Changes between Initial Version and Version 1 of Ticket #20051


Ignore:
Timestamp:
Mar 23, 2026, 10:51:30 AM (3 hours ago)
Author:
Eric Pettersen
Comment:

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  • Ticket #20051

    • Property Cc chimera-programmers added
    • Property Component Unassigned → Window Toolkit
    • Property Owner set to Zach Pearson
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → Crash in QWindowContainer::parentWasChanged

  • Ticket #20051 – Description

    initial v1  
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     675[deleted to fit within ticket limits]
     676
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    … …  
    36292191> color #1 bychain
    36302192
    3631 > color bfactor #1 palette alphafold
    3632 
    3633 5188 atoms, 653 residues, atom bfactor range 14.1 to 98.7 
    3634 
    3635 > ui tool show "Show Sequence Viewer"
    3636 
    3637 > sequence chain #1/A
    3638 
    3639 Alignment identifier is 1/A 
    3640 
    3641 > sequence chain #1/B
    3642 
    3643 Alignment identifier is 1/B 
    3644 
    3645 > select #1/B:47
    3646 
    3647 9 atoms, 8 bonds, 1 residue, 1 model selected 
    3648 
    3649 > select #1/B:47-50
    3650 
    3651 32 atoms, 31 bonds, 4 residues, 1 model selected 
    3652 
    3653 > select #1/B:138-139
    3654 
    3655 20 atoms, 20 bonds, 2 residues, 1 model selected 
    3656 
    3657 > select #1/B:138-146
    3658 
    3659 75 atoms, 76 bonds, 9 residues, 1 model selected 
    3660 
    3661 > select #1/B:1
    3662 
    3663 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3664 
    3665 > select #1/B:1-135
    3666 
    3667 1019 atoms, 1036 bonds, 135 residues, 1 model selected 
    3668 
    3669 > hide sel cartoons
    3670 
    3671 > color sel bychain
    3672 
    3673 [Repeated 1 time(s)]
    3674 
    3675 > select add #1
    3676 
    3677 5188 atoms, 5286 bonds, 653 residues, 1 model selected 
    3678 
    3679 > color sel bychain
    3680 
    3681 > color bfactor #1 palette alphafold
    3682 
    3683 5188 atoms, 653 residues, atom bfactor range 14.1 to 98.7 
    3684 
    3685 > color sel bychain
    3686 
    3687 > color bfactor #1 palette alphafold
    3688 
    3689 5188 atoms, 653 residues, atom bfactor range 14.1 to 98.7 
    3690 
    3691 > select subtract #1
    3692 
    3693 Nothing selected 
    3694 
    3695 > select #1/A:188
    3696 
    3697 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3698 
    3699 > select #1/A:259
    3700 
    3701 6 atoms, 5 bonds, 1 residue, 1 model selected 
    3702 
    3703 > select #1/A:192-259
    3704 
    3705 538 atoms, 545 bonds, 68 residues, 1 model selected 
    3706 
    3707 > hide sel cartoons
    3708 
    3709 > select #1/A:1
    3710 
    3711 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3712 
    3713 > select #1/A:1-6
    3714 
    3715 57 atoms, 58 bonds, 6 residues, 1 model selected 
    3716 
    3717 > color sel bychain
    3718 
    3719 > select add #1
    3720 
    3721 5188 atoms, 5286 bonds, 653 residues, 1 model selected 
    3722 
    3723 > color sel bychain
    3724 
    3725 > view matrix models
    3726 > #1,0.33487,-0.12445,-0.93401,-7.4476,-0.80193,0.48281,-0.35184,-5.6803,0.49474,0.86684,0.061879,-8.5074
    3727 
    3728 > view matrix models
    3729 > #1,0.33487,-0.12445,-0.93401,-9.3257,-0.80193,0.48281,-0.35184,2.7441,0.49474,0.86684,0.061879,-8.0506
    3730 
    3731 > select #1
    3732 
    3733 5188 atoms, 5286 bonds, 653 residues, 1 model selected 
    3734 
    3735 > show sel cartoons
    3736 
    3737 > undo
    3738 
    3739 > coulombic sel
    3740 
    3741 Using Amber 20 recommended default charges and atom types for standard
    3742 residues 
    3743 Coulombic values for fold_brh2_myst_model_0.cif_A SES surface #1.1: minimum,
    3744 -23.03, mean -4.12, maximum 9.12 
    3745 Coulombic values for fold_brh2_myst_model_0.cif_B SES surface #1.2: minimum,
    3746 -12.84, mean 1.69, maximum 25.66 
    3747 To also show corresponding color key, enter the above coulombic command and
    3748 add key true 
    3749 
    3750 > hide sel surfaces
    3751 
    3752 [Repeated 1 time(s)]
    3753 
    3754 > coulombic sel
    3755 
    3756 Coulombic values for fold_brh2_myst_model_0.cif_A SES surface #1.1: minimum,
    3757 -23.03, mean -4.12, maximum 9.12 
    3758 Coulombic values for fold_brh2_myst_model_0.cif_B SES surface #1.2: minimum,
    3759 -12.84, mean 1.69, maximum 25.66 
    3760 To also show corresponding color key, enter the above coulombic command and
    3761 add key true 
    3762 
    3763 > coulombic sel
    3764 
    3765 Coulombic values for fold_brh2_myst_model_0.cif_A SES surface #1.1: minimum,
    3766 -23.03, mean -4.12, maximum 9.12 
    3767 Coulombic values for fold_brh2_myst_model_0.cif_B SES surface #1.2: minimum,
    3768 -12.84, mean 1.69, maximum 25.66 
    3769 To also show corresponding color key, enter the above coulombic command and
    3770 add key true 
    3771 
    3772 > hide sel surfaces
    3773 
    3774 > select #1
    3775 
    3776 5188 atoms, 5286 bonds, 653 residues, 1 model selected 
    3777 
    3778 > show sel cartoons
    3779 
    3780 > undo
    3781 
    3782 > open
    3783 > /Users/sz140275local/Downloads/fold_brca2_spat22/fold_brca2_spat22_model_0.cif
    3784 
    3785 Chain information for fold_brca2_spat22_model_0.cif #3 
    3786 --- 
    3787 Chain | Description 
    3788 A | . 
    3789 B | . 
    3790  
    3791 Computing secondary structure 
    3792 
    3793 > hide #!1 models
    3794 
    3795 > select subtract #1
    3796 
    3797 2 models selected 
    3798 
    3799 > select #3/A
    3800 
    3801 2902 atoms, 2962 bonds, 363 residues, 1 model selected 
    3802 
    3803 > hide sel cartoons
    3804 
    3805 > mmaker #3/B to #1
    3806 
    3807 Computing secondary structure 
    3808 [Repeated 1 time(s)]  Parameters 
    3809 --- 
    3810 Chain pairing | bb 
    3811 Alignment algorithm | Needleman-Wunsch 
    3812 Similarity matrix | BLOSUM-62 
    3813 SS fraction | 0.3 
    3814 Gap open (HH/SS/other) | 18/18/6 
    3815 Gap extend | 1 
    3816 SS matrix |  |  | H | S | O 
    3817 ---|---|---|--- 
    3818 H | 6 | -9 | -6 
    3819 S |  | 6 | -6 
    3820 O |  |  | 4 
    3821 Iteration cutoff | 2 
    3822  
    3823 Matchmaker fold_brh2_myst_model_0.cif, chain B (#1) with
    3824 fold_brca2_spat22_model_0.cif, chain B (#3), sequence alignment score = 134.6 
    3825 RMSD between 11 pruned atom pairs is 1.151 angstroms; (across all 122 pairs:
    3826 68.784) 
    3827  
    3828 
    3829 > show #!1 models
    3830 
    3831 > select add #3
    3832 
    3833 12221 atoms, 12475 bonds, 1531 residues, 1 model selected 
    3834 
    3835 > select subtract #3
    3836 
    3837 Nothing selected 
    3838 
    3839 > hide #!1 models
    3840 
    3841 > select #3/B:915-1400
    3842 
    3843 1972 atoms, 2006 bonds, 254 residues, 1 model selected 
    3844 
    3845 > hide sel cartoons
    3846 
    3847 > view matrix models
    3848 > #3,0.98522,-0.11524,0.12675,-38.628,0.1099,-0.1424,-0.98369,-60.891,0.13141,0.98308,-0.12763,-42.651
    3849 
    3850 > view matrix models
    3851 > #3,0.98522,-0.11524,0.12675,-20.811,0.1099,-0.1424,-0.98369,-75.905,0.13141,0.98308,-0.12763,-23.979
    3852 
    3853 > select add #3
    3854 
    3855 12221 atoms, 12475 bonds, 1531 residues, 1 model selected 
    3856 
    3857 > select subtract #3
    3858 
    3859 Nothing selected 
    3860 
    3861 > hide #3 models
    3862 
    3863 > show #!1 models
    3864 
    3865 > show #3 models
    3866 
    3867 > hide #3 models
    3868 
    3869 > show #3 models
    3870 
    3871 > hide #3 models
    3872 
    3873 > show #3 models
    3874 
    3875 > mmaker #3/B:228-914 to #1
    3876 
    3877 Computing secondary structure 
    3878 [Repeated 1 time(s)]  Parameters 
    3879 --- 
    3880 Chain pairing | bb 
    3881 Alignment algorithm | Needleman-Wunsch 
    3882 Similarity matrix | BLOSUM-62 
    3883 SS fraction | 0.3 
    3884 Gap open (HH/SS/other) | 18/18/6 
    3885 Gap extend | 1 
    3886 SS matrix |  |  | H | S | O 
    3887 ---|---|---|--- 
    3888 H | 6 | -9 | -6 
    3889 S |  | 6 | -6 
    3890 O |  |  | 4 
    3891 Iteration cutoff | 2 
    3892  
    3893 Matchmaker fold_brh2_myst_model_0.cif, chain B (#1) with
    3894 fold_brca2_spat22_model_0.cif, chain B (#3), sequence alignment score = 50.2 
    3895 RMSD between 20 pruned atom pairs is 0.237 angstroms; (across all 23 pairs:
    3896 4.177) 
    3897  
    3898 
    3899 > hide #!1 models
    3900 
    3901 > hide #3 models
    3902 
    3903 > show #!1 models
    3904 
    3905 > show #3 models
    3906 
    3907 > hide #3 models
    3908 
    3909 > show #3 models
    3910 
    3911 > hide #!1 models
    3912 
    3913 > select #3/B:1-22!
    3914 
    3915 Expected an objects specifier or a keyword 
    3916 
    3917 > select #3/B:1-228
    3918 
    3919 1845 atoms, 1882 bonds, 228 residues, 1 model selected 
    3920 
    3921 > hide sel cartoons
    3922 
    3923 > mmaker #3/B:228-556 #1/A
    3924 
    3925 > matchmaker #3/B:228-556 #1/A
    3926 
    3927 Missing required "to" argument 
    3928 
    3929 > show #!1 models
    3930 
    3931 > mmaker #3/B:228-556 to #1/B
    3932 
    3933 Computing secondary structure 
    3934 [Repeated 1 time(s)]  Parameters 
    3935 --- 
    3936 Chain pairing | bb 
    3937 Alignment algorithm | Needleman-Wunsch 
    3938 Similarity matrix | BLOSUM-62 
    3939 SS fraction | 0.3 
    3940 Gap open (HH/SS/other) | 18/18/6 
    3941 Gap extend | 1 
    3942 SS matrix |  |  | H | S | O 
    3943 ---|---|---|--- 
    3944 H | 6 | -9 | -6 
    3945 S |  | 6 | -6 
    3946 O |  |  | 4 
    3947 Iteration cutoff | 2 
    3948  
    3949 Matchmaker fold_brh2_myst_model_0.cif, chain B (#1) with
    3950 fold_brca2_spat22_model_0.cif, chain B (#3), sequence alignment score = 50.2 
    3951 RMSD between 20 pruned atom pairs is 0.237 angstroms; (across all 23 pairs:
    3952 4.177) 
    3953  
    3954 
    3955 > mmaker #3/B:228-556 to #1/B
    3956 
    3957 Computing secondary structure 
    3958 [Repeated 1 time(s)]  Parameters 
    3959 --- 
    3960 Chain pairing | bb 
    3961 Alignment algorithm | Needleman-Wunsch 
    3962 Similarity matrix | BLOSUM-62 
    3963 SS fraction | 0.3 
    3964 Gap open (HH/SS/other) | 18/18/6 
    3965 Gap extend | 1 
    3966 SS matrix |  |  | H | S | O 
    3967 ---|---|---|--- 
    3968 H | 6 | -9 | -6 
    3969 S |  | 6 | -6 
    3970 O |  |  | 4 
    3971 Iteration cutoff | 2 
    3972  
    3973 Matchmaker fold_brh2_myst_model_0.cif, chain B (#1) with
    3974 fold_brca2_spat22_model_0.cif, chain B (#3), sequence alignment score = 50.2 
    3975 RMSD between 20 pruned atom pairs is 0.237 angstroms; (across all 23 pairs:
    3976 4.177) 
    3977  
    3978 
    3979 > view matrix models
    3980 > #3,0.301,-0.92979,0.21186,-48.674,-0.74443,-0.36795,-0.55716,-37.368,0.596,0.0099913,-0.80292,-32.751
    3981 
    3982 > hide #!1 models
    3983 
    3984 > show #2 models
    3985 
    3986 > hide #2 models
    3987 
    3988 > show #2 models
    3989 
    3990 > hide #2 models
    3991 
    3992 > mmaker #3/B:228-556 to #2/B
    3993 
    3994 Computing secondary structure 
    3995 [Repeated 1 time(s)]  Parameters 
    3996 --- 
    3997 Chain pairing | bb 
    3998 Alignment algorithm | Needleman-Wunsch 
    3999 Similarity matrix | BLOSUM-62 
    4000 SS fraction | 0.3 
    4001 Gap open (HH/SS/other) | 18/18/6 
    4002 Gap extend | 1 
    4003 SS matrix |  |  | H | S | O 
    4004 ---|---|---|--- 
    4005 H | 6 | -9 | -6 
    4006 S |  | 6 | -6 
    4007 O |  |  | 4 
    4008 Iteration cutoff | 2 
    4009  
    4010 Matchmaker
    4011 Myst_BRC2_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_97616.pdb,
    4012 chain B (#2) with fold_brca2_spat22_model_0.cif, chain B (#3), sequence
    4013 alignment score = 50.2 
    4014 RMSD between 20 pruned atom pairs is 0.332 angstroms; (across all 23 pairs:
    4015 4.056) 
    4016  
    4017 
    4018 > show #2 models
    4019 
    4020 > view matrix models
    4021 > #3,0.31129,-0.9166,0.25088,-41.935,-0.71012,-0.39979,-0.57956,-45.992,0.63153,0.0022549,-0.77535,-27.68
    4022 
    4023 > view matrix models
    4024 > #3,0.31129,-0.9166,0.25088,-54.534,-0.71012,-0.39979,-0.57956,-57.743,0.63153,0.0022549,-0.77535,-45.976
    4025 
    4026 > view matrix models
    4027 > #3,0.31129,-0.9166,0.25088,-72.304,-0.71012,-0.39979,-0.57956,-83.833,0.63153,0.0022549,-0.77535,-79.858
    4028 
    4029 > select add #3
    4030 
    4031 12221 atoms, 12475 bonds, 1531 residues, 1 model selected 
    4032 
    4033 > select subtract #3
    4034 
    4035 Nothing selected 
    4036 
    4037 > select add #1
    4038 
    4039 5188 atoms, 5286 bonds, 653 residues, 1 model selected 
    4040 
    4041 > select add #2
    4042 
    4043 10374 atoms, 10570 bonds, 1306 residues, 4 models selected 
    4044 
    4045 > select add #3
    4046 
    4047 22595 atoms, 23045 bonds, 2837 residues, 5 models selected 
    4048 
    4049 > open 7bdx
    4050 
    4051 7bdx title: 
    4052 Armadillo domain of HSF2BP in complex with BRCA2 peptide [more info...] 
    4053  
    4054 Chain information for 7bdx #4 
    4055 --- 
    4056 Chain | Description | UniProt 
    4057 A B C D | Heat shock factor 2-binding protein | HSF2B_HUMAN 122-334 
    4058 E F | Breast cancer type 2 susceptibility protein | BRCA2_HUMAN 2291-2343 
    4059  
    4060 Non-standard residues in 7bdx #4 
    4061 --- 
    4062 MG — magnesium ion 
    4063  
    4064 
    4065 > select subtract #1
    4066 
    4067 17407 atoms, 17759 bonds, 2184 residues, 4 models selected 
    4068 
    4069 > select subtract #2
    4070 
    4071 12221 atoms, 12475 bonds, 1531 residues, 1 model selected 
    4072 
    4073 > select subtract #3
    4074 
    4075 Nothing selected 
    4076 
    4077 > hide #2 models
    4078 
    4079 > hide #3 models
    4080 
    4081 > hide #!4 atoms
    4082 
    4083 > show #!4 cartoons
    4084 
    4085 > ui tool show "Show Sequence Viewer"
    4086 
    4087 > sequence chain #4/F
    4088 
    4089 Alignment identifier is 4/F 
    4090 
    4091 > select #4/F:2308
    4092 
    4093 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4094 
    4095 > select #4/F:2308
    4096 
    4097 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4098 
    4099 > select #4/F:2303
    4100 
    4101 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4102 
    4103 > select #4/F:2303
    4104 
    4105 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4106 
    4107 > style sel stick
    4108 
    4109 Changed 6 atom styles 
    4110 
    4111 > select #4/F:2307
    4112 
    4113 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4114 
    4115 > select #4/F:2307
    4116 
    4117 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4118 
    4119 > style sel stick
    4120 
    4121 Changed 6 atom styles 
    4122 
    4123 > show sel atoms
    4124 
    4125 > select #4/F:2303
    4126 
    4127 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4128 
    4129 > select #4/F:2303
    4130 
    4131 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4132 
    4133 > show sel atoms
    4134 
    4135 > select #4/F:2309
    4136 
    4137 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4138 
    4139 > select #4/F:2309-2310
    4140 
    4141 13 atoms, 12 bonds, 2 residues, 1 model selected 
    4142 
    4143 > show sel atoms
    4144 
    4145 > view matrix models #4,1,0,0,-14.296,0,1,0,10.173,0,0,1,-2.0796
    4146 
    4147 > style sel stick
    4148 
    4149 Changed 13 atom styles 
    4150 
    4151 > color sel red
    4152 
    4153 > style sel sphere
    4154 
    4155 Changed 13 atom styles 
    4156 
    4157 > select #4/F:2306-2307
    4158 
    4159 11 atoms, 10 bonds, 2 residues, 1 model selected 
    4160 
    4161 > select #4/F:2306-2307
    4162 
    4163 11 atoms, 10 bonds, 2 residues, 1 model selected 
    4164 
    4165 > select #4/F:2307
    4166 
    4167 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4168 
    4169 > select #4/F:2307
    4170 
    4171 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4172 
    4173 > show sel atoms
    4174 
    4175 > style sel sphere
    4176 
    4177 Changed 6 atom styles 
    4178 
    4179 > color sel red
    4180 
    4181 > select #4/F:2303
    4182 
    4183 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4184 
    4185 > select #4/F:2303
    4186 
    4187 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4188 
    4189 > show sel atoms
    4190 
    4191 > style sel sphere
    4192 
    4193 Changed 6 atom styles 
    4194 
    4195 > color sel red
    4196 
    4197 > select #4/D
    4198 
    4199 1603 atoms, 1604 bonds, 233 residues, 1 model selected 
    4200 
    4201 > coulombic sel
    4202 
    4203 The following residues are missing heavy (non-hydrogen) atoms, which may
    4204 result in inaccurate electrostatics: 
    4205 7bdx #4/D ALA 121 
    4206 7bdx #4/D GLN 173 
    4207 7bdx #4/D GLU 174 
    4208 7bdx #4/D LEU 175 
    4209 7bdx #4/D PHE 296 
    4210 7bdx #4/D ARG 297 
    4211 7bdx #4/D SER 298 
    4212 7bdx #4/D ARG 315 
    4213 7bdx #4/D LEU 327 
    4214 7bdx #4/D GLU 331 
    4215 
    4216 Using Amber 20 recommended default charges and atom types for standard
    4217 residues 
    4218 Coulombic values for 7bdx_D SES surface #4.2: minimum, -19.52, mean -2.41,
    4219 maximum 13.54 
    4220 To also show corresponding color key, enter the above coulombic command and
    4221 add key true 
    4222 
    4223 > view matrix models #4,1,0,0,-29.844,0,1,0,16.522,0,0,1,-7.8195
    4224 
    4225 > style sel stick
    4226 
    4227 Changed 1603 atom styles 
    4228 
    4229 > style sel stick
    4230 
    4231 Changed 1603 atom styles 
    4232 
    4233 > select add #4
    4234 
    4235 7434 atoms, 7385 bonds, 2 pseudobonds, 1110 residues, 3 models selected 
    4236 
    4237 > style sel stick
    4238 
    4239 Changed 7434 atom styles 
    4240 
    4241 > select subtract #4
    4242 
    4243 1 model selected 
    4244 
    4245 > select #4/F:2309
    4246 
    4247 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4248 
    4249 > select #4/F:2309
    4250 
    4251 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4252 
    4253 > select #4/F:2307
    4254 
    4255 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4256 
    4257 > select #4/F:2306-2307
    4258 
    4259 11 atoms, 10 bonds, 2 residues, 1 model selected 
    4260 
    4261 > select #4/F:2309
    4262 
    4263 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4264 
    4265 > select #4/F:2309
    4266 
    4267 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4268 
    4269 > select #4/F:2310
    4270 
    4271 7 atoms, 6 bonds, 1 residue, 1 model selected 
    4272 
    4273 > select #4/F:2310
    4274 
    4275 7 atoms, 6 bonds, 1 residue, 1 model selected 
    4276 
    4277 > select #4/B
    4278 
    4279 1673 atoms, 1653 bonds, 1 pseudobond, 257 residues, 2 models selected 
    4280 
    4281 > coulombic sel
    4282 
    4283 The following heavy (non-hydrogen) atoms are missing, which may result in
    4284 inaccurate electrostatics: 
    4285 7bdx #4/B ALA 121 CB 
    4286 
    4287 Using Amber 20 recommended default charges and atom types for standard
    4288 residues 
    4289 Coulombic values for 7bdx_B SES surface #4.3: minimum, -18.08, mean -2.65,
    4290 maximum 8.50 
    4291 To also show corresponding color key, enter the above coulombic command and
    4292 add key true 
    4293 
    4294 > view matrix models #4,1,0,0,-17.975,0,1,0,11.313,0,0,1,-9.6789
    4295 
    4296 > transparency sel 50
    4297 
    4298 > open
    4299 > /Users/sz140275local/Downloads/fold_brca2_plk1/fold_brca2_plk1_model_0.cif
    4300 
    4301 Chain information for fold_brca2_plk1_model_0.cif #5 
    4302 --- 
    4303 Chain | Description 
    4304 A | . 
    4305 B | . 
    4306  
    4307 Computing secondary structure 
    4308 
    4309 > hide #!4 models
    4310 
    4311 > select add #4
    4312 
    4313 7434 atoms, 7385 bonds, 2 pseudobonds, 1110 residues, 3 models selected 
    4314 
    4315 > select subtract #4
    4316 
    4317 2 models selected 
    4318 
    4319 > open 6GY2
    4320 
    4321 6gy2 title: 
    4322 Crystal structure of human Plk1-PBD in complex with WSSSLATPPTLSSpTVLI
    4323 phosphopeptide from BRCA2 [more info...] 
