28589 
    28590 24 atoms, 25 bonds, 1 residue, 1 model selected 
    28591 
    28592 > select #45/A:242
    28593 
    28594 24 atoms, 25 bonds, 1 residue, 1 model selected 
    28595 
    28596 > ui mousemode right translate
    28597 
    28598 > ui mousemode right select
    28599 
    28600 > select clear
    28601 
    28602 > select #45/A:174
    28603 
    28604 17 atoms, 16 bonds, 1 residue, 1 model selected 
    28605 
    28606 > ui mousemode right translate
    28607 
    28608 > hide sel atoms
    28609 
    28610 > ui mousemode right select
    28611 
    28612 > select #45/A:169
    28613 
    28614 22 atoms, 21 bonds, 1 residue, 1 model selected 
    28615 
    28616 > ui mousemode right translate
    28617 
    28618 > hide sel atoms
    28619 
    28620 > ui mousemode right select
    28621 
    28622 > select #45/A:148
    28623 
    28624 10 atoms, 9 bonds, 1 residue, 1 model selected 
    28625 
    28626 > hide sel atoms
    28627 
    28628 > select #45/A:145
    28629 
    28630 17 atoms, 16 bonds, 1 residue, 1 model selected 
    28631 
    28632 > hide sel atoms
    28633 
    28634 > ui mousemode right translate
    28635 
    28636 > select add #45
    28637 
    28638 4153 atoms, 4213 bonds, 259 residues, 1 model selected 
    28639 
    28640 > select subtract #45
    28641 
    28642 Nothing selected 
    28643 
    28644 > show #32 models
    28645 
    28646 > color #32 #ffef3aff
    28647 
    28648 > hide #45 models
    28649 
    28650 > ui mousemode right select
    28651 
    28652 > select #32/A:126
    28653 
    28654 12 atoms, 11 bonds, 1 residue, 1 model selected 
    28655 
    28656 > hide sel atoms
    28657 
    28658 > select #32/A:123
    28659 
    28660 15 atoms, 14 bonds, 1 residue, 1 model selected 
    28661 
    28662 > hide sel atoms
    28663 
    28664 > ui mousemode right translate
    28665 
    28666 > ui mousemode right select
    28667 
    28668 > select #50/A:236
    28669 
    28670 15 atoms, 14 bonds, 1 residue, 1 model selected 
    28671 
    28672 > select #32/A:238
    28673 
    28674 15 atoms, 14 bonds, 1 residue, 1 model selected 
    28675 
    28676 > hide sel atoms
    28677 
    28678 > select #32/A:188
    28679 
    28680 15 atoms, 14 bonds, 1 residue, 1 model selected 
    28681 
    28682 > hide sel atoms
    28683 
    28684 > ui mousemode right translate
    28685 
    28686 > ui mousemode right select
    28687 
    28688 > select #32/A:185
    28689 
    28690 15 atoms, 14 bonds, 1 residue, 1 model selected 
    28691 
    28692 > ui mousemode right translate
    28693 
    28694 > show sel atoms
    28695 
    28696 > color sel red
    28697 
    28698 > hide sel atoms
    28699 
    28700 [Repeated 1 time(s)]
    28701 
    28702 > show sel atoms
    28703 
    28704 > ui mousemode right select
    28705 
    28706 > select #32/A:249
    28707 
    28708 24 atoms, 25 bonds, 1 residue, 1 model selected 
    28709 Alignment identifier is 32/A 
    28710 
    28711 > show sel atoms
    28712 
    28713 > color sel gray
    28714 
    28715 Drag select of 4 residues 
    28716 
    28717 > select clear
    28718 
    28719 > select #32/A:182
    28720 
    28721 21 atoms, 21 bonds, 1 residue, 1 model selected 
    28722 
    28723 > show sel atoms
    28724 
    28725 > color sel gray
    28726 
    28727 > ui mousemode right translate
    28728 
    28729 > ui mousemode right select
    28730 
    28731 > select #32/A:181
    28732 
    28733 14 atoms, 13 bonds, 1 residue, 1 model selected 
    28734 
    28735 > hide sel atoms
    28736 
    28737 > select #32/A:176
    28738 
    28739 22 atoms, 21 bonds, 1 residue, 1 model selected 
    28740 
    28741 > hide sel atoms
    28742 
    28743 > select #32/A:155
    28744 
    28745 22 atoms, 21 bonds, 1 residue, 1 model selected 
    28746 
    28747 > hide sel atoms
    28748 
    28749 > select #32/A:115
    28750 
    28751 12 atoms, 11 bonds, 1 residue, 1 model selected 
    28752 
    28753 > select #32/A:152
    28754 
    28755 16 atoms, 15 bonds, 1 residue, 1 model selected 
    28756 
    28757 > hide sel atoms
    28758 
    28759 > ui mousemode right translate
    28760 
    28761 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    28762 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    28763 
    28764 ——— End of log from Wed Aug 2 13:12:02 2023 ———
    28765 
    28766 opened ChimeraX session 
    28767 
    28768 > show #33 models
    28769 
    28770 > hide #33 models
    28771 
    28772 > hide #32 models
    28773 
    28774 > select add #32
    28775 
    28776 4214 atoms, 4273 bonds, 266 residues, 1 model selected 
    28777 
    28778 > select subtract #32
    28779 
    28780 Nothing selected 
    28781 
    28782 > show #33 models
    28783 
    28784 > color #33 #ffaed9ff
    28785 
    28786 > ui mousemode right select
    28787 
    28788 > select #33/A:124
    28789 
    28790 12 atoms, 11 bonds, 1 residue, 1 model selected 
    28791 
    28792 > hide sel atoms
    28793 
    28794 > select #33/A:126
    28795 
    28796 17 atoms, 16 bonds, 1 residue, 1 model selected 
    28797 
    28798 > hide sel atoms
    28799 
    28800 > ui mousemode right translate
    28801 
    28802 > ui mousemode right select
    28803 
    28804 > select #33/A:238
    28805 
    28806 15 atoms, 14 bonds, 1 residue, 1 model selected 
    28807 
    28808 > hide sel atoms
    28809 
    28810 > ui mousemode right translate
    28811 
    28812 > ui mousemode right select
    28813 
    28814 > select #33/A:188
    28815 
    28816 15 atoms, 14 bonds, 1 residue, 1 model selected 
    28817 
    28818 > ui mousemode right translate
    28819 
    28820 > hide sel atoms
    28821 
    28822 > ui mousemode right select
    28823 
    28824 > select #33/A:185
    28825 
    28826 15 atoms, 14 bonds, 1 residue, 1 model selected 
    28827 
    28828 > select #50/A:183
    28829 
    28830 15 atoms, 14 bonds, 1 residue, 1 model selected 
    28831 Destroying pre-existing alignment with identifier 50/A 
    28832 Alignment identifier is 50/A 
    28833 
    28834 > select #33/A:185
    28835 
    28836 15 atoms, 14 bonds, 1 residue, 1 model selected 
    28837 Alignment identifier is 33/A 
    28838 
    28839 > ui mousemode right translate
    28840 
    28841 > show sel atoms
    28842 
    28843 > color sel red
    28844 
    28845 > ui mousemode right select
    28846 
    28847 > select #33/A:181
    28848 
    28849 24 atoms, 23 bonds, 1 residue, 1 model selected 
    28850 
    28851 > hide sel atoms
    28852 
    28853 > select clear
    28854 
    28855 > select #50/A:247
    28856 
    28857 24 atoms, 25 bonds, 1 residue, 1 model selected 
    28858 
    28859 > select #33/A:249
    28860 
    28861 24 atoms, 25 bonds, 1 residue, 1 model selected 
    28862 
    28863 > select #50/A:247
    28864 
    28865 24 atoms, 25 bonds, 1 residue, 1 model selected 
    28866 
    28867 > select #50/A:246
    28868 
    28869 14 atoms, 13 bonds, 1 residue, 1 model selected 
    28870 
    28871 > select #50/A:247
    28872 
    28873 24 atoms, 25 bonds, 1 residue, 1 model selected 
    28874 
    28875 > select #33/A:249
    28876 
    28877 24 atoms, 25 bonds, 1 residue, 1 model selected 
    28878 
    28879 > ui mousemode right translate
    28880 
    28881 > show sel atoms
    28882 
    28883 > color sel gray
    28884 
    28885 > ui mousemode right select
    28886 
    28887 > select #33/A:182
    28888 
    28889 21 atoms, 21 bonds, 1 residue, 1 model selected 
    28890 
    28891 > select #50/A:180
    28892 
    28893 21 atoms, 21 bonds, 1 residue, 1 model selected 
    28894 
    28895 > select #33/A:182
    28896 
    28897 21 atoms, 21 bonds, 1 residue, 1 model selected 
    28898 
    28899 > ui mousemode right translate
    28900 
    28901 > show sel atoms
    28902 
    28903 > color sel gray
    28904 
    28905 > ui mousemode right select
    28906 
    28907 > select #33/A:155
    28908 
    28909 22 atoms, 21 bonds, 1 residue, 1 model selected 
    28910 
    28911 > hide sel atoms
    28912 
    28913 > select #33/A:152
    28914 
    28915 19 atoms, 18 bonds, 1 residue, 1 model selected 
    28916 
    28917 > hide sel atoms
    28918 
    28919 > select #33/A:176
    28920 
    28921 22 atoms, 21 bonds, 1 residue, 1 model selected 
    28922 
    28923 > show sel atoms
    28924 
    28925 > hide sel atoms
    28926 
    28927 > ui mousemode right translate
    28928 
    28929 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    28930 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    28931 
    28932 > select add #33
    28933 
    28934 4198 atoms, 4258 bonds, 266 residues, 1 model selected 
    28935 
    28936 > select subtract #33
    28937 
    28938 Nothing selected 
    28939 
    28940 > hide #33 models
    28941 
    28942 > show #34 models
    28943 
    28944 > color #34 #b56d3cff
    28945 
    28946 > color #34 #b06a3bff
    28947 
    28948 > ui mousemode right select
    28949 
    28950 > select #34/A:163
    28951 
    28952 14 atoms, 13 bonds, 1 residue, 1 model selected 
    28953 
    28954 > hide sel atoms
    28955 
    28956 > select #34/A:161
    28957 
    28958 15 atoms, 14 bonds, 1 residue, 1 model selected 
    28959 
    28960 > hide sel atoms
    28961 
    28962 > select #34/A:192
    28963 
    28964 22 atoms, 21 bonds, 1 residue, 1 model selected 
    28965 
    28966 > hide sel atoms
    28967 
    28968 > ui mousemode right translate
    28969 
    28970 > ui mousemode right select
    28971 
    28972 > select #34/A:274
    28973 
    28974 11 atoms, 10 bonds, 1 residue, 1 model selected 
    28975 
    28976 > ui mousemode right translate
    28977 
    28978 > hide sel atoms
    28979 
    28980 > ui mousemode right select
    28981 
    28982 > select #34/A:218
    28983 
    28984 22 atoms, 21 bonds, 1 residue, 1 model selected 
    28985 
    28986 > hide sel atoms
    28987 
    28988 > select #34/A:189
    28989 
    28990 15 atoms, 14 bonds, 1 residue, 1 model selected 
    28991 
    28992 > hide sel atoms
    28993 
    28994 > select #34/A:213
    28995 
    28996 22 atoms, 21 bonds, 1 residue, 1 model selected 
    28997 
    28998 > hide sel atoms
    28999 
    29000 > ui mousemode right translate
    29001 
    29002 > ui mousemode right select
    29003 
    29004 > select #34/A:222
    29005 
    29006 19 atoms, 18 bonds, 1 residue, 1 model selected 
    29007 
    29008 > select #34/A:221
    29009 
    29010 14 atoms, 14 bonds, 1 residue, 1 model selected 
    29011 
    29012 > select #34/A:222
    29013 
    29014 19 atoms, 18 bonds, 1 residue, 1 model selected 
    29015 Alignment identifier is 34/A 
    29016 
    29017 > show sel atoms
    29018 
    29019 > color sel gray
    29020 
    29021 > ui mousemode right translate
    29022 
    29023 > ui mousemode right select
    29024 
    29025 > select #34/A:298
    29026 
    29027 14 atoms, 14 bonds, 1 residue, 1 model selected 
    29028 
    29029 > color #34 #bd713fff
    29030 
    29031 > color #34 #c77742ff
    29032 
    29033 > select #34/A:222
    29034 
    29035 19 atoms, 18 bonds, 1 residue, 1 model selected 
    29036 
    29037 > color sel gray
    29038 
    29039 > select #34/A:285
    29040 
    29041 20 atoms, 20 bonds, 1 residue, 1 model selected 
    29042 
    29043 > show sel atoms
    29044 
    29045 > color sel gray
    29046 
    29047 > color sel magenta
    29048 
    29049 > color sel gray
    29050 
    29051 > select #50/A:247
    29052 
    29053 24 atoms, 25 bonds, 1 residue, 1 model selected 
    29054 
    29055 > select #34/A:285
    29056 
    29057 20 atoms, 20 bonds, 1 residue, 1 model selected 
    29058 
    29059 > select #50/A:247
    29060 
    29061 24 atoms, 25 bonds, 1 residue, 1 model selected 
    29062 
    29063 > select #34/A:219
    29064 
    29065 14 atoms, 14 bonds, 1 residue, 1 model selected 
    29066 
    29067 > ui mousemode right translate
    29068 
    29069 > ui mousemode right select
    29070 
    29071 > select #50/A:180
    29072 
    29073 21 atoms, 21 bonds, 1 residue, 1 model selected 
    29074 
    29075 > select #34/A:220
    29076 
    29077 7 atoms, 6 bonds, 1 residue, 1 model selected 
    29078 
    29079 > select #34/A:219
    29080 
    29081 14 atoms, 14 bonds, 1 residue, 1 model selected 
    29082 
    29083 > color sel purple
    29084 
    29085 > color sel magenta
    29086 
    29087 > show sel atoms
    29088 
    29089 > ui mousemode right translate
    29090 
    29091 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    29092 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    29093 
    29094 > select add #34
    29095 
    29096 4798 atoms, 4847 bonds, 303 residues, 1 model selected 
    29097 
    29098 > select subtract #34
    29099 
    29100 Nothing selected 
    29101 
    29102 > hide #34 models
    29103 
    29104 > show #35 models
    29105 
    29106 > color #35 #cce83fff
    29107 
    29108 > color #35 #cae63eff
    29109 
    29110 > ui mousemode right select
    29111 
    29112 > select #35/A:97
    29113 
    29114 22 atoms, 21 bonds, 1 residue, 1 model selected 
    29115 
    29116 > hide sel atoms
    29117 
    29118 > select #35/A:95
    29119 
    29120 12 atoms, 11 bonds, 1 residue, 1 model selected 
    29121 
    29122 > hide sel atoms
    29123 
    29124 > ui mousemode right translate
    29125 
    29126 > color #35 #cbe73fff
    29127 
    29128 > ui mousemode right select
    29129 
    29130 > select #35/A:209
    29131 
    29132 15 atoms, 14 bonds, 1 residue, 1 model selected 
    29133 
    29134 > ui mousemode right translate
    29135 
    29136 > hide sel atoms
    29137 
    29138 > ui mousemode right select
    29139 
    29140 > select #35/A:173
    29141 
    29142 7 atoms, 6 bonds, 1 residue, 1 model selected 
    29143 
    29144 > select #35/A:159
    29145 
    29146 12 atoms, 11 bonds, 1 residue, 1 model selected 
    29147 
    29148 > hide sel atoms
    29149 
    29150 > select #35/A:156
    29151 
    29152 15 atoms, 14 bonds, 1 residue, 1 model selected 
    29153 
    29154 > select #50/A:183
    29155 
    29156 15 atoms, 14 bonds, 1 residue, 1 model selected 
    29157 
    29158 > select #35/A:156
    29159 
    29160 15 atoms, 14 bonds, 1 residue, 1 model selected 
    29161 
    29162 > select clear
    29163 
    29164 [Repeated 1 time(s)]
    29165 
    29166 > ui mousemode right translate
    29167 
    29168 > ui mousemode right select
    29169 
    29170 > select #35/A:157
    29171 
    29172 22 atoms, 21 bonds, 1 residue, 1 model selected 
    29173 
    29174 > select #35/A:156
    29175 
    29176 15 atoms, 14 bonds, 1 residue, 1 model selected 
    29177 
    29178 > show sel atoms
    29179 
    29180 > color sel red
    29181 
    29182 Alignment identifier is 35/A 
    29183 Drag select of 2 residues 
    29184 
    29185 > ui mousemode right translate
    29186 
    29187 > ui mousemode right select
    29188 
    29189 > select #35/A:152
    29190 
    29191 22 atoms, 21 bonds, 1 residue, 1 model selected 
    29192 
    29193 > hide sel atoms
    29194 
    29195 > select #35/A:220
    29196 
    29197 24 atoms, 25 bonds, 1 residue, 1 model selected 
    29198 
    29199 > ui mousemode right translate
    29200 
    29201 > ui mousemode right select
    29202 
    29203 > select #50/A:247
    29204 
    29205 24 atoms, 25 bonds, 1 residue, 1 model selected 
    29206 
    29207 > select #35/A:220
    29208 
    29209 24 atoms, 25 bonds, 1 residue, 1 model selected 
    29210 
    29211 > show sel atoms
    29212 
    29213 > color sel gray
    29214 
    29215 > select #50/A:180
    29216 
    29217 21 atoms, 21 bonds, 1 residue, 1 model selected 
    29218 
    29219 > select #35/A:153
    29220 
    29221 20 atoms, 20 bonds, 1 residue, 1 model selected 
    29222 
    29223 > color sel gray
    29224 
    29225 > ui mousemode right zoom
    29226 
    29227 > ui mousemode right translate
    29228 
    29229 > ui mousemode right select
    29230 
    29231 > select #35/A:147
    29232 
    29233 22 atoms, 21 bonds, 1 residue, 1 model selected 
    29234 
    29235 > hide sel atoms
    29236 
    29237 > select #35/A:123
    29238 
    29239 16 atoms, 15 bonds, 1 residue, 1 model selected 
    29240 
    29241 > hide sel atoms
    29242 
    29243 > select #35/A:126
    29244 
    29245 22 atoms, 21 bonds, 1 residue, 1 model selected 
    29246 
    29247 > hide sel atoms
    29248 
    29249 > ui mousemode right translate
    29250 
    29251 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    29252 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    29253 
    29254 > select add #35
    29255 
    29256 3771 atoms, 3815 bonds, 236 residues, 1 model selected 
    29257 
    29258 > select subtract #35
    29259 
    29260 Nothing selected 
    29261 
    29262 > hide #35 models
    29263 
    29264 > show #36 models
    29265 
    29266 > show #34 models
    29267 
    29268 > hide #34 models
    29269 
    29270 > show #34 models
    29271 
    29272 > hide #36 models
    29273 
    29274 > hide #34 models
    29275 
    29276 > show #36 models
    29277 
    29278 > color #36 #8187deff
    29279 
    29280 > color #36 #8086dcff
    29281 
    29282 > ui mousemode right rotate
    29283 
    29284 > ui mousemode right select
    29285 
    29286 > select #36/A:116
    29287 
    29288 10 atoms, 9 bonds, 1 residue, 1 model selected 
    29289 
    29290 > select #36/A:116
    29291 
    29292 10 atoms, 9 bonds, 1 residue, 1 model selected 
    29293 
    29294 > hide sel atoms
    29295 
    29296 > select clear
    29297 
    29298 [Repeated 1 time(s)]
    29299 
    29300 > select #36/A:113
    29301 
    29302 12 atoms, 11 bonds, 1 residue, 1 model selected 
    29303 
    29304 > hide sel atoms
    29305 