    4324  
    4325 Chain information for 6gy2 #6 
    4326 --- 
    4327 Chain | Description | UniProt 
    4328 A B | Serine/threonine-protein kinase PLK1 | PLK1_HUMAN 365-603 
    4329 C D | Phosphopeptide of BRCA2 |   
    4330  
    4331 Non-standard residues in 6gy2 #6 
    4332 --- 
    4333 GOL — glycerol (glycerin; propane-1,2,3-triol) 
    4334  
    4335 6gy2 mmCIF Assemblies 
    4336 --- 
    4337 1| software_defined_assembly 
    4338 2| software_defined_assembly 
    4339  
    4340 
    4341 > mmaker #5 to #6
    4342 
    4343 Computing secondary structure 
    4344 [Repeated 1 time(s)]  Parameters 
    4345 --- 
    4346 Chain pairing | bb 
    4347 Alignment algorithm | Needleman-Wunsch 
    4348 Similarity matrix | BLOSUM-62 
    4349 SS fraction | 0.3 
    4350 Gap open (HH/SS/other) | 18/18/6 
    4351 Gap extend | 1 
    4352 SS matrix |  |  | H | S | O 
    4353 ---|---|---|--- 
    4354 H | 6 | -9 | -6 
    4355 S |  | 6 | -6 
    4356 O |  |  | 4 
    4357 Iteration cutoff | 2 
    4358  
    4359 Matchmaker 6gy2, chain B (#6) with fold_brca2_plk1_model_0.cif, chain B (#5),
    4360 sequence alignment score = 1188.3 
    4361 RMSD between 216 pruned atom pairs is 0.519 angstroms; (across all 224 pairs:
    4362 1.056) 
    4363  
    4364 
    4365 > select #6/A
    4366 
    4367 1834 atoms, 1861 bonds, 235 residues, 1 model selected 
    4368 
    4369 > hide sel cartoons
    4370 
    4371 > hide sel atoms
    4372 
    4373 > select #6/D
    4374 
    4375 89 atoms, 88 bonds, 14 residues, 1 model selected 
    4376 
    4377 > hide sel cartoons
    4378 
    4379 > select add #6
    4380 
    4381 3842 atoms, 3897 bonds, 495 residues, 1 model selected 
    4382 
    4383 > hide #5 models
    4384 
    4385 > select subtract #6
    4386 
    4387 Nothing selected 
    4388 
    4389 > select #6/C
    4390 
    4391 88 atoms, 88 bonds, 13 residues, 1 model selected 
    4392 
    4393 > color sel green
    4394 
    4395 > select add #6
    4396 
    4397 3842 atoms, 3897 bonds, 495 residues, 1 model selected 
    4398 
    4399 > select subtract #6
    4400 
    4401 Nothing selected 
    4402 
    4403 > show #5 models
    4404 
    4405 > select #5/A
    4406 
    4407 265 atoms, 267 bonds, 33 residues, 1 model selected 
    4408 
    4409 > ui tool show "Show Sequence Viewer"
    4410 
    4411 > sequence chain #5/A
    4412 
    4413 Alignment identifier is 5/A 
    4414 
    4415 > select #5/A:30
    4416 
    4417 11 atoms, 10 bonds, 1 residue, 1 model selected 
    4418 
    4419 > select #5/A:30
    4420 
    4421 11 atoms, 10 bonds, 1 residue, 1 model selected 
    4422 
    4423 > show sel atoms
    4424 
    4425 > view matrix models
    4426 > #5,-0.95566,-0.26059,-0.13714,-21.364,-0.030473,0.55072,-0.83413,-19.947,0.29289,-0.79297,-0.53424,28.29
    4427 
    4428 > select add #5
    4429 
    4430 2391 atoms, 2435 bonds, 296 residues, 1 model selected 
    4431 
    4432 > select subtract #5
    4433 
    4434 Nothing selected 
    4435 
    4436 > select #6/C:207
    4437 
    4438 11 atoms, 10 bonds, 1 residue, 1 model selected 
    4439 
    4440 > show sel atoms
    4441 
    4442 > hide #5 models
    4443 
    4444 > hide #6 models
    4445 
    4446 > select add #6
    4447 
    4448 3842 atoms, 3897 bonds, 495 residues, 1 model selected 
    4449 
    4450 > show #!4 models
    4451 
    4452 > select subtract #6
    4453 
    4454 Nothing selected 
    4455 
    4456 > view #6 clip false
    4457 
    4458 > select add #4
    4459 
    4460 7434 atoms, 7385 bonds, 2 pseudobonds, 1110 residues, 2 models selected 
    4461 
    4462 > show #6 target m
    4463 
    4464 > hide #6 models
    4465 
    4466 > show #!4 target m
    4467 
    4468 > view #4 clip false
    4469 
    4470 > select subtract #4
    4471 
    4472 2 models selected 
    4473 
    4474 > hide #!4 models
    4475 
    4476 > show #!1 models
    4477 
    4478 > show #!4 target m
    4479 
    4480 > hide #!4 models
    4481 
    4482 > select add #1
    4483 
    4484 5188 atoms, 5286 bonds, 653 residues, 1 model selected 
    4485 
    4486 > show #!1 target m
    4487 
    4488 > view #1 clip false
    4489 
    4490 > select subtract #1
    4491 
    4492 2 models selected 
    4493 
    4494 > ui tool show "Show Sequence Viewer"
    4495 
    4496 > sequence chain #1/A
    4497 
    4498 Alignment identifier is 1/A 
    4499 
    4500 > sequence chain #1/B
    4501 
    4502 Alignment identifier is 1/B 
    4503 
    4504 > select #1/B:136
    4505 
    4506 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4507 
    4508 > select #1/B:136-138
    4509 
    4510 29 atoms, 29 bonds, 3 residues, 1 model selected 
    4511 
    4512 > select #1/B:136
    4513 
    4514 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4515 
    4516 > select #1/B:136-356
    4517 
    4518 1796 atoms, 1828 bonds, 221 residues, 1 model selected 
    4519 
    4520 > select #1/B:136
    4521 
    4522 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4523 
    4524 > select #1/B:136-394
    4525 
    4526 2124 atoms, 2165 bonds, 259 residues, 1 model selected 
    4527 
    4528 > select #1/A:178
    4529 
    4530 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4531 
    4532 > select #1/A:178-232
    4533 
    4534 423 atoms, 426 bonds, 55 residues, 1 model selected 
    4535 
    4536 > select #1/A:259
    4537 
    4538 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4539 
    4540 > select #1/A
    4541 
    4542 2045 atoms, 2084 bonds, 259 residues, 1 model selected 
    4543 
    4544 > select #1/A:197
    4545 
    4546 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4547 
    4548 > select #1/A:191-197
    4549 
    4550 43 atoms, 42 bonds, 7 residues, 1 model selected 
    4551 
    4552 > select #1/A:1
    4553 
    4554 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4555 
    4556 > select #1/A:1-191
    4557 
    4558 1507 atoms, 1538 bonds, 191 residues, 1 model selected 
    4559 
    4560 > open
    4561 > /Users/sz140275local/Downloads/fold_protsimer/fold_protsimer_model_0.cif
    4562 
    4563 Chain information for fold_protsimer_model_0.cif #7 
    4564 --- 
    4565 Chain | Description 
    4566 A B | . 
    4567  
    4568 Computing secondary structure 
    4569 
    4570 > hide #!1 models
    4571 
    4572 > select add #1
    4573 
    4574 5188 atoms, 5286 bonds, 653 residues, 2 models selected 
    4575 
    4576 > select subtract #1
    4577 
    4578 2 models selected 
    4579 
    4580 > select #7/A
    4581 
    4582 2214 atoms, 2260 bonds, 277 residues, 1 model selected 
    4583 
    4584 > color sel lime
    4585 
    4586 > select add #7
    4587 
    4588 4428 atoms, 4520 bonds, 554 residues, 1 model selected 
    4589 
    4590 > select subtract #7
    4591 
    4592 Nothing selected 
    4593 
    4594 > select #7/B
    4595 
    4596 2214 atoms, 2260 bonds, 277 residues, 1 model selected 
    4597 
    4598 > color bfactor #7/B palette alphafold
    4599 
    4600 2214 atoms, 277 residues, atom bfactor range 20.2 to 97.4 
    4601 
    4602 > select add #7
    4603 
    4604 4428 atoms, 4520 bonds, 554 residues, 1 model selected 
    4605 
    4606 > select subtract #7
    4607 
    4608 Nothing selected 
    4609 
    4610 > select #1/A:195
    4611 
    4612 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4613 
    4614 > select #1/A:195-254
    4615 
    4616 477 atoms, 483 bonds, 60 residues, 1 model selected 
    4617 
    4618 > ui tool show "Show Sequence Viewer"
    4619 
    4620 > sequence chain #7/A
    4621 
    4622 Alignment identifier is 7/A 
    4623 
    4624 > select #7/A:251-277
    4625 
    4626 226 atoms, 230 bonds, 27 residues, 1 model selected 
    4627 
    4628 > select #7/A:198-277
    4629 
    4630 623 atoms, 640 bonds, 80 residues, 1 model selected 
    4631 
    4632 > view matrix models #7,1,0,0,-12.479,0,1,0,-6.7066,0,0,1,-23.359
    4633 
    4634 > view matrix models #7,1,0,0,12.034,0,1,0,-10.279,0,0,1,2.7897
    4635 
    4636 > view matrix models #7,1,0,0,26.561,0,1,0,-12.856,0,0,1,43.524
    4637 
    4638 > view matrix models #7,1,0,0,31.721,0,1,0,-20.189,0,0,1,28.966
    4639 
    4640 > select #7/B:83
    4641 
    4642 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4643 
    4644 > select #7/B:80
    4645 
    4646 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4647 
    4648 > select #7/A:80
    4649 
    4650 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4651 
    4652 > color #7/B pinlk
    4653 
    4654 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    4655 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    4656 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    4657 
    4658 > color #7/B pink
    4659 
    4660 > view matrix models #7,1,0,0,6.1539,0,1,0,-29.134,0,0,1,13.662
    4661 
    4662 > open /Users/sz140275local/Downloads/AF-Q86WS4-F1-model_v4.pdb
    4663 
    4664 AF-Q86WS4-F1-model_v4.pdb title: 
    4665 Alphafold monomer V2.0 prediction for uncharacterized protein C12ORF40
    4666 (Q86WS4) [more info...] 
    4667  
    4668 Chain information for AF-Q86WS4-F1-model_v4.pdb #8 
    4669 --- 
    4670 Chain | Description | UniProt 
    4671 A | uncharacterized protein C12ORF40 | CL040_HUMAN 1-652 
    4672  
    4673 Computing secondary structure 
    4674 
    4675 > hide #7 models
    4676 
    4677 > select add #7
    4678 
    4679 4428 atoms, 4520 bonds, 554 residues, 1 model selected 
    4680 
    4681 > select subtract #7
    4682 
    4683 Nothing selected 
    4684 
    4685 > color bfactor #7/ palette alphafold
    4686 
    4687 > color byattribute bfactor #7/ palette alphafold
    4688 
    4689 Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
    4690 or a keyword 
    4691 
    4692 > color bfactor #8 palette alphafold
    4693 
    4694 5207 atoms, 652 residues, atom bfactor range 27.4 to 92.7 
    4695 
    4696 > hide #8 models
    4697 
    4698 > show #7 models
    4699 
    4700 > select #7/A:1
    4701 
    4702 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4703 
    4704 > select #7/A:1-197
    4705 
    4706 1591 atoms, 1619 bonds, 197 residues, 1 model selected 
    4707 
    4708 > select #7/A:1
    4709 
    4710 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4711 
    4712 > select #7/A:1-81
    4713 
    4714 620 atoms, 631 bonds, 81 residues, 1 model selected 
    4715 
    4716 > select #7/A:196-197
    4717 
    4718 16 atoms, 16 bonds, 2 residues, 1 model selected 
    4719 
    4720 > select #7/A:1-197
    4721 
    4722 1591 atoms, 1619 bonds, 197 residues, 1 model selected 
    4723 
    4724 > open
    4725 > /Users/sz140275local/Downloads/fold_complexehei10foldnterdimer_redicnterdimer/fold_complexehei10foldnterdimer_redicnterdimer_model_0.cif
    4726 
    4727 Chain information for
    4728 fold_complexehei10foldnterdimer_redicnterdimer_model_0.cif #9 
    4729 --- 
    4730 Chain | Description 
    4731 A B | . 
    4732 C D | . 
    4733  
    4734 Computing secondary structure 
    4735 
    4736 > hide #7 models
    4737 
    4738 > select add #7
    4739 
    4740 4428 atoms, 4520 bonds, 554 residues, 1 model selected 
    4741 
    4742 > select subtract #7
    4743 
    4744 Nothing selected 
    4745 
    4746 > ui tool show "Show Sequence Viewer"
    4747 
    4748 > sequence chain #9/C
    4749 
    4750 Alignment identifier is 9/C 
    4751 
    4752 > select #9/C:100
    4753 
    4754 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4755 
    4756 > select #9/C:63-100
    4757 
    4758 314 atoms, 320 bonds, 38 residues, 1 model selected 
    4759 
    4760 > open
    4761 > /Users/sz140275local/Downloads/fold_complexehei10foldntershortdimer_redicnterdimer/fold_complexehei10foldntershortdimer_redicnterdimer_model_0.cif
    4762 
    4763 Chain information for
    4764 fold_complexehei10foldntershortdimer_redicnterdimer_model_0.cif #10 
    4765 --- 
    4766 Chain | Description 
    4767 A B | . 
    4768 C D | . 
    4769  
    4770 Computing secondary structure 
    4771 
    4772 > hide #9 models
    4773 
    4774 > select add #9
    4775 
    4776 4820 atoms, 4902 bonds, 594 residues, 1 model selected 
    4777 
    4778 > color #10 bychain
    4779 
    4780 > view matrix models #9,1,0,0,27.223,0,1,0,11.668,0,0,1,1.7485
    4781 
    4782 > view matrix models #9,1,0,0,59.533,0,1,0,28.672,0,0,1,5.8463
    4783 
    4784 > view matrix models #9,1,0,0,75.016,0,1,0,35.933,0,0,1,7.2413
    4785 
    4786 > color bfactor #10 palette alphafold
    4787 
    4788 2510 atoms, 320 residues, atom bfactor range 18.5 to 98.1 
    4789 
    4790 > view matrix models #9,1,0,0,88.609,0,1,0,10.762,0,0,1,11.708
    4791 
    4792 > ui mousemode right zoom
    4793 
    4794 > ui tool show "Show Sequence Viewer"
    4795 
    4796 > sequence chain #10/C
    4797 
    4798 Alignment identifier is 10/C 
    4799 
    4800 > select clear
    4801 
    4802 > select #10/C:19
    4803 
    4804 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4805 
    4806 > select #10/C:13
    4807 
    4808 7 atoms, 7 bonds, 1 residue, 1 model selected 
    4809 
    4810 > select clear
    4811 
    4812 [Repeated 3 time(s)]
    4813 
    4814 > select #10/C:19
    4815 
    4816 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4817 
    4818 > select #10/C:13
    4819 
    4820 7 atoms, 7 bonds, 1 residue, 1 model selected 
    4821 
    4822 > select #10/C:13-19
    4823 
    4824 55 atoms, 56 bonds, 7 residues, 1 model selected 
    4825 
    4826 > select #10/C:24-25
    4827 
    4828 15 atoms, 15 bonds, 2 residues, 1 model selected 
    4829 
    4830 > select #10/C:15-25
    4831 
    4832 92 atoms, 93 bonds, 11 residues, 1 model selected 
    4833 
    4834 > open
    4835 > /Users/sz140275local/Downloads/MinComplex_cff0e/predictions/MinComplex/models/MinComplex_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_59653.pdb
    4836 
    4837 Chain information for
    4838 MinComplex_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_59653.pdb
    4839 #11 
    4840 --- 
    4841 Chain | Description 
    4842 A | No description available 
    4843 B | No description available 
    4844  
    4845 Computing secondary structure 
    4846 
    4847 > hide #10 models
    4848 
    4849 > select add #10
    4850 
    4851 2510 atoms, 2556 bonds, 320 residues, 1 model selected 
    4852 
    4853 > select subtract #10
    4854 
    4855 Nothing selected 
    4856 
    4857 > color #11 bychain
    4858 
    4859 > select #11/A
    4860 
    4861 620 atoms, 631 bonds, 81 residues, 1 model selected 
    4862 
    4863 > color sel lime
    4864 
    4865 > select add #11
    4866 
    4867 964 atoms, 978 bonds, 124 residues, 1 model selected 
    4868 
    4869 > select subtract #11
    4870 
    4871 Nothing selected 
    4872 
    4873 > color bfactor #11/B palette alphafold
    4874 
    4875 344 atoms, 43 residues, atom bfactor range 26.5 to 82.9 
    4876 
    4877 > ui tool show "Show Sequence Viewer"
    4878 
    4879 > sequence chain #11/B
    4880 
    4881 Alignment identifier is 11/B 
    4882 
    4883 > select #11/B:27
    4884 
    4885 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4886 
    4887 > select #11/B:27-43
    4888 
    4889 142 atoms, 143 bonds, 17 residues, 1 model selected 
    4890 
    4891 > hide #11 models
    4892 
    4893 > select add #11
    4894 
    4895 964 atoms, 978 bonds, 124 residues, 1 model selected 
    4896 
    4897 > show #10 models
    4898 
    4899 > select subtract #11
    4900 
    4901 Nothing selected 
    4902 
    4903 > color #10 bychain
    4904 
    4905 > hide #10 models
    4906 
    4907 > show #11 models
    4908 
    4909 > select #11/B:2
    4910 
    4911 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4912 
    4913 > select #11/B:2
    4914 
    4915 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4916 
    4917 > select #11/B:21-22
    4918 
    4919 15 atoms, 14 bonds, 2 residues, 1 model selected 
    4920 
    4921 > select #11/B:21-24
    4922 
    4923 33 atoms, 32 bonds, 4 residues, 1 model selected 
    4924 
    4925 > select #11/B:2-3
    4926 
    4927 17 atoms, 16 bonds, 2 residues, 1 model selected 
    4928 
    4929 > select #11/B:2-3
    4930 
    4931 17 atoms, 16 bonds, 2 residues, 1 model selected 
    4932 
    4933 > select #11/B:21-22
    4934 
    4935 15 atoms, 14 bonds, 2 residues, 1 model selected 
    4936 
    4937 > select #11/B:21-23
    4938 
    4939 24 atoms, 23 bonds, 3 residues, 1 model selected 
    4940 
    4941 > select #11/B:24
    4942 
    4943 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4944 
    4945 > select #11/B:22-24
    4946 
    4947 27 atoms, 26 bonds, 3 residues, 1 model selected 
    4948 
    4949 > show sel atoms
    4950 
    4951 > select #11/B:9
    4952 
    4953 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4954 
    4955 > select #11/B:9
    4956 
    4957 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4958 
    4959 > show sel atoms
    4960 
    4961 > select #11/A
    4962 
    4963 620 atoms, 631 bonds, 81 residues, 1 model selected 
    4964 
    4965 > coulombic sel
    4966 
    4967 Using Amber 20 recommended default charges and atom types for standard
    4968 residues 
    4969 Coulombic values for
    4970 MinComplex_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_59653.pdb_A
    4971 SES surface #11.1: minimum, -12.42, mean -0.56, maximum 9.15 
    4972 To also show corresponding color key, enter the above coulombic command and
    4973 add key true 
    4974 
    4975 > hide #!11 models
    4976 
    4977 > select add #11
    4978 
    4979 964 atoms, 978 bonds, 124 residues, 2 models selected 
    4980 
    4981 > select subtract #11
    4982 
    4983 1 model selected 
    4984 
    4985 > show #10 models
    4986 
    4987 > mmaker #11/B to #10
    4988 
    4989 Computing secondary structure 
    4990 [Repeated 1 time(s)]  Parameters 
    4991 --- 
    4992 Chain pairing | bb 
    4993 Alignment algorithm | Needleman-Wunsch 
    4994 Similarity matrix | BLOSUM-62 
    4995 SS fraction | 0.3 
    4996 Gap open (HH/SS/other) | 18/18/6 
    4997 Gap extend | 1 
    4998 SS matrix |  |  | H | S | O 
    4999 ---|---|---|--- 
    5000 H | 6 | -9 | -6 
    5001 S |  | 6 | -6 
    5002 O |  |  | 4 
    5003 Iteration cutoff | 2 
    5004  
    5005 Matchmaker fold_complexehei10foldntershortdimer_redicnterdimer_model_0.cif,
    5006 chain C (#10) with
    5007 MinComplex_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_59653.pdb,
    5008 chain B (#11), sequence alignment score = 92.1 
    5009 RMSD between 7 pruned atom pairs is 1.211 angstroms; (across all 24 pairs:
    5010 9.433) 
    5011  
    5012 
    5013 > show #!11 models
    5014 
    5015 > ui mousemode right translate
    5016 
    5017 > hide #10 models
    5018 
    5019 > show #10 models
    5020 
    5021 > hide #10#!11 surfaces
    5022 
    5023 [Repeated 1 time(s)]
    5024 
    5025 > hide #10 models
    5026 
    5027 > show #10 models
    5028 
    5029 > hide #10 models
    5030 
    5031 > show #10 models
    5032 
    5033 > mmaker #11/B to #10/A
    5034 
    5035 Computing secondary structure 
    5036 [Repeated 1 time(s)]  Parameters 
    5037 --- 
    5038 Chain pairing | bb 
    5039 Alignment algorithm | Needleman-Wunsch 
    5040 Similarity matrix | BLOSUM-62 
    5041 SS fraction | 0.3 
    5042 Gap open (HH/SS/other) | 18/18/6 
    5043 Gap extend | 1 
    5044 SS matrix |  |  | H | S | O 
    5045 ---|---|---|--- 
    5046 H | 6 | -9 | -6 
    5047 S |  | 6 | -6 
    5048 O |  |  | 4 
    5049 Iteration cutoff | 2 
    5050  
    5051 Matchmaker fold_complexehei10foldntershortdimer_redicnterdimer_model_0.cif,
    5052 chain A (#10) with
    5053 MinComplex_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_59653.pdb,
    5054 chain B (#11), sequence alignment score = 23 
    5055 RMSD between 19 pruned atom pairs is 0.314 angstroms; (across all 21 pairs:
    5056 2.062) 
    5057  
    5058 
    5059 > select add #11
    5060 
    5061 964 atoms, 978 bonds, 124 residues, 1 model selected 
    5062 
    5063 > ui mousemode right "translate selected models"
    5064 
    5065 > view matrix models
    5066 > #11,0.45417,0.17343,-0.87387,-7.6896,-0.21821,-0.92934,-0.29784,-6.1638,-0.86378,0.32596,-0.38423,-6.7588
    5067 
    5068 > view matrix models
    5069 > #11,0.45417,0.17343,-0.87387,-9.0774,-0.21821,-0.92934,-0.29784,-10.446,-0.86378,0.32596,-0.38423,-4.0281
    5070 
    5071 > ui mousemode right "rotate selected models"
    5072 
    5073 > view matrix models
    5074 > #11,0.75776,0.22696,-0.61179,-11.227,-0.17588,-0.83183,-0.52643,-8.4392,-0.62838,0.50651,-0.59041,-2.1338
    5075 
    5076 > ui mousemode right "translate selected models"
    5077 
    5078 > view matrix models
    5079 > #11,0.75776,0.22696,-0.61179,-11.483,-0.17588,-0.83183,-0.52643,-13.357,-0.62838,0.50651,-0.59041,-6.6171
    5080 
    5081 > ui mousemode right "rotate selected models"
    5082 
    5083 > view matrix models
    5084 > #11,0.92185,-0.22361,-0.31652,-10.061,-0.35913,-0.79989,-0.48084,-15.057,-0.14566,0.55693,-0.81769,-2.1088
    5085 
    5086 > ui mousemode right "translate selected models"
    5087 
    5088 > view matrix models
    5089 > #11,0.92185,-0.22361,-0.31652,-7.9745,-0.35913,-0.79989,-0.48084,-11.144,-0.14566,0.55693,-0.81769,-9.1072
    5090 
    5091 > view matrix models
    5092 > #11,0.92185,-0.22361,-0.31652,-4.7457,-0.35913,-0.79989,-0.48084,-12.185,-0.14566,0.55693,-0.81769,-7.597
    5093 
    5094 > ui mousemode right "rotate selected models"
    5095 
    5096 > view matrix models
    5097 > #11,0.58872,-0.34667,-0.73023,-0.3068,-0.62533,-0.76776,-0.13967,-17.771,-0.51222,0.53886,-0.66878,-10.926
    5098 
    5099 > ui mousemode right "translate selected models"
    5100 
    5101 > view matrix models
    5102 > #11,0.58872,-0.34667,-0.73023,-2.8607,-0.62533,-0.76776,-0.13967,-18.042,-0.51222,0.53886,-0.66878,-11.237
    5103 
    5104 > view matrix models
    5105 > #11,0.58872,-0.34667,-0.73023,-5.4691,-0.62533,-0.76776,-0.13967,-10.92,-0.51222,0.53886,-0.66878,-10.008
    5106 
    5107 > view matrix models
    5108 > #11,0.58872,-0.34667,-0.73023,-5.9244,-0.62533,-0.76776,-0.13967,-9.4818,-0.51222,0.53886,-0.66878,-9.2632
    5109 
    5110 > view matrix models
    5111 > #11,0.58872,-0.34667,-0.73023,-7.0168,-0.62533,-0.76776,-0.13967,-9.3366,-0.51222,0.53886,-0.66878,-9.0932
    5112 
    5113 > ui mousemode right "rotate selected models"
    5114 
    5115 > view matrix models
    5116 > #11,0.60946,-0.49396,-0.62012,-6.8682,-0.74675,-0.62039,-0.23974,-10.081,-0.2663,0.60919,-0.74697,-7.65
    5117 
    5118 > select subtract #11
    5119 
    5120 1 model selected 
    5121 
    5122 > ui mousemode right zoom
    5123 
    5124 > hide #!11 models
    5125 
    5126 > show #!11 models
    5127 
    5128 > hide #!11 models
    5129 
    5130 > show #!11 models
    5131 
    5132 > hide #!11 models
    5133 
    5134 > show #!11 models
    5135 
    5136 > hide #10 models
    5137 
    5138 > show #7 models
    5139 
    5140 > hide #!11 models
    5141 
    5142 > show #!11 models
    5143 
    5144 > hide #!11 models
    5145 
    5146 > show #!11 models
    5147 
    5148 > select add #11
    5149 
    5150 964 atoms, 978 bonds, 124 residues, 1 model selected 
    5151 
    5152 > ui mousemode right "translate selected models"
    5153 
    5154 > view matrix models
    5155 > #11,0.60946,-0.49396,-0.62012,-5.0789,-0.74675,-0.62039,-0.23974,-12.86,-0.2663,0.60919,-0.74697,-19.599
    5156 
    5157 > view matrix models
    5158 > #11,0.60946,-0.49396,-0.62012,-10.025,-0.74675,-0.62039,-0.23974,-23.461,-0.2663,0.60919,-0.74697,-15.959
    5159 
    5160 > ui mousemode right "rotate selected models"
    5161 
    5162 > view matrix models
    5163 > #11,-0.5001,-0.78903,0.35683,-24.114,-0.86467,0.47752,-0.15596,-35.081,-0.04734,-0.38654,-0.92106,-3.7318
    5164 
    5165 > view matrix models
    5166 > #11,-0.86805,-0.37548,0.32482,-29.272,-0.49639,0.64332,-0.58287,-29.814,0.0098938,-0.6672,-0.74482,-2.9684
    5167 
    5168 > view matrix models
    5169 > #11,-0.81472,0.47872,0.32719,-36.883,0.035261,0.60413,-0.7961,-24.418,-0.57878,-0.63707,-0.50908,-8.8173
    5170 
    5171 > ui mousemode right "translate selected models"
    5172 
    5173 > view matrix models
    5174 > #11,-0.81472,0.47872,0.32719,-28.458,0.035261,0.60413,-0.7961,-19.19,-0.57878,-0.63707,-0.50908,-22.659
    5175 
    5176 > view matrix models
    5177 > #11,-0.81472,0.47872,0.32719,-28.584,0.035261,0.60413,-0.7961,-12.041,-0.57878,-0.63707,-0.50908,-26.684
    5178 
    5179 > view matrix models
    5180 > #11,-0.81472,0.47872,0.32719,-22.139,0.035261,0.60413,-0.7961,-19.132,-0.57878,-0.63707,-0.50908,-24.143
    5181 
    5182 > view matrix models
    5183 > #11,-0.81472,0.47872,0.32719,-30.491,0.035261,0.60413,-0.7961,-28.714,-0.57878,-0.63707,-0.50908,-16.793
    5184 
    5185 > view matrix models
    5186 > #11,-0.81472,0.47872,0.32719,-29.135,0.035261,0.60413,-0.7961,-23.604,-0.57878,-0.63707,-0.50908,-14.034
    5187 
    5188 > ui mousemode right translate
    5189 
    5190 > ui mousemode right "rotate selected models"
    5191 
    5192 > view matrix models
    5193 > #11,-0.75974,0.46914,-0.45023,-19.602,0.28528,-0.38171,-0.87915,-12.396,-0.5843,-0.79637,0.15616,-20.458
    5194 
    5195 > view matrix models
    5196 > #11,-0.34315,0.54622,-0.76413,-14.628,0.49887,-0.58332,-0.64099,-12.349,-0.79585,-0.60116,-0.07233,-20.551
    5197 
    5198 > ui mousemode right "translate selected models"
    5199 
    5200 > view matrix models
    5201 > #11,-0.34315,0.54622,-0.76413,-15.814,0.49887,-0.58332,-0.64099,-18.705,-0.79585,-0.60116,-0.07233,-21.537
    5202 
    5203 > view matrix models
    5204 > #11,-0.34315,0.54622,-0.76413,-16.508,0.49887,-0.58332,-0.64099,-21.067,-0.79585,-0.60116,-0.07233,-22.136
    5205 
    5206 > view matrix models
    5207 > #11,-0.34315,0.54622,-0.76413,-16.657,0.49887,-0.58332,-0.64099,-22.026,-0.79585,-0.60116,-0.07233,-22.257
    5208 
    5209 > ui mousemode right "rotate selected models"
    5210 
    5211 > view matrix models
    5212 > #11,-0.92723,0.31326,-0.2052,-23.889,0.30484,0.31311,-0.89946,-28.115,-0.21751,-0.89657,-0.38582,-13.105
    5213 
    5214 > ui mousemode right "translate selected models"
    5215 
    5216 > view matrix models
    5217 > #11,-0.92723,0.31326,-0.2052,-27.671,0.30484,0.31311,-0.89946,-22.477,-0.21751,-0.89657,-0.38582,-16.682
    5218 
    5219 > view matrix models
    5220 > #11,-0.92723,0.31326,-0.2052,-25.736,0.30484,0.31311,-0.89946,-19.062,-0.21751,-0.89657,-0.38582,-22.092
    5221 
    5222 > ui mousemode right "rotate selected models"
    5223 
    5224 > view matrix models
    5225 > #11,0.57665,0.13065,-0.80647,-9.8366,0.040993,0.98126,0.18828,-39.291,0.81596,-0.14163,0.56049,-35.303
    5226 
    5227 > ui mousemode right "translate selected models"
    5228 
    5229 > view matrix models
    5230 > #11,0.57665,0.13065,-0.80647,-10.183,0.040993,0.98126,0.18828,-29.954,0.81596,-0.14163,0.56049,-31.515
    5231 
    5232 > ui mousemode right "translate selected models"
    5233 
    5234 > ui mousemode right "rotate selected models"
    5235 
    5236 > view matrix models
    5237 > #11,0.9282,-0.34226,0.14594,-15.432,0.23645,0.84545,0.47887,-31.216,-0.28728,-0.40998,0.86567,-37.883
    5238 
    5239 > view matrix models
    5240 > #11,0.91745,0.007446,0.39777,-21.666,0.018868,0.99789,-0.062197,-27.252,-0.3974,0.064568,0.91537,-43.345
    5241 
    5242 > view matrix models
    5243 > #11,0.90846,0.060592,0.41355,-22.382,-0.0036715,0.99055,-0.13707,-26.407,-0.41795,0.123,0.9001,-43.798
    5244 
    5245 > view matrix models
    5246 > #11,0.90063,0.10119,0.42265,-22.899,-0.019506,0.98095,-0.1933,-25.73,-0.43416,0.16584,0.88544,-44.094
    5247 
    5248 > view matrix models
    5249 > #11,0.88244,0.18279,0.43347,-23.862,-0.047836,0.95151,-0.30386,-24.288,-0.46799,0.2474,0.84839,-44.565
    5250 
    5251 > view matrix models
    5252 > #11,0.12024,0.89703,0.42531,-33.926,-0.81638,0.33311,-0.47177,-20.27,-0.56486,-0.29049,0.77237,-39.191
    5253 
    5254 > view matrix models
    5255 > #11,0.23492,0.92442,0.30042,-32.159,-0.90485,0.32088,-0.2798,-22.845,-0.35505,-0.2061,0.91184,-40.62
    5256 
    5257 > ui mousemode right "translate selected models"
    5258 
    5259 > view matrix models
    5260 > #11,0.23492,0.92442,0.30042,-28.316,-0.90485,0.32088,-0.2798,-20.032,-0.35505,-0.2061,0.91184,-11.358
    5261 
    5262 > view matrix models
    5263 > #11,0.23492,0.92442,0.30042,-21.791,-0.90485,0.32088,-0.2798,-20.582,-0.35505,-0.2061,0.91184,-15.337
    5264 
    5265 > view matrix models
    5266 > #11,0.23492,0.92442,0.30042,-22.627,-0.90485,0.32088,-0.2798,-15.199,-0.35505,-0.2061,0.91184,-13.084
    5267 
    5268 > view matrix models
    5269 > #11,0.23492,0.92442,0.30042,-23.105,-0.90485,0.32088,-0.2798,-14.499,-0.35505,-0.2061,0.91184,-13.587
    5270 
    5271 > select subtract #11
    5272 
    5273 1 model selected 
    5274 
    5275 > hide #7 models
    5276 
    5277 > show #7 models
    5278 
    5279 > hide #7 models
    5280 
    5281 > show #7 models
    5282 
    5283 > hide #7 models
    5284 
    5285 > show #7 models
    5286 
    5287 > hide #7 models
    5288 
    5289 > select #11/B:2-24,27-30
    5290 
    5291 214 atoms, 213 bonds, 27 residues, 1 model selected 
    5292 
    5293 > select #11/A
    5294 
    5295 620 atoms, 631 bonds, 81 residues, 1 model selected 
    5296 
    5297 > coulombic sel
    5298 
    5299 Coulombic values for
    5300 MinComplex_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_59653.pdb_A
    5301 SES surface #11.1: minimum, -12.42, mean -0.56, maximum 9.15 
    5302 To also show corresponding color key, enter the above coulombic command and
    5303 add key true 
    5304 
    5305 > select add #11
    5306 
    5307 964 atoms, 978 bonds, 124 residues, 2 models selected 
    5308 
    5309 > select subtract #11
    5310 
    5311 1 model selected 
    5312 
    5313 > select #11/B:4
    5314 
    5315 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5316 
    5317 > select #11/B:4
    5318 
    5319 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5320 
    5321 > show sel atoms
    5322 
    5323 > select #11/B:7
    5324 
    5325 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5326 
    5327 > select #11/B:7
    5328 
    5329 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5330 
    5331 > show sel atoms
    5332 
    5333 > select #11/B:20
    5334 
    5335 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5336 
    5337 > select #11/B:20
    5338 
    5339 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5340 
    5341 > show sel atoms
    5342 
    5343 > select #11/B:2-24,27-30
    5344 
    5345 214 atoms, 213 bonds, 27 residues, 1 model selected 
    5346 
    5347 > select #11/B:28
    5348 
    5349 7 atoms, 6 bonds, 1 residue, 1 model selected 
    5350 
    5351 > select #11/B:28
    5352 
    5353 7 atoms, 6 bonds, 1 residue, 1 model selected 
    5354 
    5355 > select #11/B:7
    5356 
    5357 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5358 
    5359 > select #11/B:7
    5360 
    5361 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5362 
    5363 > open
    5364 > /Users/sz140275local/Downloads/Hop1_Mnd1_8398f/predictions/Hop1_Mnd1/models/Hop1_Mnd1_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_82003.pdb
    5365 
    5366 Chain information for
    5367 Hop1_Mnd1_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_82003.pdb #12 
    5368 --- 
    5369 Chain | Description 
    5370 A | No description available 
    5371 B | No description available 
    5372  
    5373 Computing secondary structure 
    5374 
    5375 > select add #11
    5376 
    5377 964 atoms, 978 bonds, 124 residues, 1 model selected 
    5378 
    5379 > select subtract #11
    5380 
    5381 1 model selected 
    5382 
    5383 > hide #!11 models
    5384 
    5385 > ui mousemode right zoom
    5386 
    5387 > ui tool show "Show Sequence Viewer"
    5388 
    5389 > sequence chain #12/A
    5390 
    5391 Alignment identifier is 12/A 
    5392 
    5393 > sequence chain #12/B
    5394 
    5395 Alignment identifier is 12/B 
    5396 
    5397 > select #12/B:72
    5398 
    5399 14 atoms, 15 bonds, 1 residue, 1 model selected 
    5400 
    5401 > select #12/B:72-75
    5402 
    5403 37 atoms, 40 bonds, 4 residues, 1 model selected 
    5404 
    5405 > show sel atoms
    5406 
    5407 > select #12/B:195
    5408 
    5409 11 atoms, 11 bonds, 1 residue, 1 model selected 
    5410 
    5411 > select #12/B:195-198
    5412 
    5413 30 atoms, 31 bonds, 4 residues, 1 model selected 
    5414 
    5415 > show sel atoms
    5416 
    5417 > select #12/B:187
    5418 
    5419 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5420 
    5421 > select #12/B:187-205
    5422 
    5423 163 atoms, 166 bonds, 19 residues, 1 model selected 
    5424 
    5425 > ui mousemode right translate
    5426 
    5427 > select #12/B:185
    5428 
    5429 4 atoms, 3 bonds, 1 residue, 1 model selected 
    5430 
    5431 > select #12/B:185-205
    5432 
    5433 178 atoms, 182 bonds, 21 residues, 1 model selected 
    5434 
    5435 > hide #12 models
    5436 
    5437 > select add #12
    5438 
    5439 3412 atoms, 3460 bonds, 422 residues, 1 model selected 
    5440 
    5441 > select subtract #12
    5442 
    5443 Nothing selected 
    5444 
    5445 > show #!11 models
    5446 
    5447 > ui mousemode right zoom
    5448 
    5449 > ui mousemode right translate
    5450 
    5451 > ui tool show "Show Sequence Viewer"
    5452 
    5453 > sequence chain #11/B
    5454 
    5455 Alignment identifier is 11/B 
    5456 
    5457 > select #11/B:20
    5458 
    5459 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5460 
    5461 > select #11/B:20
    5462 
    5463 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5464 
    5465 > color sel green
    5466 
    5467 > select add #11
    5468 
    5469 964 atoms, 978 bonds, 124 residues, 1 model selected 
    5470 
    5471 > select subtract #11
    5472 
    5473 1 model selected 
    5474 
    5475 > transparency #11.1 50
    5476 
    5477 > open
    5478 > /Users/sz140275local/Downloads/MinComplexP_6bcbe/predictions/MinComplexP/models/MinComplexP_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_14081.pdb
    5479 
    5480 Chain information for
    5481 MinComplexP_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_14081.pdb
    5482 #13 
    5483 --- 
    5484 Chain | Description 
    5485 A | No description available 
    5486 B | No description available 
    5487  
    5488 Computing secondary structure 
    5489 
    5490 > mmaker #12 to #11
    5491 
    5492 Computing secondary structure 
    5493 [Repeated 1 time(s)]  Parameters 
    5494 --- 
    5495 Chain pairing | bb 
    5496 Alignment algorithm | Needleman-Wunsch 
    5497 Similarity matrix | BLOSUM-62 
    5498 SS fraction | 0.3 
    5499 Gap open (HH/SS/other) | 18/18/6 
    5500 Gap extend | 1 
    5501 SS matrix |  |  | H | S | O 
    5502 ---|---|---|--- 
    5503 H | 6 | -9 | -6 
    5504 S |  | 6 | -6 
    5505 O |  |  | 4 
    5506 Iteration cutoff | 2 
    5507  
    5508 Matchmaker
    5509 MinComplex_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_59653.pdb,
    5510 chain B (#11) with
    5511 Hop1_Mnd1_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_82003.pdb,
    5512 chain B (#12), sequence alignment score = 46 
    5513 RMSD between 23 pruned atom pairs is 0.617 angstroms; (across all 42 pairs:
    5514 24.380) 
    5515  
    5516 
    5517 > mmaker #12 to #11
    5518 
    5519 Computing secondary structure 
    5520 [Repeated 1 time(s)]  Parameters 
    5521 --- 
    5522 Chain pairing | bb 
    5523 Alignment algorithm | Needleman-Wunsch 
    5524 Similarity matrix | BLOSUM-62 
    5525 SS fraction | 0.3 
    5526 Gap open (HH/SS/other) | 18/18/6 
    5527 Gap extend | 1 
    5528 SS matrix |  |  | H | S | O 
    5529 ---|---|---|--- 
    5530 H | 6 | -9 | -6 
    5531 S |  | 6 | -6 
    5532 O |  |  | 4 
    5533 Iteration cutoff | 2 
    5534  
    5535 Matchmaker
    5536 MinComplex_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_59653.pdb,
    5537 chain B (#11) with
    5538 Hop1_Mnd1_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_82003.pdb,
    5539 chain B (#12), sequence alignment score = 46 
    5540 RMSD between 23 pruned atom pairs is 0.617 angstroms; (across all 42 pairs:
    5541 24.380) 
    5542  
    5543 
    5544 > mmaker #13 to #11
    5545 
    5546 Computing secondary structure 
    5547 [Repeated 1 time(s)]  Parameters 
    5548 --- 
    5549 Chain pairing | bb 
    5550 Alignment algorithm | Needleman-Wunsch 
    5551 Similarity matrix | BLOSUM-62 
    5552 SS fraction | 0.3 
    5553 Gap open (HH/SS/other) | 18/18/6 
    5554 Gap extend | 1 
    5555 SS matrix |  |  | H | S | O 
    5556 ---|---|---|--- 
    5557 H | 6 | -9 | -6 
    5558 S |  | 6 | -6 
    5559 O |  |  | 4 
    5560 Iteration cutoff | 2 
    5561  
    5562 Matchmaker
    5563 MinComplex_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_59653.pdb,
    5564 chain A (#11) with
    5565 MinComplexP_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_14081.pdb,
    5566 chain A (#13), sequence alignment score = 425.3 
    5567 RMSD between 80 pruned atom pairs is 0.615 angstroms; (across all 81 pairs:
    5568 0.655) 
    5569  
    5570 
    5571 > hide #!11 models
    5572 
    5573 > show #!11 models
    5574 
    5575 > hide #!11 models
    5576 
    5577 > color #13/A green
    5578 
    5579 > select #13/A
    5580 
    5581 620 atoms, 631 bonds, 81 residues, 1 model selected 
    5582 
    5583 > coulombic sel
    5584 
    5585 Using Amber 20 recommended default charges and atom types for standard
    5586 residues 
    5587 Coulombic values for
    5588 MinComplexP_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_14081.pdb_A
    5589 SES surface #13.1: minimum, -14.04, mean -0.47, maximum 9.17 
    5590 To also show corresponding color key, enter the above coulombic command and
    5591 add key true 
    5592 
    5593 > color bfactor #113B palette alphafold
    5594 
    5595 > color byattribute bfactor #113B palette alphafold
    5596 
    5597 Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
    5598 or a keyword 
    5599 
    5600 > color bfactor #13/B palette alphafold
    5601 
    5602 347 atoms, 43 residues, atom bfactor range 25.8 to 83.8 
    5603 
    5604 > select add #13
    5605 
    5606 967 atoms, 981 bonds, 124 residues, 2 models selected 
    5607 
    5608 > select #13/B:20
    5609 
    5610 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5611 
    5612 > show sel atoms
    5613 
    5614 > color sel green
    5615 
    5616 > select add #13
    5617 
    5618 967 atoms, 981 bonds, 124 residues, 1 model selected 
    5619 
    5620 > select subtract #13
    5621 
    5622 1 model selected 
    5623 
    5624 > hide #!13 models
    5625 
    5626 > show #!13 models
    5627 
    5628 > open
    5629 > /Users/sz140275local/Downloads/fold_complexehei10foldntershort_redicnterb_phospho/fold_complexehei10foldntershort_redicnterb_phospho_model_0.cif
    5630 
    5631 Chain information for
    5632 fold_complexehei10foldntershort_redicnterb_phospho_model_0.cif #14 
    5633 --- 
    5634 Chain | Description 
    5635 A | . 
    5636 B | . 
    5637  
    5638 Computing secondary structure 
    5639 
    5640 > mmaker #14 to #13
    5641 
    5642 Computing secondary structure 
    5643 [Repeated 1 time(s)]  Parameters 
    5644 --- 
    5645 Chain pairing | bb 
    5646 Alignment algorithm | Needleman-Wunsch 
    5647 Similarity matrix | BLOSUM-62 
    5648 SS fraction | 0.3 
    5649 Gap open (HH/SS/other) | 18/18/6 
    5650 Gap extend | 1 
    5651 SS matrix |  |  | H | S | O 
    5652 ---|---|---|--- 
    5653 H | 6 | -9 | -6 
    5654 S |  | 6 | -6 
    5655 O |  |  | 4 
    5656 Iteration cutoff | 2 
    5657  
    5658 Matchmaker
    5659 MinComplexP_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_14081.pdb,
    5660 chain A (#13) with
    5661 fold_complexehei10foldntershort_redicnterb_phospho_model_0.cif, chain A (#14),
    5662 sequence alignment score = 368.9 
    5663 RMSD between 60 pruned atom pairs is 0.906 angstroms; (across all 81 pairs:
    5664 5.001) 
    5665  
    5666 
    5667 > hide #!13 models
    5668 
    5669 > select #14/B:20
    5670 
    5671 10 atoms, 9 bonds, 1 residue, 1 model selected 
    5672 
    5673 > show sel atoms
    5674 
    5675 > show #!13 models
    5676 
    5677 > hide #!13 models
    5678 
    5679 > show #!13 models
    5680 
    5681 > hide #!13 models
    5682 
    5683 > select add #14
    5684 
    5685 970 atoms, 984 bonds, 124 residues, 1 model selected 
    5686 
    5687 > select subtract #14
    5688 
    5689 Nothing selected 
    5690 
    5691 > select #14/A
    5692 
    5693 621 atoms, 632 bonds, 81 residues, 1 model selected 
    5694 
    5695 > color sel green
    5696 
    5697 > select add #14
    5698 
    5699 970 atoms, 984 bonds, 124 residues, 1 model selected 
    5700 
    5701 > select subtract #14
    5702 
    5703 Nothing selected 
    5704 
    5705 > show #!13 models
    5706 
    5707 > hide #14#!13 surfaces
    5708 
    5709 > hide #!13 models
    5710 
    5711 > coulombic #14
    5712 
    5713 Using Amber 20 recommended default charges and atom types for standard
    5714 residues 
    5715 Assigning partial charges to residue SEP (net charge -1) with am1-bcc method 
    5716 Running ANTECHAMBER command:
    5717 /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber -ek
    5718 qm_theory='AM1', -i
    5719 /var/folders/dd/q54xxd8s6h7cd69lnrz0_1bc0000gn/T/tmpb2ugs2q5/ante.in.mol2 -fi
    5720 mol2 -o
    5721 /var/folders/dd/q54xxd8s6h7cd69lnrz0_1bc0000gn/T/tmpb2ugs2q5/ante.out.mol2 -fo
    5722 mol2 -c bcc -nc -1 -j 5 -s 2 -dr n 
    5723 (SEP) `` 
    5724 (SEP) `Welcome to antechamber 20.0: molecular input file processor.` 
    5725 (SEP) `` 
    5726 (SEP) `Info: Finished reading file
    5727 (/var/folders/dd/q54xxd8s6h7cd69lnrz0_1bc0000gn/T/tmpb2ugs2q5/ante.in.mol2);
    5728 atoms read (27), bonds read (26).` 
    5729 (SEP) `Info: Determining atomic numbers from atomic symbols which are case
    5730 sensitive.` 
    5731 (SEP) `Running:
    5732 /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/bondtype -j part -i
    5733 ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` 
    5734 (SEP) `` 
    5735 (SEP) `` 
    5736 (SEP) `Running:
    5737 /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -i
    5738 ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` 
    5739 (SEP) `Info: Total number of electrons: 126; net charge: -1` 
    5740 (SEP) `` 
    5741 (SEP) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O
    5742 -i sqm.in -o sqm.out` 
    5743 (SEP) `` 
    5744 (SEP) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/am1bcc
    5745 -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
    5746 /Applications/ChimeraX-1.9.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
    5747 -s 2 -j 1` 
    5748 (SEP) `` 
    5749 (SEP) `Running:
    5750 /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
    5751 -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` 
    5752 (SEP) `` 
    5753 Charges for residue SEP determined 
    5754 Coulombic values for
    5755 fold_complexehei10foldntershort_redicnterb_phospho_model_0.cif_A SES surface
    5756 #14.1: minimum, -11.49, mean -0.49, maximum 10.98 
    5757 Coulombic values for
    5758 fold_complexehei10foldntershort_redicnterb_phospho_model_0.cif_B SES surface
    5759 #14.2: minimum, -9.14, mean 1.34, maximum 11.25 
    5760 To also show corresponding color key, enter the above coulombic command and
    5761 add key true 
    5762 
    5763 > select #14/B
    5764 
    5765 349 atoms, 352 bonds, 43 residues, 1 model selected 
    5766 
    5767 > hide sel surfaces
    5768 
    5769 > show sel atoms
    5770 
    5771 > label residues
    5772 
    5773 > label sel
    5774 
    5775 > open /Users/sz140275local/Downloads/AF-Q9Y620-F1-model_v4.pdb
    5776 
    5777 AF-Q9Y620-F1-model_v4.pdb title: 
    5778 Alphafold monomer V2.0 prediction for DNA repair and recombination protein
    5779 RAD54B (Q9Y620) [more info...] 
    5780  
    5781 Chain information for AF-Q9Y620-F1-model_v4.pdb #15 
    5782 --- 
    5783 Chain | Description | UniProt 
    5784 A | DNA repair and recombination protein RAD54B | RA54B_HUMAN 1-910 
    5785  
    5786 Computing secondary structure 
    5787 
    5788 > hide #!14 models
    5789 
    5790 > select add #14
    5791 
    5792 970 atoms, 984 bonds, 124 residues, 3 models selected 
    5793 
    5794 > select subtract #14
    5795 
    5796 2 models selected 
    5797 
    5798 > color bfactor #15 palette alphafold
    5799 
    5800 7236 atoms, 910 residues, atom bfactor range 23.5 to 96.1 
    5801 
    5802 > ui tool show "Show Sequence Viewer"
    5803 
    5804 > sequence chain #15/A
    5805 
    5806 Alignment identifier is 15/A 
    5807 
    5808 > select #15/A:228
    5809 
    5810 11 atoms, 11 bonds, 1 residue, 1 model selected 
    5811 
    5812 > select #15/A:228-231
    5813 
    5814 32 atoms, 33 bonds, 4 residues, 1 model selected 
    5815 
    5816 > show sel atoms
    5817 
    5818 > open "/Users/sz140275local/Downloads/AF-Q9Y620-F1-model_v4 (1).pdb"