    29306 > ui mousemode right translate
    29307 
    29308 > ui mousemode right rotate
    29309 
    29310 > ui mousemode right select
    29311 
    29312 > select #36/A:228
    29313 
    29314 15 atoms, 14 bonds, 1 residue, 1 model selected 
    29315 
    29316 > ui mousemode right translate
    29317 
    29318 > hide sel atoms
    29319 
    29320 > ui mousemode right select
    29321 
    29322 > select #36/A:178
    29323 
    29324 12 atoms, 11 bonds, 1 residue, 1 model selected 
    29325 
    29326 > hide sel atoms
    29327 
    29328 > select #36/A:175
    29329 
    29330 15 atoms, 14 bonds, 1 residue, 1 model selected 
    29331 
    29332 > select #50/A:183
    29333 
    29334 15 atoms, 14 bonds, 1 residue, 1 model selected 
    29335 
    29336 > select #36/A:175
    29337 
    29338 15 atoms, 14 bonds, 1 residue, 1 model selected 
    29339 
    29340 > show sel atoms
    29341 
    29342 > color sel red
    29343 
    29344 Alignment identifier is 36/A 
    29345 
    29346 > ui mousemode right translate
    29347 
    29348 > ui mousemode right select
    29349 
    29350 > select #50/A:247
    29351 
    29352 24 atoms, 25 bonds, 1 residue, 1 model selected 
    29353 
    29354 > select #36/A:239
    29355 
    29356 24 atoms, 25 bonds, 1 residue, 1 model selected 
    29357 
    29358 > show sel atoms
    29359 
    29360 > color sel gray
    29361 
    29362 Drag select of 3 residues, 1 atoms 
    29363 
    29364 > select #50/A:180
    29365 
    29366 21 atoms, 21 bonds, 1 residue, 1 model selected 
    29367 
    29368 > select #36/A:172
    29369 
    29370 21 atoms, 21 bonds, 1 residue, 1 model selected 
    29371 
    29372 > show sel atoms
    29373 
    29374 > color sel gray
    29375 
    29376 > select #36/A:171
    29377 
    29378 14 atoms, 13 bonds, 1 residue, 1 model selected 
    29379 
    29380 > hide sel atoms
    29381 
    29382 > select #36/A:166
    29383 
    29384 24 atoms, 23 bonds, 1 residue, 1 model selected 
    29385 
    29386 > hide sel atoms
    29387 
    29388 > ui mousemode right translate
    29389 
    29390 > ui mousemode right select
    29391 
    29392 > select #36/A:145
    29393 
    29394 14 atoms, 13 bonds, 1 residue, 1 model selected 
    29395 
    29396 > hide sel atoms
    29397 
    29398 > select #36/A:142
    29399 
    29400 19 atoms, 18 bonds, 1 residue, 1 model selected 
    29401 
    29402 > hide sel atoms
    29403 
    29404 > ui mousemode right rotate
    29405 
    29406 > ui mousemode right translate
    29407 
    29408 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    29409 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    29410 
    29411 > select add #36
    29412 
    29413 3980 atoms, 4027 bonds, 256 residues, 1 model selected 
    29414 
    29415 > select subtract #36
    29416 
    29417 Nothing selected 
    29418 
    29419 > hide #36 models
    29420 
    29421 > show #40 models
    29422 
    29423 > color #40 #b18732ff
    29424 
    29425 > color #40 #b88c34ff
    29426 
    29427 > ui mousemode right select
    29428 
    29429 > select #40/A:142
    29430 
    29431 10 atoms, 9 bonds, 1 residue, 1 model selected 
    29432 
    29433 > hide sel atoms
    29434 
    29435 > select #40/A:140
    29436 
    29437 12 atoms, 11 bonds, 1 residue, 1 model selected 
    29438 
    29439 > hide sel atoms
    29440 
    29441 > select #40/A:253
    29442 
    29443 12 atoms, 11 bonds, 1 residue, 1 model selected 
    29444 
    29445 > hide sel atoms
    29446 
    29447 > ui mousemode right translate
    29448 
    29449 > ui mousemode right select
    29450 
    29451 > select #40/A:203
    29452 
    29453 12 atoms, 11 bonds, 1 residue, 1 model selected 
    29454 
    29455 > hide sel atoms
    29456 
    29457 > select #40/A:201
    29458 
    29459 17 atoms, 16 bonds, 1 residue, 1 model selected 
    29460 
    29461 > select #40/A:200
    29462 
    29463 14 atoms, 13 bonds, 1 residue, 1 model selected 
    29464 Alignment identifier is 40/A 
    29465 
    29466 > select #40/A:201
    29467 
    29468 17 atoms, 16 bonds, 1 residue, 1 model selected 
    29469 
    29470 > show sel atoms
    29471 
    29472 > color sel gray
    29473 
    29474 > ui mousemode right translate
    29475 
    29476 > ui mousemode right select
    29477 
    29478 > select #50/A:253
    29479 
    29480 14 atoms, 13 bonds, 1 residue, 1 model selected 
    29481 
    29482 > ui mousemode right translate
    29483 
    29484 > color #40 #c19336ff
    29485 
    29486 > color #40 #c69738ff
    29487 
    29488 > ui mousemode right select
    29489 
    29490 > select #40/A:201
    29491 
    29492 17 atoms, 16 bonds, 1 residue, 1 model selected 
    29493 
    29494 > color sel red
    29495 
    29496 > color sel gray
    29497 
    29498 > select #50/A:247
    29499 
    29500 24 atoms, 25 bonds, 1 residue, 1 model selected 
    29501 
    29502 > select #40/A:264
    29503 
    29504 20 atoms, 20 bonds, 1 residue, 1 model selected 
    29505 
    29506 > ui mousemode right translate
    29507 
    29508 > show sel atoms
    29509 
    29510 > color sel gray
    29511 
    29512 > ui mousemode right select
    29513 
    29514 > select #50/A:180
    29515 
    29516 21 atoms, 21 bonds, 1 residue, 1 model selected 
    29517 
    29518 > select #40/A:198
    29519 
    29520 14 atoms, 14 bonds, 1 residue, 1 model selected 
    29521 
    29522 > ui mousemode right translate
    29523 
    29524 > show sel atoms
    29525 
    29526 > color sel magenta
    29527 
    29528 > ui mousemode right rotate
    29529 
    29530 > ui mousemode right select
    29531 
    29532 > select #40/A:197
    29533 
    29534 15 atoms, 14 bonds, 1 residue, 1 model selected 
    29535 
    29536 > hide sel atoms
    29537 
    29538 > select #40/A:192
    29539 
    29540 24 atoms, 23 bonds, 1 residue, 1 model selected 
    29541 
    29542 > hide sel atoms
    29543 
    29544 > select #40/A:171
    29545 
    29546 12 atoms, 11 bonds, 1 residue, 1 model selected 
    29547 
    29548 > hide sel atoms
    29549 
    29550 > select #40/A:168
    29551 
    29552 15 atoms, 14 bonds, 1 residue, 1 model selected 
    29553 
    29554 > hide sel atoms
    29555 
    29556 > ui mousemode right translate
    29557 
    29558 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    29559 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    29560 
    29561 > select add #40
    29562 
    29563 4420 atoms, 4461 bonds, 281 residues, 1 model selected 
    29564 
    29565 > select subtract #40
    29566 
    29567 Nothing selected 
    29568 
    29569 > show #37 models
    29570 
    29571 > hide #40 models
    29572 
    29573 > color #37 #6edf42ff
    29574 
    29575 > color #37 #6ddc41ff
    29576 
    29577 > ui mousemode right select
    29578 
    29579 > select #37/A:136
    29580 
    29581 22 atoms, 21 bonds, 1 residue, 1 model selected 
    29582 
    29583 > hide sel atoms
    29584 
    29585 > select #37/A:134
    29586 
    29587 12 atoms, 11 bonds, 1 residue, 1 model selected 
    29588 
    29589 > hide sel atoms
    29590 
    29591 > ui mousemode right translate
    29592 
    29593 > ui mousemode right select
    29594 
    29595 > select #37/A:248
    29596 
    29597 15 atoms, 14 bonds, 1 residue, 1 model selected 
    29598 
    29599 > hide sel atoms
    29600 
    29601 > ui mousemode right translate
    29602 
    29603 > ui mousemode right select
    29604 
    29605 > select #37/A:198
    29606 
    29607 17 atoms, 16 bonds, 1 residue, 1 model selected 
    29608 
    29609 > ui mousemode right translate
    29610 
    29611 > hide sel atoms
    29612 
    29613 > ui mousemode right select
    29614 
    29615 > select #37/A:195
    29616 
    29617 15 atoms, 14 bonds, 1 residue, 1 model selected 
    29618 Alignment identifier is 37/A 
    29619 
    29620 > show sel atoms
    29621 
    29622 > color sel red
    29623 
    29624 > select #50/A:247
    29625 
    29626 24 atoms, 25 bonds, 1 residue, 1 model selected 
    29627 
    29628 > select #37/A:259
    29629 
    29630 24 atoms, 25 bonds, 1 residue, 1 model selected 
    29631 
    29632 > show sel atoms
    29633 
    29634 > color sel dark gray
    29635 
    29636 > color sel gray
    29637 
    29638 > select #50/A:180
    29639 
    29640 21 atoms, 21 bonds, 1 residue, 1 model selected 
    29641 
    29642 > select #50/A:180
    29643 
    29644 21 atoms, 21 bonds, 1 residue, 1 model selected 
    29645 
    29646 > select #37/A:192
    29647 
    29648 21 atoms, 21 bonds, 1 residue, 1 model selected 
    29649 
    29650 > show sel atoms
    29651 
    29652 > color sel gray
    29653 
    29654 > select #37/A:191
    29655 
    29656 22 atoms, 21 bonds, 1 residue, 1 model selected 
    29657 
    29658 > hide sel atoms
    29659 
    29660 > select #37/A:186
    29661 
    29662 24 atoms, 23 bonds, 1 residue, 1 model selected 
    29663 
    29664 > hide sel atoms
    29665 
    29666 > select #37/A:162
    29667 
    29668 14 atoms, 13 bonds, 1 residue, 1 model selected 
    29669 
    29670 > hide sel atoms
    29671 
    29672 > select #37/A:165
    29673 
    29674 11 atoms, 10 bonds, 1 residue, 1 model selected 
    29675 
    29676 > hide sel atoms
    29677 
    29678 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    29679 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    29680 
    29681 > select add #37
    29682 
    29683 4402 atoms, 4459 bonds, 276 residues, 1 model selected 
    29684 
    29685 > select subtract #37
    29686 
    29687 Nothing selected 
    29688 
    29689 > show #36 models
    29690 
    29691 > hide #36 models
    29692 
    29693 > show #40 models
    29694 
    29695 > hide #37 models
    29696 
    29697 > hide #40 models
    29698 
    29699 > show #37 models
    29700 
    29701 > hide #37 models
    29702 
    29703 > show #38 models
    29704 
    29705 > color #38 #a7a756ff
    29706 
    29707 > color #38 #a6a655ff
    29708 
    29709 > color #38 #b0b05aff
    29710 
    29711 Drag select of 15 atoms, 22 residues, 15 bonds 
    29712 Drag select of 19 residues, 2 atoms, 1 bonds 
    29713 
    29714 > ui mousemode right translate
    29715 
    29716 > ui mousemode right select
    29717 
    29718 > select #38/A:117
    29719 
    29720 16 atoms, 15 bonds, 1 residue, 1 model selected 
    29721 
    29722 > hide sel atoms
    29723 
    29724 > select #38/A:114
    29725 
    29726 12 atoms, 11 bonds, 1 residue, 1 model selected 
    29727 
    29728 > hide sel atoms
    29729 
    29730 > ui mousemode right rotate
    29731 
    29732 > ui mousemode right translate
    29733 
    29734 > ui mousemode right select
    29735 
    29736 > select #38/A:229
    29737 
    29738 15 atoms, 14 bonds, 1 residue, 1 model selected 
    29739 
    29740 > hide sel atoms
    29741 
    29742 > select #38/A:179
    29743 
    29744 12 atoms, 11 bonds, 1 residue, 1 model selected 
    29745 
    29746 > hide sel atoms
    29747 
    29748 > ui mousemode right translate
    29749 
    29750 > ui mousemode right select
    29751 
    29752 > select #38/A:176
    29753 
    29754 15 atoms, 14 bonds, 1 residue, 1 model selected 
    29755 Alignment identifier is 38/A 
    29756 
    29757 > show sel atoms
    29758 
    29759 > color sel gray
    29760 
    29761 > color sel red
    29762 
    29763 > select #50/A:247
    29764 
    29765 24 atoms, 25 bonds, 1 residue, 1 model selected 
    29766 
    29767 > select #38/A:240
    29768 
    29769 24 atoms, 25 bonds, 1 residue, 1 model selected 
    29770 
    29771 > ui mousemode right translate
    29772 
    29773 > show sel atoms
    29774 
    29775 > color sel gray
    29776 
    29777 > ui mousemode right select
    29778 
    29779 > select #50/A:180
    29780 
    29781 21 atoms, 21 bonds, 1 residue, 1 model selected 
    29782 
    29783 > select #38/A:173
    29784 
    29785 21 atoms, 21 bonds, 1 residue, 1 model selected 
    29786 
    29787 > show sel atoms
    29788 
    29789 > color sel gray
    29790 
    29791 > select #38/A:172
    29792 
    29793 11 atoms, 10 bonds, 1 residue, 1 model selected 
    29794 
    29795 > hide sel atoms
    29796 
    29797 > select #38/A:167
    29798 
    29799 24 atoms, 23 bonds, 1 residue, 1 model selected 
    29800 
    29801 > hide sel atoms
    29802 
    29803 > select #38/A:143
    29804 
    29805 19 atoms, 18 bonds, 1 residue, 1 model selected 
    29806 
    29807 > hide sel atoms
    29808 
    29809 > select #38/A:146
    29810 
    29811 11 atoms, 10 bonds, 1 residue, 1 model selected 
    29812 
    29813 > hide sel atoms
    29814 
    29815 > ui mousemode right translate
    29816 
    29817 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    29818 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    29819 
    29820 > select add #38
    29821 
    29822 4010 atoms, 4055 bonds, 257 residues, 1 model selected 
    29823 
    29824 > select subtract #38
    29825 
    29826 Nothing selected 
    29827 
    29828 > show #39 models
    29829 
    29830 > hide #38 models
    29831 
    29832 > color #39 #9e5552ff
    29833 
    29834 > color #39 #a35855ff
    29835 
    29836 > ui mousemode right select
    29837 
    29838 > select #39/A:186
    29839 
    29840 15 atoms, 14 bonds, 1 residue, 1 model selected 
    29841 
    29842 > show sel atoms
    29843 
    29844 > hide sel atoms
    29845 
    29846 > select #39/A:217
    29847 
    29848 14 atoms, 13 bonds, 1 residue, 1 model selected 
    29849 
    29850 > hide sel atoms
    29851 
    29852 > ui mousemode right translate
    29853 
    29854 > ui mousemode right select
    29855 
    29856 > select #39/A:299
    29857 
    29858 12 atoms, 11 bonds, 1 residue, 1 model selected 
    29859 
    29860 > hide sel atoms
    29861 
    29862 > select #39/A:249
    29863 
    29864 12 atoms, 11 bonds, 1 residue, 1 model selected 
    29865 
    29866 > hide sel atoms
    29867 
    29868 > ui mousemode right translate
    29869 
    29870 > ui mousemode right select
    29871 
    29872 > select #50/A:183
    29873 
    29874 15 atoms, 14 bonds, 1 residue, 1 model selected 
    29875 
    29876 > select #39/A:246
    29877 
    29878 10 atoms, 9 bonds, 1 residue, 1 model selected 
    29879 
    29880 > select #39/A:247
    29881 
    29882 17 atoms, 16 bonds, 1 residue, 1 model selected 
    29883 
    29884 > select #39/A:246
    29885 
    29886 10 atoms, 9 bonds, 1 residue, 1 model selected 
    29887 
    29888 > select #39/A:245
    29889 
    29890 10 atoms, 9 bonds, 1 residue, 1 model selected 
    29891 
    29892 > select #39/A:246
    29893 
    29894 10 atoms, 9 bonds, 1 residue, 1 model selected 
    29895 Alignment identifier is 39/A 
    29896 
    29897 > select #39/A:245
    29898 
    29899 10 atoms, 9 bonds, 1 residue, 1 model selected 
    29900 
    29901 > select #39/A:246
    29902 
    29903 10 atoms, 9 bonds, 1 residue, 1 model selected 
    29904 
    29905 > select #39/A:245
    29906 
    29907 10 atoms, 9 bonds, 1 residue, 1 model selected 
    29908 
    29909 > select #39/A:246
    29910 
    29911 10 atoms, 9 bonds, 1 residue, 1 model selected 
    29912 
    29913 > ui mousemode right translate
    29914 
    29915 > show sel atoms
    29916 
    29917 > color sel gray
    29918 
    29919 > ui mousemode right select
    29920 
    29921 > select #39/A:214
    29922 
    29923 12 atoms, 11 bonds, 1 residue, 1 model selected 
    29924 
    29925 > hide sel atoms
    29926 
    29927 > select #39/A:238
    29928 
    29929 24 atoms, 23 bonds, 1 residue, 1 model selected 
    29930 
    29931 > hide sel atoms
    29932 
    29933 > select #39/A:243
    29934 
    29935 22 atoms, 21 bonds, 1 residue, 1 model selected 
    29936 
    29937 > hide sel atoms
    29938 
    29939 > select #39/A:244
    29940 
    29941 14 atoms, 14 bonds, 1 residue, 1 model selected 
    29942 
    29943 > show sel atoms
    29944 
    29945 > color sel magenta
    29946 
    29947 > ui mousemode right translate
    29948 
    29949 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    29950 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    29951 
    29952 > select add #39
    29953 
    29954 4950 atoms, 4999 bonds, 312 residues, 1 model selected 
    29955 
    29956 > select subtract #39
    29957 
    29958 Nothing selected 
    29959 
    29960 > hide #39 models
    29961 
    29962 > show #41 models
    29963 
    29964 > color #41 #2c731cff
    29965 
    29966 > color #41 #399123ff
    29967 
    29968 > ui mousemode right select
    29969 
    29970 > select #41/A:158
    29971 
    29972 14 atoms, 13 bonds, 1 residue, 1 model selected 
    29973 
    29974 > ui mousemode right select
    29975 
    29976 > hide sel atoms
    29977 
    29978 > select #41/A:156
    29979 
    29980 22 atoms, 21 bonds, 1 residue, 1 model selected 
    29981 
    29982 > hide sel atoms
    29983 
    29984 > ui mousemode right translate
    29985 
    29986 > ui mousemode right select
    29987 
    29988 > select #41/A:269
    29989 
    29990 15 atoms, 14 bonds, 1 residue, 1 model selected 
    29991 
    29992 > hide sel atoms
    29993 
    29994 > ui mousemode right translate
    29995 
    29996 > ui mousemode right select
    29997 
    29998 > select #41/A:219
    29999 
    30000 15 atoms, 14 bonds, 1 residue, 1 model selected 
    30001 
    30002 > hide sel atoms
    30003 
    30004 > select #41/A:217
    30005 
    30006 21 atoms, 21 bonds, 1 residue, 1 model selected 
    30007 Alignment identifier is 41/A 
    30008 
    30009 > select #41/A:221
    30010 
    30011 10 atoms, 9 bonds, 1 residue, 1 model selected 
    30012 
    30013 > select #41/A:221
    30014 
    30015 10 atoms, 9 bonds, 1 residue, 1 model selected 
    30016 
    30017 > ui mousemode right translate
    30018 
    30019 > ui mousemode right select
    30020 
    30021 > select #41/A:217
    30022 
    30023 21 atoms, 21 bonds, 1 residue, 1 model selected 
    30024 
    30025 > select #41/A:216
    30026 
    30027 22 atoms, 21 bonds, 1 residue, 1 model selected 
    30028 
    30029 > select #41/A:217
    30030 
    30031 21 atoms, 21 bonds, 1 residue, 1 model selected 
    30032 
    30033 > select #41/A:218
    30034 
    30035 22 atoms, 21 bonds, 1 residue, 1 model selected 
    30036 Drag select of 2 residues 
    30037 
    30038 > ui mousemode right rotate
    30039 
    30040 > ui mousemode right translate
    30041 
    30042 > ui mousemode right select
    30043 
    30044 > select #41/A:217
    30045 
    30046 21 atoms, 21 bonds, 1 residue, 1 model selected 
    30047 
    30048 > select #41/A:217
    30049 
    30050 21 atoms, 21 bonds, 1 residue, 1 model selected 
    30051 
    30052 > ui mousemode right translate
    30053 
    30054 > show sel atoms
    30055 
    30056 > color sel gray
    30057 
    30058 > ui mousemode right rotate
    30059 
    30060 > ui mousemode right select
    30061 
    30062 > select #41/A:161
    30063 
    30064 7 atoms, 6 bonds, 1 residue, 1 model selected 
    30065 
    30066 > color #41 #45b02bff
    30067 
    30068 > color #41 #54d634ff
    30069 
    30070 > select #41/A:217
    30071 
    30072 21 atoms, 21 bonds, 1 residue, 1 model selected 
    30073 
    30074 > color sel gray
    30075 
    30076 > select #50/A:180
    30077 
    30078 21 atoms, 21 bonds, 1 residue, 1 model selected 
    30079 
    30080 > select #41/A:214
    30081 
    30082 21 atoms, 21 bonds, 1 residue, 1 model selected 
    30083 
    30084 > show sel atoms
    30085 
    30086 > color sel gray
    30087 
    30088 > ui mousemode right translate
    30089 
    30090 > ui mousemode right select
    30091 
    30092 > select #50/A:247
    30093 
    30094 24 atoms, 25 bonds, 1 residue, 1 model selected 
    30095 
    30096 > select #41/A:280
    30097 
    30098 20 atoms, 20 bonds, 1 residue, 1 model selected 
    30099 
    30100 > select #41/A:281
    30101 
    30102 14 atoms, 13 bonds, 1 residue, 1 model selected 
    30103 
    30104 > ui mousemode right translate
    30105 
    30106 > ui mousemode right select
    30107 
    30108 > select #41/A:280
    30109 
    30110 20 atoms, 20 bonds, 1 residue, 1 model selected 
    30111 
    30112 > hide sel atoms
    30113 
    30114 > show sel atoms
    30115 
    30116 > color sel gray
    30117 
    30118 > select #41/A:217
    30119 
    30120 21 atoms, 21 bonds, 1 residue, 1 model selected 
    30121 
    30122 > select #41/A:214
    30123 
    30124 21 atoms, 21 bonds, 1 residue, 1 model selected 
    30125 
    30126 > ui mousemode right translate
    30127 
    30128 > ui mousemode right select
    30129 
    30130 > select #41/A:187
    30131 
    30132 15 atoms, 14 bonds, 1 residue, 1 model selected 
    30133 
    30134 > ui mousemode right translate
    30135 
    30136 > hide sel atoms
    30137 
    30138 > ui mousemode right select
    30139 
    30140 > select #41/A:184
    30141 
    30142 19 atoms, 18 bonds, 1 residue, 1 model selected 
    30143 
    30144 > hide sel atoms
    30145 
    30146 > select #41/A:213
    30147 
    30148 10 atoms, 9 bonds, 1 residue, 1 model selected 
    30149 
    30150 > hide sel atoms
    30151 
    30152 > select #41/A:208
    30153 
    30154 17 atoms, 17 bonds, 1 residue, 1 model selected 
    30155 
    30156 > hide sel atoms
    30157 
    30158 > ui mousemode right translate
    30159 
    30160 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    30161 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    30162 
    30163 > hide #41 models
    30164 
    30165 > select add #41
    30166 
    30167 4748 atoms, 4801 bonds, 296 residues, 1 model selected 
    30168 
    30169 > select subtract #41
    30170 
    30171 Nothing selected 
    30172 
    30173 > show #42 models
    30174 
    30175 > color #42 #a1cfb9ff
    30176 
    30177 [Repeated 1 time(s)]
    30178 
    30179 > color #42 #9bc7b2ff
    30180 
    30181 > ui mousemode right rotate
    30182 
    30183 > ui mousemode right select
    30184 
    30185 > select #42/A:128
    30186 
    30187 24 atoms, 23 bonds, 1 residue, 1 model selected 
    30188 
    30189 > hide sel atoms
    30190 
    30191 > select #42/A:125@CA
    30192 
    30193 1 atom, 1 residue, 1 model selected 
    30194 
    30195 > hide sel atoms
    30196 
    30197 > select #42/A:125
    30198 
    30199 15 atoms, 14 bonds, 1 residue, 1 model selected 
    30200 
    30201 > hide sel cartoons
    30202 
    30203 > show sel cartoons
    30204 
    30205 > hide sel atoms
    30206 
    30207 > ui mousemode right translate
    30208 
    30209 > ui mousemode right select
    30210 
    30211 > select #42/A:240
    30212 
    30213 15 atoms, 14 bonds, 1 residue, 1 model selected 
    30214 
    30215 > ui mousemode right translate
    30216 
    30217 > hide sel atoms
    30218 
    30219 > ui mousemode right select
    30220 
    30221 > select #42/A:190
    30222 
    30223 12 atoms, 11 bonds, 1 residue, 1 model selected 
    30224 
    30225 > hide sel atoms
    30226 
    30227 > select #42/A:187
    30228 
    30229 22 atoms, 21 bonds, 1 residue, 1 model selected 
    30230 
    30231 > select #50/A:183
    30232 
    30233 15 atoms, 14 bonds, 1 residue, 1 model selected 
    30234 
    30235 > select #42/A:187
    30236 
    30237 22 atoms, 21 bonds, 1 residue, 1 model selected 
    30238 Alignment identifier is 42/A 
    30239 
    30240 > show sel atoms
    30241 
    30242 > color sel blue
    30243 
    30244 > ui mousemode right translate
    30245 
    30246 > ui mousemode right select
    30247 
    30248 > select #42/A:183
    30249 
    30250 10 atoms, 9 bonds, 1 residue, 1 model selected 
    30251 
    30252 > hide sel atoms
    30253 
    30254 > select #42/A:251
    30255 
    30256 24 atoms, 25 bonds, 1 residue, 1 model selected 
    30257 
    30258 > show sel atoms
    30259 
    30260 > color sel gray
    30261 
    30262 > select #42/A:184
    30263 
    30264 21 atoms, 21 bonds, 1 residue, 1 model selected 
    30265 
    30266 > show sel atoms
    30267 
    30268 > color sel gray
    30269 
    30270 > select #42/A:178
    30271 
    30272 24 atoms, 23 bonds, 1 residue, 1 model selected 
    30273 
    30274 > hide sel atoms
    30275 
    30276 > select #42/A:154
    30277 
    30278 14 atoms, 13 bonds, 1 residue, 1 model selected 
    30279 
    30280 > hide sel atoms
    30281 
    30282 > ui mousemode right translate
    30283 
    30284 > ui mousemode right select
    30285 
    30286 > select #42/A:157
    30287 
    30288 11 atoms, 10 bonds, 1 residue, 1 model selected 
    30289 
    30290 > hide sel atoms
    30291 
    30292 > ui mousemode right translate
    30293 
    30294 > ui mousemode right select
    30295 
    30296 > select #42/A:187
    30297 
    30298 22 atoms, 21 bonds, 1 residue, 1 model selected 
    30299 
    30300 > ui mousemode right translate
    30301 
    30302 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    30303 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    30304 
    30305 > show #34 models
    30306 
    30307 > hide #50 models
    30308 
    30309 > ui mousemode right select
    30310 
    30311 > select #34/A:222
    30312 
    30313 19 atoms, 18 bonds, 1 residue, 1 model selected 
    30314 
    30315 > ui mousemode right translate
    30316 
    30317 Alignment identifier is 34/A 
    30318 
    30319 > select add #34
    30320 
    30321 4798 atoms, 4847 bonds, 303 residues, 1 model selected 
    30322 
    30323 > select subtract #34
    30324 
    30325 Nothing selected 
    30326 
    30327 > hide #34 models
    30328 
    30329 > show #50 models
    30330 
    30331 > show #34 models
    30332 
    30333 > ui mousemode right select
    30334 
    30335 > select #34/A:222
    30336 
    30337 19 atoms, 18 bonds, 1 residue, 1 model selected 
    30338 
    30339 > select add #34
    30340 
    30341 4798 atoms, 4847 bonds, 303 residues, 1 model selected 
    30342 
    30343 > select subtract #34
    30344 
    30345 Nothing selected 
    30346 
    30347 > hide #34 models
    30348 
    30349 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    30350 > UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
    30351 
    30352 ——— End of log from Wed Aug 9 11:27:54 2023 ———
    30353 
    30354 > view name session-start
    30355 
    30356 opened ChimeraX session 
    30357 
    30358 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    30359 > UASLP/Lab Virología/AlphaFold3/fold_sec1_model_0.cif"
    30360 
    30361 Chain information for fold_sec1_model_0.cif #53 
    30362 --- 
    30363 Chain | Description 
    30364 A | . 
    30365  
    30366 Computing secondary structure 
    30367 
    30368 > hide #50 models
    30369 
    30370 > hide #42 models
    30371 
    30372 > show #1 models
    30373 
    30374 > show #2 models
    30375 
    30376 > hide #1 models
    30377 
    30378 > hide #2 models
    30379 
    30380 > show #2 models
    30381 
    30382 > ui tool show Matchmaker
    30383 
    30384 > matchmaker #53 to #2
    30385 
    30386 Computing secondary structure 
    30387 Parameters 
    30388 --- 
    30389 Chain pairing | bb 
    30390 Alignment algorithm | Needleman-Wunsch 
    30391 Similarity matrix | BLOSUM-62 
    30392 SS fraction | 0.3 
    30393 Gap open (HH/SS/other) | 18/18/6 
    30394 Gap extend | 1 
    30395 SS matrix |  |  | H | S | O 
    30396 ---|---|---|--- 
    30397 H | 6 | -9 | -6 
    30398 S |  | 6 | -6 
    30399 O |  |  | 4 
    30400 Iteration cutoff | 2 
    30401  
    30402 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec1_model_0.cif, chain A (#53),
    30403 sequence alignment score = 527.8 
    30404 RMSD between 147 pruned atom pairs is 0.715 angstroms; (across all 148 pairs:
    30405 0.768) 
    30406  
    30407 
    30408 > select ~sel & ##selected
    30409 
    30410 Nothing selected 
    30411 
    30412 > select ~sel & ##selected
    30413 
    30414 Nothing selected 
    30415 
    30416 > select ~sel & ##selected
    30417 
    30418 Nothing selected 
    30419 
    30420 > show target m
    30421 
    30422 > view clip false
    30423 
    30424 > log metadata #1
    30425 
    30426 The model has no metadata
    30427 
    30428 > log chains #1
    30429 
    30430 Chain information for 7vga.pdb #1 
    30431 --- 
    30432 Chain | Description | UniProt 
    30433 A D G J | No description available | POLS_GETV 1-438 
    30434 B E H K | No description available | POLS_GETV 1-422 
    30435 C F I L | No description available | POLS_GETV 1-268 
    30436  
    30437 
    30438 > log metadata #2
    30439 
    30440 The model has no metadata
    30441 
    30442 > log chains #2
    30443 
    30444 Chain information for 3j2w.pdb #2 
    30445 --- 
    30446 Chain | Description | UniProt 
    30447 A B C D | No description available | Q1H8W5_CHIKV 1-393 1001-1393 2001-2393 3001-3393 
    30448 E F G H | No description available | POLS_CHIK3 394-439 1394-1439 2394-2439 3394-3439 
    30449 I | capsid protein | POLS_CHIK3 119-267 
    30450 J K L | No description available | POLS_CHIK3 1119-1267 2119-2267 3119-3267 
    30451 M N O | No description available | Q1H8W5_CHIKV 507-842 1507-1842 2507-2842 
    30452 P | No description available | Q1H8W5_CHIKV 3507-3842 
    30453 Q R S T | No description available | POLS_CHIK3 843-923 1843-1923 2843-2923 3843-3923 
    30454  
    30455 
    30456 > log metadata #3
    30457 
    30458 The model has no metadata
    30459 
    30460 > log chains #3
    30461 
    30462 Chain information for 1kxf.pdb #3 
    30463 --- 
    30464 Chain | Description | UniProt 
    30465 A | No description available | POLS_SINDV 106-264 
    30466  
    30467 
    30468 > log metadata #4
    30469 
    30470 The model has no metadata
    30471 
    30472 > log chains #4
    30473 
    30474 Chain information for 7sfu.pdb #4 
    30475 --- 
    30476 Chain | Description | UniProt 
    30477 A D G J | No description available | POLS_EEVV8 1-442 
    30478 B E H K | No description available | POLS_EEVV8 1-423 
    30479 C F I L | No description available | POLS_EEVV8 114-275 
    30480  
    30481 
    30482 > log metadata #5
    30483 
    30484 No models had metadata
    30485 
    30486 > log chains #5
    30487 
    30488 Chain information for 6xo4.pdb #5 
    30489 --- 
    30490 Chain | Description | UniProt 
    30491 A D G J | No description available | Q88678_EEEV 1-441 
    30492 B E H K | No description available | Q88678_EEEV 1-420 
    30493 C F I L | No description available | Q88678_EEEV 1-261 
    30494  
    30495 
    30496 > log metadata #6
    30497 
    30498 The model has no metadata
    30499 
    30500 > log chains #6
    30501 
    30502 Chain information for 4agk.pdb #6 
    30503 --- 
    30504 Chain | Description | UniProt 
    30505 A | No description available | POLS_AURAV 110-267 
    30506  
    30507 
    30508 > log metadata #7
    30509 
    30510 No models had metadata
    30511 
    30512 > log chains #7
    30513 
    30514 Chain information for 1vcp.pdb #7 
    30515 --- 
    30516 Chain | Description | UniProt 
    30517 A B C | No description available | POLS_SFV 119-267 
    30518  
    30519 
    30520 > log metadata #8
    30521 
    30522 No models had metadata
    30523 
    30524 > log chains #8
    30525 
    30526 Chain information for 2yew.pdb #8 
    30527 --- 
    30528 Chain | Description | UniProt 
    30529 A D G J | No description available | POLS_BFV 1-253 
    30530 B E H K | No description available | POLS_BFV 1-439 
    30531 C F I L | No description available | POLS_BFV 1-421 
    30532  
    30533 
    30534 > log metadata #9
    30535 
    30536 The model has no metadata
    30537 
    30538 > log chains #9
    30539 
    30540 Chain information for 7ko8.pdb #9 
    30541 --- 
    30542 Chain | Description 
    30543 A D G J | No description available 
    30544 B E H L | No description available 
    30545 C F I M | No description available 
    30546  
    30547 
    30548 > log metadata #10
    30549 
    30550 The model has no metadata
    30551 
    30552 > log chains #10
    30553 
    30554 Chain information for AlphFold Colaboratory Ross River.pdb #10 
    30555 --- 
    30556 Chain | Description 
    30557 A | No description available 
    30558  
    30559 
    30560 > log metadata #11
    30561 
    30562 The model has no metadata
    30563 
    30564 > log chains #11
    30565 
    30566 Chain information for AlphaFold Colaboratory Middelburg virus.pdb #11 
    30567 --- 
    30568 Chain | Description 
    30569 A | No description available 
    30570  
    30571 
    30572 > log metadata #12
    30573 
    30574 The model has no metadata
    30575 
    30576 > log chains #12
    30577 
    30578 Chain information for AlphaFold Colaboratory Everglades virus.pdb #12 
    30579 --- 
    30580 Chain | Description 
    30581 A | No description available 
    30582  
    30583 
    30584 > log metadata #13
    30585 
    30586 The model has no metadata
    30587 
    30588 > log chains #13
    30589 
    30590 Chain information for Alpha Fold Collaboratory Salmon Pancrease Disease.pdb
    30591 #13 
    30592 --- 
    30593 Chain | Description 
    30594 A | No description available 
    30595  
    30596 
    30597 > log metadata #14
    30598 
    30599 The model has no metadata
    30600 
    30601 > log chains #14
    30602 
    30603 Chain information for Alpha Fold Collaboratory Fort Morgan virus.pdb #14 
    30604 --- 
    30605 Chain | Description 
    30606 A | No description available 
    30607  
    30608 
    30609 > log metadata #15
    30610 
    30611 The model has no metadata
    30612 
    30613 > log chains #15
    30614 
    30615 Chain information for Ndumu virus Alphafold.pdb #15 
    30616 --- 
    30617 Chain | Description 
    30618 A | No description available 
    30619  
    30620 
    30621 > log metadata #16
    30622 
    30623 The model has no metadata
    30624 
    30625 > log chains #16
    30626 
    30627 Chain information for Everglades virus Alphafold.pdb #16 
    30628 --- 
    30629 Chain | Description 
    30630 A | No description available 
    30631  
    30632 
    30633 > log metadata #17
    30634 
    30635 The model has no metadata
    30636 
    30637 > log chains #17
    30638 
    30639 Chain information for Bebaru virus Alphafold.pdb #17 
    30640 --- 
    30641 Chain | Description 
    30642 A | No description available 
    30643  
    30644 
    30645 > log metadata #18
    30646 
    30647 The model has no metadata
    30648 
    30649 > log chains #18
    30650 
    30651 Chain information for Caaingua virus AlphaFold.pdb #18 
    30652 --- 
    30653 Chain | Description 
    30654 A | No description available 
    30655  
    30656 
    30657 > log metadata #19
    30658 
    30659 The model has no metadata
    30660 
    30661 > log chains #19
    30662 
    30663 Chain information for Cabassou virus Alphafold.pdb #19 
    30664 --- 
    30665 Chain | Description 
    30666 A | No description available 
    30667  
    30668 
    30669 > log metadata #20
    30670 
    30671 The model has no metadata
    30672 
    30673 > log chains #20
    30674 
    30675 Chain information for Eilat virus Alphafold.pdb #20 
    30676 --- 
    30677 Chain | Description 
    30678 A | No description available 
    30679  
    30680 
    30681 > log metadata #21
    30682 
    30683 The model has no metadata
    30684 
    30685 > log chains #21
    30686 
    30687 Chain information for Highlands J. virus Alphafold.pdb #21 
    30688 --- 
    30689 Chain | Description 
    30690 A | No description available 
    30691  
    30692 