    5819 
    5820 AF-Q9Y620-F1-model_v4 (1).pdb title: 
    5821 Alphafold monomer V2.0 prediction for DNA repair and recombination protein
    5822 RAD54B (Q9Y620) [more info...] 
    5823  
    5824 Chain information for AF-Q9Y620-F1-model_v4 (1).pdb #16 
    5825 --- 
    5826 Chain | Description | UniProt 
    5827 A | DNA repair and recombination protein RAD54B | RA54B_HUMAN 1-910 
    5828  
    5829 Computing secondary structure 
    5830 
    5831 > hide #15 models
    5832 
    5833 > select add #15
    5834 
    5835 7236 atoms, 7387 bonds, 910 residues, 1 model selected 
    5836 
    5837 > select subtract #15
    5838 
    5839 Nothing selected 
    5840 
    5841 > close #16
    5842 
    5843 > show #15 models
    5844 
    5845 > ui tool show "Show Sequence Viewer"
    5846 
    5847 > sequence chain #15/A
    5848 
    5849 Alignment identifier is 15/A 
    5850 
    5851 > select #15/A:26-27
    5852 
    5853 14 atoms, 13 bonds, 2 residues, 1 model selected 
    5854 
    5855 > select #15/A:26-225
    5856 
    5857 1549 atoms, 1577 bonds, 200 residues, 1 model selected 
    5858 
    5859 > select clear
    5860 
    5861 > select #15/A:123
    5862 
    5863 7 atoms, 6 bonds, 1 residue, 1 model selected 
    5864 
    5865 > select #15/A:197
    5866 
    5867 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5868 
    5869 > select clear
    5870 
    5871 [Repeated 1 time(s)]
    5872 
    5873 > select #15/A:207
    5874 
    5875 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5876 
    5877 > select #15/A:208
    5878 
    5879 11 atoms, 11 bonds, 1 residue, 1 model selected 
    5880 
    5881 > select #15/A:123
    5882 
    5883 7 atoms, 6 bonds, 1 residue, 1 model selected 
    5884 
    5885 > select #15/A:123-211
    5886 
    5887 705 atoms, 718 bonds, 89 residues, 1 model selected 
    5888 
    5889 > select #15/A:207
    5890 
    5891 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5892 
    5893 > select #15/A:123-207
    5894 
    5895 673 atoms, 685 bonds, 85 residues, 1 model selected 
    5896 
    5897 > select #15/A:251
    5898 
    5899 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5900 
    5901 > select #15/A:251-803
    5902 
    5903 4433 atoms, 4525 bonds, 553 residues, 1 model selected 
    5904 
    5905 > select #15/A:26
    5906 
    5907 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5908 
    5909 > select #15/A:26-225
    5910 
    5911 1549 atoms, 1577 bonds, 200 residues, 1 model selected 
    5912 
    5913 > select #15/A:476
    5914 
    5915 11 atoms, 11 bonds, 1 residue, 1 model selected 
    5916 
    5917 > select #15/A:476-479
    5918 
    5919 33 atoms, 34 bonds, 4 residues, 1 model selected 
    5920 
    5921 > open
    5922 > /Users/sz140275local/Documents/Collab_Fred_Baudat/RAD54BnterDMC1_85bb9/predictions/RAD54BnterDMC1/models/RAD54BnterDMC1_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_29694.pdb
    5923 
    5924 Chain information for
    5925 RAD54BnterDMC1_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_29694.pdb
    5926 #16 
    5927 --- 
    5928 Chain | Description 
    5929 A | No description available 
    5930 B | No description available 
    5931  
    5932 Computing secondary structure 
    5933 
    5934 > hide #15 models
    5935 
    5936 > select add #15
    5937 
    5938 7236 atoms, 7387 bonds, 910 residues, 1 model selected 
    5939 
    5940 > select subtract #15
    5941 
    5942 Nothing selected 
    5943 
    5944 > select #6/B
    5945 
    5946 1831 atoms, 1860 bonds, 233 residues, 1 model selected 
    5947 
    5948 > select #16/B
    5949 
    5950 2646 atoms, 2688 bonds, 340 residues, 1 model selected 
    5951 
    5952 > color bfactor #16/B palette alphafold
    5953 
    5954 2646 atoms, 340 residues, atom bfactor range 32.7 to 98.9 
    5955 
    5956 > color bfactor #16/A palette alphafold
    5957 
    5958 387 atoms, 50 residues, atom bfactor range 15.1 to 89 
    5959 
    5960 > open
    5961 > /Users/sz140275local/Documents/Collab_Fred_Baudat/RAD54B200DMC1_1afb7/predictions/RAD54B200DMC1/models/RAD54B200DMC1_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_60027.pdb
    5962 
    5963 Chain information for
    5964 RAD54B200DMC1_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_60027.pdb
    5965 #17 
    5966 --- 
    5967 Chain | Description 
    5968 A | No description available 
    5969 B | No description available 
    5970  
    5971 Computing secondary structure 
    5972 
    5973 > mmaker #16 to #17
    5974 
    5975 Computing secondary structure 
    5976 [Repeated 1 time(s)]  Parameters 
    5977 --- 
    5978 Chain pairing | bb 
    5979 Alignment algorithm | Needleman-Wunsch 
    5980 Similarity matrix | BLOSUM-62 
    5981 SS fraction | 0.3 
    5982 Gap open (HH/SS/other) | 18/18/6 
    5983 Gap extend | 1 
    5984 SS matrix |  |  | H | S | O 
    5985 ---|---|---|--- 
    5986 H | 6 | -9 | -6 
    5987 S |  | 6 | -6 
    5988 O |  |  | 4 
    5989 Iteration cutoff | 2 
    5990  
    5991 Matchmaker
    5992 RAD54B200DMC1_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_60027.pdb,
    5993 chain B (#17) with
    5994 RAD54BnterDMC1_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_29694.pdb,
    5995 chain B (#16), sequence alignment score = 1724.4 
    5996 RMSD between 329 pruned atom pairs is 0.225 angstroms; (across all 340 pairs:
    5997 0.771) 
    5998  
    5999 
    6000 > color bfactor #17/A palette alphafold
    6001 
    6002 382 atoms, 50 residues, atom bfactor range 14.7 to 84.4 
    6003 
    6004 > select add #16
    6005 
    6006 3033 atoms, 3083 bonds, 390 residues, 1 model selected 
    6007 
    6008 > select subtract #16
    6009 
    6010 Nothing selected 
    6011 
    6012 > select #17/A:32
    6013 
    6014 11 atoms, 11 bonds, 1 residue, 1 model selected 
    6015 
    6016 > show sel atoms
    6017 
    6018 > select #17/A:28
    6019 
    6020 11 atoms, 11 bonds, 1 residue, 1 model selected 
    6021 
    6022 > show sel atoms
    6023 
    6024 > select #17/A:31
    6025 
    6026 7 atoms, 7 bonds, 1 residue, 1 model selected 
    6027 
    6028 > show sel atoms
    6029 
    6030 > select #16/A:20
    6031 
    6032 11 atoms, 11 bonds, 1 residue, 1 model selected 
    6033 
    6034 > show sel atoms
    6035 
    6036 > select #16/A:22
    6037 
    6038 7 atoms, 7 bonds, 1 residue, 1 model selected 
    6039 
    6040 > show sel atoms
    6041 
    6042 > select #16/A:23
    6043 
    6044 7 atoms, 7 bonds, 1 residue, 1 model selected 
    6045 
    6046 > show sel atoms
    6047 
    6048 > select #16/A:24
    6049 
    6050 4 atoms, 3 bonds, 1 residue, 1 model selected 
    6051 
    6052 > show sel atoms
    6053 
    6054 [Repeated 2 time(s)]
    6055 
    6056 > open
    6057 > /Users/sz140275local/Downloads/RAD54BnterRAD51_aef71/predictions/RAD54BnterRAD51/models/RAD54BnterRAD51_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_85478.pdb
    6058 
    6059 Chain information for
    6060 RAD54BnterRAD51_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_85478.pdb
    6061 #18 
    6062 --- 
    6063 Chain | Description 
    6064 A | No description available 
    6065 B | No description available 
    6066  
    6067 Computing secondary structure 
    6068 
    6069 > select add #16
    6070 
    6071 3033 atoms, 3083 bonds, 390 residues, 1 model selected 
    6072 
    6073 > select subtract #16
    6074 
    6075 Nothing selected 
    6076 
    6077 > mmaker #18 to #16
    6078 
    6079 Computing secondary structure 
    6080 [Repeated 1 time(s)]  Parameters 
    6081 --- 
    6082 Chain pairing | bb 
    6083 Alignment algorithm | Needleman-Wunsch 
    6084 Similarity matrix | BLOSUM-62 
    6085 SS fraction | 0.3 
    6086 Gap open (HH/SS/other) | 18/18/6 
    6087 Gap extend | 1 
    6088 SS matrix |  |  | H | S | O 
    6089 ---|---|---|--- 
    6090 H | 6 | -9 | -6 
    6091 S |  | 6 | -6 
    6092 O |  |  | 4 
    6093 Iteration cutoff | 2 
    6094  
    6095 Matchmaker
    6096 RAD54BnterDMC1_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_29694.pdb,
    6097 chain B (#16) with
    6098 RAD54BnterRAD51_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_85478.pdb,
    6099 chain B (#18), sequence alignment score = 1085.9 
    6100 RMSD between 274 pruned atom pairs is 0.889 angstroms; (across all 336 pairs:
    6101 3.231) 
    6102  
    6103 
    6104 > hide #16 models
    6105 
    6106 > hide #17 models
    6107 
    6108 > color bfactor #1<!/A palette alphafold
    6109 
    6110 > color byattribute bfactor #1<!/A palette alphafold
    6111 
    6112 Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
    6113 or a keyword 
    6114 
    6115 > color bfactor #18/A palette alphafold
    6116 
    6117 387 atoms, 50 residues, atom bfactor range 15.5 to 82.3 
    6118 
    6119 > show #17 models
    6120 
    6121 > hide #17 models
    6122 
    6123 > show #16 models
    6124 
    6125 > select #18/A:23
    6126 
    6127 7 atoms, 7 bonds, 1 residue, 1 model selected 
    6128 
    6129 > show sel atoms
    6130 
    6131 > select #18/A:22
    6132 
    6133 7 atoms, 7 bonds, 1 residue, 1 model selected 
    6134 
    6135 > show sel atoms
    6136 
    6137 > select #18/A:20
    6138 
    6139 11 atoms, 11 bonds, 1 residue, 1 model selected 
    6140 
    6141 > show sel atoms
    6142 
    6143 > open
    6144 > /Users/sz140275local/Downloads/RAD54B200RAD51_0825e/predictions/RAD54B200RAD51/models/RAD54B200RAD51_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_63869.pdb
    6145 
    6146 Chain information for
    6147 RAD54B200RAD51_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_63869.pdb
    6148 #19 
    6149 --- 
    6150 Chain | Description 
    6151 A | No description available 
    6152 B | No description available 
    6153  
    6154 Computing secondary structure 
    6155 
    6156 > color bfactor #19/A palette alphafold
    6157 
    6158 382 atoms, 50 residues, atom bfactor range 15.8 to 69.8 
    6159 
    6160 > mmaker #19 to #16
    6161 
    6162 Computing secondary structure 
    6163 [Repeated 1 time(s)]  Parameters 
    6164 --- 
    6165 Chain pairing | bb 
    6166 Alignment algorithm | Needleman-Wunsch 
    6167 Similarity matrix | BLOSUM-62 
    6168 SS fraction | 0.3 
    6169 Gap open (HH/SS/other) | 18/18/6 
    6170 Gap extend | 1 
    6171 SS matrix |  |  | H | S | O 
    6172 ---|---|---|--- 
    6173 H | 6 | -9 | -6 
    6174 S |  | 6 | -6 
    6175 O |  |  | 4 
    6176 Iteration cutoff | 2 
    6177  
    6178 Matchmaker
    6179 RAD54BnterDMC1_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_29694.pdb,
    6180 chain B (#16) with
    6181 RAD54B200RAD51_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_63869.pdb,
    6182 chain B (#19), sequence alignment score = 1075.2 
    6183 RMSD between 287 pruned atom pairs is 0.863 angstroms; (across all 338 pairs:
    6184 2.588) 
    6185  
    6186 
    6187 > select add #18
    6188 
    6189 2975 atoms, 3020 bonds, 389 residues, 1 model selected 
    6190 
    6191 > hide #16 models
    6192 
    6193 > show #17 models
    6194 
    6195 > hide #18 models
    6196 
    6197 > select subtract #18
    6198 
    6199 Nothing selected 
    6200 
    6201 > select #19/A:32
    6202 
    6203 11 atoms, 11 bonds, 1 residue, 1 model selected 
    6204 
    6205 > show sel atoms
    6206 
    6207 > select #19/A:35
    6208 
    6209 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6210 
    6211 > show sel atoms
    6212 
    6213 > hide #17 models
    6214 
    6215 > ui tool show "Show Sequence Viewer"
    6216 
    6217 > sequence chain #19/A
    6218 
    6219 Alignment identifier is 19/A 
    6220 
    6221 > select #19/A:32
    6222 
    6223 11 atoms, 11 bonds, 1 residue, 1 model selected 
    6224 
    6225 > select #19/A:32-35
    6226 
    6227 33 atoms, 33 bonds, 4 residues, 1 model selected 
    6228 
    6229 > show #17 models
    6230 
    6231 > hide #17 models
    6232 
    6233 > show #17 models
    6234 
    6235 > close #2-3,5-10,12,15-19#1,4,11,13-14
    6236 
    6237 > open
    6238 > /Users/sz140275local/Downloads/cryosparc_P26_J216_011_volume_map_sharp.mrc
    6239 
    6240 Opened cryosparc_P26_J216_011_volume_map_sharp.mrc as #1, grid size
    6241 336,336,336, pixel 0.745, shown at level 0.0337, step 2, values float32 
    6242 
    6243 > open /Users/sz140275local/Downloads/cryosparc_P26_J216_011_volume_map.mrc
    6244 
    6245 Opened cryosparc_P26_J216_011_volume_map.mrc as #2, grid size 336,336,336,
    6246 pixel 0.745, shown at level 0.0204, step 2, values float32 
    6247 
    6248 > open /Users/sz140275local/Downloads/J216_011_volume_map_ABCEF.pdb
    6249 
    6250 Chain information for J216_011_volume_map_ABCEF.pdb #3 
    6251 --- 
    6252 Chain | Description 
    6253 A B C D E F | No description available 
    6254 M N O P Q R | No description available 
    6255 X | No description available 
    6256  
    6257 
    6258 > hide #!2 models
    6259 
    6260 > hide #!1 models
    6261 
    6262 > hide atoms
    6263 
    6264 > show cartoons
    6265 
    6266 Computing secondary structure 
    6267 
    6268 > show #!2 models
    6269 
    6270 > hide #!2 models
    6271 
    6272 > show #!2 models
    6273 
    6274 > transparency #2.1 50
    6275 
    6276 > ui mousemode right zoom
    6277 
    6278 > ui tool show "Show Sequence Viewer"
    6279 
    6280 > hide #!2 models
    6281 
    6282 > ui tool show "Show Sequence Viewer"
    6283 
    6284 > sequence chain /O
    6285 
    6286 Alignment identifier is 3/O 
    6287 
    6288 > select #3/X
    6289 
    6290 360 atoms, 395 bonds, 18 residues, 1 model selected 
    6291 
    6292 > color sel black
    6293 
    6294 > select add #3
    6295 
    6296 15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 2 models selected 
    6297 
    6298 > select subtract #3
    6299 
    6300 Nothing selected 
    6301 
    6302 > color #3/A,C,E,G,I royal blue
    6303 
    6304 > select clear
    6305 
    6306 [Repeated 1 time(s)]
    6307 
    6308 > color #3/M,N,O,P,Q red
    6309 
    6310 > color #3/F,D,B wheat
    6311 
    6312 > lighting soft
    6313 
    6314 > graphics silhouettes true width 2
    6315 
    6316 > background white
    6317 
    6318 Unknown command: background white 
    6319 
    6320 > cartoon style strand width 3 thickness 1
    6321 
    6322 > cartoon style helix width 3 thickness 1
    6323 
    6324 > cartoon style coil width 2 thickness 1.5
    6325 
    6326 > cartoon style nucleic width 1.2 thickness 1.2 xsection section oval
    6327 
    6328 Invalid "xsection" argument: Should be one of 'barbell', 'oval', 'piping',
    6329 'rectangle', 'round', or 'square' 
    6330 
    6331 > select #3/M,N,O,P,Q
    6332 
    6333 275 atoms, 290 bonds, 35 residues, 1 model selected 
    6334 
    6335 > show sel atoms
    6336 
    6337 > size #3/M,N,O,P,Q stickRadius 2
    6338 
    6339 Changed 290 bond radii 
    6340 
    6341 > size #3/M,N,O,P,Q stickRadius 0.5
    6342 
    6343 Changed 290 bond radii 
    6344 
    6345 > select add #3
    6346 
    6347 15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 2 models selected 
    6348 
    6349 > select subtract #3
    6350 
    6351 Nothing selected 
    6352 
    6353 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    6354 > RAD54/FVdmc1BRCA2.tif" width 884 height 589 supersample 3
    6355 
    6356 > show #!1 models
    6357 
    6358 > surface dust #1 size 7.45
    6359 
    6360 > transparency #1.1 50
    6361 
    6362 > color zone #1 near #3 distance 4.47
    6363 
    6364 > transparency #1.1 0
    6365 
    6366 > transparency #1.1 50
    6367 
    6368 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    6369 > RAD54/FVdmc1BRCA2withMap.tif" width 884 height 589 supersample 3
    6370 
    6371 > ui mousemode right translate
    6372 
    6373 > ui mousemode right zoom
    6374 
    6375 > hide #!3 models
    6376 
    6377 > show #!3 models
    6378 
    6379 > hide #!3 models
    6380 
    6381 > preset "overall look" "publication 1 (silhouettes)"
    6382 
    6383 Using preset: Overall Look / Publication 1 (Silhouettes) 
    6384 Preset expands to these ChimeraX commands:
    6385 
    6386    
    6387    
    6388     set bg white
    6389     graphics silhouettes t
    6390     lighting depthCue f
    6391 
    6392  
    6393 
    6394 > preset "overall look" "publication 2 (depth-cued)"
    6395 
    6396 Using preset: Overall Look / Publication 2 (Depth-Cued) 
    6397 Preset expands to these ChimeraX commands:
    6398 
    6399    
    6400    
    6401     set bg white
    6402     graphics silhouettes f
    6403     lighting depthCue t
    6404 
    6405  
    6406 
    6407 > preset "overall look" "publication 1 (silhouettes)"
    6408 
    6409 Using preset: Overall Look / Publication 1 (Silhouettes) 
    6410 Preset expands to these ChimeraX commands:
    6411 
    6412    
    6413    
    6414     set bg white
    6415     graphics silhouettes t
    6416     lighting depthCue f
    6417 
    6418  
    6419 
    6420 > graphics silhouettes true width 1
    6421 
    6422 > graphics silhouettes true width 3
    6423 
    6424 > graphics silhouettes false width 3
    6425 
    6426 > graphics silhouettes true width 3
    6427 
    6428 > lighting
    6429 
    6430 Intensity: 0 
    6431 Direction: 0.577,-0.577,-0.577 
    6432 Color: 100,100,100 
    6433 Fill intensity: 0 
    6434 Fill direction: -0.2,-0.2,-0.959 
    6435 Fill color: 100,100,100 
    6436 Ambient intensity: 1.5 
    6437 Ambient color: 100,100,100 
    6438 Depth cue: 0, start 0.5, end 1, color 100,100,100 
    6439 Shadow: False (depth map size 2048, depth bias 0.005) 
    6440 Multishadows: 64 (max 1024, depth map size 1024, depth bias 0.01) 
    6441 
    6442 > lighting simple
    6443 
    6444 > show #!3 models
    6445 
    6446 > hide #!3 models
    6447 
    6448 > show #!3 models
    6449 
    6450 > hide #!3 models
    6451 
    6452 > show #!3 models
    6453 
    6454 > hide #!3 models
    6455 
    6456 > volume #!1 showOutlineBox true
    6457 
    6458 > volume #!1 showOutlineBox false
    6459 
    6460 > transparency #1.1 0
    6461 
    6462 > transparency #1.1 50
    6463 
    6464 > show #!3 models
    6465 
    6466 > volume #1 level 0.02152
    6467 
    6468 > volume #1 level 0.02422
    6469 
    6470 > color zone #1 near #3 distance 4.47
    6471 
    6472 > surface dust #1 size 7.45
    6473 
    6474 > transparency #1.1 0
    6475 
    6476 > transparency #1.1 50
    6477 
    6478 > ui mousemode right translate
    6479 
    6480 > volume #1 level 0.02692
    6481 
    6482 > color zone #1 near #3 distance 4.47
    6483 
    6484 > surface dust #1 size 7.45
    6485 
    6486 > transparency #1.1 0
    6487 
    6488 > transparency #1.1 50
    6489 
    6490 > ui mousemode right zoom
    6491 
    6492 > ui mousemode right translate
    6493 
    6494 > ui mousemode right zoom
    6495 
    6496 > ui mousemode right translate
    6497 
    6498 > hide #!3 models
    6499 
    6500 > ui mousemode right zoom
    6501 
    6502 > transparency #1.1 0
    6503 
    6504 > ui mousemode right translate
    6505 
    6506 > ui mousemode right zoom
    6507 
    6508 > ui mousemode right translate
    6509 
    6510 > ui mousemode right zoom
    6511 
    6512 > ui mousemode right translate
    6513 
    6514 > transparency #1.1 50
    6515 
    6516 > transparency #1.1 0
    6517 
    6518 > show #!3 models
    6519 
    6520 > hide #!3 models
    6521 
    6522 > show #!3 models
    6523 
    6524 > hide #!3 models
    6525 
    6526 > show #!3 models
    6527 
    6528 > hide #!3 models
    6529 
    6530 > transparency #1.1 50
    6531 
    6532 > transparency #1.1 0
    6533 
    6534 > transparency #1.1 50
    6535 
    6536 > transparency #1.1 0
    6537 
    6538 > show #!2 models
    6539 
    6540 > hide #!1 models
    6541 
    6542 > show #!3 models
    6543 
    6544 > color zone #2 near #3 distance 4.47
    6545 
    6546 > volume #2 level 0.01243
    6547 
    6548 > surface dust #2 size 7.45
    6549 
    6550 > transparency #2.1 0
    6551 
    6552 > transparency #2.1 50
    6553 
    6554 > transparency #2.1 0
    6555 
    6556 > hide #!3 models
    6557 
    6558 > volume #2 level 0.01409
    6559 
    6560 Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
    6561 models, 1 maps. 