    30693 > log metadata #22
    30694 
    30695 The model has no metadata
    30696 
    30697 > log chains #22
    30698 
    30699 Chain information for Madariaga virus Alpha Fold.pdb #22 
    30700 --- 
    30701 Chain | Description 
    30702 A | No description available 
    30703  
    30704 
    30705 > log metadata #23
    30706 
    30707 The model has no metadata
    30708 
    30709 > log chains #23
    30710 
    30711 Chain information for Mosso das Pedras virus AlphaFold.pdb #23 
    30712 --- 
    30713 Chain | Description 
    30714 A | No description available 
    30715  
    30716 
    30717 > log metadata #24
    30718 
    30719 The model has no metadata
    30720 
    30721 > log chains #24
    30722 
    30723 Chain information for Southern Elephant Seal virus AlphaFold.pdb #24 
    30724 --- 
    30725 Chain | Description 
    30726 A | No description available 
    30727  
    30728 
    30729 > log metadata #25
    30730 
    30731 The model has no metadata
    30732 
    30733 > log chains #25
    30734 
    30735 Chain information for Mucambo virus AlphaFold.pdb #25 
    30736 --- 
    30737 Chain | Description 
    30738 A | No description available 
    30739  
    30740 
    30741 > log metadata #26
    30742 
    30743 The model has no metadata
    30744 
    30745 > log chains #26
    30746 
    30747 Chain information for Onyong-nyong virus AlphaFold.pdb #26 
    30748 --- 
    30749 Chain | Description 
    30750 A | No description available 
    30751  
    30752 
    30753 > log metadata #27
    30754 
    30755 The model has no metadata
    30756 
    30757 > log chains #27
    30758 
    30759 Chain information for Pixuna virus AlphaFold.pdb #27 
    30760 --- 
    30761 Chain | Description 
    30762 A | No description available 
    30763  
    30764 
    30765 > log metadata #28
    30766 
    30767 The model has no metadata
    30768 
    30769 > log chains #28
    30770 
    30771 Chain information for RioNegro virus AlphaFold.pdb #28 
    30772 --- 
    30773 Chain | Description 
    30774 A | No description available 
    30775  
    30776 
    30777 > log metadata #29
    30778 
    30779 The model has no metadata
    30780 
    30781 > log chains #29
    30782 
    30783 Chain information for Tonate virus AlphaFold.pdb #29 
    30784 --- 
    30785 Chain | Description 
    30786 A | No description available 
    30787  
    30788 
    30789 > log metadata #30
    30790 
    30791 The model has no metadata
    30792 
    30793 > log chains #30
    30794 
    30795 Chain information for Trocara virus AlphaFold.pdb #30 
    30796 --- 
    30797 Chain | Description 
    30798 A | No description available 
    30799  
    30800 
    30801 > log metadata #31
    30802 
    30803 The model has no metadata
    30804 
    30805 > log chains #31
    30806 
    30807 Chain information for Una virus AlphaFold.pdb #31 
    30808 --- 
    30809 Chain | Description 
    30810 A | No description available 
    30811  
    30812 
    30813 > log metadata #32
    30814 
    30815 The model has no metadata
    30816 
    30817 > log chains #32
    30818 
    30819 Chain information for Whataroa virus AlphaFold.pdb #32 
    30820 --- 
    30821 Chain | Description 
    30822 A | No description available 
    30823  
    30824 
    30825 > log metadata #33
    30826 
    30827 The model has no metadata
    30828 
    30829 > log chains #33
    30830 
    30831 Chain information for AguaSalud alphavirus AlphaFold.pdb #33 
    30832 --- 
    30833 Chain | Description 
    30834 A | No description available 
    30835  
    30836 
    30837 > log metadata #34
    30838 
    30839 The model has no metadata
    30840 
    30841 > log chains #34
    30842 
    30843 Chain information for Comber alphavirus AlphaFold.pdb #34 
    30844 --- 
    30845 Chain | Description 
    30846 A | No description available 
    30847  
    30848 
    30849 > log metadata #35
    30850 
    30851 The model has no metadata
    30852 
    30853 > log chains #35
    30854 
    30855 Chain information for Harbor porpoise alphavirus AlphaFold.pdb #35 
    30856 --- 
    30857 Chain | Description 
    30858 A | No description available 
    30859  
    30860 
    30861 > log metadata #36
    30862 
    30863 The model has no metadata
    30864 
    30865 > log chains #36
    30866 
    30867 Chain information for Mwinilunga alphavirus AlphaFold.pdb #36 
    30868 --- 
    30869 Chain | Description 
    30870 A | No description available 
    30871  
    30872 
    30873 > log metadata #37
    30874 
    30875 The model has no metadata
    30876 
    30877 > log chains #37
    30878 
    30879 Chain information for selected_prediction Pirahy virus.pdb #37 
    30880 --- 
    30881 Chain | Description 
    30882 A | No description available 
    30883  
    30884 
    30885 > log metadata #38
    30886 
    30887 The model has no metadata
    30888 
    30889 > log chains #38
    30890 
    30891 Chain information for selected_prediction tai forest alphavirus .pdb #38 
    30892 --- 
    30893 Chain | Description 
    30894 A | No description available 
    30895  
    30896 
    30897 > log metadata #39
    30898 
    30899 The model has no metadata
    30900 
    30901 > log chains #39
    30902 
    30903 Chain information for selected_prediction Weglinng hagfish alphavirus
    30904 consensus.pdb #39 
    30905 --- 
    30906 Chain | Description 
    30907 A | No description available 
    30908  
    30909 
    30910 > log metadata #40
    30911 
    30912 The model has no metadata
    30913 
    30914 > log chains #40
    30915 
    30916 Chain information for Norwegian salmonid alphavirus AlphaFold.pdb #40 
    30917 --- 
    30918 Chain | Description 
    30919 A | No description available 
    30920  
    30921 
    30922 > log metadata #41
    30923 
    30924 The model has no metadata
    30925 
    30926 > log chains #41
    30927 
    30928 Chain information for selected_prediction Wenling fish alphavirus.pdb #41 
    30929 --- 
    30930 Chain | Description 
    30931 A | No description available 
    30932  
    30933 
    30934 > log metadata #42
    30935 
    30936 The model has no metadata
    30937 
    30938 > log chains #42
    30939 
    30940 Chain information for Yada yada virus AlphaFold.pdb #42 
    30941 --- 
    30942 Chain | Description 
    30943 A | No description available 
    30944  
    30945 
    30946 > log metadata #43
    30947 
    30948 The model has no metadata
    30949 
    30950 > log chains #43
    30951 
    30952 Chain information for Aura virus AlphaFold.pdb #43 
    30953 --- 
    30954 Chain | Description 
    30955 A | No description available 
    30956  
    30957 
    30958 > log metadata #44
    30959 
    30960 The model has no metadata
    30961 
    30962 > log chains #44
    30963 
    30964 Chain information for BFV AlphaFold.pdb #44 
    30965 --- 
    30966 Chain | Description 
    30967 A | No description available 
    30968  
    30969 
    30970 > log metadata #45
    30971 
    30972 The model has no metadata
    30973 
    30974 > log chains #45
    30975 
    30976 Chain information for WEEV AlphaFold.pdb #45 
    30977 --- 
    30978 Chain | Description 
    30979 A | No description available 
    30980  
    30981 
    30982 > log metadata #46
    30983 
    30984 The model has no metadata
    30985 
    30986 > log chains #46
    30987 
    30988 Chain information for EEEV AlphaFold.pdb #46 
    30989 --- 
    30990 Chain | Description 
    30991 A | No description available 
    30992  
    30993 
    30994 > log metadata #47
    30995 
    30996 The model has no metadata
    30997 
    30998 > log chains #47
    30999 
    31000 Chain information for Getah virus AlphaFold.pdb #47 
    31001 --- 
    31002 Chain | Description 
    31003 A | No description available 
    31004  
    31005 
    31006 > log metadata #48
    31007 
    31008 The model has no metadata
    31009 
    31010 > log chains #48
    31011 
    31012 Chain information for Mayaro virus AlphaFold.pdb #48 
    31013 --- 
    31014 Chain | Description 
    31015 A | No description available 
    31016  
    31017 
    31018 > log metadata #49
    31019 
    31020 The model has no metadata
    31021 
    31022 > log chains #49
    31023 
    31024 Chain information for SFV AlphaFold.pdb #49 
    31025 --- 
    31026 Chain | Description 
    31027 A | No description available 
    31028  
    31029 
    31030 > log metadata #50
    31031 
    31032 The model has no metadata
    31033 
    31034 > log chains #50
    31035 
    31036 Chain information for Sindbis virus AlphaFold.pdb #50 
    31037 --- 
    31038 Chain | Description 
    31039 A | No description available 
    31040  
    31041 
    31042 > log metadata #51
    31043 
    31044 The model has no metadata
    31045 
    31046 > log chains #51
    31047 
    31048 Chain information for Fort Morgan virus AlphaFold.pdb #51 
    31049 --- 
    31050 Chain | Description 
    31051 A | No description available 
    31052  
    31053 
    31054 > log metadata #52
    31055 
    31056 The model has no metadata
    31057 
    31058 > log chains #52
    31059 
    31060 Chain information for VEEV AlphaFold.pdb #52 
    31061 --- 
    31062 Chain | Description 
    31063 A | No description available 
    31064  
    31065 
    31066 > log metadata #53
    31067 
    31068 The model has no metadata
    31069 
    31070 > log chains #53
    31071 
    31072 Chain information for fold_sec1_model_0.cif #53 
    31073 --- 
    31074 Chain | Description 
    31075 A | . 
    31076  
    31077 
    31078 > hide target m
    31079 
    31080 > show #2 models
    31081 
    31082 > show #53 models
    31083 
    31084 > ui tool show Distances
    31085 
    31086 > ui tool show "Similar Structures"
    31087 
    31088 Must choose a chain in the similar structures panel before running search 
    31089 You must press the similar structures Search button before you can open
    31090 matching structures. 
    31091 Must run search first 
    31092 
    31093 > similarstructures blast #2/A
    31094 
    31095 Webservices job id: BNOXPZ45QADI1K8E 
    31096 Must run search first 
    31097 Found 441 similar structures to 3j2w.pdb #2/A in pdb database using blast,
    31098 name bl1 
    31099 
    31100 > save "C:/Users/Carolina/Documents/Prueba Chimera.cxs"
    31101 
    31102 [Repeated 1 time(s)]
    31103 
    31104 ——— End of log from Tue Jan 21 18:31:41 2025 ———
    31105 
    31106 > view name session-start
    31107 
    31108 opened ChimeraX session 
    31109 
    31110 > ui tool show "Show Sequence Viewer"
    31111 
    31112 > sequence chain #53/A
    31113 
    31114 Alignment identifier is 53/A 
    31115 
    31116 > ui tool show "Show Sequence Viewer"
    31117 
    31118 > sequence chain #2/I
    31119 
    31120 Alignment identifier is 2/I 
    31121 
    31122 > ui mousemode right select
    31123 
    31124 > select #2/I:187
    31125 
    31126 9 atoms, 8 bonds, 1 residue, 1 model selected 
    31127 
    31128 > select clear
    31129 
    31130 [Repeated 1 time(s)]
    31131 
    31132 > ui mousemode right select
    31133 
    31134 > select #2/I:187
    31135 
    31136 9 atoms, 8 bonds, 1 residue, 1 model selected 
    31137 
    31138 > ui mousemode right rotate
    31139 
    31140 > ui mousemode right select
    31141 
    31142 > select #2/I:251
    31143 
    31144 14 atoms, 15 bonds, 1 residue, 1 model selected 
    31145 
    31146 > select clear
    31147 
    31148 > select #2/I:187
    31149 
    31150 9 atoms, 8 bonds, 1 residue, 1 model selected 
    31151 
    31152 > select #2/I:251
    31153 
    31154 14 atoms, 15 bonds, 1 residue, 1 model selected 
    31155 
    31156 > ui mousemode right select
    31157 
    31158 [Repeated 1 time(s)]
    31159 
    31160 > select #2/I:240
    31161 
    31162 9 atoms, 8 bonds, 1 residue, 1 model selected 
    31163 
    31164 > show sel cartoons
    31165 
    31166 > show sel atoms
    31167 
    31168 > color sel red
    31169 
    31170 > select #2/I:189
    31171 
    31172 7 atoms, 7 bonds, 1 residue, 1 model selected 
    31173 
    31174 > select clear
    31175 
    31176 > select #2/I:190
    31177 
    31178 9 atoms, 8 bonds, 1 residue, 1 model selected 
    31179 
    31180 > show sel cartoons
    31181 
    31182 > show sel atoms
    31183 
    31184 > color sel red
    31185 
    31186 > select #2/I:187
    31187 
    31188 9 atoms, 8 bonds, 1 residue, 1 model selected 
    31189 
    31190 > hide sel atoms
    31191 
    31192 > select #2/I:190@CG
    31193 
    31194 1 atom, 1 residue, 1 model selected 
    31195 
    31196 > select #2/I:251
    31197 
    31198 14 atoms, 15 bonds, 1 residue, 1 model selected 
    31199 
    31200 > hide sel atoms
    31201 
    31202 > select #2/I:184
    31203 
    31204 11 atoms, 11 bonds, 1 residue, 1 model selected 
    31205 
    31206 > hide sel atoms
    31207 
    31208 > select #2/I:183
    31209 
    31210 9 atoms, 8 bonds, 1 residue, 1 model selected 
    31211 
    31212 > hide sel atoms
    31213 
    31214 > show sel atoms
    31215 
    31216 > color sel blue
    31217 
    31218 > ui mousemode right select
    31219 
    31220 > select #2/I:178
    31221 
    31222 9 atoms, 8 bonds, 1 residue, 1 model selected 
    31223 
    31224 > show sel atoms
    31225 
    31226 > color sel blue
    31227 
    31228 > select #2/I:157
    31229 
    31230 9 atoms, 8 bonds, 1 residue, 1 model selected 
    31231 
    31232 > show sel atoms
    31233 
    31234 > color sel blue
    31235 
    31236 > select #2/I:154
    31237 
    31238 8 atoms, 7 bonds, 1 residue, 1 model selected 
    31239 
    31240 > show sel atoms
    31241 
    31242 > color sel red
    31243 
    31244 > select #2/I:126
    31245 
    31246 9 atoms, 8 bonds, 1 residue, 1 model selected 
    31247 
    31248 > show sel atoms
    31249 
    31250 > color sel red
    31251 
    31252 > select #2/I:128
    31253 
    31254 9 atoms, 8 bonds, 1 residue, 1 model selected 
    31255 
    31256 > show sel atoms
    31257 
    31258 > color sel blue
    31259 
    31260 > save C:/Users/Carolina/Documents/CHIKVaaint.cxs
    31261 
    31262 > hide #53 models
    31263 
    31264 > select #2/I:187
    31265 
    31266 9 atoms, 8 bonds, 1 residue, 1 model selected 
    31267 
    31268 > hide sel atoms
    31269 
    31270 > color sel cyan
    31271 
    31272 > select #2/I:251
    31273 
    31274 14 atoms, 15 bonds, 1 residue, 1 model selected 
    31275 
    31276 > color sel cyan
    31277 
    31278 > select #2/I:184
    31279 
    31280 11 atoms, 11 bonds, 1 residue, 1 model selected 
    31281 
    31282 > color sel cyan
    31283 
    31284 > save C:/Users/Carolina/Documents/CHIKVaaint.cxs
    31285 
    31286 ——— End of log from Wed Jan 29 09:08:51 2025 ———
    31287 
    31288 > view name session-start
    31289 
    31290 opened ChimeraX session 
    31291 
    31292 > show #53 models
    31293 
    31294 > ui tool show Matchmaker
    31295 
    31296 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    31297 > UASLP/Lab Virología/AlphaFold3/32/fold_sec1_summary_confidences_1.json"
    31298 
    31299 Opening an AlphaFold PAE file requires first opening the predicted atomic
    31300 model. Did not find an open atomic model from the same directory. If the
    31301 atomic model is already open choose it using menu 
    31302  
    31303 Tools / Structure Prediction / AlphaFold Error Plot 
    31304  
    31305 or use the open command structure option, for example 
    31306  
    31307 open C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    31308 UASLP/Lab Virología/AlphaFold3/32/fold_sec1_summary_confidences_1.json
    31309 structure #1 
    31310  
    31311 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    31312 need to specify the specific JSON format such as 
    31313  
    31314 open mole_channels.json format mole 
    31315 
    31316 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    31317 > UASLP/Lab Virología/AlphaFold3/32/fold_sec1_model_1.cif"
    31318 
    31319 Chain information for fold_sec1_model_1.cif #54 
    31320 --- 
    31321 Chain | Description 
    31322 A | . 
    31323  
    31324 Computing secondary structure 
    31325 
    31326 > ui tool show Matchmaker
    31327 
    31328 > matchmaker #54 to #2
    31329 
    31330 Computing secondary structure 
    31331 Parameters 
    31332 --- 
    31333 Chain pairing | bb 
    31334 Alignment algorithm | Needleman-Wunsch 
    31335 Similarity matrix | BLOSUM-62 
    31336 SS fraction | 0.3 
    31337 Gap open (HH/SS/other) | 18/18/6 
    31338 Gap extend | 1 
    31339 SS matrix |  |  | H | S | O 
    31340 ---|---|---|--- 
    31341 H | 6 | -9 | -6 
    31342 S |  | 6 | -6 
    31343 O |  |  | 4 
    31344 Iteration cutoff | 2 
    31345  
    31346 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec1_model_1.cif, chain A (#54),
    31347 sequence alignment score = 527.8 
    31348 RMSD between 147 pruned atom pairs is 0.713 angstroms; (across all 148 pairs:
    31349 0.764) 
    31350  
    31351 
    31352 > hide #53 models
    31353 
    31354 > show #53 models
    31355 
    31356 > hide #53 models
    31357 
    31358 > hide #54 models
    31359 
    31360 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    31361 > UASLP/Lab Virología/AlphaFold3/32/fold_sec1_summary_confidences_2.json"
    31362 
    31363 JSON file "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis
    31364 Potosi - UASLP/Lab
    31365 Virología/AlphaFold3/32/fold_sec1_summary_confidences_2.json" is not AlphaFold
    31366 predicted aligned error data, expected a top level list 
    31367 
    31368 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    31369 > UASLP/Lab Virología/AlphaFold3/32/fold_sec1_model_2.cif"