    6562 
    6563 [Repeated 1 time(s)]
    6564 
    6565 > show #!3 models
    6566 
    6567 > color zone #2 near #3 distance 4.47
    6568 
    6569 > hide #!3 models
    6570 
    6571 > color #2 #fbffd180 models
    6572 
    6573 > color #2 #ffeeef80 models
    6574 
    6575 > color #2 #ffeef080 models
    6576 
    6577 > color #2 #dccdcf80 models
    6578 
    6579 > show #!3 models
    6580 
    6581 > color zone #2 near #3 distance 4.47
    6582 
    6583 > hide #!3 models
    6584 
    6585 > show #!1 models
    6586 
    6587 > hide #!2 models
    6588 
    6589 > show #!2 models
    6590 
    6591 > hide #!1 models
    6592 
    6593 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    6594 > RAD54/FVdmc1BRCA2zoom1.tif" width 884 height 589 supersample 3
    6595 
    6596 > show #!3 models
    6597 
    6598 > transparency #2.1 0
    6599 
    6600 > transparency #2.1 50
    6601 
    6602 > ui mousemode right zoom
    6603 
    6604 > ui mousemode right translate
    6605 
    6606 > ui mousemode right zoom
    6607 
    6608 > ui mousemode right translate
    6609 
    6610 > ui mousemode right zoom
    6611 
    6612 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    6613 > RAD54/FVdmc1BRCA2withMap2.tif" width 884 height 589 supersample 3
    6614 
    6615 > ui mousemode right translate
    6616 
    6617 > ui mousemode right zoom
    6618 
    6619 > show #!1 models
    6620 
    6621 > hide #!2 models
    6622 
    6623 > transparency #1.1 50
    6624 
    6625 > transparency #1.1 0
    6626 
    6627 > transparency #1.1 50
    6628 
    6629 > transparency #1.1 0
    6630 
    6631 > transparency #1.1 50
    6632 
    6633 > ui mousemode right translate
    6634 
    6635 > show #!2 models
    6636 
    6637 > hide #!1 models
    6638 
    6639 > show #!1 models
    6640 
    6641 > hide #!2 models
    6642 
    6643 > hide #!1 models
    6644 
    6645 > show #!2 models
    6646 
    6647 > hide #!2 models
    6648 
    6649 > show #!1 models
    6650 
    6651 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    6652 > RAD54/FVdmc1BRCA2withMapZ3.tif" width 884 height 589 supersample 3
    6653 
    6654 > hide #!1 models
    6655 
    6656 > label #3/O
    6657 
    6658 > show #!1 models
    6659 
    6660 > hide #!3 models
    6661 
    6662 > show #!3 models
    6663 
    6664 > ui mousemode right zoom
    6665 
    6666 > ui mousemode right translate
    6667 
    6668 > ui mousemode right zoom
    6669 
    6670 > select #3/O
    6671 
    6672 55 atoms, 58 bonds, 7 residues, 1 model selected 
    6673 
    6674 > ~label sel residues
    6675 
    6676 > select add #3
    6677 
    6678 15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 2 models selected 
    6679 
    6680 > select subtract #3
    6681 
    6682 Nothing selected 
    6683 
    6684 > ui mousemode right translate
    6685 
    6686 > hide #!3 models
    6687 
    6688 > show #!3 models
    6689 
    6690 > hide #!1 models
    6691 
    6692 > show #!1 models
    6693 
    6694 > hide #!1 models
    6695 
    6696 > show #!1 models
    6697 
    6698 > hide #!1 models
    6699 
    6700 > ui mousemode right zoom
    6701 
    6702 > ui mousemode right translate
    6703 
    6704 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    6705 > RAD54/BRCA2struct1.tif" width 884 height 589 supersample 3
    6706 
    6707 > show #!1 models
    6708 
    6709 > hide #!1 models
    6710 
    6711 > show #!1 models
    6712 
    6713 > hide #!1 models
    6714 
    6715 > show #!2 models
    6716 
    6717 > hide #!2 models
    6718 
    6719 > show #!2 models
    6720 
    6721 > volume #2 level 0.01143
    6722 
    6723 > color zone #2 near #3 distance 4.47
    6724 
    6725 > transparency #2.1 0
    6726 
    6727 > transparency #2.1 50
    6728 
    6729 > hide #!2 models
    6730 
    6731 > select /D:85
    6732 
    6733 11 atoms, 11 bonds, 1 residue, 1 model selected 
    6734 
    6735 > show sel atoms
    6736 
    6737 > select /D:89
    6738 
    6739 11 atoms, 11 bonds, 1 residue, 1 model selected 
    6740 
    6741 > show sel atoms
    6742 
    6743 > hide sel atoms
    6744 
    6745 > select /D:85@CD2
    6746 
    6747 1 atom, 1 residue, 1 model selected 
    6748 
    6749 > hide sel atoms
    6750 
    6751 [Repeated 1 time(s)]
    6752 
    6753 > select /D:85@CA
    6754 
    6755 1 atom, 1 residue, 1 model selected 
    6756 
    6757 > hide sel atoms
    6758 
    6759 > select /D:85@CB
    6760 
    6761 1 atom, 1 residue, 1 model selected 
    6762 
    6763 > select /D:85@CG
    6764 
    6765 1 atom, 1 residue, 1 model selected 
    6766 
    6767 > select /D:85@CE2
    6768 
    6769 1 atom, 1 residue, 1 model selected 
    6770 
    6771 > hide sel atoms
    6772 
    6773 > select /D:85@CB
    6774 
    6775 1 atom, 1 residue, 1 model selected 
    6776 
    6777 > hide sel atoms
    6778 
    6779 > select /D:85@CG
    6780 
    6781 1 atom, 1 residue, 1 model selected 
    6782 
    6783 > hide sel atoms
    6784 
    6785 > select /D:85@CD1
    6786 
    6787 1 atom, 1 residue, 1 model selected 
    6788 
    6789 > hide sel atoms
    6790 
    6791 > select /D:85@CZ
    6792 
    6793 1 atom, 1 residue, 1 model selected 
    6794 
    6795 > hide sel atoms
    6796 
    6797 > select /D:85@CE1
    6798 
    6799 1 atom, 1 residue, 1 model selected 
    6800 
    6801 > hide sel atoms
    6802 
    6803 > select #3/C,D
    6804 
    6805 4876 atoms, 4952 bonds, 2 pseudobonds, 628 residues, 2 models selected 
    6806 
    6807 > coulombic sel
    6808 
    6809 Using Amber 20 recommended default charges and atom types for standard
    6810 residues 
    6811 Coulombic values for J216_011_volume_map_ABCEF.pdb_C SES surface #3.2:
    6812 minimum, -26.80, mean -0.75, maximum 13.88 
    6813 Coulombic values for J216_011_volume_map_ABCEF.pdb_D SES surface #3.3:
    6814 minimum, -27.43, mean -0.73, maximum 14.12 
    6815 To also show corresponding color key, enter the above coulombic command and
    6816 add key true 
    6817 
    6818 > transparency sel 50
    6819 
    6820 > select add #3
    6821 
    6822 15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 4 models selected 
    6823 
    6824 > transparency sel 0
    6825 
    6826 > transparency sel 50
    6827 
    6828 > select /C:20@N
    6829 
    6830 1 atom, 1 residue, 1 model selected 
    6831 
    6832 > show sel atoms
    6833 
    6834 [Repeated 1 time(s)]
    6835 
    6836 > transparency sel 0
    6837 
    6838 > select add #3
    6839 
    6840 15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 3 models selected 
    6841 
    6842 > select subtract #3
    6843 
    6844 2 models selected 
    6845 
    6846 > select add #3
    6847 
    6848 15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 2 models selected 
    6849 
    6850 > transparency sel 0
    6851 
    6852 > transparency sel 50
    6853 
    6854 > transparency sel 0
    6855 
    6856 > transparency sel 50
    6857 
    6858 > transparency sel 0
    6859 
    6860 > transparency sel 50
    6861 
    6862 > transparency sel 0
    6863 
    6864 > transparency sel 50
    6865 
    6866 > transparency sel 0
    6867 
    6868 > select subtract #3
    6869 
    6870 2 models selected 
    6871 
    6872 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    6873 > RAD54/BRCA2elec1.tif" width 884 height 589 supersample 3
    6874 
    6875 > hide surfaces
    6876 
    6877 > ui mousemode right zoom
    6878 
    6879 > ui mousemode right translate
    6880 
    6881 > select #3/A
    6882 
    6883 2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected 
    6884 
    6885 > hide sel cartoons
    6886 
    6887 > select #3/B
    6888 
    6889 2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected 
    6890 
    6891 > hide sel cartoons
    6892 
    6893 > select #3/M
    6894 
    6895 55 atoms, 58 bonds, 7 residues, 1 model selected 
    6896 
    6897 > hide sel atoms
    6898 
    6899 > hide sel cartoons
    6900 
    6901 > select #3/E,P
    6902 
    6903 2493 atoms, 2534 bonds, 1 pseudobond, 321 residues, 2 models selected 
    6904 
    6905 > hide sel cartoons
    6906 
    6907 > hide sel atoms
    6908 
    6909 > select #3/D:85,89
    6910 
    6911 22 atoms, 22 bonds, 2 residues, 1 model selected 
    6912 
    6913 > show sel atoms
    6914 
    6915 > style sel stick
    6916 
    6917 Changed 22 atom styles 
    6918 
    6919 > size #3/D stickRadius 2
    6920 
    6921 Changed 2476 bond radii 
    6922 
    6923 > style sel stick
    6924 
    6925 Changed 22 atom styles 
    6926 
    6927 > style sel stick
    6928 
    6929 Changed 22 atom styles 
    6930 
    6931 > style sel stick
    6932 
    6933 Changed 22 atom styles 
    6934 
    6935 > size #3/D stickRadius 0.5
    6936 
    6937 Changed 2476 bond radii 
    6938 
    6939 > select add #3
    6940 
    6941 15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 3 models selected 
    6942 
    6943 > select subtract #3
    6944 
    6945 2 models selected 
    6946 
    6947 > select #3/A
    6948 
    6949 2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected 
    6950 
    6951 > show sel cartoons
    6952 
    6953 [Repeated 1 time(s)]
    6954 
    6955 > hide sel cartoons
    6956 
    6957 > select #3/B
    6958 
    6959 2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected 
    6960 
    6961 > show sel cartoons
    6962 
    6963 > select add #3
    6964 
    6965 15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 2 models selected 
    6966 
    6967 > select subtract #3
    6968 
    6969 2 models selected 
    6970 
    6971 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    6972 > RAD54/BRCA2struct1.tif" width 884 height 589 supersample 3
    6973 
    6974 > select #3/C,D
    6975 
    6976 4876 atoms, 4952 bonds, 2 pseudobonds, 628 residues, 2 models selected 
    6977 
    6978 > coulombic sel
    6979 
    6980 Coulombic values for J216_011_volume_map_ABCEF.pdb_C SES surface #3.2:
    6981 minimum, -26.80, mean -0.75, maximum 13.88 
    6982 Coulombic values for J216_011_volume_map_ABCEF.pdb_D SES surface #3.3:
    6983 minimum, -27.43, mean -0.73, maximum 14.12 
    6984 To also show corresponding color key, enter the above coulombic command and
    6985 add key true 
    6986 
    6987 > coulombic sel
    6988 
    6989 Coulombic values for J216_011_volume_map_ABCEF.pdb_C SES surface #3.2:
    6990 minimum, -26.80, mean -0.75, maximum 13.88 
    6991 Coulombic values for J216_011_volume_map_ABCEF.pdb_D SES surface #3.3:
    6992 minimum, -27.43, mean -0.73, maximum 14.12 
    6993 To also show corresponding color key, enter the above coulombic command and
    6994 add key true 
    6995 
    6996 > hide sel surfaces
    6997 
    6998 > show sel surfaces
    6999 
    7000 > hide sel surfaces
    7001 
    7002 > show sel surfaces
    7003 
    7004 > hide sel surfaces
    7005 
    7006 [Repeated 2 time(s)]
    7007 
    7008 > show sel surfaces
    7009 
    7010 > ui mousemode right zoom
    7011 
    7012 > ui mousemode right translate
    7013 
    7014 > ui mousemode right zoom
    7015 
    7016 > transparency sel 50
    7017 
    7018 > transparency sel 0
    7019 
    7020 > select #3/C:175
    7021 
    7022 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7023 
    7024 > transparency sel 50
    7025 
    7026 > show sel atoms
    7027 
    7028 [Repeated 2 time(s)]
    7029 
    7030 > style sel stick
    7031 
    7032 Changed 8 atom styles 
    7033 
    7034 > hide sel surfaces
    7035 
    7036 > select #3/C
    7037 
    7038 2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected 
    7039 
    7040 > hide sel surfaces
    7041 
    7042 [Repeated 2 time(s)]
    7043 
    7044 > show sel surfaces
    7045 
    7046 > select #3/C:213
    7047 
    7048 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7049 
    7050 > show sel atoms
    7051 
    7052 > hide sel surfaces
    7053 
    7054 > style sel stick
    7055 
    7056 Changed 9 atom styles 
    7057 
    7058 > select #3/C
    7059 
    7060 2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected 
    7061 
    7062 > hide sel surfaces
    7063 
    7064 > select #3/C
    7065 
    7066 2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected 
    7067 
    7068 > select #3/B,D
    7069 
    7070 4876 atoms, 4952 bonds, 2 pseudobonds, 628 residues, 2 models selected 
    7071 
    7072 > show sel surfaces
    7073 
    7074 > select #3/B,D
    7075 
    7076 4876 atoms, 4952 bonds, 2 pseudobonds, 628 residues, 2 models selected 
    7077 
    7078 > color sel wheat
    7079 
    7080 > select add #3
    7081 
    7082 15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 4 models selected 
    7083 
    7084 > select subtract #3
    7085 
    7086 3 models selected 
    7087 
    7088 > hide atoms
    7089 
    7090 > select #3/O
    7091 
    7092 55 atoms, 58 bonds, 7 residues, 1 model selected 
    7093 
    7094 > show sel atoms
    7095 
    7096 > select add #3
    7097 
    7098 15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 2 models selected 
    7099 
    7100 > select subtract #3
    7101 
    7102 3 models selected 
    7103 
    7104 > ui mousemode right translate
    7105 
    7106 > ui mousemode right zoom
    7107 
    7108 > select #3/O,P,M,N
    7109 
    7110 220 atoms, 232 bonds, 28 residues, 1 model selected 
    7111 
    7112 > show sel cartoons
    7113 
    7114 [Repeated 2 time(s)]
    7115 
    7116 > select add #3
    7117 
    7118 15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 2 models selected 
    7119 
    7120 > select subtract #3
    7121 
    7122 3 models selected 
    7123 
    7124 > ui mousemode right translate
    7125 
    7126 > select #3/F
    7127 
    7128 2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected 
    7129 
    7130 > hide sel cartoons
    7131 
    7132 > select #3/D:85,89
    7133 
    7134 22 atoms, 22 bonds, 2 residues, 1 model selected 
    7135 
    7136 > color sel green
    7137 
    7138 > select add #3
    7139 
    7140 15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 3 models selected 
    7141 
    7142 > select subtract #3
    7143 
    7144 3 models selected 
    7145 
    7146 > color sel orange
    7147 
    7148 > select #3/D:85,89
    7149 
    7150 22 atoms, 22 bonds, 2 residues, 1 model selected 
    7151 
    7152 > color sel orange
    7153 
    7154 > select add #3
    7155 
    7156 15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 3 models selected 
    7157 
    7158 > select subtract #3
    7159 
    7160 3 models selected 
    7161 
    7162 > select #3/X
    7163 
    7164 360 atoms, 395 bonds, 18 residues, 1 model selected 
    7165 
    7166 > hide sel cartoons
    7167 
    7168 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    7169 > RAD54/BRCA2mono.tif" width 670 height 583 supersample 3
    7170 
    7171 > select #3/C:179,180,183
    7172 
    7173 20 atoms, 18 bonds, 3 residues, 1 model selected 
    7174 
    7175 > show sel atoms
    7176 
    7177 > style sel stick
    7178 
    7179 Changed 20 atom styles 
    7180 
    7181 > ui mousemode right zoom
    7182 
    7183 > show #!1 models
    7184 
    7185 > select add #3
    7186 
    7187 15318 atoms, 15599 bonds, 6 pseudobonds, 1944 residues, 3 models selected 
    7188 
    7189 > select subtract #3
    7190 
    7191 3 models selected 
    7192 
    7193 > hide #!1 models
    7194 
    7195 > show #!2 models
    7196 
    7197 > hide #!2 models
    7198 
    7199 > show #!1 models
    7200 
    7201 > open /Users/sz140275local/Downloads/newPDBfit-
    7202 > coot-10_real_space_refined_002.pdb
    7203 
    7204 Chain information for newPDBfit-coot-10_real_space_refined_002.pdb #4 
    7205 --- 
    7206 Chain | Description 
    7207 A B C D E F | No description available 
    7208 M N O P Q R | No description available 
    7209 X | No description available 
    7210  
    7211 
    7212 > hide #!3 models
    7213 
    7214 > hide #!1 models
    7215 
    7216 > open /Users/sz140275local/Downloads/cryosparc_P26_J362_012_volume_map.mrc
    7217 
    7218 Opened cryosparc_P26_J362_012_volume_map.mrc as #5, grid size 336,336,336,
    7219 pixel 0.73, shown at level 0.0236, step 2, values float32 
    7220 
    7221 > open
    7222 > /Users/sz140275local/Downloads/cryosparc_P26_J362_012_volume_map_sharp.mrc
    7223 
    7224 Opened cryosparc_P26_J362_012_volume_map_sharp.mrc as #6, grid size
    7225 336,336,336, pixel 0.73, shown at level 0.0403, step 2, values float32 
    7226 
    7227 > hide #!4 models
    7228 
    7229 > hide #!5 models
    7230 
    7231 > surface dust #6 size 7.3
    7232 
    7233 > show #!4 models
    7234 
    7235 > hide #!4 atoms
    7236 
    7237 > show #!4 cartoons
    7238 
    7239 > transparency #6.1 50
    7240 
    7241 > select #6/O,P,M,N
    7242 
    7243 Nothing selected 
    7244 
    7245 > color sel red
    7246 
    7247 > select #6/R,P,Q,
    7248 
    7249 Expected an objects specifier or a keyword 
    7250 
    7251 > select #6/R,P,Q,M,N,O
    7252 
    7253 Nothing selected 
    7254 
    7255 > select #4/R,P,Q,M,N,O
    7256 
    7257 408 atoms, 426 bonds, 48 residues, 1 model selected 
    7258 
    7259 > color sel red
    7260 
    7261 > select add #4
    7262 
    7263 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    7264 
    7265 > select subtract #4
    7266 
    7267 Nothing selected 
    7268 
    7269 > ui mousemode right translate
    7270 
    7271 > color zone #6 near #4 distance 4.38
    7272 
    7273 > transparency #6.1 0
    7274 
    7275 > transparency #6.1 50
    7276 
    7277 > hide #!6 models
    7278 
    7279 > select #4/R,P,Q,M,N,O
    7280 
    7281 408 atoms, 426 bonds, 48 residues, 1 model selected 
    7282 
    7283 > show sel atoms
    7284 
    7285 > select add #4
    7286 
    7287 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    7288 
    7289 > select subtract #4
    7290 
    7291 Nothing selected 
    7292 
    7293 > show #!6 models
    7294 
    7295 > ui mousemode right zoom
    7296 
    7297 > volume #6 level 0.0257
    7298 
    7299 > color zone #6 near #4 distance 4.38
    7300 
    7301 > transparency #6.1 0
    7302 
    7303 > transparency #6.1 50
    7304 
    7305 > ui mousemode right translate
    7306 
    7307 > volume #6 level 0.04401
    7308 
    7309 > color zone #6 near #4 distance 4.38
    7310 
    7311 > transparency #6.1 0
    7312 
    7313 > transparency #6.1 50
    7314 
    7315 > volume #6 level 0.03485
    7316 
    7317 > color zone #6 near #4 distance 4.38
    7318 
    7319 > transparency #6.1 0
    7320 
    7321 > transparency #6.1 50
    7322 
    7323 > hide #!4 models
    7324 
    7325 > show #!5 models
    7326 
    7327 > hide #!6 models
    7328 
    7329 > show #!4 models
    7330 
    7331 > color zone #5 near #4 distance 4.38
    7332 
    7333 > transparency #5.1 50
    7334 
    7335 > ui mousemode right zoom
    7336 
    7337 > select #4/ATP*
    7338 
    7339 Nothing selected 
    7340 
    7341 > hide #!5 models
    7342 
    7343 > select #4/ATP
    7344 
    7345 Nothing selected 
    7346 
    7347 > select #4/A:ATP*
    7348 
    7349 31 atoms, 33 bonds, 1 residue, 1 model selected 
    7350 
    7351 > show sel atoms
    7352 
    7353 > select #4/B,C,D:ATP*
    7354 
    7355 93 atoms, 99 bonds, 3 residues, 1 model selected 
    7356 
    7357 > show sel atoms
    7358 
    7359 > select #4/A,B,C,D:Mg*
    7360 
    7361 8 atoms, 8 residues, 1 model selected 
    7362 
    7363 > show sel atoms
    7364 
    7365 > select add #4
    7366 
    7367 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    7368 
    7369 > select subtract #4
    7370 
    7371 Nothing selected 
    7372 
    7373 > show #!5 models
    7374 
    7375 > volume #6 level 0.04767
    7376 
    7377 > hide #!6 models
    7378 
    7379 > volume #5 level 0.0359
    7380 
    7381 > color zone #5 near #4 distance 4.38
    7382 
    7383 > transparency #5.1 50
    7384 
    7385 > ui mousemode right translate
    7386 
    7387 > ui mousemode right zoom
    7388 
    7389 > select #4/X
    7390 
    7391 360 atoms, 395 bonds, 18 residues, 1 model selected 
    7392 
    7393 > show sel atoms
    7394 
    7395 > style sel stick
    7396 
    7397 Changed 360 atom styles 
    7398 
    7399 > select add #4
    7400 
    7401 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    7402 
    7403 > select subtract #4
    7404 
    7405 Nothing selected 
    7406 
    7407 > close #2-3
    7408 
    7409 > close #1
    7410 
    7411 > open "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
    7412 > structure RAD54B 07072025/cryosparc_P26_J402_011_volume_map.mrc"
    7413 
    7414 Opened cryosparc_P26_J402_011_volume_map.mrc as #1, grid size 336,336,336,
    7415 pixel 0.745, shown at level 0.0227, step 2, values float32 
    7416 
    7417 > open "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
    7418 > structure RAD54B 07072025/cryosparc_P26_J402_011_volume_map_sharp.mrc"
    7419 
    7420 Opened cryosparc_P26_J402_011_volume_map_sharp.mrc as #2, grid size
    7421 336,336,336, pixel 0.745, shown at level 0.0343, step 2, values float32 
    7422 
    7423 > hide #!4 models
    7424 
    7425 > hide #!2 models
    7426 
    7427 > hide #!1 models
    7428 
    7429 > show #!6 models
    7430 
    7431 > hide #!6 models
    7432 
    7433 > open "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
    7434 > structure RAD54B 07072025/newPDBfit-coot-10_real_space_refined_002.pdb"
    7435 
    7436 Chain information for newPDBfit-coot-10_real_space_refined_002.pdb #3 
    7437 --- 
    7438 Chain | Description 
    7439 A B C D E F | No description available 
    7440 M N O P Q R | No description available 
    7441 X | No description available 
    7442  
    7443 
    7444 > hide #!5 models
    7445 
    7446 > close #4
    7447 
    7448 > hide atoms
    7449 
    7450 > show cartoons
    7451 
    7452 > hide #!3 models
    7453 
    7454 > show #!5 models
    7455 
    7456 > show #!1 models
    7457 
    7458 > hide #!1 models
    7459 
    7460 > show #!1 models
    7461 
    7462 > hide #!1 models
    7463 
    7464 > show #!3 models
    7465 
    7466 > hide #!3 models
    7467 
    7468 > show #!3 models
    7469 
    7470 > hide #!3 models
    7471 
    7472 > show #!3 models
    7473 
    7474 > hide #!3 models
    7475 
    7476 > hide #!5 models
    7477 
    7478 > show #!6 models
    7479 
    7480 > color #6 #95d3fa80 models
    7481 
    7482 > color #6 #decffa80 models
    7483 
    7484 > color #6 #fac9bb80 models
    7485 
    7486 > show #!3 models
    7487 
    7488 > hide cartoons
    7489 
    7490 > select #3/X
    7491 
    7492 360 atoms, 395 bonds, 18 residues, 1 model selected 
    7493 
    7494 > show sel cartoons
    7495 
    7496 > color sel lime
    7497 
    7498 > select #3/A=ATP*
    7499 
    7500 Expected an objects specifier or a keyword 
    7501 
    7502 > select #3/A:ATP*
    7503 
    7504 31 atoms, 33 bonds, 1 residue, 1 model selected 
    7505 
    7506 > select #3/A,B,C,D,E,F:ATP*
    7507 
    7508 124 atoms, 132 bonds, 4 residues, 1 model selected 
    7509 
    7510 > select #3/A,B,C,D,E,F,G:ATP*
    7511 
    7512 124 atoms, 132 bonds, 4 residues, 1 model selected 
    7513 
    7514 > style sel stick
    7515 
    7516 Changed 124 atom styles 
    7517 
    7518 > style sel stick
    7519 
    7520 Changed 124 atom styles 
    7521 
    7522 > show sel atoms
    7523 
    7524 > color sel blue
    7525 
    7526 > select #3/M,N,O,P,Q,R,S,T
    7527 
    7528 408 atoms, 426 bonds, 48 residues, 1 model selected 
    7529 
    7530 > show sel cartoons
    7531 
    7532 > show sel atoms
    7533 
    7534 > select #3/M,N,O,P,Q,R,S,T
    7535 
    7536 408 atoms, 426 bonds, 48 residues, 1 model selected 
    7537 
    7538 > color sel red
    7539 
    7540 > select #3/X
    7541 
    7542 360 atoms, 395 bonds, 18 residues, 1 model selected 
    7543 
    7544 > show sel atoms
    7545 
    7546 > style sel stick
    7547 
    7548 Changed 360 atom styles 
    7549 
    7550 > select add #3
    7551 
    7552 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    7553 
    7554 > select subtract #3
    7555 
    7556 Nothing selected 
    7557 
    7558 > volume #6 level 0.03485
    7559 
    7560 > color zone #6 near #3 distance 4.38
    7561 
    7562 > transparency #6.1 0
    7563 
    7564 > transparency #6.1 50
    7565 
    7566 > ui mousemode right translate
    7567 
    7568 > volume #6 level 0.03
    7569 
    7570 > volume #6 level 0.02
    7571 
    7572 > volume #6 level 0.04
    7573 
    7574 > color zone #6 near #3 distance 4.38
    7575 
    7576 > transparency #6.1 0
    7577 
    7578 > transparency #6.1 50
    7579 
    7580 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    7581 > RAD54/BRCA2filaments.tif" width 769 height 709 supersample 3
    7582 
    7583 > select #3/M,N,O,P,Q,R,S,T:10
    7584 
    7585 54 atoms, 48 bonds, 6 residues, 1 model selected 
    7586 
    7587 > hide sel atoms
    7588 
    7589 > select add #3
    7590 
    7591 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    7592 
    7593 > select subtract #3
    7594 
    7595 Nothing selected 
    7596 
    7597 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    7598 > RAD54/BRCA2filaments.tif" width 769 height 709 supersample 3
    7599 
    7600 [Repeated 1 time(s)]
    7601 
    7602 > hide #!3 models
    7603 
    7604 > show #!3 models
    7605 
    7606 > hide #!6 models
    7607 
    7608 > select #3/D
    7609 
    7610 2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 2 models selected 
    7611 
    7612 > show sel cartoons
    7613 
    7614 [Repeated 1 time(s)]
    7615 
    7616 > hide sel cartoons
    7617 
    7618 > select #3/E