    31370 
    31371 Chain information for fold_sec1_model_2.cif #55 
    31372 --- 
    31373 Chain | Description 
    31374 A | . 
    31375  
    31376 Computing secondary structure 
    31377 
    31378 > ui tool show Matchmaker
    31379 
    31380 > matchmaker #55 to #2
    31381 
    31382 Computing secondary structure 
    31383 Parameters 
    31384 --- 
    31385 Chain pairing | bb 
    31386 Alignment algorithm | Needleman-Wunsch 
    31387 Similarity matrix | BLOSUM-62 
    31388 SS fraction | 0.3 
    31389 Gap open (HH/SS/other) | 18/18/6 
    31390 Gap extend | 1 
    31391 SS matrix |  |  | H | S | O 
    31392 ---|---|---|--- 
    31393 H | 6 | -9 | -6 
    31394 S |  | 6 | -6 
    31395 O |  |  | 4 
    31396 Iteration cutoff | 2 
    31397  
    31398 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec1_model_2.cif, chain A (#55),
    31399 sequence alignment score = 527.8 
    31400 RMSD between 146 pruned atom pairs is 0.727 angstroms; (across all 148 pairs:
    31401 0.814) 
    31402  
    31403 
    31404 > hide #55 models
    31405 
    31406 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    31407 > UASLP/Lab Virología/AlphaFold3/32/fold_sec1_model_3.cif"
    31408 
    31409 Chain information for fold_sec1_model_3.cif #56 
    31410 --- 
    31411 Chain | Description 
    31412 A | . 
    31413  
    31414 Computing secondary structure 
    31415 
    31416 > ui tool show Matchmaker
    31417 
    31418 > matchmaker #56 to #2
    31419 
    31420 Computing secondary structure 
    31421 Parameters 
    31422 --- 
    31423 Chain pairing | bb 
    31424 Alignment algorithm | Needleman-Wunsch 
    31425 Similarity matrix | BLOSUM-62 
    31426 SS fraction | 0.3 
    31427 Gap open (HH/SS/other) | 18/18/6 
    31428 Gap extend | 1 
    31429 SS matrix |  |  | H | S | O 
    31430 ---|---|---|--- 
    31431 H | 6 | -9 | -6 
    31432 S |  | 6 | -6 
    31433 O |  |  | 4 
    31434 Iteration cutoff | 2 
    31435  
    31436 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec1_model_3.cif, chain A (#56),
    31437 sequence alignment score = 527.8 
    31438 RMSD between 145 pruned atom pairs is 0.737 angstroms; (across all 148 pairs:
    31439 0.823) 
    31440  
    31441 
    31442 > hide #56 models
    31443 
    31444 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    31445 > UASLP/Lab Virología/AlphaFold3/32/fold_sec1_model_4.cif"
    31446 
    31447 Chain information for fold_sec1_model_4.cif #57 
    31448 --- 
    31449 Chain | Description 
    31450 A | . 
    31451  
    31452 Computing secondary structure 
    31453 
    31454 > ui tool show Matchmaker
    31455 
    31456 > matchmaker #57 to #2
    31457 
    31458 Computing secondary structure 
    31459 Parameters 
    31460 --- 
    31461 Chain pairing | bb 
    31462 Alignment algorithm | Needleman-Wunsch 
    31463 Similarity matrix | BLOSUM-62 
    31464 SS fraction | 0.3 
    31465 Gap open (HH/SS/other) | 18/18/6 
    31466 Gap extend | 1 
    31467 SS matrix |  |  | H | S | O 
    31468 ---|---|---|--- 
    31469 H | 6 | -9 | -6 
    31470 S |  | 6 | -6 
    31471 O |  |  | 4 
    31472 Iteration cutoff | 2 
    31473  
    31474 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec1_model_4.cif, chain A (#57),
    31475 sequence alignment score = 527.8 
    31476 RMSD between 145 pruned atom pairs is 0.742 angstroms; (across all 148 pairs:
    31477 0.906) 
    31478  
    31479 
    31480 > hide #57 models
    31481 
    31482 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    31483 > UASLP/Lab Virología/AlphaFold3/35/fold_sec2_model_0.cif"
    31484 
    31485 Chain information for fold_sec2_model_0.cif #58 
    31486 --- 
    31487 Chain | Description 
    31488 A | . 
    31489  
    31490 Computing secondary structure 
    31491 
    31492 > ui tool show Matchmaker
    31493 
    31494 > matchmaker #58 to #2
    31495 
    31496 Computing secondary structure 
    31497 Parameters 
    31498 --- 
    31499 Chain pairing | bb 
    31500 Alignment algorithm | Needleman-Wunsch 
    31501 Similarity matrix | BLOSUM-62 
    31502 SS fraction | 0.3 
    31503 Gap open (HH/SS/other) | 18/18/6 
    31504 Gap extend | 1 
    31505 SS matrix |  |  | H | S | O 
    31506 ---|---|---|--- 
    31507 H | 6 | -9 | -6 
    31508 S |  | 6 | -6 
    31509 O |  |  | 4 
    31510 Iteration cutoff | 2 
    31511  
    31512 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec2_model_0.cif, chain A (#58),
    31513 sequence alignment score = 547.5 
    31514 RMSD between 148 pruned atom pairs is 0.718 angstroms; (across all 149 pairs:
    31515 0.771) 
    31516  
    31517 
    31518 > hide #58 models
    31519 
    31520 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    31521 > UASLP/Lab Virología/AlphaFold3/35/fold_sec2_model_1.cif"
    31522 
    31523 Chain information for fold_sec2_model_1.cif #59 
    31524 --- 
    31525 Chain | Description 
    31526 A | . 
    31527  
    31528 Computing secondary structure 
    31529 
    31530 > ui tool show Matchmaker
    31531 
    31532 > matchmaker #59 to #2
    31533 
    31534 Computing secondary structure 
    31535 Parameters 
    31536 --- 
    31537 Chain pairing | bb 
    31538 Alignment algorithm | Needleman-Wunsch 
    31539 Similarity matrix | BLOSUM-62 
    31540 SS fraction | 0.3 
    31541 Gap open (HH/SS/other) | 18/18/6 
    31542 Gap extend | 1 
    31543 SS matrix |  |  | H | S | O 
    31544 ---|---|---|--- 
    31545 H | 6 | -9 | -6 
    31546 S |  | 6 | -6 
    31547 O |  |  | 4 
    31548 Iteration cutoff | 2 
    31549  
    31550 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec2_model_1.cif, chain A (#59),
    31551 sequence alignment score = 536.7 
    31552 RMSD between 148 pruned atom pairs is 0.686 angstroms; (across all 149 pairs:
    31553 0.740) 
    31554  
    31555 
    31556 > hide #59 models
    31557 
    31558 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    31559 > UASLP/Lab Virología/AlphaFold3/35/fold_sec2_model_2.cif"
    31560 
    31561 Chain information for fold_sec2_model_2.cif #60 
    31562 --- 
    31563 Chain | Description 
    31564 A | . 
    31565  
    31566 Computing secondary structure 
    31567 
    31568 > ui tool show Matchmaker
    31569 
    31570 > matchmaker #60 to #2
    31571 
    31572 Computing secondary structure 
    31573 Parameters 
    31574 --- 
    31575 Chain pairing | bb 
    31576 Alignment algorithm | Needleman-Wunsch 
    31577 Similarity matrix | BLOSUM-62 
    31578 SS fraction | 0.3 
    31579 Gap open (HH/SS/other) | 18/18/6 
    31580 Gap extend | 1 
    31581 SS matrix |  |  | H | S | O 
    31582 ---|---|---|--- 
    31583 H | 6 | -9 | -6 
    31584 S |  | 6 | -6 
    31585 O |  |  | 4 
    31586 Iteration cutoff | 2 
    31587  
    31588 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec2_model_2.cif, chain A (#60),
    31589 sequence alignment score = 536.7 
    31590 RMSD between 148 pruned atom pairs is 0.686 angstroms; (across all 149 pairs:
    31591 0.733) 
    31592  
    31593 
    31594 > hide #60 models
    31595 
    31596 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    31597 > UASLP/Lab Virología/AlphaFold3/35/fold_sec2_model_3.cif"
    31598 
    31599 Chain information for fold_sec2_model_3.cif #61 
    31600 --- 
    31601 Chain | Description 
    31602 A | . 
    31603  
    31604 Computing secondary structure 
    31605 
    31606 > ui tool show Matchmaker
    31607 
    31608 > matchmaker #61 to #2
    31609 
    31610 Computing secondary structure 
    31611 Parameters 
    31612 --- 
    31613 Chain pairing | bb 
    31614 Alignment algorithm | Needleman-Wunsch 
    31615 Similarity matrix | BLOSUM-62 
    31616 SS fraction | 0.3 
    31617 Gap open (HH/SS/other) | 18/18/6 
    31618 Gap extend | 1 
    31619 SS matrix |  |  | H | S | O 
    31620 ---|---|---|--- 
    31621 H | 6 | -9 | -6 
    31622 S |  | 6 | -6 
    31623 O |  |  | 4 
    31624 Iteration cutoff | 2 
    31625  
    31626 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec2_model_3.cif, chain A (#61),
    31627 sequence alignment score = 536.7 
    31628 RMSD between 148 pruned atom pairs is 0.663 angstroms; (across all 149 pairs:
    31629 0.706) 
    31630  
    31631 
    31632 > hide #61 models
    31633 
    31634 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    31635 > UASLP/Lab Virología/AlphaFold3/35/fold_sec2_summary_confidences_4.json"
    31636 
    31637 Opening an AlphaFold PAE file requires first opening the predicted atomic
    31638 model. Did not find an open atomic model from the same directory. If the
    31639 atomic model is already open choose it using menu 
    31640  
    31641 Tools / Structure Prediction / AlphaFold Error Plot 
    31642  
    31643 or use the open command structure option, for example 
    31644  
    31645 open C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    31646 UASLP/Lab Virología/AlphaFold3/35/fold_sec2_summary_confidences_4.json
    31647 structure #1 
    31648  
    31649 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    31650 need to specify the specific JSON format such as 
    31651  
    31652 open mole_channels.json format mole 
    31653 
    31654 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    31655 > UASLP/Lab Virología/AlphaFold3/35/fold_sec2_model_4.cif"
    31656 
    31657 Chain information for fold_sec2_model_4.cif #62 
    31658 --- 
    31659 Chain | Description 
    31660 A | . 
    31661  
    31662 Computing secondary structure 
    31663 
    31664 > ui tool show Matchmaker
    31665 
    31666 > matchmaker #62 to #2
    31667 
    31668 Computing secondary structure 
    31669 Parameters 
    31670 --- 
    31671 Chain pairing | bb 
    31672 Alignment algorithm | Needleman-Wunsch 
    31673 Similarity matrix | BLOSUM-62 
    31674 SS fraction | 0.3 
    31675 Gap open (HH/SS/other) | 18/18/6 
    31676 Gap extend | 1 
    31677 SS matrix |  |  | H | S | O 
    31678 ---|---|---|--- 
    31679 H | 6 | -9 | -6 
    31680 S |  | 6 | -6 
    31681 O |  |  | 4 
    31682 Iteration cutoff | 2 
    31683  
    31684 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec2_model_4.cif, chain A (#62),
    31685 sequence alignment score = 536.7 
    31686 RMSD between 148 pruned atom pairs is 0.666 angstroms; (across all 149 pairs:
    31687 0.699) 
    31688  
    31689 
    31690 > color #60 white
    31691 
    31692 > color #60 #d4d4d4ff
    31693 
    31694 > color #62 #737f82ff
    31695 
    31696 > color #62 #757682ff
    31697 
    31698 > show #61 models
    31699 
    31700 > hide #62 models
    31701 
    31702 > color #59 #bfd6d8ff
    31703 
    31704 > color #58 #53605cff
    31705 
    31706 > color #58 #5b5e60ff
    31707 
    31708 > color #58 #5e605eff
    31709 
    31710 > color #58 white
    31711 
    31712 > color #58 #c2c2c2ff
    31713 
    31714 > color #58 #d6d6d6ff
    31715 
    31716 > hide #61 models
    31717 
    31718 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    31719 > UASLP/Lab Virología/AlphaFold3/41/fold_sec3_model_0.cif"
    31720 
    31721 Chain information for fold_sec3_model_0.cif #63 
    31722 --- 
    31723 Chain | Description 
    31724 A | . 
    31725  
    31726 Computing secondary structure 
    31727 
    31728 > ui tool show Matchmaker
    31729 
    31730 > matchmaker #63 to #2
    31731 
    31732 Computing secondary structure 
    31733 Parameters 
    31734 --- 
    31735 Chain pairing | bb 
    31736 Alignment algorithm | Needleman-Wunsch 
    31737 Similarity matrix | BLOSUM-62 
    31738 SS fraction | 0.3 
    31739 Gap open (HH/SS/other) | 18/18/6 
    31740 Gap extend | 1 
    31741 SS matrix |  |  | H | S | O 
    31742 ---|---|---|--- 
    31743 H | 6 | -9 | -6 
    31744 S |  | 6 | -6 
    31745 O |  |  | 4 
    31746 Iteration cutoff | 2 
    31747  
    31748 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec3_model_0.cif, chain A (#63),
    31749 sequence alignment score = 544.6 
    31750 RMSD between 148 pruned atom pairs is 0.694 angstroms; (across all 149 pairs:
    31751 0.756) 
    31752  
    31753 
    31754 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    31755 > UASLP/Lab Virología/AlphaFold3/41/fold_sec3_full_data_1.json"
    31756 
    31757 Opened AlphaFold PAE with values for 270 residues and atoms 
    31758 
    31759 > color #63/A:126-184 lime
    31760 
    31761 > ui tool show Matchmaker
    31762 
    31763 > matchmaker #63 to #2
    31764 
    31765 Computing secondary structure 
    31766 Parameters 
    31767 --- 
    31768 Chain pairing | bb 
    31769 Alignment algorithm | Needleman-Wunsch 
    31770 Similarity matrix | BLOSUM-62 
    31771 SS fraction | 0.3 
    31772 Gap open (HH/SS/other) | 18/18/6 
    31773 Gap extend | 1 
    31774 SS matrix |  |  | H | S | O 
    31775 ---|---|---|--- 
    31776 H | 6 | -9 | -6 
    31777 S |  | 6 | -6 
    31778 O |  |  | 4 
    31779 Iteration cutoff | 2 
    31780  
    31781 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec3_model_0.cif, chain A (#63),
    31782 sequence alignment score = 544.6 
    31783 RMSD between 148 pruned atom pairs is 0.694 angstroms; (across all 149 pairs:
    31784 0.756) 
    31785  
    31786 
    31787 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    31788 > UASLP/Lab Virología/AlphaFold3/41/fold_sec3_model_1.cif"
    31789 
    31790 Chain information for fold_sec3_model_1.cif #64 
    31791 --- 
    31792 Chain | Description 
    31793 A | . 
    31794  
    31795 Computing secondary structure 
    31796 
    31797 > ui mousemode right select
    31798 
    31799 > select #63/A:167
    31800 
    31801 9 atoms, 8 bonds, 1 residue, 1 model selected 
    31802 
    31803 > hide sel atoms
    31804 
    31805 > show sel atoms
    31806 
    31807 [Repeated 1 time(s)]
    31808 
    31809 > hide sel atoms
    31810 
    31811 > hide sel cartoons
    31812 
    31813 > hide sel surfaces
    31814 
    31815 > show sel surfaces
    31816 
    31817 > hide sel cartoons
    31818 
    31819 > show sel cartoons
    31820 
    31821 > hide sel surfaces
    31822 
    31823 > hide #!63 models
    31824 
    31825 > ui tool show Matchmaker
    31826 
    31827 > matchmaker #64 to #2
    31828 
    31829 Computing secondary structure 
    31830 Parameters 
    31831 --- 
    31832 Chain pairing | bb 
    31833 Alignment algorithm | Needleman-Wunsch 
    31834 Similarity matrix | BLOSUM-62 
    31835 SS fraction | 0.3 
    31836 Gap open (HH/SS/other) | 18/18/6 
    31837 Gap extend | 1 
    31838 SS matrix |  |  | H | S | O 
    31839 ---|---|---|--- 
    31840 H | 6 | -9 | -6 
    31841 S |  | 6 | -6 
    31842 O |  |  | 4 
    31843 Iteration cutoff | 2 
    31844  
    31845 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec3_model_1.cif, chain A (#64),
    31846 sequence alignment score = 544.6 
    31847 RMSD between 148 pruned atom pairs is 0.678 angstroms; (across all 149 pairs:
    31848 0.736) 
    31849  
    31850 
    31851 > select add #63
    31852 
    31853 2159 atoms, 2218 bonds, 270 residues, 2 models selected 
    31854 
    31855 > select subtract #63
    31856 
    31857 1 model selected 
    31858 
    31859 > hide #64 models
    31860 
    31861 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    31862 > UASLP/Lab Virología/AlphaFold3/41/fold_sec3_model_2.cif"
    31863 
    31864 Chain information for fold_sec3_model_2.cif #65 
    31865 --- 
    31866 Chain | Description 
    31867 A | . 
    31868  
    31869 Computing secondary structure 
    31870 
    31871 > ui tool show Matchmaker
    31872 
    31873 > matchmaker #65 to #2
    31874 
    31875 Computing secondary structure 
    31876 Parameters 
    31877 --- 
    31878 Chain pairing | bb 
    31879 Alignment algorithm | Needleman-Wunsch 
    31880 Similarity matrix | BLOSUM-62 
    31881 SS fraction | 0.3 
    31882 Gap open (HH/SS/other) | 18/18/6 
    31883 Gap extend | 1 
    31884 SS matrix |  |  | H | S | O 
    31885 ---|---|---|--- 
    31886 H | 6 | -9 | -6 
    31887 S |  | 6 | -6 
    31888 O |  |  | 4 
    31889 Iteration cutoff | 2 
    31890  
    31891 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec3_model_2.cif, chain A (#65),
    31892 sequence alignment score = 544.6 
    31893 RMSD between 148 pruned atom pairs is 0.697 angstroms; (across all 149 pairs:
    31894 0.753) 
    31895  
    31896 
    31897 > color #65 #d5bbd7ff
    31898 
    31899 > color #65 #d7cccdff
    31900 
    31901 > hide #65 models
    31902 
    31903 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    31904 > UASLP/Lab Virología/AlphaFold3/41/fold_sec3_model_3.cif"
    31905 
    31906 Chain information for fold_sec3_model_3.cif #66 
    31907 --- 
    31908 Chain | Description 
    31909 A | . 
    31910  
    31911 Computing secondary structure 
    31912 
    31913 > ui tool show Matchmaker
    31914 
    31915 > matchmaker #66 to #2
    31916 
    31917 Computing secondary structure 
    31918 Parameters 
    31919 --- 
    31920 Chain pairing | bb 
    31921 Alignment algorithm | Needleman-Wunsch 
    31922 Similarity matrix | BLOSUM-62 
    31923 SS fraction | 0.3 
    31924 Gap open (HH/SS/other) | 18/18/6 
    31925 Gap extend | 1 
    31926 SS matrix |  |  | H | S | O 
    31927 ---|---|---|--- 
    31928 H | 6 | -9 | -6 
    31929 S |  | 6 | -6 
    31930 O |  |  | 4 
    31931 Iteration cutoff | 2 
    31932  
    31933 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec3_model_3.cif, chain A (#66),
    31934 sequence alignment score = 544.6 
    31935 RMSD between 148 pruned atom pairs is 0.695 angstroms; (across all 149 pairs:
    31936 0.742) 
    31937  
    31938 
    31939 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    31940 > UASLP/Lab Virología/AlphaFold3/41/fold_sec3_model_4.cif"