    7619 
    7620 2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected 
    7621 
    7622 > show sel cartoons
    7623 
    7624 [Repeated 1 time(s)]
    7625 
    7626 > hide sel cartoons
    7627 
    7628 > select #3/C
    7629 
    7630 2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 2 models selected 
    7631 
    7632 > show sel cartoons
    7633 
    7634 > select #3
    7635 
    7636 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    7637 
    7638 > show sel surfaces
    7639 
    7640 > select #3/C
    7641 
    7642 2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 2 models selected 
    7643 
    7644 > hide sel surfaces
    7645 
    7646 > select #3/O
    7647 
    7648 68 atoms, 71 bonds, 8 residues, 1 model selected 
    7649 
    7650 > hide sel surfaces
    7651 
    7652 > select add #3
    7653 
    7654 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected 
    7655 
    7656 > select subtract #3
    7657 
    7658 13 models selected 
    7659 
    7660 > select #3/X
    7661 
    7662 360 atoms, 395 bonds, 18 residues, 1 model selected 
    7663 
    7664 > hide sel surfaces
    7665 
    7666 > select add #3
    7667 
    7668 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected 
    7669 
    7670 > select subtract #3
    7671 
    7672 13 models selected 
    7673 
    7674 > cartoon style coil width 2 thickness 1.5
    7675 
    7676 > cartoon style coil width 1.5 thickness 1.5
    7677 
    7678 > cartoon style coil width 1.5 thickness 1
    7679 
    7680 > cartoon style helix width 1.5 thickness 1
    7681 
    7682 > cartoon style strand width 1.5 thickness 1
    7683 
    7684 > cartoon style coil width 1 thickness 1
    7685 
    7686 > cartoon style coil width 1 thickness 0.8
    7687 
    7688 > size #3/D stickRadius 0.5
    7689 
    7690 Changed 2509 bond radii 
    7691 
    7692 > size #3/D stickRadius 1
    7693 
    7694 Changed 2509 bond radii 
    7695 
    7696 > size #3 stickRadius 1
    7697 
    7698 Changed 15810 bond radii 
    7699 
    7700 > size #3 stickRadius 0.4
    7701 
    7702 Changed 15810 bond radii 
    7703 
    7704 > select #3/C
    7705 
    7706 2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 2 models selected 
    7707 
    7708 > color sel wheat
    7709 
    7710 > select add #3
    7711 
    7712 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected 
    7713 
    7714 > select subtract #3
    7715 
    7716 13 models selected 
    7717 
    7718 > select #3/D
    7719 
    7720 2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 2 models selected 
    7721 
    7722 > color #3/D:85,89
    7723 
    7724 > color #3/D:85,89 orange
    7725 
    7726 > select add #3
    7727 
    7728 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected 
    7729 
    7730 > select subtract #3
    7731 
    7732 13 models selected 
    7733 
    7734 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    7735 > RAD54/BRCA2filaments2.tif" width 769 height 709 supersample 3
    7736 
    7737 > show #!6 models
    7738 
    7739 > volume #2 level 0.02615
    7740 
    7741 > hide #!2 models
    7742 
    7743 > hide #!6 models
    7744 
    7745 > show #!6 models
    7746 
    7747 > volume #2 level 0.01936
    7748 
    7749 > hide #!6 models
    7750 
    7751 > show #!6 models
    7752 
    7753 > hide #!2 models
    7754 
    7755 > volume #6 level 0.03451
    7756 
    7757 > color zone #6 near #3 distance 4.38
    7758 
    7759 > transparency #3.2-14#6.1 0
    7760 
    7761 > transparency #3.2-14#6.1 50
    7762 
    7763 > volume #6 level 0.02169
    7764 
    7765 > color zone #6 near #3 distance 4.38
    7766 
    7767 > transparency #3.2-14#6.1 0
    7768 
    7769 > transparency #3.2-14#6.1 50
    7770 
    7771 > volume #6 level 0.03267
    7772 
    7773 > color zone #6 near #3 distance 4.38
    7774 
    7775 > transparency #3.2-14#6.1 0
    7776 
    7777 > transparency #3.2-14#6.1 50
    7778 
    7779 > hide #!6 models
    7780 
    7781 > show #!5 models
    7782 
    7783 > volume #5 level 0.0125
    7784 
    7785 > color zone #5 near #3 distance 4.38
    7786 
    7787 > transparency #3.2-14#5.1 0
    7788 
    7789 > transparency #3.2-14#5.1 50
    7790 
    7791 > hide #!5 models
    7792 
    7793 > select /O:10
    7794 
    7795 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7796 
    7797 > show sel atoms
    7798 
    7799 > select add #3
    7800 
    7801 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected 
    7802 
    7803 > select subtract #3
    7804 
    7805 13 models selected 
    7806 
    7807 > show #!5 models
    7808 
    7809 > volume #5 level 0.01455
    7810 
    7811 > color zone #5 near #3 distance 4.38
    7812 
    7813 > transparency #3.2-14#5.1 0
    7814 
    7815 > transparency #3.2-14#5.1 50
    7816 
    7817 > hide #!5 models
    7818 
    7819 > show #!6 models
    7820 
    7821 > volume #6 level 0.04
    7822 
    7823 > color zone #6 near #3 distance 4.38
    7824 
    7825 > transparency #3.2-14#6.1 0
    7826 
    7827 > transparency #3.2-14#6.1 50
    7828 
    7829 > color #3/O:3,10
    7830 
    7831 > show atoms
    7832 
    7833 [Repeated 1 time(s)]
    7834 
    7835 > hide atoms
    7836 
    7837 > color #3/O
    7838 
    7839 > hide #!6 models
    7840 
    7841 > color #3/O
    7842 
    7843 > show atoms
    7844 
    7845 > hide atoms
    7846 
    7847 > select add #3
    7848 
    7849 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    7850 
    7851 > color #3/O
    7852 
    7853 > select #3/O
    7854 
    7855 68 atoms, 71 bonds, 8 residues, 1 model selected 
    7856 
    7857 > show sel atoms
    7858 
    7859 > select #3/O:3,10
    7860 
    7861 18 atoms, 16 bonds, 2 residues, 1 model selected 
    7862 
    7863 > hide sel atoms
    7864 
    7865 > select add #3
    7866 
    7867 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected 
    7868 
    7869 > select subtract #3
    7870 
    7871 13 models selected 
    7872 
    7873 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    7874 > RAD54/BRCA2filaments2.tif" width 769 height 709 supersample 3
    7875 
    7876 > select #3/O:C
    7877 
    7878 Nothing selected 
    7879 
    7880 > hide cartoons
    7881 
    7882 > show surfaces
    7883 
    7884 > hide surfaces
    7885 
    7886 > select #3/
    7887 
    7888 Expected an objects specifier or a keyword 
    7889 
    7890 > hide surfaces
    7891 
    7892 > show cartoons
    7893 
    7894 > hide #!3 models
    7895 
    7896 > show #!6 models
    7897 
    7898 > select #3/M,N,O,P,Q,R,S,T
    7899 
    7900 408 atoms, 426 bonds, 48 residues, 1 model selected 
    7901 
    7902 > select #3/M,N,O,P,Q,R,S,T
    7903 
    7904 408 atoms, 426 bonds, 48 residues, 1 model selected 
    7905 
    7906 > transparency #6.1 0
    7907 
    7908 > transparency #6.1 50
    7909 
    7910 > show #!3 models
    7911 
    7912 > select #3/
    7913 
    7914 Expected an objects specifier or a keyword 
    7915 
    7916 > hide sel cartoons
    7917 
    7918 > hide sel atoms
    7919 
    7920 > hide sel surfaces
    7921 
    7922 > hide sel cartoons
    7923 
    7924 > select #3
    7925 
    7926 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    7927 
    7928 > hide sel cartoons
    7929 
    7930 > select #3/M,N,O,P,Q,R,S,T
    7931 
    7932 408 atoms, 426 bonds, 48 residues, 1 model selected 
    7933 
    7934 > show sel cartoons
    7935 
    7936 > show sel atoms
    7937 
    7938 > select #3/M,N,O,P,Q,R,S,T:3,10
    7939 
    7940 108 atoms, 96 bonds, 12 residues, 1 model selected 
    7941 
    7942 > hide sel atoms
    7943 
    7944 > select #3/X
    7945 
    7946 360 atoms, 395 bonds, 18 residues, 1 model selected 
    7947 
    7948 > hide sel atoms
    7949 
    7950 > show sel atoms
    7951 
    7952 > select #3/A,B,C,D,E,F,G:ATP*
    7953 
    7954 124 atoms, 132 bonds, 4 residues, 1 model selected 
    7955 
    7956 > show sel atoms
    7957 
    7958 > select add #3
    7959 
    7960 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    7961 
    7962 > select subtract #3
    7963 
    7964 13 models selected 
    7965 
    7966 > hide #!6 models
    7967 
    7968 > select #3/A,B,C,D,E,F,G:ATP*
    7969 
    7970 124 atoms, 132 bonds, 4 residues, 1 model selected 
    7971 
    7972 > color sel blue
    7973 
    7974 > select add #3
    7975 
    7976 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    7977 
    7978 > select subtract #3
    7979 
    7980 13 models selected 
    7981 
    7982 > show #!6 models
    7983 
    7984 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    7985 > RAD54/BRCA2filaments.tif" width 769 height 709 supersample 3
    7986 
    7987 > color #3/C
    7988 
    7989 > hide surfaces
    7990 
    7991 [Repeated 1 time(s)]
    7992 
    7993 > select #3/C
    7994 
    7995 2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 2 models selected 
    7996 
    7997 > hide sel surfaces
    7998 
    7999 > show sel cartoons
    8000 
    8001 > hide sel surfaces
    8002 
    8003 > select add #3
    8004 
    8005 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected 
    8006 
    8007 > select subtract #3
    8008 
    8009 13 models selected 
    8010 
    8011 > hide #!6 models
    8012 
    8013 > show surfaces
    8014 
    8015 > select #3/D:85,89
    8016 
    8017 22 atoms, 22 bonds, 2 residues, 1 model selected 
    8018 
    8019 > show sel atoms
    8020 
    8021 > style sel stick
    8022 
    8023 Changed 22 atom styles 
    8024 
    8025 > select add #3
    8026 
    8027 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected 
    8028 
    8029 > select subtract #3
    8030 
    8031 13 models selected 
    8032 
    8033 > select #3/M,N,O,P,Q,R,S,T
    8034 
    8035 408 atoms, 426 bonds, 48 residues, 1 model selected 
    8036 
    8037 > hide sel surfaces
    8038 
    8039 > select add #3
    8040 
    8041 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 8 models selected 
    8042 
    8043 > select subtract #3
    8044 
    8045 13 models selected 
    8046 
    8047 > select #3/Z
    8048 
    8049 Nothing selected 
    8050 
    8051 > hide surfaces
    8052 
    8053 > show surfaces
    8054 
    8055 > select #3/X
    8056 
    8057 360 atoms, 395 bonds, 18 residues, 1 model selected 
    8058 
    8059 > hide sel surfaces
    8060 
    8061 > select #3/M,N,O,P,Q,R,S,T
    8062 
    8063 408 atoms, 426 bonds, 48 residues, 1 model selected 
    8064 
    8065 > hide sel surfaces
    8066 
    8067 > select add #3
    8068 
    8069 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 8 models selected 
    8070 
    8071 > select subtract #3
    8072 
    8073 13 models selected 
    8074 
    8075 > select #3/C
    8076 
    8077 2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 2 models selected 
    8078 
    8079 > hide sel surfaces
    8080 
    8081 > select add #3
    8082 
    8083 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected 
    8084 
    8085 > select subtract #3
    8086 
    8087 13 models selected 
    8088 
    8089 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    8090 > RAD54/BRCA2filaments2.tif" width 769 height 709 supersample 3
    8091 
    8092 > select #3/
    8093 
    8094 Expected an objects specifier or a keyword 
    8095 
    8096 > transparency #3.2-14 0
    8097 
    8098 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    8099 > RAD54/BRCA2filaments2.tif" width 769 height 709 supersample 3
    8100 
    8101 > open /Users/sz140275local/Downloads/RAD54-J402_m1_real_space_refined_001.pdb
    8102 
    8103 Chain information for RAD54-J402_m1_real_space_refined_001.pdb #4 
    8104 --- 
    8105 Chain | Description 
    8106 A B C D E F | No description available 
    8107 M N O P Q R | No description available 
    8108 X | No description available 
    8109  
    8110 
    8111 > hide #!4 models
    8112 
    8113 > hide #!3 models
    8114 
    8115 > show #!4 models
    8116 
    8117 > hide #!4 cartoons
    8118 
    8119 > hide #!4 atoms
    8120 
    8121 > show #!4 cartoons
    8122 
    8123 > ui tool show "Show Sequence Viewer"
    8124 
    8125 > sequence chain #4/O
    8126 
    8127 Alignment identifier is 4/O 
    8128 
    8129 > hide #!4 models
    8130 
    8131 > show #!3 models
    8132 
    8133 > select #3/C:85,89
    8134 
    8135 22 atoms, 22 bonds, 2 residues, 1 model selected 
    8136 
    8137 > show sel atoms
    8138 
    8139 > style sel stick
    8140 
    8141 Changed 22 atom styles 
    8142 
    8143 > select add #3
    8144 
    8145 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected 
    8146 
    8147 > select subtract #3
    8148 
    8149 13 models selected 
    8150 
    8151 > select #3/C:85,89
    8152 
    8153 22 atoms, 22 bonds, 2 residues, 1 model selected 
    8154 
    8155 > color sel orange
    8156 
    8157 > select add #3
    8158 
    8159 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected 
    8160 
    8161 > select subtract #3
    8162 
    8163 13 models selected 
    8164 
    8165 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    8166 > RAD54/BRCA2filaments2.tif" width 560 height 701 supersample 3
    8167 
    8168 > open 7C9C
    8169 
    8170 7c9c title: 
    8171 Human DMC1 pre-synaptic complexes [more info...] 
    8172  
    8173 Chain information for 7c9c #7 
    8174 --- 
    8175 Chain | Description | UniProt 
    8176 A B C | Meiotic recombination protein DMC1/LIM15 homolog | DMC1_HUMAN 1-340 
    8177 D | DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') |   
    8178  
    8179 Non-standard residues in 7c9c #7 
    8180 --- 
    8181 ANP — phosphoaminophosphonic acid-adenylate ester 
    8182 CA — calcium ion 
    8183  
    8184 
    8185 > mmaker #7 to #3
    8186 
    8187 Computing secondary structure 
    8188 [Repeated 1 time(s)]  Parameters 
    8189 --- 
    8190 Chain pairing | bb 
    8191 Alignment algorithm | Needleman-Wunsch 
    8192 Similarity matrix | BLOSUM-62 
    8193 SS fraction | 0.3 
    8194 Gap open (HH/SS/other) | 18/18/6 
    8195 Gap extend | 1 
    8196 SS matrix |  |  | H | S | O 
    8197 ---|---|---|--- 
    8198 H | 6 | -9 | -6 
    8199 S |  | 6 | -6 
    8200 O |  |  | 4 
    8201 Iteration cutoff | 2 
    8202  
    8203 Matchmaker newPDBfit-coot-10_real_space_refined_002.pdb, chain E (#3) with
    8204 7c9c, chain B (#7), sequence alignment score = 1478.4 
    8205 RMSD between 302 pruned atom pairs is 0.679 angstroms; (across all 308 pairs:
    8206 0.775) 
    8207  
    8208 
    8209 > select #3
    8210 
    8211 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    8212 
    8213 > hide sel surfaces
    8214 
    8215 > show sel cartoons
    8216 
    8217 > select subtract #3
    8218 
    8219 13 models selected 
    8220 
    8221 > select #3/A,B,C
    8222 
    8223 7413 atoms, 7528 bonds, 3 pseudobonds, 951 residues, 2 models selected 
    8224 
    8225 > hide sel cartoons
    8226 
    8227 > hide sel atoms
    8228 
    8229 > select #3/M,N,O
    8230 
    8231 204 atoms, 213 bonds, 24 residues, 1 model selected 
    8232 
    8233 > hide sel atoms
    8234 
    8235 > hide sel cartoons
    8236 
    8237 > ~label (#!3 & sel) residues
    8238 
    8239 > ~label (#!3 & sel) atoms
    8240 
    8241 > hide #!7 models
    8242 
    8243 > show #!7 models
    8244 
    8245 > select #7
    8246 
    8247 7452 atoms, 7586 bonds, 10 pseudobonds, 939 residues, 4 models selected 
    8248 
    8249 > ~label (#!7 & sel) residues
    8250 
    8251 > ~label (#!7 & sel) atoms
    8252 
    8253 > select subtract #7
    8254 
    8255 Nothing selected 
    8256 
    8257 > select #3/C,D,E,F,G:85,89
    8258 
    8259 88 atoms, 88 bonds, 8 residues, 1 model selected 
    8260 
    8261 > hide sel atoms
    8262 
    8263 > color sel palegreen blue
    8264 
    8265 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
    8266 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword 
    8267 
    8268 > color sel light blue
    8269 
    8270 > select add #3
    8271 
    8272 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 6 models selected 
    8273 
    8274 > select subtract #3
    8275 
    8276 13 models selected 
    8277 
    8278 > select #7
    8279 
    8280 7452 atoms, 7586 bonds, 10 pseudobonds, 939 residues, 4 models selected 
    8281 
    8282 > ui tool show "Selection Inspector"
    8283 
    8284 > delete label
    8285 
    8286 Missing or invalid "atoms" argument: invalid atoms specifier 
    8287 
    8288 > delete
    8289 
    8290 Missing or invalid "atoms" argument: empty atom specifier 
    8291 
    8292 > delete #7/B:276-282
    8293 
    8294 > select #7/B:275-283
    8295 
    8296 4 atoms, 3 bonds, 1 residue, 1 model selected 
    8297 
    8298 > ~label sel residues
    8299 
    8300 > ~label sel atoms
    8301 
    8302 > select add #7
    8303 
    8304 7452 atoms, 7586 bonds, 10 pseudobonds, 939 residues, 4 models selected 
    8305 
    8306 > select subtract #7
    8307 
    8308 Nothing selected 
    8309 
    8310 > select #3/M,N,O,P,Q,R,S,T
    8311 
    8312 408 atoms, 426 bonds, 48 residues, 1 model selected 
    8313 
    8314 > hide sel atoms
    8315 
    8316 > hide sel cartoons
    8317 
    8318 > hide #!3 models
    8319 
    8320 > show #!3 models
    8321 
    8322 > hide #!3 models
    8323 
    8324 > show #!3 models
    8325 
    8326 > hide #!3 models
    8327 
    8328 > show #!3 models
    8329 
    8330 > hide #!3 models
    8331 
    8332 > show #!3 models
    8333 
    8334 > hide #!3 models
    8335 
    8336 > show #!3 models
    8337 
    8338 > select #3/D:132
    8339 
    8340 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8341 
    8342 > show sel atoms
    8343 
    8344 > style sel stick
    8345 
    8346 Changed 9 atom styles 
    8347 
    8348 > select #3/D:162
    8349 
    8350 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8351 
    8352 > show sel atoms
    8353 
    8354 > style sel stick
    8355 
    8356 Changed 9 atom styles 
    8357 
    8358 > select #3/D:133
    8359 
    8360 7 atoms, 6 bonds, 1 residue, 1 model selected 
    8361 
    8362 > show sel atoms
    8363 
    8364 > style sel stick
    8365 
    8366 Changed 7 atom styles 
    8367 
    8368 > select #7
    8369 
    8370 7452 atoms, 7586 bonds, 10 pseudobonds, 939 residues, 4 models selected 
    8371 
    8372 > hide sel atoms
    8373 
    8374 > show sel atoms
    8375 
    8376 > hide sel atoms
    8377 
    8378 > show sel atoms
    8379 
    8380 > hide sel atoms
    8381 
    8382 > select #7/D
    8383 
    8384 180 atoms, 197 bonds, 9 residues, 1 model selected 
    8385 
    8386 > show sel atoms
    8387 
    8388 > select #7/A,B,C:ANP*
    8389 
    8390 93 atoms, 99 bonds, 3 residues, 1 model selected 
    8391 
    8392 > show sel atoms
    8393 
    8394 > select add #7
    8395 
    8396 7452 atoms, 7586 bonds, 10 pseudobonds, 939 residues, 4 models selected 
    8397 
    8398 > select subtract #7
    8399 
    8400 Nothing selected 
    8401 
    8402 > select #7/A,B,C:
    8403 
    8404 Expected an objects specifier or a keyword 
    8405 
    8406 > select #7/A,B,C
    8407 
    8408 7272 atoms, 7389 bonds, 10 pseudobonds, 930 residues, 3 models selected 
    8409 
    8410 > label delete
    8411 
    8412 > select add #7
    8413 
    8414 7452 atoms, 7586 bonds, 10 pseudobonds, 939 residues, 3 models selected 
    8415 
    8416 > select subtract #7
    8417 
    8418 Nothing selected 
    8419 
    8420 > select #7/D
    8421 
    8422 180 atoms, 197 bonds, 9 residues, 1 model selected 
    8423 
    8424 > show sel cartoons
    8425 
    8426 > select add #7
    8427 
    8428 7452 atoms, 7586 bonds, 10 pseudobonds, 939 residues, 3 models selected 
    8429 
    8430 > select subtract #7
    8431 
    8432 Nothing selected 
    8433 
    8434 > show #!5 models
    8435 
    8436 > hide #!5 models
    8437 
    8438 > show #!5 models
    8439 
    8440 > hide #!5 models
    8441 
    8442 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    8443 > RAD54/BRCA2compC9C7.tif" width 890 height 709 supersample 3
    8444 
    8445 > select #7/P
    8446 
    8447 Nothing selected 
    8448 
    8449 > show #!3,7 cartoons
    8450 
    8451 > hide #!3,7 cartoons
    8452 
    8453 > show #!3,7 cartoons
    8454 
    8455 > hide #!3,7 cartoons
    8456 
    8457 > hide #!3 models
    8458 
    8459 > show #!3 models
    8460 
    8461 > hide #!7 models
    8462 
    8463 > show #!7 models
    8464 
    8465 > hide #!7 models
    8466 
    8467 > show #!7 models
    8468 
    8469 > select #7
    8470 
    8471 7452 atoms, 7586 bonds, 10 pseudobonds, 939 residues, 3 models selected 
    8472 
    8473 > show sel cartoons
    8474 
    8475 > select #3/A,B,C
    8476 
    8477 7413 atoms, 7528 bonds, 3 pseudobonds, 951 residues, 2 models selected 
    8478 
    8479 > show sel cartoons
    8480 
    8481 [Repeated 1 time(s)]
    8482 
    8483 > hide sel cartoons
    8484 
    8485 > select #3/D,E,F
    8486 
    8487 7347 atoms, 7461 bonds, 3 pseudobonds, 945 residues, 2 models selected 
    8488 
    8489 > show sel cartoons
    8490 
    8491 > select add #3
    8492 
    8493 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 5 models selected 
    8494 
    8495 > select subtract #3
    8496 
    8497 13 models selected 
    8498 
    8499 > select #3/O,P
    8500 
    8501 136 atoms, 142 bonds, 16 residues, 1 model selected 
    8502 
    8503 > show sel cartoons
    8504 
    8505 > hide sel cartoons
    8506 
    8507 > select #3/P
    8508 
    8509 68 atoms, 71 bonds, 8 residues, 1 model selected 
    8510 
    8511 > show sel cartoons
    8512 
    8513 > select add #3
    8514 
    8515 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected 
    8516 
    8517 > select subtract #3
    8518 
    8519 13 models selected 
    8520 
    8521 > mmaker #7/A to #3/D
    8522 
    8523 Computing secondary structure 
    8524 [Repeated 1 time(s)]  Parameters 
    8525 --- 
    8526 Chain pairing | bb 
    8527 Alignment algorithm | Needleman-Wunsch 
    8528 Similarity matrix | BLOSUM-62 
    8529 SS fraction | 0.3 
    8530 Gap open (HH/SS/other) | 18/18/6 
    8531 Gap extend | 1 
    8532 SS matrix |  |  | H | S | O 
    8533 ---|---|---|--- 
    8534 H | 6 | -9 | -6 
    8535 S |  | 6 | -6 
    8536 O |  |  | 4 
    8537 Iteration cutoff | 2 
    8538  
    8539 Matchmaker newPDBfit-coot-10_real_space_refined_002.pdb, chain D (#3) with
    8540 7c9c, chain A (#7), sequence alignment score = 1458.6 
    8541 RMSD between 301 pruned atom pairs is 0.668 angstroms; (across all 308 pairs:
    8542 0.819) 
    8543  
    8544 
    8545 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    8546 > RAD54/BRCA2compC9C7.zoomtif.tif" width 890 height 709 supersample 3
    8547 
    8548 > select #3/P
    8549 
    8550 68 atoms, 71 bonds, 8 residues, 1 model selected 
    8551 
    8552 > hide sel cartoons
    8553 
    8554 > select #3/D:ATP*
    8555 
    8556 31 atoms, 33 bonds, 1 residue, 1 model selected 
    8557 
    8558 > hide sel atoms
    8559 
    8560 > select #3/X
    8561 
    8562 360 atoms, 395 bonds, 18 residues, 1 model selected 
    8563 
    8564 > hide sel cartoons
    8565 
    8566 > hide sel atoms
    8567 
    8568 > select #7/D
    8569 
    8570 180 atoms, 197 bonds, 9 residues, 1 model selected 
    8571 
    8572 > color sel black
    8573 
    8574 > select add #7
    8575 
    8576 7452 atoms, 7586 bonds, 10 pseudobonds, 939 residues, 3 models selected 
    8577 
    8578 > select subtract #7
    8579 
    8580 Nothing selected 
    8581 
    8582 > select #7/*ATP*
    8583 
    8584 Nothing selected 
    8585 
    8586 > select #7/*ANP*
    8587 
    8588 Nothing selected 
    8589 
    8590 > select #7/A,B,C,D:ANP*
    8591 
    8592 93 atoms, 99 bonds, 3 residues, 1 model selected 
    8593 
    8594 > color sel black
    8595 
    8596 > select add #7
    8597 
    8598 7452 atoms, 7586 bonds, 10 pseudobonds, 939 residues, 3 models selected 
    8599 
    8600 > select subtract #7
    8601 
    8602 Nothing selected 
    8603 
    8604 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    8605 > RAD54/BRCA2compC9C7.tif" width 890 height 709 supersample 3
    8606 
    8607 > mmaker #7/A,B,C to #3/D,E,F
    8608 
    8609 Computing secondary structure 
    8610 [Repeated 1 time(s)]  Parameters 
    8611 --- 
    8612 Chain pairing | bb 
    8613 Alignment algorithm | Needleman-Wunsch 
    8614 Similarity matrix | BLOSUM-62 
    8615 SS fraction | 0.3 
    8616 Gap open (HH/SS/other) | 18/18/6 
    8617 Gap extend | 1 
    8618 SS matrix |  |  | H | S | O 
    8619 ---|---|---|--- 
    8620 H | 6 | -9 | -6 
    8621 S |  | 6 | -6 
    8622 O |  |  | 4 
    8623 Iteration cutoff | 2 
    8624  
    8625 Matchmaker newPDBfit-coot-10_real_space_refined_002.pdb, chain E (#3) with
    8626 7c9c, chain B (#7), sequence alignment score = 1478.4 
    8627 RMSD between 302 pruned atom pairs is 0.679 angstroms; (across all 308 pairs:
    8628 0.775) 
    8629  
    8630 
    8631 > mmaker #7/A,B,C to #3/D,E,F
    8632 
    8633 Computing secondary structure 
    8634 [Repeated 1 time(s)]  Parameters 
    8635 --- 
    8636 Chain pairing | bb 
    8637 Alignment algorithm | Needleman-Wunsch 
    8638 Similarity matrix | BLOSUM-62 
    8639 SS fraction | 0.3 
    8640 Gap open (HH/SS/other) | 18/18/6 
    8641 Gap extend | 1 
    8642 SS matrix |  |  | H | S | O 
    8643 ---|---|---|--- 
    8644 H | 6 | -9 | -6 
    8645 S |  | 6 | -6 
    8646 O |  |  | 4 
    8647 Iteration cutoff | 2 
    8648  
    8649 Matchmaker newPDBfit-coot-10_real_space_refined_002.pdb, chain E (#3) with
    8650 7c9c, chain B (#7), sequence alignment score = 1478.4 
    8651 RMSD between 302 pruned atom pairs is 0.679 angstroms; (across all 308 pairs:
    8652 0.775) 
    8653  
    8654 
    8655 > mmaker #7/A,B,C to #3/D,E,F
    8656 
    8657 Computing secondary structure 
    8658 [Repeated 1 time(s)]  Parameters 
    8659 --- 
    8660 Chain pairing | bb 
    8661 Alignment algorithm | Needleman-Wunsch 
    8662 Similarity matrix | BLOSUM-62 
    8663 SS fraction | 0.3 
    8664 Gap open (HH/SS/other) | 18/18/6 
    8665 Gap extend | 1 
    8666 SS matrix |  |  | H | S | O 
    8667 ---|---|---|--- 
    8668 H | 6 | -9 | -6 
    8669 S |  | 6 | -6 
    8670 O |  |  | 4 
    8671 Iteration cutoff | 2 
    8672  
    8673 Matchmaker newPDBfit-coot-10_real_space_refined_002.pdb, chain E (#3) with
    8674 7c9c, chain B (#7), sequence alignment score = 1478.4 
    8675 RMSD between 302 pruned atom pairs is 0.679 angstroms; (across all 308 pairs:
    8676 0.775) 
    8677  
    8678 
    8679 > mmaker #7/A,B,C to #3/D,E,F
    8680 
    8681 Computing secondary structure 
    8682 [Repeated 1 time(s)]  Parameters 
    8683 --- 
    8684 Chain pairing | bb 
    8685 Alignment algorithm | Needleman-Wunsch 
    8686 Similarity matrix | BLOSUM-62 
    8687 SS fraction | 0.3 
    8688 Gap open (HH/SS/other) | 18/18/6 
    8689 Gap extend | 1 
    8690 SS matrix |  |  | H | S | O 
    8691 ---|---|---|--- 
    8692 H | 6 | -9 | -6 
    8693 S |  | 6 | -6 
    8694 O |  |  | 4 
    8695 Iteration cutoff | 2 
    8696  
    8697 Matchmaker newPDBfit-coot-10_real_space_refined_002.pdb, chain E (#3) with
    8698 7c9c, chain B (#7), sequence alignment score = 1478.4 
    8699 RMSD between 302 pruned atom pairs is 0.679 angstroms; (across all 308 pairs:
    8700 0.775) 
    8701  
    8702 
    8703 > mmaker #7/A,B,C to #3/D,E,F
    8704 
    8705 Computing secondary structure 
    8706 [Repeated 1 time(s)]  Parameters 
    8707 --- 
    8708 Chain pairing | bb 
    8709 Alignment algorithm | Needleman-Wunsch 
    8710 Similarity matrix | BLOSUM-62 
    8711 SS fraction | 0.3 
    8712 Gap open (HH/SS/other) | 18/18/6 
    8713 Gap extend | 1 
    8714 SS matrix |  |  | H | S | O 
    8715 ---|---|---|--- 
    8716 H | 6 | -9 | -6 
    8717 S |  | 6 | -6 
    8718 O |  |  | 4 
    8719 Iteration cutoff | 2 
    8720  
    8721 Matchmaker newPDBfit-coot-10_real_space_refined_002.pdb, chain E (#3) with
    8722 7c9c, chain B (#7), sequence alignment score = 1478.4 
    8723 RMSD between 302 pruned atom pairs is 0.679 angstroms; (across all 308 pairs:
    8724 0.775) 
    8725  
    8726 
    8727 > mmaker #7/A to #3/D
    8728 
    8729 Computing secondary structure 
    8730 [Repeated 1 time(s)]  Parameters 
    8731 --- 
    8732 Chain pairing | bb 
    8733 Alignment algorithm | Needleman-Wunsch 
    8734 Similarity matrix | BLOSUM-62 
    8735 SS fraction | 0.3 
    8736 Gap open (HH/SS/other) | 18/18/6 
    8737 Gap extend | 1 
    8738 SS matrix |  |  | H | S | O 
    8739 ---|---|---|--- 
    8740 H | 6 | -9 | -6 
    8741 S |  | 6 | -6 
    8742 O |  |  | 4 
    8743 Iteration cutoff | 2 
    8744  
    8745 Matchmaker newPDBfit-coot-10_real_space_refined_002.pdb, chain D (#3) with
    8746 7c9c, chain A (#7), sequence alignment score = 1458.6 
    8747 RMSD between 301 pruned atom pairs is 0.668 angstroms; (across all 308 pairs:
    8748 0.819) 
    8749  
    8750 
    8751 > mmaker #7/A,B,C to #3/D,E,F
    8752 
    8753 Computing secondary structure 
    8754 [Repeated 1 time(s)]  Parameters 
    8755 --- 
    8756 Chain pairing | bb 
    8757 Alignment algorithm | Needleman-Wunsch 
    8758 Similarity matrix | BLOSUM-62 
    8759 SS fraction | 0.3 
    8760 Gap open (HH/SS/other) | 18/18/6 
    8761 Gap extend | 1 
    8762 SS matrix |  |  | H | S | O 
    8763 ---|---|---|--- 
    8764 H | 6 | -9 | -6 
    8765 S |  | 6 | -6 
    8766 O |  |  | 4 
    8767 Iteration cutoff | 2 
    8768  
    8769 Matchmaker newPDBfit-coot-10_real_space_refined_002.pdb, chain E (#3) with
    8770 7c9c, chain B (#7), sequence alignment score = 1478.4 
    8771 RMSD between 302 pruned atom pairs is 0.679 angstroms; (across all 308 pairs:
    8772 0.775) 
    8773  
    8774 
    8775 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    8776 > RAD54/BRCA2compC9C7.tif" width 890 height 709 supersample 3
    8777 
    8778 > hide #!7 models
    8779 
    8780 > hide #!3 models
    8781 
    8782 > show #!6 models
    8783 
    8784 > show #!3 models
    8785 
    8786 > show #!4 models
    8787 
    8788 > hide #!4 models
    8789 
    8790 > show #!4 models
    8791 
    8792 > hide #!3 models
    8793 
    8794 > hide #!6 models
    8795 
    8796 > show #!7 models
    8797 
    8798 > hide #!4 models
    8799 
    8800 > show #!3 models
    8801 
    8802 > select #3/E:ATP*
    8803 
    8804 Nothing selected 
    8805 
    8806 > show #!3,7 atoms
    8807 
    8808 > hide #!3,7 atoms
    8809 
    8810 > select #3/*:ATP*
    8811 
    8812 124 atoms, 132 bonds, 4 residues, 1 model selected 
    8813 
    8814 > show sel atoms
    8815 
    8816 > hide sel atoms
    8817 
    8818 > select #3/D:ATP*
    8819 
    8820 31 atoms, 33 bonds, 1 residue, 1 model selected 
    8821 
    8822 > show sel atoms
    8823 
    8824 > select #7/*:ATP*
    8825 
    8826 Nothing selected 
    8827 
    8828 > select #7/*:ANP*
    8829 
    8830 93 atoms, 99 bonds, 3 residues, 1 model selected 
    8831 
    8832 > show sel atoms
    8833 
    8834 > select add #7
    8835 
    8836 7452 atoms, 7586 bonds, 10 pseudobonds, 939 residues, 3 models selected 
    8837 
    8838 > select subtract #7
    8839 
    8840 Nothing selected 
    8841 
    8842 > select #3/O*
    8843 
    8844 68 atoms, 71 bonds, 8 residues, 1 model selected 
    8845 
    8846 > show sel cartoons
    8847 
    8848 > hide sel cartoons
    8849 
    8850 > select #3/M*
    8851 
    8852 68 atoms, 71 bonds, 8 residues, 1 model selected 
    8853 
    8854 > show sel atoms
    8855 
    8856 > hide sel atoms
    8857 
    8858 > select #3/R*
    8859 
    8860 68 atoms, 71 bonds, 8 residues, 1 model selected 
    8861 
    8862 > show sel atoms
    8863 
    8864 > hide sel atoms
    8865 
    8866 > select #3/Q*
    8867 
    8868 68 atoms, 71 bonds, 8 residues, 1 model selected 
    8869 
    8870 > show sel atoms
    8871 
    8872 > hide sel atoms
    8873 
    8874 > hide sel cartoons
    8875 
    8876 > hide sel atoms
    8877 
    8878 > select #3/P*
    8879 
    8880 68 atoms, 71 bonds, 8 residues, 1 model selected 
    8881 
    8882 > show sel atoms
    8883 
    8884 > select #3/P,Q*
    8885 
    8886 136 atoms, 142 bonds, 16 residues, 1 model selected 
    8887 
    8888 > show sel atoms
    8889 
    8890 > select add #3
    8891 
    8892 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 4 models selected 
    8893 
    8894 > select subtract #3
    8895 
    8896 13 models selected 
    8897 
    8898 > select #3/X
    8899 
    8900 360 atoms, 395 bonds, 18 residues, 1 model selected 
    8901 
    8902 > show sel atoms
    8903 
    8904 > select add #3
    8905 
    8906 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected 
    8907 
    8908 > hide #!3 models
    8909 
    8910 > show #!3 models
    8911 
    8912 > select subtract #3
    8913 
    8914 13 models selected 
    8915 
    8916 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    8917 > RAD54/BRCA2compC9C7.zoomtif.tif" width 890 height 709 supersample 3
    8918 
    8919 > select #3/P,Q:3,10
    8920 
    8921 36 atoms, 32 bonds, 4 residues, 1 model selected 
    8922 
    8923 > hide sel atoms
    8924 
    8925 > select #3/P,Q
    8926 
    8927 136 atoms, 142 bonds, 16 residues, 1 model selected 
    8928 
    8929 > show sel cartoons
    8930 
    8931 > select add #3
    8932 
    8933 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 4 models selected 
    8934 
    8935 > select subtract #3
    8936 
    8937 13 models selected 
    8938 
    8939 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    8940 > RAD54/BRCA2compC9C7.zoomtif.tif" width 875 height 694 supersample 3
    8941 
    8942 > hide #!7 models
    8943 
    8944 > select add #7
    8945 
    8946 7452 atoms, 7586 bonds, 10 pseudobonds, 939 residues, 3 models selected 
    8947 
    8948 > select subtract #7
    8949 
    8950 Nothing selected 
    8951 
    8952 > select #3/F:ATP*
    8953 
    8954 Nothing selected 
    8955 
    8956 > show #!3 atoms
    8957 
    8958 > hide #!3 atoms
    8959 
    8960 > select #3/E:ATP*
    8961 
    8962 Nothing selected 
    8963 
    8964 > hide #!3 atoms
    8965 
    8966 [Repeated 1 time(s)]
    8967 
    8968 > show #!3 atoms
    8969 
    8970 > hide #!3 atoms
    8971 
    8972 > select #3/E:ATP*
    8973 
    8974 Nothing selected 
    8975 
    8976 > show #!3 atoms
    8977 
    8978 > hide #!3 atoms
    8979 
    8980 > select #3/E
    8981 
    8982 2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected 
    8983 
    8984 > show sel atoms
    8985 
    8986 > hide sel atoms
    8987 
    8988 > select #3/E:ATP*
    8989 
    8990 Nothing selected 
    8991 
    8992 > show #!3 atoms
    8993 
    8994 > hide #!3 atoms
    8995 
    8996 > select #3/E:ATP*
    8997 
    8998 Nothing selected 
    8999 
    9000 > select #3/D:ATP*
    9001 
    9002 31 atoms, 33 bonds, 1 residue, 1 model selected 
    9003 
    9004 > show sel atoms
    9005 
    9006 > select #3/B,D:ATP*
    9007 
    9008 62 atoms, 66 bonds, 2 residues, 1 model selected 
    9009 
    9010 > show sel atoms
    9011 
    9012 > select #3/C,D:ATP*
    9013 
    9014 62 atoms, 66 bonds, 2 residues, 1 model selected 
    9015 
    9016 > show sel atoms
    9017 
    9018 > select #3/Q
    9019 
    9020 68 atoms, 71 bonds, 8 residues, 1 model selected 
    9021 
    9022 > hide sel cartoons
    9023 
    9024 > select #3/E
    9025 
    9026 2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected 
    9027 
    9028 > hide sel cartoons
    9029 
    9030 > show sel cartoons
    9031 
    9032 > select #3/F
    9033 
    9034 2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected 
    9035 
    9036 > hide sel cartoons
    9037 
    9038 > select #3/F
    9039 
    9040 2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected 
    9041 
    9042 > select #3/P
    9043 
    9044 68 atoms, 71 bonds, 8 residues, 1 model selected 
    9045 
    9046 > select #3/Q
    9047 
    9048 68 atoms, 71 bonds, 8 residues, 1 model selected 
    9049 
    9050 > show sel cartoons
    9051 
    9052 > select #3/B,C
    9053 
    9054 4942 atoms, 5018 bonds, 2 pseudobonds, 634 residues, 2 models selected 
    9055 
    9056 > show sel cartoons
    9057 
    9058 > select #3/O,N
    9059 
    9060 136 atoms, 142 bonds, 16 residues, 1 model selected 
    9061 
    9062 > show sel cartoons
    9063 
    9064 > select #3/M,A
    9065 
    9066 2539 atoms, 2581 bonds, 1 pseudobond, 325 residues, 2 models selected 
    9067 
    9068 > show sel cartoons
    9069 
    9070 > select #3/A:ATP*
    9071 
    9072 31 atoms, 33 bonds, 1 residue, 1 model selected 
    9073 
    9074 > show sel cartoons
    9075 
    9076 > show sel atoms
    9077 
    9078 > select add #3
    9079 
    9080 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    9081 
    9082 > select subtract #3
    9083 
    9084 13 models selected 
    9085 
    9086 > show #!6 models
    9087 
    9088 > hide #!6 models
    9089 
    9090 > show #!6 models
    9091 
    9092 > select #3/X
    9093 
    9094 360 atoms, 395 bonds, 18 residues, 1 model selected 
    9095 
    9096 > show sel atoms
    9097 
    9098 > select add #3
    9099 
    9100 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected 
    9101 
    9102 > select subtract #3
    9103 
    9104 13 models selected 
    9105 
    9106 > hide #!6 models
    9107 
    9108 > select #3/B:85,89
    9109 
    9110 22 atoms, 22 bonds, 2 residues, 1 model selected 
    9111 
    9112 > hide sel atoms
    9113 
    9114 > color sel light blue
    9115 
    9116 > show #!6 models
    9117 
    9118 > hide #!6 models
    9119 
    9120 > select #3/C:85,89
    9121 
    9122 22 atoms, 22 bonds, 2 residues, 1 model selected 
    9123 
    9124 > color sel wheat
    9125 
    9126 > show #!6 models
    9127 
    9128 > color zone #6 near sel & #3 distance 4.38
    9129 
    9130 [Repeated 3 time(s)]
    9131 
    9132 > transparency sel 50
    9133 
    9134 > select add #3
    9135 
    9136 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected 
    9137 
    9138 > select subtract #3
    9139 
    9140 13 models selected 
    9141 
    9142 > color zone #6 near #3 distance 4.38
    9143 
    9144 > transparency #3.2-14#6.1 0
    9145 
    9146 > transparency #3.2-14#6.1 50
    9147 
    9148 > color #3/A,C,F
    9149 
    9150 > color #3/A,C,F wheat
    9151 
    9152 > color #3/B,D royal blue
    9153 
    9154 > color zone #6 near #3 distance 4.38
    9155 
    9156 > color #3/A,C,E wheat
    9157 
    9158 > color zone #6 near #3 distance 4.38
    9159 
    9160 > color #6 #f5dec980 models
    9161 
    9162 > color #3/F wheat
    9163 
    9164 > color #3/F misty rose
    9165 
    9166 > color zone #6 near #3 distance 4.38
    9167 
    9168 > hide #!6 models
    9169 
    9170 > show #!6 models
    9171 
    9172 > hide #!6 models
    9173 
    9174 > show #!6 models
    9175 
    9176 > hide #!6 models
    9177 
    9178 > show #!6 models
    9179 
    9180 > hide #!6 models
    9181 
    9182 > show #!6 models
    9183 
    9184 > hide #!6 models
    9185 
    9186 > show #!6 models
    9187 
    9188 > hide #!6 models
    9189 
    9190 > show #!6 models
    9191 
    9192 > hide #!6 models
    9193 
    9194 > show #!6 models
    9195 
    9196 > hide #!6 models
    9197 
    9198 > show #!6 models
    9199 
    9200 > hide #!6 models
    9201 
    9202 > show #!6 models
    9203 
    9204 > hide #!6 models
    9205 
    9206 > color #3/R misty rose
    9207 
    9208 > show #!6 models
    9209 
    9210 > color zone #6 near #3 distance 4.38
    9211 
    9212 > color #3/M,N,O,P,Q misty rose
    9213 
    9214 > show #!3 cartoons
    9215 
    9216 > show #!3 atoms
    9217 
    9218 > hide #!3 atoms
    9219 
    9220 > select #3/M,N,O,P,Q
    9221 
    9222 340 atoms, 355 bonds, 40 residues, 1 model selected 
    9223 
    9224 > select #3/M,N,O,P,Q
    9225 
    9226 340 atoms, 355 bonds, 40 residues, 1 model selected 
    9227 
    9228 > show sel atoms
    9229 
    9230 > select #3/M,N,O,P,Q:3,10
    9231 
    9232 90 atoms, 80 bonds, 10 residues, 1 model selected 
    9233 
    9234 > hide sel atoms
    9235 
    9236 > select #3/A,B,C,D,E:ATP*
    9237 
    9238 124 atoms, 132 bonds, 4 residues, 1 model selected 
    9239 
    9240 > show sel atoms
    9241 
    9242 > transparency #3.2-14#6.1 0
    9243 
    9244 > transparency #3.2-14#6.1 50
    9245 
    9246 > select #3/A,B,C,D,E:ATP*
    9247 
    9248 124 atoms, 132 bonds, 4 residues, 1 model selected 
    9249 
    9250 > color sel black
    9251 
    9252 > select #3/M,N,O,P,Q
    9253 
    9254 340 atoms, 355 bonds, 40 residues, 1 model selected 
    9255 
    9256 > color sel red
    9257 
    9258 > select add #3
    9259 
    9260 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 7 models selected 
    9261 
    9262 > select subtract #3
    9263 
    9264 13 models selected 
    9265 
    9266 > select #3/X
    9267 
    9268 360 atoms, 395 bonds, 18 residues, 1 model selected 
    9269 
    9270 > show sel atoms
    9271 
    9272 > select add #3
    9273 
    9274 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected 
    9275 
    9276 > select subtract #3
    9277 
    9278 13 models selected 
    9279 
    9280 > surface dust #6 size 7.3
    9281 
    9282 [Repeated 3 time(s)]
    9283 
    9284 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    9285 > RAD54/BRCA2struct1.tif" width 890 height 709 supersample 3
    9286 
    9287 > surface dust #6 size 7.3
    9288 
    9289 [Repeated 1 time(s)]
    9290 
    9291 > hide #!6 models
    9292 
    9293 > show #!6 models
    9294 
    9295 > hide #!6 models
    9296 
    9297 > show #!6 models
    9298 
    9299 > ui mousemode right zoom
    9300 
    9301 > ui mousemode right translate
    9302 
    9303 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    9304 > RAD54/BRCA2struct1.tif" width 890 height 709 supersample 3
    9305 
    9306 > select #3/A,M
    9307 
    9308 2539 atoms, 2581 bonds, 1 pseudobond, 325 residues, 2 models selected 
    9309 
    9310 > hide sel cartoons
    9311 
    9312 > color #3/A,M mistyrose pink
    9313 
    9314 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
    9315 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword 
    9316 
    9317 > hide sel cartoons
    9318 
    9319 > hide sel atoms
    9320 
    9321 > hide #!6 models
    9322 
    9323 > color #3/F dodger blue
    9324 
    9325 > color #3/F royal blue
    9326 
    9327 > select #3/R
    9328 
    9329 68 atoms, 71 bonds, 8 residues, 1 model selected 
    9330 
    9331 > show sel atoms
    9332 
    9333 > select #3/R:3,10
    9334 
    9335 18 atoms, 16 bonds, 2 residues, 1 model selected 
    9336 
    9337 > hide sel atoms
    9338 
    9339 > color #3/R red
    9340 
    9341 > show #!6 models
    9342 
    9343 > color #6 #f4e7ce80 models
    9344 
    9345 > color zone #6 near sel & #3 distance 4.38
    9346 
    9347 [Repeated 1 time(s)]
    9348 
    9349 > select add #6
    9350 
    9351 18 atoms, 16 bonds, 2 residues, 4 models selected 
    9352 
    9353 > select add #3
    9354 
    9355 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 5 models selected 
    9356 
    9357 > select subtract #3
    9358 
    9359 15 models selected 
    9360 
    9361 > color zone #6 near #3 distance 4.38
    9362 
    9363 > select subtract #6
    9364 
    9365 Nothing selected 
    9366 
    9367 > select add #6
    9368 
    9369 2 models selected 
    9370 
    9371 > select subtract #6
    9372 
    9373 Nothing selected 
    9374 
    9375 > hide #!3 models
    9376 
    9377 > show #!3 models
    9378 
    9379 > color #6 #f4f5d380 models
    9380 
    9381 > color #3/A,M misty rose
    9382 
    9383 > color zone #6 near #3 distance 4.38
    9384 
    9385 > color #3/A,M white
    9386 
    9387 > color zone #6 near #3 distance 4.38
    9388 
    9389 > color #3/A,M lemon chiffon
    9390 
    9391 > color zone #6 near #3 distance 4.38
    9392 
    9393 > color #3/A,M light yellow
    9394 
    9395 > color zone #6 near #3 distance 4.38
    9396 
    9397 > hide #!3 models
    9398 
    9399 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    9400 > RAD54/BRCA2struct0.tif" width 890 height 709 supersample 3
    9401 
    9402 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    9403 > RAD54/BRCA2struct0b.tif" width 890 height 709 supersample 3
    9404 
    9405 > ui mousemode right zoom
    9406 
    9407 > ui mousemode right translate
    9408 
    9409 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    9410 > RAD54/BRCA2struct0b.tif" width 890 height 709 supersample 3
    9411 
    9412 [Repeated 1 time(s)]
    9413 
    9414 > show #!3 models
    9415 
    9416 > transparency #3.2-14#6.1 0
    9417 
    9418 > transparency #3.2-14#6.1 50
    9419 
    9420 > select #3/D
    9421 
    9422 2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 2 models selected 
    9423 
    9424 > transparency sel 0
    9425 
    9426 > transparency sel 50
    9427 
    9428 > select add #3
    9429 
    9430 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected 
    9431 
    9432 > select subtract #3
    9433 
    9434 13 models selected 
    9435 
    9436 > hide #!6 models
    9437 
    9438 > select #3/X
    9439 
    9440 360 atoms, 395 bonds, 18 residues, 1 model selected 
    9441 
    9442 > hide sel cartoons
    9443 
    9444 > hide sel atoms
    9445 
    9446 > show #!6 models
    9447 
    9448 > hide #!6 models
    9449 
    9450 > show #!6 models
    9451 
    9452 > hide #!6 models
    9453 
    9454 > select #3/E:85,89
    9455 
    9456 22 atoms, 22 bonds, 2 residues, 1 model selected 
    9457 
    9458 > show sel atoms
    9459 
    9460 > style sel stick
    9461 
    9462 Changed 22 atom styles 
    9463 
    9464 > color sel orange
    9465 
    9466 > select add #3
    9467 
    9468 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected 
    9469 
    9470 > select subtract #3
    9471 
    9472 13 models selected 
    9473 
    9474 > show #!6 models
    9475 
    9476 > volume #6 level 0.02869
    9477 
    9478 > color zone #6 near #3 distance 4.38
    9479 
    9480 > transparency #3.2-14#6.1 0
    9481 
    9482 > transparency #3.2-14#6.1 50
    9483 
    9484 > volume #6 level 0.05131
    9485 
    9486 > volume #6 level 0.03
    9487 
    9488 > color zone #6 near #3 distance 4.38
    9489 
    9490 > volume #6 level 0.035
    9491 
    9492 > transparency #3.2-14#6.1 0
    9493 
    9494 > transparency #3.2-14#6.1 50
    9495 
    9496 > hide #!6 models
    9497 
    9498 > show #!6 models
    9499 
    9500 > select #3/F
    9501 
    9502 2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected 
    9503 
    9504 > hide sel cartoons
    9505 
    9506 > hide #!6 models
    9507 
    9508 > show #!6 models
    9509 
    9510 > select #3/D:85,89
    9511 
    9512 22 atoms, 22 bonds, 2 residues, 1 model selected 
    9513 
    9514 > show sel atoms
    9515 
    9516 > color sel orange
    9517 
    9518 > hide #!6 models
    9519 
    9520 > show #!6 models
    9521 
    9522 > color zone #6 near sel & #3 distance 4.38
    9523 
    9524 [Repeated 1 time(s)]
    9525 
    9526 > select add #3
    9527 
    9528 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected 
    9529 
    9530 > select subtract #3
    9531 
    9532 13 models selected 
    9533 
    9534 > select add #3
    9535 
    9536 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    9537 
    9538 > color zone #6 near sel & #3 distance 4.38
    9539 
    9540 > transparency sel 0
    9541 
    9542 > transparency sel 50
    9543 
    9544 > select subtract #3
    9545 
    9546 13 models selected 
    9547 
    9548 > transparency #3.2-14#6.1 0
    9549 
    9550 > transparency #3.2-14#6.1 50
    9551 
    9552 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    9553 > RAD54/BRCA2struct0c.tif" width 890 height 709 supersample 3
    9554 
    9555 > hide #!6 models
    9556 
    9557 > show #!6 models
    9558 
    9559 > hide #!6 models
    9560 
    9561 > select #3/C,E
    9562 
    9563 4909 atoms, 4985 bonds, 2 pseudobonds, 631 residues, 2 models selected 
    9564 
    9565 > show sel surfaces
    9566 
    9567 > select add #3.1
    9568 
    9569 4909 atoms, 4985 bonds, 6 pseudobonds, 631 residues, 4 models selected 
    9570 
    9571 > select subtract #3.1
    9572 
    9573 4909 atoms, 4985 bonds, 631 residues, 3 models selected 
    9574 
    9575 > select add #3
    9576 
    9577 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 4 models selected 
    9578 
    9579 > select subtract #3
    9580 
    9581 13 models selected 
    9582 
    9583 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    9584 > RAD54/BRCA2struct0d.tif" width 890 height 709 supersample 3
    9585 
    9586 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    9587 > RAD54/BRCA2-07072025.cxs"
    9588 
    9589 ——— End of log from Mon Jul 7 15:58:39 2025 ———
    9590 
    9591 opened ChimeraX session 
    9592 
    9593 > show #!7 models
    9594 
    9595 > hide #!7 models
    9596 
    9597 > show #!6 models
    9598 
    9599 > hide #!6 models
    9600 
    9601 > show #!6 models
    9602 
    9603 > select #3/P:3,10
    9604 
    9605 18 atoms, 16 bonds, 2 residues, 1 model selected 
    9606 
    9607 > show sel atoms
    9608 
    9609 > volume #6 level 0.02208
    9610 
    9611 > color zone #6 near sel & #3 distance 4.38
    9612 
    9613 > select add #3
    9614 
    9615 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected 
    9616 
    9617 > select subtract #3
    9618 
    9619 13 models selected 
    9620 
    9621 > color zone #6 near #3 distance 4.38
    9622 
    9623 [Repeated 1 time(s)]
    9624 
    9625 > transparency #3.2-14#6.1 0
    9626 
    9627 > transparency #3.2-14#6.1 50
    9628 
    9629 > volume #6 level 0.02854
    9630 
    9631 > color zone #6 near #3 distance 4.38
    9632 
    9633 > transparency #3.2-14#6.1 0
    9634 
    9635 > transparency #3.2-14#6.1 50
    9636 
    9637 > volume #6 level 0.03
    9638 
    9639 > color zone #6 near #3 distance 4.38
    9640 
    9641 > transparency #3.2-14#6.1 0
    9642 
    9643 > transparency #3.2-14#6.1 50
    9644 
    9645 > volume #6 level 0.035
    9646 
    9647 > color zone #6 near #3 distance 4.38
    9648 
    9649 > transparency #3.2-14#6.1 0
    9650 
    9651 > transparency #3.2-14#6.1 50
    9652 
    9653 > hide #!6 models
    9654 
    9655 > color bfactor #3/B
    9656 
    9657 2471 atoms, 317 residues, 1 surfaces, atom bfactor range 59.1 to 203 
    9658 
    9659 > color bfactor #3/BD
    9660 
    9661 No atoms specified 
    9662 
    9663 > color bfactor #3/D
    9664 
    9665 2471 atoms, 317 residues, 1 surfaces, atom bfactor range 52.2 to 170 
    9666 
    9667 > color bfactor #3/B
    9668 
    9669 2471 atoms, 317 residues, 1 surfaces, atom bfactor range 59.1 to 203 
    9670 
    9671 > hide #!3 cartoons
    9672 
    9673 > show #!3 cartoons
    9674 
    9675 > color #3/B royal blue
    9676 
    9677 > color bfactor #3/P
    9678 
    9679 68 atoms, 8 residues, 1 surfaces, atom bfactor range 104 to 145 
    9680 
    9681 > color #3/O wheat
    9682 
    9683 > color #3/B wheat
    9684 
    9685 > color #3/F wheat
    9686 
    9687 > hide #!3 models
    9688 
    9689 > show #!2 models
    9690 
    9691 > volume #2 level 0.04171
    9692 
    9693 Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
    9694 models, 1 maps. 