    31941 
    31942 Chain information for fold_sec3_model_4.cif #67 
    31943 --- 
    31944 Chain | Description 
    31945 A | . 
    31946  
    31947 Computing secondary structure 
    31948 
    31949 > hide #66 models
    31950 
    31951 > ui tool show Matchmaker
    31952 
    31953 > matchmaker #67 to #2
    31954 
    31955 Computing secondary structure 
    31956 Parameters 
    31957 --- 
    31958 Chain pairing | bb 
    31959 Alignment algorithm | Needleman-Wunsch 
    31960 Similarity matrix | BLOSUM-62 
    31961 SS fraction | 0.3 
    31962 Gap open (HH/SS/other) | 18/18/6 
    31963 Gap extend | 1 
    31964 SS matrix |  |  | H | S | O 
    31965 ---|---|---|--- 
    31966 H | 6 | -9 | -6 
    31967 S |  | 6 | -6 
    31968 O |  |  | 4 
    31969 Iteration cutoff | 2 
    31970  
    31971 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec3_model_4.cif, chain A (#67),
    31972 sequence alignment score = 544.6 
    31973 RMSD between 148 pruned atom pairs is 0.675 angstroms; (across all 149 pairs:
    31974 0.740) 
    31975  
    31976 
    31977 > color #66 white
    31978 
    31979 > color #66 #eeeeeeff
    31980 
    31981 > color #64 white
    31982 
    31983 > color #64 #e3e3e3ff
    31984 
    31985 > color #61 #ffaa00ff
    31986 
    31987 > color #61 #ffaa7fff
    31988 
    31989 > hide #67 models
    31990 
    31991 > show #54 models
    31992 
    31993 > color #53 #656770ff
    31994 
    31995 > color #55 white
    31996 
    31997 > color #55 #e6e6e6ff
    31998 
    31999 > color #56 white
    32000 
    32001 > color #56 #f3f3f3ff
    32002 
    32003 > color #57 white
    32004 
    32005 > color #57 #f1f1f1ff
    32006 
    32007 > color #53 #bdc0d1ff
    32008 
    32009 > show #67 models
    32010 
    32011 > hide #54 models
    32012 
    32013 > save C:/Users/Carolina/Documents/CHIKVaaint.cxs
    32014 
    32015 ——— End of log from Wed Jan 29 14:59:10 2025 ———
    32016 
    32017 > view name session-start
    32018 
    32019 opened ChimeraX session 
    32020 
    32021 > hide #67 models
    32022 
    32023 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    32024 > UASLP/Lab Virología/AlphaFold3/43/fold_sec4_model_0.cif"
    32025 
    32026 Chain information for fold_sec4_model_0.cif #68 
    32027 --- 
    32028 Chain | Description 
    32029 A | . 
    32030  
    32031 Computing secondary structure 
    32032 
    32033 > ui tool show Matchmaker
    32034 
    32035 > matchmaker #68 to #2
    32036 
    32037 Computing secondary structure 
    32038 Parameters 
    32039 --- 
    32040 Chain pairing | bb 
    32041 Alignment algorithm | Needleman-Wunsch 
    32042 Similarity matrix | BLOSUM-62 
    32043 SS fraction | 0.3 
    32044 Gap open (HH/SS/other) | 18/18/6 
    32045 Gap extend | 1 
    32046 SS matrix |  |  | H | S | O 
    32047 ---|---|---|--- 
    32048 H | 6 | -9 | -6 
    32049 S |  | 6 | -6 
    32050 O |  |  | 4 
    32051 Iteration cutoff | 2 
    32052  
    32053 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec4_model_0.cif, chain A (#68),
    32054 sequence alignment score = 556.6 
    32055 RMSD between 147 pruned atom pairs is 0.631 angstroms; (across all 149 pairs:
    32056 0.720) 
    32057  
    32058 
    32059 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    32060 > UASLP/Lab Virología/AlphaFold3/43/fold_sec4_model_1.cif"
    32061 
    32062 Chain information for fold_sec4_model_1.cif #69 
    32063 --- 
    32064 Chain | Description 
    32065 A | . 
    32066  
    32067 Computing secondary structure 
    32068 
    32069 > ui tool show Matchmaker
    32070 
    32071 > matchmaker #69 to #2
    32072 
    32073 Computing secondary structure 
    32074 Parameters 
    32075 --- 
    32076 Chain pairing | bb 
    32077 Alignment algorithm | Needleman-Wunsch 
    32078 Similarity matrix | BLOSUM-62 
    32079 SS fraction | 0.3 
    32080 Gap open (HH/SS/other) | 18/18/6 
    32081 Gap extend | 1 
    32082 SS matrix |  |  | H | S | O 
    32083 ---|---|---|--- 
    32084 H | 6 | -9 | -6 
    32085 S |  | 6 | -6 
    32086 O |  |  | 4 
    32087 Iteration cutoff | 2 
    32088  
    32089 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec4_model_1.cif, chain A (#69),
    32090 sequence alignment score = 545.8 
    32091 RMSD between 147 pruned atom pairs is 0.669 angstroms; (across all 149 pairs:
    32092 0.764) 
    32093  
    32094 
    32095 > hide #68 models
    32096 
    32097 > hide #69 models
    32098 
    32099 > color #69 white
    32100 
    32101 > color #69 #ffe4edff
    32102 
    32103 > color #69 white
    32104 
    32105 > color #69 #fff7f9ff
    32106 
    32107 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    32108 > UASLP/Lab Virología/AlphaFold3/43/fold_sec4_model_2.cif"
    32109 
    32110 Chain information for fold_sec4_model_2.cif #70 
    32111 --- 
    32112 Chain | Description 
    32113 A | . 
    32114  
    32115 Computing secondary structure 
    32116 
    32117 > ui tool show Matchmaker
    32118 
    32119 > matchmaker #70 to #2
    32120 
    32121 Computing secondary structure 
    32122 Parameters 
    32123 --- 
    32124 Chain pairing | bb 
    32125 Alignment algorithm | Needleman-Wunsch 
    32126 Similarity matrix | BLOSUM-62 
    32127 SS fraction | 0.3 
    32128 Gap open (HH/SS/other) | 18/18/6 
    32129 Gap extend | 1 
    32130 SS matrix |  |  | H | S | O 
    32131 ---|---|---|--- 
    32132 H | 6 | -9 | -6 
    32133 S |  | 6 | -6 
    32134 O |  |  | 4 
    32135 Iteration cutoff | 2 
    32136  
    32137 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec4_model_2.cif, chain A (#70),
    32138 sequence alignment score = 567.4 
    32139 RMSD between 147 pruned atom pairs is 0.660 angstroms; (across all 149 pairs:
    32140 0.753) 
    32141  
    32142 
    32143 > color #70 white
    32144 
    32145 > color #70 #fae9ffff
    32146 
    32147 > color #70 #fbf0ffff
    32148 
    32149 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    32150 > UASLP/Lab Virología/AlphaFold3/43/fold_sec4_model_3.cif"
    32151 
    32152 Chain information for fold_sec4_model_3.cif #71 
    32153 --- 
    32154 Chain | Description 
    32155 A | . 
    32156  
    32157 Computing secondary structure 
    32158 
    32159 > hide #70 models
    32160 
    32161 > ui tool show Matchmaker
    32162 
    32163 > matchmaker #71 to #2
    32164 
    32165 Computing secondary structure 
    32166 Parameters 
    32167 --- 
    32168 Chain pairing | bb 
    32169 Alignment algorithm | Needleman-Wunsch 
    32170 Similarity matrix | BLOSUM-62 
    32171 SS fraction | 0.3 
    32172 Gap open (HH/SS/other) | 18/18/6 
    32173 Gap extend | 1 
    32174 SS matrix |  |  | H | S | O 
    32175 ---|---|---|--- 
    32176 H | 6 | -9 | -6 
    32177 S |  | 6 | -6 
    32178 O |  |  | 4 
    32179 Iteration cutoff | 2 
    32180  
    32181 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec4_model_3.cif, chain A (#71),
    32182 sequence alignment score = 556.6 
    32183 RMSD between 146 pruned atom pairs is 0.623 angstroms; (across all 149 pairs:
    32184 0.740) 
    32185  
    32186 
    32187 > color #68 #d3dbd3ff
    32188 
    32189 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    32190 > UASLP/Lab Virología/AlphaFold3/43/fold_sec4_model_4.cif"
    32191 
    32192 Chain information for fold_sec4_model_4.cif #72 
    32193 --- 
    32194 Chain | Description 
    32195 A | . 
    32196  
    32197 Computing secondary structure 
    32198 
    32199 > ui tool show Matchmaker
    32200 
    32201 > matchmaker #72 to #2
    32202 
    32203 Computing secondary structure 
    32204 Parameters 
    32205 --- 
    32206 Chain pairing | bb 
    32207 Alignment algorithm | Needleman-Wunsch 
    32208 Similarity matrix | BLOSUM-62 
    32209 SS fraction | 0.3 
    32210 Gap open (HH/SS/other) | 18/18/6 
    32211 Gap extend | 1 
    32212 SS matrix |  |  | H | S | O 
    32213 ---|---|---|--- 
    32214 H | 6 | -9 | -6 
    32215 S |  | 6 | -6 
    32216 O |  |  | 4 
    32217 Iteration cutoff | 2 
    32218  
    32219 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec4_model_4.cif, chain A (#72),
    32220 sequence alignment score = 567.4 
    32221 RMSD between 147 pruned atom pairs is 0.619 angstroms; (across all 149 pairs:
    32222 0.709) 
    32223  
    32224 
    32225 > hide #71-72 target m
    32226 
    32227 > show #1 target m
    32228 
    32229 > hide #2 target m
    32230 
    32231 > show #72 target m
    32232 
    32233 > hide #1 target m
    32234 
    32235 > show #71 target m
    32236 
    32237 > hide #72 target m
    32238 
    32239 > show #2 models
    32240 
    32241 > show #72 models
    32242 
    32243 > hide #71 models
    32244 
    32245 > color #71 #969e96ff
    32246 
    32247 > color #71 #9c9e9cff
    32248 
    32249 > color #71 #969e96ff
    32250 
    32251 > color #71 #bbc5bbff
    32252 
    32253 > color #71 #ced9ceff
    32254 
    32255 > hide #72 models
    32256 
    32257 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    32258 > UASLP/Lab Virología/AlphaFold3/44/fold_sec5_model_0.cif"
    32259 
    32260 Chain information for fold_sec5_model_0.cif #73 
    32261 --- 
    32262 Chain | Description 
    32263 A | . 
    32264  
    32265 Computing secondary structure 
    32266 
    32267 > ui tool show Matchmaker
    32268 
    32269 > matchmaker #73 to #2
    32270 
    32271 Computing secondary structure 
    32272 Parameters 
    32273 --- 
    32274 Chain pairing | bb 
    32275 Alignment algorithm | Needleman-Wunsch 
    32276 Similarity matrix | BLOSUM-62 
    32277 SS fraction | 0.3 
    32278 Gap open (HH/SS/other) | 18/18/6 
    32279 Gap extend | 1 
    32280 SS matrix |  |  | H | S | O 
    32281 ---|---|---|--- 
    32282 H | 6 | -9 | -6 
    32283 S |  | 6 | -6 
    32284 O |  |  | 4 
    32285 Iteration cutoff | 2 
    32286  
    32287 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec5_model_0.cif, chain A (#73),
    32288 sequence alignment score = 651.1 
    32289 RMSD between 148 pruned atom pairs is 0.618 angstroms; (across all 149 pairs:
    32290 0.661) 
    32291  
    32292 
    32293 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    32294 > UASLP/Lab Virología/AlphaFold3/44/fold_sec5_model_1.cif"
    32295 
    32296 Chain information for fold_sec5_model_1.cif #74 
    32297 --- 
    32298 Chain | Description 
    32299 A | . 
    32300  
    32301 Computing secondary structure 
    32302 
    32303 > hide #73 models
    32304 
    32305 > ui tool show H-Bonds
    32306 
    32307 > ui tool show Matchmaker
    32308 
    32309 > matchmaker #74 to #2
    32310 
    32311 Computing secondary structure 
    32312 Parameters 
    32313 --- 
    32314 Chain pairing | bb 
    32315 Alignment algorithm | Needleman-Wunsch 
    32316 Similarity matrix | BLOSUM-62 
    32317 SS fraction | 0.3 
    32318 Gap open (HH/SS/other) | 18/18/6 
    32319 Gap extend | 1 
    32320 SS matrix |  |  | H | S | O 
    32321 ---|---|---|--- 
    32322 H | 6 | -9 | -6 
    32323 S |  | 6 | -6 
    32324 O |  |  | 4 
    32325 Iteration cutoff | 2 
    32326  
    32327 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec5_model_1.cif, chain A (#74),
    32328 sequence alignment score = 661.9 
    32329 RMSD between 148 pruned atom pairs is 0.611 angstroms; (across all 149 pairs:
    32330 0.654) 
    32331  
    32332 
    32333 > color #73 #7f8b8dff
    32334 
    32335 > color #73 #c8dbdeff
    32336 
    32337 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    32338 > UASLP/Lab Virología/AlphaFold3/44/fold_sec5_model_2.cif"
    32339 
    32340 Chain information for fold_sec5_model_2.cif #75 
    32341 --- 
    32342 Chain | Description 
    32343 A | . 
    32344  
    32345 Computing secondary structure 
    32346 
    32347 > ui tool show Matchmaker
    32348 
    32349 > matchmaker #75 to #2
    32350 
    32351 Computing secondary structure 
    32352 Parameters 
    32353 --- 
    32354 Chain pairing | bb 
    32355 Alignment algorithm | Needleman-Wunsch 
    32356 Similarity matrix | BLOSUM-62 
    32357 SS fraction | 0.3 
    32358 Gap open (HH/SS/other) | 18/18/6 
    32359 Gap extend | 1 
    32360 SS matrix |  |  | H | S | O 
    32361 ---|---|---|--- 
    32362 H | 6 | -9 | -6 
    32363 S |  | 6 | -6 
    32364 O |  |  | 4 
    32365 Iteration cutoff | 2 
    32366  
    32367 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec5_model_2.cif, chain A (#75),
    32368 sequence alignment score = 670.9 
    32369 RMSD between 148 pruned atom pairs is 0.595 angstroms; (across all 149 pairs:
    32370 0.636) 
    32371  
    32372 
    32373 > color #74 #7c8078ff
    32374 
    32375 > color #74 #e1e7d9ff
    32376 
    32377 > hide #74 models
    32378 
    32379 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    32380 > UASLP/Lab Virología/AlphaFold3/44/fold_sec5_model_3.cif"
    32381 
    32382 Chain information for fold_sec5_model_3.cif #76 
    32383 --- 
    32384 Chain | Description 
    32385 A | . 
    32386  
    32387 Computing secondary structure 
    32388 
    32389 > hide #75 models
    32390 
    32391 > ui tool show Matchmaker
    32392 
    32393 > matchmaker #76 to #2
    32394 
    32395 Computing secondary structure 
    32396 Parameters 
    32397 --- 
    32398 Chain pairing | bb 
    32399 Alignment algorithm | Needleman-Wunsch 
    32400 Similarity matrix | BLOSUM-62 
    32401 SS fraction | 0.3 
    32402 Gap open (HH/SS/other) | 18/18/6 
    32403 Gap extend | 1 
    32404 SS matrix |  |  | H | S | O 
    32405 ---|---|---|--- 
    32406 H | 6 | -9 | -6 
    32407 S |  | 6 | -6 
    32408 O |  |  | 4 
    32409 Iteration cutoff | 2 
    32410  
    32411 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec5_model_3.cif, chain A (#76),
    32412 sequence alignment score = 651.1 
    32413 RMSD between 148 pruned atom pairs is 0.598 angstroms; (across all 149 pairs:
    32414 0.637) 
    32415  
    32416 
    32417 > color #76 #676b65ff
    32418 
    32419 > color #76 #d6ded1ff
    32420 
    32421 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    32422 > UASLP/Lab Virología/AlphaFold3/44/fold_sec5_model_4.cif"
    32423 
    32424 Chain information for fold_sec5_model_4.cif #77 
    32425 --- 
    32426 Chain | Description 
    32427 A | . 
    32428  
    32429 Computing secondary structure 
    32430 
    32431 > ui tool show Matchmaker
    32432 
    32433 > matchmaker #77 to #2
    32434 
    32435 Computing secondary structure 
    32436 Parameters 
    32437 --- 
    32438 Chain pairing | bb 
    32439 Alignment algorithm | Needleman-Wunsch 
    32440 Similarity matrix | BLOSUM-62 
    32441 SS fraction | 0.3 
    32442 Gap open (HH/SS/other) | 18/18/6 
    32443 Gap extend | 1 
    32444 SS matrix |  |  | H | S | O 
    32445 ---|---|---|--- 
    32446 H | 6 | -9 | -6 
    32447 S |  | 6 | -6 
    32448 O |  |  | 4 
    32449 Iteration cutoff | 2 
    32450  
    32451 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec5_model_4.cif, chain A (#77),
    32452 sequence alignment score = 640.3 
    32453 RMSD between 148 pruned atom pairs is 0.642 angstroms; (across all 149 pairs:
    32454 0.683) 
    32455  
    32456 
    32457 > color #77 #44523cff
    32458 
    32459 > color #77 #cef8b7ff
    32460 
    32461 > color #77 #d3ffbcff
    32462 
    32463 > select ~sel & ##selected
    32464 
    32465 Nothing selected 
    32466 
    32467 > select ~sel & ##selected
    32468 
    32469 Nothing selected 
    32470 
    32471 > select ~sel & ##selected
    32472 
    32473 Nothing selected 
    32474 
    32475 > color #77 #edffe1ff
    32476 
    32477 > hide #77 models
    32478 
    32479 > hide #76 models
    32480 
    32481 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    32482 > UASLP/Lab Virología/AlphaFold3/45/fold_sec6_model_0.cif"
    32483 
    32484 Chain information for fold_sec6_model_0.cif #78 
    32485 --- 
    32486 Chain | Description 
    32487 A | . 
    32488  
    32489 Computing secondary structure 
    32490 
    32491 > ui tool show Matchmaker
    32492 
    32493 > matchmaker #78 to #2
    32494 
    32495 Computing secondary structure 
    32496 Parameters 
    32497 --- 
    32498 Chain pairing | bb 
    32499 Alignment algorithm | Needleman-Wunsch 
    32500 Similarity matrix | BLOSUM-62 
    32501 SS fraction | 0.3 
    32502 Gap open (HH/SS/other) | 18/18/6 
    32503 Gap extend | 1 
    32504 SS matrix |  |  | H | S | O 
    32505 ---|---|---|--- 
    32506 H | 6 | -9 | -6 
    32507 S |  | 6 | -6 
    32508 O |  |  | 4 
    32509 Iteration cutoff | 2 
    32510  
    32511 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec6_model_0.cif, chain A (#78),
    32512 sequence alignment score = 627.1 
    32513 RMSD between 148 pruned atom pairs is 0.614 angstroms; (across all 149 pairs:
    32514 0.681) 
    32515  
    32516 
    32517 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    32518 > UASLP/Lab Virología/AlphaFold3/45/fold_sec6_model_1.cif"
    32519 
    32520 Chain information for fold_sec6_model_1.cif #79 
    32521 --- 
    32522 Chain | Description 
    32523 A | . 
    32524  
    32525 Computing secondary structure 
    32526 
    32527 > ui tool show Matchmaker
    32528 
    32529 > matchmaker #79 to #2
    32530 
    32531 Computing secondary structure 
    32532 Parameters 
    32533 --- 
    32534 Chain pairing | bb 
    32535 Alignment algorithm | Needleman-Wunsch 
    32536 Similarity matrix | BLOSUM-62 
    32537 SS fraction | 0.3 
    32538 Gap open (HH/SS/other) | 18/18/6 
    32539 Gap extend | 1 
    32540 SS matrix |  |  | H | S | O 
    32541 ---|---|---|--- 
    32542 H | 6 | -9 | -6 
    32543 S |  | 6 | -6 
    32544 O |  |  | 4 
    32545 Iteration cutoff | 2 
    32546  
    32547 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec6_model_1.cif, chain A (#79),
    32548 sequence alignment score = 631.3 
    32549 RMSD between 148 pruned atom pairs is 0.635 angstroms; (across all 149 pairs:
    32550 0.703) 
    32551  
    32552 
    32553 > hide #78 models
    32554 
    32555 > color #79 #b1a7a0ff
    32556 
    32557 > color #79 #f4e7dcff
    32558 
    32559 > hide #79 models
    32560 
    32561 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    32562 > UASLP/Lab Virología/AlphaFold3/45/fold_sec6_model_2.cif"
    32563 
    32564 Chain information for fold_sec6_model_2.cif #80 
    32565 --- 
    32566 Chain | Description 
    32567 A | . 
    32568  
    32569 Computing secondary structure 
    32570 
    32571 > ui tool show Matchmaker
    32572 
    32573 > matchmaker #80 to #2
    32574 
    32575 Computing secondary structure 
    32576 Parameters 
    32577 --- 
    32578 Chain pairing | bb 
    32579 Alignment algorithm | Needleman-Wunsch 
    32580 Similarity matrix | BLOSUM-62 
    32581 SS fraction | 0.3 
    32582 Gap open (HH/SS/other) | 18/18/6 
    32583 Gap extend | 1 
    32584 SS matrix |  |  | H | S | O 
    32585 ---|---|---|--- 
    32586 H | 6 | -9 | -6 
    32587 S |  | 6 | -6 
    32588 O |  |  | 4 
    32589 Iteration cutoff | 2 
    32590  
    32591 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec6_model_2.cif, chain A (#80),
    32592 sequence alignment score = 630.7 
    32593 RMSD between 148 pruned atom pairs is 0.627 angstroms; (across all 149 pairs:
    32594 0.699) 
    32595  
    32596 
    32597 > color #80 #e1e6f1ff
    32598 
    32599 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    32600 > UASLP/Lab Virología/AlphaFold3/45/fold_sec6_model_3.cif"
    32601 
    32602 Chain information for fold_sec6_model_3.cif #81 
    32603 --- 
    32604 Chain | Description 
    32605 A | . 
    32606  
    32607 Computing secondary structure 
    32608 
    32609 > hide #80 models
    32610 
    32611 > ui tool show H-Bonds
    32612 
    32613 > ui tool show Matchmaker
    32614 
    32615 > matchmaker #81 to #2
    32616 
    32617 Computing secondary structure 
    32618 Parameters 
    32619 --- 
    32620 Chain pairing | bb 
    32621 Alignment algorithm | Needleman-Wunsch 
    32622 Similarity matrix | BLOSUM-62 
    32623 SS fraction | 0.3 
    32624 Gap open (HH/SS/other) | 18/18/6 
    32625 Gap extend | 1 
    32626 SS matrix |  |  | H | S | O 
    32627 ---|---|---|--- 
    32628 H | 6 | -9 | -6 
    32629 S |  | 6 | -6 
    32630 O |  |  | 4 
    32631 Iteration cutoff | 2 
    32632  
    32633 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec6_model_3.cif, chain A (#81),
    32634 sequence alignment score = 631.3 
    32635 RMSD between 148 pruned atom pairs is 0.632 angstroms; (across all 149 pairs:
    32636 0.694) 
    32637  
    32638 
    32639 > color #81 #88838eff
    32640 
    32641 > color #81 #d0c8d9ff
    32642 
    32643 > hide #81 models
    32644 
    32645 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    32646 > UASLP/Lab Virología/AlphaFold3/45/fold_sec6_model_4.cif"
    32647 
    32648 Chain information for fold_sec6_model_4.cif #82 
    32649 --- 
    32650 Chain | Description 
    32651 A | . 
    32652  
    32653 Computing secondary structure 
    32654 
    32655 > ui tool show Matchmaker
    32656 
    32657 > matchmaker #82 to #2
    32658 
    32659 Computing secondary structure 
    32660 Parameters 
    32661 --- 
    32662 Chain pairing | bb 
    32663 Alignment algorithm | Needleman-Wunsch 
    32664 Similarity matrix | BLOSUM-62 
    32665 SS fraction | 0.3 
    32666 Gap open (HH/SS/other) | 18/18/6 
    32667 Gap extend | 1 
    32668 SS matrix |  |  | H | S | O 
    32669 ---|---|---|--- 
    32670 H | 6 | -9 | -6 
    32671 S |  | 6 | -6 
    32672 O |  |  | 4 
    32673 Iteration cutoff | 2 
    32674  
    32675 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec6_model_4.cif, chain A (#82),
    32676 sequence alignment score = 630.7 
    32677 RMSD between 148 pruned atom pairs is 0.634 angstroms; (across all 149 pairs:
    32678 0.696) 
    32679  
    32680 
    32681 > color #82 #baf82aff
    32682 
    32683 > color #82 #e2f8b8ff
    32684 
    32685 > hide #82 models
    32686 
    32687 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    32688 > UASLP/Lab Virología/AlphaFold3/50/fold_sec7_model_0.cif"
    32689 
    32690 Chain information for fold_sec7_model_0.cif #83 
    32691 --- 
    32692 Chain | Description 
    32693 A | . 
    32694  
    32695 Computing secondary structure 
    32696 
    32697 > ui tool show Matchmaker
    32698 
    32699 > matchmaker #83 to #2
    32700 
    32701 Computing secondary structure 
    32702 Parameters 
    32703 --- 
    32704 Chain pairing | bb 
    32705 Alignment algorithm | Needleman-Wunsch 
    32706 Similarity matrix | BLOSUM-62 
    32707 SS fraction | 0.3 
    32708 Gap open (HH/SS/other) | 18/18/6 
    32709 Gap extend | 1 
    32710 SS matrix |  |  | H | S | O 
    32711 ---|---|---|--- 
    32712 H | 6 | -9 | -6 
    32713 S |  | 6 | -6 
    32714 O |  |  | 4 
    32715 Iteration cutoff | 2 
    32716  
    32717 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec7_model_0.cif, chain A (#83),
    32718 sequence alignment score = 680.9 
    32719 RMSD between 148 pruned atom pairs is 0.665 angstroms; (across all 149 pairs:
    32720 0.690) 
    32721  
    32722 
    32723 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    32724 > UASLP/Lab Virología/AlphaFold3/50/fold_sec7_model_1.cif"
    32725 
    32726 Chain information for fold_sec7_model_1.cif #84 
    32727 --- 
    32728 Chain | Description 
    32729 A | . 
    32730  
    32731 Computing secondary structure 
    32732 
    32733 > ui tool show Matchmaker
    32734 
    32735 > matchmaker #84 to #2
    32736 
    32737 Computing secondary structure 
    32738 Parameters 
    32739 --- 
    32740 Chain pairing | bb 
    32741 Alignment algorithm | Needleman-Wunsch 
    32742 Similarity matrix | BLOSUM-62 
    32743 SS fraction | 0.3 
    32744 Gap open (HH/SS/other) | 18/18/6 
    32745 Gap extend | 1 
    32746 SS matrix |  |  | H | S | O 
    32747 ---|---|---|--- 
    32748 H | 6 | -9 | -6 
    32749 S |  | 6 | -6 
    32750 O |  |  | 4 
    32751 Iteration cutoff | 2 
    32752  
    32753 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec7_model_1.cif, chain A (#84),
    32754 sequence alignment score = 689.9 
    32755 RMSD between 148 pruned atom pairs is 0.674 angstroms; (across all 149 pairs:
    32756 0.722) 
    32757  
    32758 
    32759 > color #84 #c192aaff
    32760 
    32761 > color #84 #f8bcdbff
    32762 
    32763 > color #84 #f8dbe7ff
    32764 
    32765 > hide #84 models
    32766 
    32767 > hide #83 models
    32768 
    32769 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    32770 > UASLP/Lab Virología/AlphaFold3/50/fold_sec7_model_2.cif"
    32771 
    32772 Chain information for fold_sec7_model_2.cif #85 
    32773 --- 
    32774 Chain | Description 
    32775 A | . 
    32776  
    32777 Computing secondary structure 
    32778 
    32779 > ui tool show Matchmaker
    32780 
    32781 > matchmaker #85 to #2
    32782 
    32783 Computing secondary structure 
    32784 Parameters 
    32785 --- 
    32786 Chain pairing | bb 
    32787 Alignment algorithm | Needleman-Wunsch 
    32788 Similarity matrix | BLOSUM-62 
    32789 SS fraction | 0.3 
    32790 Gap open (HH/SS/other) | 18/18/6 
    32791 Gap extend | 1 
    32792 SS matrix |  |  | H | S | O 
    32793 ---|---|---|--- 
    32794 H | 6 | -9 | -6 
    32795 S |  | 6 | -6 
    32796 O |  |  | 4 
    32797 Iteration cutoff | 2 
    32798  
    32799 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec7_model_2.cif, chain A (#85),
    32800 sequence alignment score = 683.9 
    32801 RMSD between 148 pruned atom pairs is 0.676 angstroms; (across all 149 pairs:
    32802 0.695) 
    32803  
    32804 
    32805 > color #85 #777571ff
    32806 
    32807 > color #85 #f8f5ecff
    32808 
    32809 > hide #85 models
    32810 
    32811 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    32812 > UASLP/Lab Virología/AlphaFold3/50/fold_sec7_model_3.cif"
    32813 
    32814 Chain information for fold_sec7_model_3.cif #86 
    32815 --- 
    32816 Chain | Description 
    32817 A | . 
    32818  
    32819 Computing secondary structure 
    32820 
    32821 > ui tool show Matchmaker
    32822 
    32823 > matchmaker #86 to #2
    32824 
    32825 Computing secondary structure 
    32826 Parameters 
    32827 --- 
    32828 Chain pairing | bb 
    32829 Alignment algorithm | Needleman-Wunsch 
    32830 Similarity matrix | BLOSUM-62 
    32831 SS fraction | 0.3 
    32832 Gap open (HH/SS/other) | 18/18/6 
    32833 Gap extend | 1 
    32834 SS matrix |  |  | H | S | O 
    32835 ---|---|---|--- 
    32836 H | 6 | -9 | -6 
    32837 S |  | 6 | -6 
    32838 O |  |  | 4 
    32839 Iteration cutoff | 2 
    32840  
    32841 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec7_model_3.cif, chain A (#86),
    32842 sequence alignment score = 680.9 
    32843 RMSD between 148 pruned atom pairs is 0.641 angstroms; (across all 149 pairs:
    32844 0.694) 
    32845  
    32846 
    32847 > color #83 #bbbdd1ff
    32848 
    32849 > color #83 #dee0f8ff
    32850 
    32851 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    32852 > UASLP/Lab Virología/AlphaFold3/50/fold_sec7_model_4.cif"
    32853 
    32854 Chain information for fold_sec7_model_4.cif #87 
    32855 --- 
    32856 Chain | Description 
    32857 A | . 
    32858  
    32859 Computing secondary structure 
    32860 
    32861 > ui tool show Matchmaker
    32862 
    32863 > matchmaker #87 to #2
    32864 
    32865 Computing secondary structure 
    32866 Parameters 
    32867 --- 
    32868 Chain pairing | bb 
    32869 Alignment algorithm | Needleman-Wunsch 
    32870 Similarity matrix | BLOSUM-62 
    32871 SS fraction | 0.3 
    32872 Gap open (HH/SS/other) | 18/18/6 
    32873 Gap extend | 1 
    32874 SS matrix |  |  | H | S | O 
    32875 ---|---|---|--- 
    32876 H | 6 | -9 | -6 
    32877 S |  | 6 | -6 
    32878 O |  |  | 4 
    32879 Iteration cutoff | 2 
    32880  
    32881 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec7_model_4.cif, chain A (#87),
    32882 sequence alignment score = 702.5 
    32883 RMSD between 148 pruned atom pairs is 0.659 angstroms; (across all 149 pairs:
    32884 0.696) 
    32885  
    32886 
    32887 > hide #86 models
    32888 
    32889 > color #87 #4e5d56ff
    32890 
    32891 > color #87 #cdf5e2ff
    32892 
    32893 > color #86 #13a85eff
    32894 
    32895 > hide #87 models
    32896 
    32897 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    32898 > UASLP/Lab Virología/AlphaFold3/54/fold_sec8_model_0.cif"
    32899 
    32900 Chain information for fold_sec8_model_0.cif #88 
    32901 --- 
    32902 Chain | Description 
    32903 A | . 
    32904  
    32905 Computing secondary structure 
    32906 
    32907 > ui tool show Matchmaker
    32908 
    32909 > matchmaker #88 to #2
    32910 
    32911 Computing secondary structure 
    32912 Parameters 
    32913 --- 
    32914 Chain pairing | bb 
    32915 Alignment algorithm | Needleman-Wunsch 
    32916 Similarity matrix | BLOSUM-62 
    32917 SS fraction | 0.3 
    32918 Gap open (HH/SS/other) | 18/18/6 
    32919 Gap extend | 1 
    32920 SS matrix |  |  | H | S | O 
    32921 ---|---|---|--- 
    32922 H | 6 | -9 | -6 
    32923 S |  | 6 | -6 
    32924 O |  |  | 4 
    32925 Iteration cutoff | 2 
    32926  
    32927 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec8_model_0.cif, chain A (#88),
    32928 sequence alignment score = 685.7 
    32929 RMSD between 149 pruned atom pairs is 0.662 angstroms; (across all 149 pairs:
    32930 0.662) 
    32931  
    32932 
    32933 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    32934 > UASLP/Lab Virología/AlphaFold3/54/fold_sec8_model_1.cif"
    32935 
    32936 Chain information for fold_sec8_model_1.cif #89 
    32937 --- 
    32938 Chain | Description 
    32939 A | . 
    32940  
    32941 Computing secondary structure 
    32942 
    32943 > ui tool show Matchmaker
    32944 
    32945 > matchmaker #89 to #2
    32946 
    32947 Computing secondary structure 
    32948 Parameters 
    32949 --- 
    32950 Chain pairing | bb 
    32951 Alignment algorithm | Needleman-Wunsch 
    32952 Similarity matrix | BLOSUM-62 
    32953 SS fraction | 0.3 
    32954 Gap open (HH/SS/other) | 18/18/6 
    32955 Gap extend | 1 
    32956 SS matrix |  |  | H | S | O 
    32957 ---|---|---|--- 
    32958 H | 6 | -9 | -6 
    32959 S |  | 6 | -6 
    32960 O |  |  | 4 
    32961 Iteration cutoff | 2 
    32962  
    32963 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec8_model_1.cif, chain A (#89),
    32964 sequence alignment score = 700.7 
    32965 RMSD between 148 pruned atom pairs is 0.648 angstroms; (across all 149 pairs:
    32966 0.684) 
    32967  
    32968 
    32969 > hide #88 models
    32970 
    32971 > color #88 #666776ff
    32972 
    32973 > color #88 #d6d9f8ff
    32974 
    32975 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    32976 > UASLP/Lab Virología/AlphaFold3/54/fold_sec8_model_1.cif"
    32977 
    32978 Chain information for fold_sec8_model_1.cif #90 
    32979 --- 
    32980 Chain | Description 
    32981 A | . 
    32982  
    32983 Computing secondary structure 
    32984 
    32985 > ui tool show Matchmaker
    32986 
    32987 > matchmaker #90 to #2
    32988 
    32989 Computing secondary structure 
    32990 Parameters 
    32991 --- 
    32992 Chain pairing | bb 
    32993 Alignment algorithm | Needleman-Wunsch 
    32994 Similarity matrix | BLOSUM-62 
    32995 SS fraction | 0.3 
    32996 Gap open (HH/SS/other) | 18/18/6 
    32997 Gap extend | 1 
    32998 SS matrix |  |  | H | S | O 
    32999 ---|---|---|--- 
    33000 H | 6 | -9 | -6 
    33001 S |  | 6 | -6 
    33002 O |  |  | 4 
    33003 Iteration cutoff | 2 
    33004  
    33005 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec8_model_1.cif, chain A (#90),
    33006 sequence alignment score = 700.7 
    33007 RMSD between 148 pruned atom pairs is 0.648 angstroms; (across all 149 pairs:
    33008 0.684) 
    33009  
    33010 
    33011 > hide #90 models
    33012 
    33013 > color #90 white
    33014 
    33015 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    33016 > UASLP/Lab Virología/AlphaFold3/54/fold_sec8_model_2.cif"
    33017 
    33018 Chain information for fold_sec8_model_2.cif #91 
    33019 --- 
    33020 Chain | Description 
    33021 A | . 
    33022  
    33023 Computing secondary structure 
    33024 
    33025 > ui tool show Matchmaker
    33026 
    33027 > matchmaker #91 to #2
    33028 
    33029 Computing secondary structure 
    33030 Parameters 
    33031 --- 
    33032 Chain pairing | bb 
    33033 Alignment algorithm | Needleman-Wunsch 
    33034 Similarity matrix | BLOSUM-62 
    33035 SS fraction | 0.3 
    33036 Gap open (HH/SS/other) | 18/18/6 
    33037 Gap extend | 1 
    33038 SS matrix |  |  | H | S | O 
    33039 ---|---|---|--- 
    33040 H | 6 | -9 | -6 
    33041 S |  | 6 | -6 
    33042 O |  |  | 4 
    33043 Iteration cutoff | 2 
    33044  
    33045 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec8_model_2.cif, chain A (#91),
    33046 sequence alignment score = 691.7 
    33047 RMSD between 148 pruned atom pairs is 0.679 angstroms; (across all 149 pairs:
    33048 0.714) 
    33049  
    33050 
    33051 > color #91 #a0a0aeff
    33052 
    33053 > color #91 #e1e2f5ff
    33054 
    33055 > hide #91 models
    33056 
    33057 > show #91 models
    33058 
    33059 > hide #91 models
    33060 
    33061 > hide #89 models
    33062 
    33063 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    33064 > UASLP/Lab Virología/AlphaFold3/54/fold_sec8_model_3.cif"
    33065 
    33066 Chain information for fold_sec8_model_3.cif #92 
    33067 --- 
    33068 Chain | Description 
    33069 A | . 
    33070  
    33071 Computing secondary structure 
    33072 
    33073 > ui tool show Matchmaker
    33074 
    33075 > matchmaker #92 to #1
    33076 
    33077 Computing secondary structure 
    33078 Parameters 
    33079 --- 
    33080 Chain pairing | bb 
    33081 Alignment algorithm | Needleman-Wunsch 
    33082 Similarity matrix | BLOSUM-62 
    33083 SS fraction | 0.3 
    33084 Gap open (HH/SS/other) | 18/18/6 
    33085 Gap extend | 1 
    33086 SS matrix |  |  | H | S | O 
    33087 ---|---|---|--- 
    33088 H | 6 | -9 | -6 
    33089 S |  | 6 | -6 
    33090 O |  |  | 4 
    33091 Iteration cutoff | 2 
    33092  
    33093 Matchmaker 7vga.pdb, chain C (#1) with fold_sec8_model_3.cif, chain A (#92),
    33094 sequence alignment score = 838.6 
    33095 RMSD between 151 pruned atom pairs is 0.830 angstroms; (across all 158 pairs:
    33096 1.156) 
    33097  
    33098 
    33099 > color #89 #dbb4dbff
    33100 
    33101 > color #89 #f8ccf8ff
    33102 
    33103 > color #89 #e975f8ff
    33104 
    33105 > color #89 #f87cc7ff
    33106 
    33107 > color #92 #9da198ff
    33108 
    33109 > color #92 #f3faebff
    33110 
    33111 > hide #92 models
    33112 
    33113 > show #92 models
    33114 
    33115 > hide #92 models
    33116 
    33117 > open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    33118 > UASLP/Lab Virología/AlphaFold3/54/fold_sec8_model_4.cif"
    33119 
    33120 Chain information for fold_sec8_model_4.cif #93 
    33121 --- 
    33122 Chain | Description 
    33123 A | . 
    33124  
    33125 Computing secondary structure 
    33126 
    33127 > ui tool show Matchmaker
    33128 
    33129 > matchmaker #93 to #2
    33130 
    33131 Computing secondary structure 
    33132 Parameters 
    33133 --- 
    33134 Chain pairing | bb 
    33135 Alignment algorithm | Needleman-Wunsch 
    33136 Similarity matrix | BLOSUM-62 
    33137 SS fraction | 0.3 
    33138 Gap open (HH/SS/other) | 18/18/6 
    33139 Gap extend | 1 
    33140 SS matrix |  |  | H | S | O 
    33141 ---|---|---|--- 
    33142 H | 6 | -9 | -6 
    33143 S |  | 6 | -6 
    33144 O |  |  | 4 
    33145 Iteration cutoff | 2 
    33146  
    33147 Matchmaker 3j2w.pdb, chain I (#2) with fold_sec8_model_4.cif, chain A (#93),
    33148 sequence alignment score = 679.7 
    33149 RMSD between 148 pruned atom pairs is 0.624 angstroms; (across all 149 pairs:
    33150 0.678) 
    33151  
    33152 
    33153 > color #89 #f8e5efff
    33154 
    33155 > color #93 #8d3e78ff
    33156 
    33157 > color #93 #f16acdff
    33158 
    33159 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    33160 > UASLP/Lab Virología/AlphaFold3/CHIKVaaint.cxs"
    33161 
    33162 ——— End of log from Sun Feb 2 22:29:43 2025 ———
    33163 
    33164 > view name session-start
    33165 
    33166 opened ChimeraX session 
    33167 
    33168 > show #54 models
    33169 
    33170 > hide #93 models
    33171 
    33172 > ui mousemode right select
    33173 
    33174 > select #54/A:134
    33175 
    33176 8 atoms, 7 bonds, 1 residue, 1 model selected 
    33177 
    33178 > show sel cartoons
    33179 
    33180 [Repeated 1 time(s)]
    33181 
    33182 > show sel atoms
    33183 
    33184 Alignment identifier is 54/A 
    33185 
    33186 > color sel red
    33187 
    33188 > ui mousemode right translate
    33189 
    33190 > ui mousemode right rotate
    33191 
    33192 > ui mousemode right select
    33193 
    33194 [Repeated 1 time(s)]
    33195 
    33196 > ui mousemode right zoom
    33197 
    33198 > ui mousemode right select
    33199 
    33200 > select #2/I:240
    33201 
    33202 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33203 
    33204 > select #54/A:248
    33205 
    33206 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33207 
    33208 > show sel atoms
    33209 
    33210 > color sel red
    33211 
    33212 > ui mousemode right rotate
    33213 
    33214 > ui mousemode right select
    33215 
    33216 > select #2/I:190
    33217 
    33218 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33219 
    33220 > select #54/A:198
    33221 
    33222 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33223 
    33224 > select #54/A:199
    33225 
    33226 4 atoms, 3 bonds, 1 residue, 1 model selected 
    33227 
    33228 > select #54/A:198
    33229 
    33230 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33231 
    33232 > show sel atoms
    33233 
    33234 > color sel orange
    33235 
    33236 > ui mousemode right translate
    33237 
    33238 > ui mousemode right zoom
    33239 
    33240 > ui mousemode right translate
    33241 
    33242 > ui mousemode right "translate selected models"
    33243 
    33244 > ui mousemode right translate
    33245 
    33246 > ui mousemode right rotate
    33247 
    33248 > ui mousemode right translate
    33249 
    33250 > ui mousemode right select
    33251 
    33252 > ui mousemode right rotate
    33253 
    33254 > ui mousemode right translate
    33255 
    33256 > ui mousemode right select
    33257 
    33258 [Repeated 1 time(s)]
    33259 
    33260 > select clear
    33261 
    33262 > select #2/I:183
    33263 
    33264 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33265 
    33266 > select #54/A:191
    33267 
    33268 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33269 
    33270 > show sel atoms
    33271 
    33272 > color sel blue
    33273 
    33274 > select #54/A:186
    33275 
    33276 11 atoms, 10 bonds, 1 residue, 1 model selected 
    33277 
    33278 > select #2/I:180
    33279 
    33280 8 atoms, 7 bonds, 1 residue, 1 model selected 
    33281 
    33282 > select #2/I:178
    33283 
    33284 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33285 
    33286 > select #54/A:186
    33287 
    33288 11 atoms, 10 bonds, 1 residue, 1 model selected 
    33289 
    33290 > show sel atoms
    33291 
    33292 > color sel blue
    33293 
    33294 > select #54/A:162
    33295 
    33296 7 atoms, 6 bonds, 1 residue, 1 model selected 
    33297 
    33298 > select #2/I:154
    33299 
    33300 8 atoms, 7 bonds, 1 residue, 1 model selected 
    33301 
    33302 > select #54/A:162
    33303 
    33304 7 atoms, 6 bonds, 1 residue, 1 model selected 
    33305 
    33306 > show sel atoms
    33307 
    33308 > color sel orange
    33309 
    33310 > ui mousemode right select
    33311 
    33312 > select #2/I:128
    33313 
    33314 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33315 
    33316 > select #54/A:136
    33317 
    33318 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33319 
    33320 > select #2/I:128
    33321 
    33322 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33323 
    33324 > select #54/A:136
    33325 
    33326 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33327 
    33328 > show sel atoms
    33329 
    33330 > color sel blue
    33331 
    33332 > ui mousemode right rotate
    33333 
    33334 > ui mousemode right translate
    33335 
    33336 > ui mousemode right rotate
    33337 
    33338 > ui mousemode right select
    33339 
    33340 > ui mousemode right translate
    33341 
    33342 > ui mousemode right rotate
    33343 
    33344 > ui mousemode right translate
    33345 
    33346 > ui mousemode right select
    33347 
    33348 > select #2/I:157
    33349 
    33350 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33351 
    33352 > select #54/A:165
    33353 
    33354 6 atoms, 5 bonds, 1 residue, 1 model selected 
    33355 
    33356 > ui mousemode right rotate
    33357 
    33358 > ui mousemode right translate
    33359 
    33360 > ui mousemode right rotate
    33361 
    33362 > show sel atoms
    33363 
    33364 > color sel orange
    33365 
    33366 > ui mousemode right select
    33367 
    33368 > select #54/A:162
    33369 
    33370 7 atoms, 6 bonds, 1 residue, 1 model selected 
    33371 
    33372 > select #54/A:198
    33373 
    33374 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33375 
    33376 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    33377 > UASLP/Lab Virología/AlphaFold3/CHIKVaaint.cxs"
    33378 
    33379 ——— End of log from Tue Feb 11 09:48:29 2025 ———
    33380 
    33381 > view name session-start
    33382 
    33383 opened ChimeraX session 
    33384 
    33385 > show #61 models
    33386 
    33387 > hide #61 models
    33388 
    33389 > show #61 models
    33390 
    33391 > hide #54 models
    33392 
    33393 > ui mousemode right select
    33394 
    33395 > select #61/A:242
    33396 
    33397 7 atoms, 6 bonds, 1 residue, 1 model selected 
    33398 
    33399 > ui tool show "Show Sequence Viewer"
    33400 
    33401 > sequence chain #61/A
    33402 
    33403 Alignment identifier is 61/A 
    33404 
    33405 > ui mousemode right rotate
    33406 
    33407 > ui mousemode right translate
    33408 
    33409 > ui mousemode right select
    33410 
    33411 > select #61/A:234
    33412 
    33413 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33414 
    33415 > select #2/I:240
    33416 
    33417 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33418 
    33419 > select #61/A:234
    33420 
    33421 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33422 
    33423 > show sel atoms
    33424 
    33425 > color sel red
    33426 
    33427 Drag select of 1 residues 
    33428 
    33429 > ui mousemode right translate
    33430 
    33431 > ui mousemode right select
    33432 
    33433 > select #61/A:184
    33434 
    33435 7 atoms, 7 bonds, 1 residue, 1 model selected 
    33436 
    33437 > select #2/I:190
    33438 
    33439 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33440 
    33441 > select #61/A:184
    33442 
    33443 7 atoms, 7 bonds, 1 residue, 1 model selected 
    33444 
    33445 > select #61/A:185
    33446 
    33447 4 atoms, 3 bonds, 1 residue, 1 model selected 
    33448 
    33449 > select #61/A:184
    33450 
    33451 7 atoms, 7 bonds, 1 residue, 1 model selected 
    33452 
    33453 > select #2/I:190
    33454 
    33455 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33456 
    33457 > show sel atoms
    33458 
    33459 [Repeated 1 time(s)]
    33460 
    33461 > show sel cartoons
    33462 
    33463 > show sel atoms
    33464 
    33465 > show sel cartoons
    33466 
    33467 > show sel atoms
    33468 
    33469 > hide sel atoms
    33470 
    33471 > show sel atoms
    33472 
    33473 > select #61/A:184
    33474 
    33475 7 atoms, 7 bonds, 1 residue, 1 model selected 
    33476 
    33477 > show sel atoms
    33478 
    33479 > color sel magenta
    33480 
    33481 > ui mousemode right translate
    33482 
    33483 > ui mousemode right select
    33484 
    33485 > select #2/I:183
    33486 
    33487 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33488 
    33489 > select #61/A:177
    33490 
    33491 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33492 
    33493 > show sel atoms
    33494 
    33495 > color sel orange
    33496 
    33497 > ui mousemode right translate
    33498 
    33499 > ui mousemode right select
    33500 
    33501 > select #2/I:178
    33502 
    33503 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33504 
    33505 > select #61/A:172
    33506 
    33507 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33508 
    33509 > show sel cartoons
    33510 
    33511 > show sel atoms
    33512 
    33513 > color sel blue
    33514 
    33515 > ui mousemode right translate
    33516 
    33517 > color #61 #d18b68ff
    33518 
    33519 > color #61 #d48d6aff
    33520 
    33521 > color #61 #ff5500ff
    33522 
    33523 > color #61 #ff7c11ff
    33524 
    33525 > color #61 #ff7f23ff
    33526 
    33527 > color #61 #ffc44fff
    33528 
    33529 > color #61 #ffaa7fff
    33530 
    33531 > color #61 #ffa86eff
    33532 
    33533 > color #61 #ff9580ff
    33534 
    33535 > ui mousemode right "crop volume"
    33536 
    33537 > ui mousemode right translate
    33538 
    33539 > ui mousemode right select
    33540 
    33541 > select #61/A:234
    33542 
    33543 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33544 
    33545 > color sel red
    33546 
    33547 > ui mousemode right "translate selected atoms"
    33548 
    33549 > ui mousemode right select
    33550 
    33551 > select #61/A:184
    33552 
    33553 7 atoms, 7 bonds, 1 residue, 1 model selected 
    33554 
    33555 > color sel magenta
    33556 
    33557 > select #61/A:177
    33558 
    33559 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33560 
    33561 > color sel orange
    33562 
    33563 > ui mousemode right translate
    33564 
    33565 > ui mousemode right select
    33566 
    33567 > select #61/A:172
    33568 
    33569 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33570 
    33571 > color sel blue
    33572 
    33573 > select clear
    33574 
    33575 > select #2/I:178
    33576 
    33577 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33578 
    33579 > ui mousemode right select
    33580 
    33581 > select #61/A:172
    33582 
    33583 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33584 
    33585 > select #2/I:178
    33586 
    33587 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33588 
    33589 > select #61/A:172
    33590 
    33591 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33592 
    33593 > ui mousemode right translate
    33594 
    33595 > ui mousemode right select
    33596 
    33597 > select #61/A:151
    33598 
    33599 5 atoms, 4 bonds, 1 residue, 1 model selected 
    33600 
    33601 > select #2/I:157
    33602 
    33603 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33604 
    33605 > select #61/A:151
    33606 
    33607 5 atoms, 4 bonds, 1 residue, 1 model selected 
    33608 
    33609 > select #2/I:157
    33610 
    33611 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33612 
    33613 > select #61/A:151
    33614 
    33615 5 atoms, 4 bonds, 1 residue, 1 model selected 
    33616 
    33617 > show sel atoms
    33618 
    33619 > color sel gray
    33620 
    33621 > ui mousemode right select
    33622 
    33623 > select #2/I:154
    33624 
    33625 8 atoms, 7 bonds, 1 residue, 1 model selected 
    33626 
    33627 > select #61/A:148
    33628 
    33629 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33630 
    33631 > show sel atoms
    33632 
    33633 > color sel orange
    33634 
    33635 > ui mousemode right translate
    33636 
    33637 [Repeated 1 time(s)]
    33638 
    33639 > ui mousemode right select
    33640 
    33641 > select #61/A:172
    33642 
    33643 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33644 
    33645 > select #61/A:148
    33646 
    33647 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33648 
    33649 > ui mousemode right translate
    33650 
    33651 > ui mousemode right select
    33652 
    33653 > select #61/A:151
    33654 
    33655 5 atoms, 4 bonds, 1 residue, 1 model selected 
    33656 
    33657 > ui mousemode right translate
    33658 
    33659 > show sel atoms
    33660 
    33661 > hide sel atoms
    33662 
    33663 > show sel atoms
    33664 
    33665 [Repeated 1 time(s)]
    33666 
    33667 > ui mousemode right select
    33668 
    33669 > select clear
    33670 
    33671 > ui mousemode right translate
    33672 
    33673 > ui mousemode right select
    33674 
    33675 > select #2/I:128
    33676 
    33677 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33678 
    33679 > select clear
    33680 
    33681 > select #61/A:122
    33682 
    33683 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33684 
    33685 > show sel atoms
    33686 
    33687 > color sel orange
    33688 
    33689 > ui mousemode right translate
    33690 
    33691 > ui mousemode right select
    33692 
    33693 > select #2/I:126
    33694 
    33695 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33696 
    33697 > select #61/A:120
    33698 
    33699 8 atoms, 7 bonds, 1 residue, 1 model selected 
    33700 
    33701 > show sel atoms
    33702 
    33703 > color sel orange
    33704 
    33705 > ui mousemode right rotate
    33706 
    33707 > ui mousemode right translate
    33708 
    33709 > ui mousemode right select
    33710 
    33711 > select #2/I:240
    33712 
    33713 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33714 
    33715 > select #61/A:234
    33716 
    33717 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33718 
    33719 > ui mousemode right translate
    33720 
    33721 > ui mousemode right select
    33722 
    33723 > ui mousemode right translate
    33724 
    33725 > ui mousemode right select
    33726 
    33727 > select #2/I:183
    33728 
    33729 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33730 
    33731 > select #61/A:177
    33732 
    33733 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33734 
    33735 > ui mousemode right translate
    33736 
    33737 > ui mousemode right select
    33738 
    33739 > select #61/A:172
    33740 
    33741 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33742 
    33743 > select #2/I:178
    33744 
    33745 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33746 
    33747 > ui mousemode right translate
    33748 
    33749 > ui mousemode right rotate
    33750 
    33751 > ui mousemode right select
    33752 
    33753 > select #61/A:151
    33754 
    33755 5 atoms, 4 bonds, 1 residue, 1 model selected 
    33756 
    33757 > select #2/I:157
    33758 
    33759 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33760 
    33761 > select #2/I:154
    33762 
    33763 8 atoms, 7 bonds, 1 residue, 1 model selected 
    33764 
    33765 > select #2/I:154
    33766 
    33767 8 atoms, 7 bonds, 1 residue, 1 model selected 
    33768 
    33769 > select #2/I:154
    33770 
    33771 8 atoms, 7 bonds, 1 residue, 1 model selected 
    33772 
    33773 > select #61/A:148
    33774 
    33775 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33776 
    33777 > ui mousemode right translate
    33778 
    33779 > ui mousemode right select
    33780 
    33781 > select #2/I:128
    33782 
    33783 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33784 
    33785 > ui mousemode right select
    33786 
    33787 > select #2/I:128
    33788 
    33789 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33790 
    33791 > select #61/A:122
    33792 
    33793 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33794 
    33795 > select #61/A:120
    33796 
    33797 8 atoms, 7 bonds, 1 residue, 1 model selected 
    33798 
    33799 > select #2/I:126
    33800 
    33801 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33802 
    33803 > select #61/A:120
    33804 
    33805 8 atoms, 7 bonds, 1 residue, 1 model selected 
    33806 
    33807 > ui mousemode right translate
    33808 
    33809 > save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
    33810 > UASLP/Lab Virología/AlphaFold3/CHIKVaaint.cxs"
    33811 
    33812 ——— End of log from Fri Feb 21 21:14:08 2025 ———
    33813 
    33814 > view name session-start
    33815 
    33816 opened ChimeraX session 
    33817 
    33818 > hide #61 models
    33819 
    33820 > show #67 models
    33821 
    33822 > ui mousemode right rotate
    33823 
    33824 [Repeated 1 time(s)]
    33825 
    33826 > ui mousemode right translate
    33827 
    33828 > ui mousemode right select
    33829 
    33830 > select #67/A:242
    33831 
    33832 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33833 
    33834 > select #2/I:240
    33835 
    33836 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33837 
    33838 > select #2/I:240
    33839 
    33840 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33841 
    33842 > select #67/A:242
    33843 
    33844 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33845 
    33846 > ui tool show "Show Sequence Viewer"
    33847 
    33848 > sequence chain #67/A
    33849 
    33850 Alignment identifier is 67/A 
    33851 
    33852 > show sel atoms
    33853 
    33854 > color sel red
    33855 
    33856 > select #2/I:240
    33857 
    33858 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33859 
    33860 > ui mousemode right translate
    33861 
    33862 > ui mousemode right select
    33863 
    33864 > select #2/I:190
    33865 
    33866 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33867 
    33868 > select #67/A:192
    33869 
    33870 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33871 
    33872 > show sel atoms
    33873 
    33874 > select #2/I:190
    33875 
    33876 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33877 
    33878 > select #67/A:192
    33879 
    33880 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33881 
    33882 > color sel orange
    33883 
    33884 > ui mousemode right translate
    33885 
    33886 > ui mousemode right select
    33887 
    33888 > select #2/I:183
    33889 
    33890 9 atoms, 8 bonds, 1 residue, 1 model selected 
    33891 
    33892 > select #67/A:185
    33893 
    33894 9 atoms, 8 bonds, 1 residue, 1 model selected 
     3589[deleted to fit within ticket limits]
     3590
    338953591
    338963592> show sel atoms