    9695 
    9696 > surface dust #2 size 7.45
    9697 
    9698 > show #!4 models
    9699 
    9700 > ui tool show "Map Statistics"
    9701 
    9702 > measure mapstats #!2
    9703 
    9704 Map cryosparc_P26_J402_011_volume_map_sharp.mrc #2, step 2, minimum -0.2938,
    9705 maximum 0.57, mean 0.0008808, SD 0.01263, RMS 0.01266 
    9706 
    9707 > ui tool show "Map Coordinates"
    9708 
    9709 > ui tool show "Fit in Map"
    9710 
    9711 > fitmap #4 inMap #2
    9712 
    9713 Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#4) to map
    9714 cryosparc_P26_J402_011_volume_map_sharp.mrc (#2) using 15528 atoms 
    9715 average map value = 0.02136, steps = 72 
    9716 shifted from previous position = 2.7 
    9717 rotated from previous position = 2.26 degrees 
    9718 atoms outside contour = 12054, contour level = 0.041713 
    9719  
    9720 Position of RAD54-J402_m1_real_space_refined_001.pdb (#4) relative to
    9721 cryosparc_P26_J402_011_volume_map_sharp.mrc (#2) coordinates: 
    9722 Matrix rotation and translation 
    9723 0.99982960 -0.01832214 -0.00225362 4.55188201 
    9724 0.01823221 0.99922246 -0.03495810 0.83149762 
    9725 0.00289238 0.03491105 0.99938624 -5.85964538 
    9726 Axis 0.88417881 -0.06512155 0.46258730 
    9727 Axis point 0.00000000 184.92677295 22.01943861 
    9728 Rotation angle (degrees) 2.26438918 
    9729 Shift along axis 1.25993170 
    9730  
    9731 
    9732 > select #4/A,M
    9733 
    9734 2539 atoms, 2581 bonds, 1 pseudobond, 325 residues, 2 models selected 
    9735 
    9736 > fitmap sel inMap #2
    9737 
    9738 Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#4) to map
    9739 cryosparc_P26_J402_011_volume_map_sharp.mrc (#2) using 2539 atoms 
    9740 average map value = 0.02261, steps = 116 
    9741 shifted from previous position = 1.45 
    9742 rotated from previous position = 9.84 degrees 
    9743 atoms outside contour = 1967, contour level = 0.041713 
    9744  
    9745 Position of RAD54-J402_m1_real_space_refined_001.pdb (#4) relative to
    9746 cryosparc_P26_J402_011_volume_map_sharp.mrc (#2) coordinates: 
    9747 Matrix rotation and translation 
    9748 0.98424810 -0.09316819 -0.15025098 41.07304687 
    9749 0.09430536 0.99554322 0.00044532 -15.27352811 
    9750 0.14953986 -0.01460778 0.98864779 -19.15376273 
    9751 Axis -0.04253453 -0.84709842 0.52973115 
    9752 Axis point 151.35584707 0.00000000 257.79096684 
    9753 Rotation angle (degrees) 10.19224918 
    9754 Shift along axis 1.04481421 
    9755  
    9756 
    9757 > fitmap sel inMap #2
    9758 
    9759 Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#4) to map
    9760 cryosparc_P26_J402_011_volume_map_sharp.mrc (#2) using 2539 atoms 
    9761 average map value = 0.02261, steps = 64 
    9762 shifted from previous position = 0.0104 
    9763 rotated from previous position = 0.0175 degrees 
    9764 atoms outside contour = 1962, contour level = 0.041713 
    9765  
    9766 Position of RAD54-J402_m1_real_space_refined_001.pdb (#4) relative to
    9767 cryosparc_P26_J402_011_volume_map_sharp.mrc (#2) coordinates: 
    9768 Matrix rotation and translation 
    9769 0.98430158 -0.09301129 -0.14999768 41.01143653 
    9770 0.09414090 0.99555879 0.00043217 -15.25193280 
    9771 0.14929131 -0.01454631 0.98868625 -19.13386900 
    9772 Axis -0.04239536 -0.84711300 0.52971898 
    9773 Axis point 151.41713045 0.00000000 257.86243105 
    9774 Rotation angle (degrees) 10.17482829 
    9775 Shift along axis 1.04584245 
    9776  
    9777 
    9778 > select #4/A,M
    9779 
    9780 2539 atoms, 2581 bonds, 1 pseudobond, 325 residues, 2 models selected 
    9781 
    9782 > select #4/B,N
    9783 
    9784 2539 atoms, 2580 bonds, 1 pseudobond, 325 residues, 2 models selected 
    9785 
    9786 > select #4/C,O
    9787 
    9788 2539 atoms, 2580 bonds, 1 pseudobond, 325 residues, 2 models selected 
    9789 
    9790 > select #4/D,P
    9791 
    9792 2539 atoms, 2580 bonds, 1 pseudobond, 325 residues, 2 models selected 
    9793 
    9794 > select #4/E,Q
    9795 
    9796 2506 atoms, 2547 bonds, 1 pseudobond, 322 residues, 2 models selected 
    9797 
    9798 > select #4/F,R
    9799 
    9800 2506 atoms, 2547 bonds, 1 pseudobond, 322 residues, 2 models selected 
    9801 
    9802 > select #4/F,R
    9803 
    9804 2506 atoms, 2547 bonds, 1 pseudobond, 322 residues, 2 models selected 
    9805 
    9806 > fitmap sel inMap #2 moveWholeMolecules false
    9807 
    9808 Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#4) to map
    9809 cryosparc_P26_J402_011_volume_map_sharp.mrc (#2) using 2506 atoms 
    9810 average map value = 0.01676, steps = 100 
    9811 shifted from previous position = 1.8 
    9812 rotated from previous position = 8.28 degrees 
    9813 atoms outside contour = 2133, contour level = 0.041713 
    9814  
    9815 
    9816 > fitmap sel inMap #2 moveWholeMolecules false
    9817 
    9818 Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#4) to map
    9819 cryosparc_P26_J402_011_volume_map_sharp.mrc (#2) using 2506 atoms 
    9820 average map value = 0.01676, steps = 60 
    9821 shifted from previous position = 0.0175 
    9822 rotated from previous position = 0.0306 degrees 
    9823 atoms outside contour = 2134, contour level = 0.041713 
    9824  
    9825 
    9826 > fitmap sel inMap #2 moveWholeMolecules false
    9827 
    9828 Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#4) to map
    9829 cryosparc_P26_J402_011_volume_map_sharp.mrc (#2) using 2506 atoms 
    9830 average map value = 0.01676, steps = 44 
    9831 shifted from previous position = 0.0118 
    9832 rotated from previous position = 0.0214 degrees 
    9833 atoms outside contour = 2135, contour level = 0.041713 
    9834  
    9835 
    9836 > fitmap sel inMap #2 moveWholeMolecules false
    9837 
    9838 Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#4) to map
    9839 cryosparc_P26_J402_011_volume_map_sharp.mrc (#2) using 2506 atoms 
    9840 average map value = 0.01676, steps = 64 
    9841 shifted from previous position = 0.0021 
    9842 rotated from previous position = 0.0043 degrees 
    9843 atoms outside contour = 2133, contour level = 0.041713 
    9844  
    9845 
    9846 > fitmap sel inMap #2 moveWholeMolecules false
    9847 
    9848 Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#4) to map
    9849 cryosparc_P26_J402_011_volume_map_sharp.mrc (#2) using 2506 atoms 
    9850 average map value = 0.01676, steps = 64 
    9851 shifted from previous position = 0.00268 
    9852 rotated from previous position = 0.0039 degrees 
    9853 atoms outside contour = 2135, contour level = 0.041713 
    9854  
    9855 
    9856 > close #2
    9857 
    9858 > close #4
    9859 
    9860 > open "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
    9861 > structure RAD54B 07072025/newPDBfit-coot-10_real_space_refined_002.pdb"
    9862 
    9863 Chain information for newPDBfit-coot-10_real_space_refined_002.pdb #2 
    9864 --- 
    9865 Chain | Description 
    9866 A B C D E F | No description available 
    9867 M N O P Q R | No description available 
    9868 X | No description available 
    9869  
    9870 
    9871 > open "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
    9872 > structure RAD54B 07072025/cryosparc_P26_J402_011_volume_map_sharp.mrc"
    9873 
    9874 Opened cryosparc_P26_J402_011_volume_map_sharp.mrc as #4, grid size
    9875 336,336,336, pixel 0.745, shown at level 0.0343, step 2, values float32 
    9876 
    9877 > surface dust #4 size 7.45
    9878 
    9879 > hide #!2 atoms
    9880 
    9881 > show #!2 atoms
    9882 
    9883 [Repeated 1 time(s)]
    9884 
    9885 > hide #!2 atoms
    9886 
    9887 > hide #!2 cartoons
    9888 
    9889 > show #!2 cartoons
    9890 
    9891 > hide #!2 models
    9892 
    9893 > open "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
    9894 > structure RAD54B 07072025/RAD54-J402_m1_real_space_refined_001.pdb"
    9895 
    9896 Chain information for RAD54-J402_m1_real_space_refined_001.pdb #5 
    9897 --- 
    9898 Chain | Description 
    9899 A B C D E F | No description available 
    9900 M N O P Q R | No description available 
    9901 X | No description available 
    9902  
    9903 
    9904 > select add #5
    9905 
    9906 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    9907 
    9908 > hide sel atoms
    9909 
    9910 > show sel cartoons
    9911 
    9912 > select #4/A,M
    9913 
    9914 Nothing selected 
    9915 
    9916 > select #5/A,M
    9917 
    9918 2539 atoms, 2581 bonds, 1 pseudobond, 325 residues, 2 models selected 
    9919 
    9920 > fitmap sel inMap #4 moveWholeMolecules false
    9921 
    9922 Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#5) to map
    9923 cryosparc_P26_J402_011_volume_map_sharp.mrc (#4) using 2539 atoms 
    9924 average map value = 0.02263, steps = 116 
    9925 shifted from previous position = 2.54 
    9926 rotated from previous position = 6.47 degrees 
    9927 atoms outside contour = 1924, contour level = 0.0343 
    9928  
    9929 
    9930 > ui mousemode right "translate selected models"
    9931 
    9932 > view matrix models #5,1,0,0,2.953,0,1,0,-4.242,0,0,1,-0.79188
    9933 
    9934 > fitmap sel inMap #4 moveWholeMolecules false
    9935 
    9936 Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#5) to map
    9937 cryosparc_P26_J402_011_volume_map_sharp.mrc (#4) using 2539 atoms 
    9938 average map value = 0.0212, steps = 116 
    9939 shifted from previous position = 1.4 
    9940 rotated from previous position = 8.19 degrees 
    9941 atoms outside contour = 1949, contour level = 0.0343 
    9942  
    9943 
    9944 > view matrix models #5,1,0,0,1.0377,0,1,0,-0.69388,0,0,1,-1.3528
    9945 
    9946 > view matrix models #5,1,0,0,-0.13682,0,1,0,-2.2411,0,0,1,-0.70572
    9947 
    9948 > select #5/A,M
    9949 
    9950 2539 atoms, 2581 bonds, 1 pseudobond, 325 residues, 2 models selected 
    9951 
    9952 > fitmap sel inMap #4 moveWholeMolecules false
    9953 
    9954 Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#5) to map
    9955 cryosparc_P26_J402_011_volume_map_sharp.mrc (#4) using 2539 atoms 
    9956 average map value = 0.1051, steps = 72 
    9957 shifted from previous position = 2.02 
    9958 rotated from previous position = 2.45 degrees 
    9959 atoms outside contour = 452, contour level = 0.0343 
    9960  
    9961 
    9962 > select #5/B,N
    9963 
    9964 2539 atoms, 2580 bonds, 1 pseudobond, 325 residues, 2 models selected 
    9965 
    9966 > fitmap sel inMap #4 moveWholeMolecules false
    9967 
    9968 Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#5) to map
    9969 cryosparc_P26_J402_011_volume_map_sharp.mrc (#4) using 2539 atoms 
    9970 average map value = 0.02419, steps = 104 
    9971 shifted from previous position = 1.99 
    9972 rotated from previous position = 7.47 degrees 
    9973 atoms outside contour = 1881, contour level = 0.0343 
    9974  
    9975 
    9976 > view matrix models #5,1,0,0,-2.8013,0,1,0,-6.3378,0,0,1,-1.9553
    9977 
    9978 > fitmap sel inMap #4 moveWholeMolecules false
    9979 
    9980 Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#5) to map
    9981 cryosparc_P26_J402_011_volume_map_sharp.mrc (#4) using 2539 atoms 
    9982 average map value = 0.1297, steps = 140 
    9983 shifted from previous position = 4.11 
    9984 rotated from previous position = 7.46 degrees 
    9985 atoms outside contour = 322, contour level = 0.0343 
    9986  
    9987 
    9988 > select #5/A,M
    9989 
    9990 2539 atoms, 2581 bonds, 1 pseudobond, 325 residues, 2 models selected 
    9991 
    9992 > fitmap sel inMap #4 moveWholeMolecules false
    9993 
    9994 Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#5) to map
    9995 cryosparc_P26_J402_011_volume_map_sharp.mrc (#4) using 2539 atoms 
    9996 average map value = 0.02559, steps = 80 
    9997 shifted from previous position = 0.958 
    9998 rotated from previous position = 5.73 degrees 
    9999 atoms outside contour = 1806, contour level = 0.0343 
    10000  
    10001 
    10002 > select #5/A,M
    10003 
    10004 2539 atoms, 2581 bonds, 1 pseudobond, 325 residues, 2 models selected 
    10005 
    10006 > view matrix models #5,1,0,0,-0.91106,0,1,0,-1.7616,0,0,1,-4.2822
    10007 
    10008 > select #5/A,M
    10009 
    10010 2539 atoms, 2581 bonds, 1 pseudobond, 325 residues, 2 models selected 
    10011 
    10012 > fitmap sel inMap #4 moveWholeMolecules false
    10013 
    10014 Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#5) to map
    10015 cryosparc_P26_J402_011_volume_map_sharp.mrc (#4) using 2539 atoms 
    10016 average map value = 0.1051, steps = 68 
    10017 shifted from previous position = 2.78 
    10018 rotated from previous position = 5.72 degrees 
    10019 atoms outside contour = 451, contour level = 0.0343 
    10020  
    10021 
    10022 > select #5/B,N
    10023 
    10024 2539 atoms, 2580 bonds, 1 pseudobond, 325 residues, 2 models selected 
    10025 
    10026 > fitmap sel inMap #4 moveWholeMolecules false
    10027 
    10028 Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#5) to map
    10029 cryosparc_P26_J402_011_volume_map_sharp.mrc (#4) using 2539 atoms 
    10030 average map value = 0.0267, steps = 108 
    10031 shifted from previous position = 1.2 
    10032 rotated from previous position = 5.25 degrees 
    10033 atoms outside contour = 1812, contour level = 0.0343 
    10034  
    10035 
    10036 > fitmap sel inMap #4 moveWholeMolecules false
    10037 
    10038 Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#5) to map
    10039 cryosparc_P26_J402_011_volume_map_sharp.mrc (#4) using 2539 atoms 
    10040 average map value = 0.0267, steps = 48 
    10041 shifted from previous position = 0.0131 
    10042 rotated from previous position = 0.00744 degrees 
    10043 atoms outside contour = 1811, contour level = 0.0343 
    10044  
    10045 
    10046 > transparency #4.1 50
    10047 
    10048 > view matrix models #5,1,0,0,-0.92563,0,1,0,-1.9541,0,0,1,-5.7241
    10049 
    10050 > fitmap sel inMap #4 moveWholeMolecules false
    10051 
    10052 Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#5) to map
    10053 cryosparc_P26_J402_011_volume_map_sharp.mrc (#4) using 2539 atoms 
    10054 average map value = 0.0267, steps = 56 
    10055 shifted from previous position = 1.45 
    10056 rotated from previous position = 0.00861 degrees 
    10057 atoms outside contour = 1812, contour level = 0.0343 
    10058  
    10059 
    10060 > fitmap sel inMap #4 moveWholeMolecules false
    10061 
    10062 Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#5) to map
    10063 cryosparc_P26_J402_011_volume_map_sharp.mrc (#4) using 2539 atoms 
    10064 average map value = 0.0267, steps = 28 
    10065 shifted from previous position = 0.00957 
    10066 rotated from previous position = 0.0268 degrees 
    10067 atoms outside contour = 1811, contour level = 0.0343 
    10068  
    10069 
    10070 > select add #5
    10071 
    10072 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    10073 
    10074 > select subtract #5
    10075 
    10076 Nothing selected 
    10077 
    10078 > ui tool show "Show Sequence Viewer"
    10079 
    10080 > sequence chain #5/M
    10081 
    10082 Alignment identifier is 5/M 
    10083 
    10084 > select #5/M:5
    10085 
    10086 11 atoms, 11 bonds, 1 residue, 1 model selected 
    10087 
    10088 > select #5/M:5
    10089 
    10090 11 atoms, 11 bonds, 1 residue, 1 model selected 
    10091 
    10092 > select #5/M:5-8
    10093 
    10094 32 atoms, 34 bonds, 4 residues, 1 model selected 
    10095 
    10096 > select #5/M:6
    10097 
    10098 7 atoms, 6 bonds, 1 residue, 1 model selected 
    10099 
    10100 > select #5/M:6
    10101 
    10102 7 atoms, 6 bonds, 1 residue, 1 model selected 
    10103 
    10104 > show sel atoms
    10105 
    10106 > select ::name="ILE"
    10107 
    10108 4536 atoms, 4011 bonds, 567 residues, 4 models selected 
    10109 
    10110 > toolshed show
    10111 
    10112 Downloading bundle ChimeraX_PhenixUI-1.3.7-py3-none-any.whl 
    10113 Installed ChimeraX-PhenixUI (1.3.7) 
    10114 
    10115 > swapaa #5/M:6 ile
    10116 
    10117 Using Dunbrack library 
    10118 RAD54-J402_m1_real_space_refined_001.pdb #5/M VAL 6: phi -104.4, psi 112.3
    10119 trans 
    10120 Density criteria with multiple volume models open; 
    10121 Need to specify one to use via 'density' keyword. 
    10122 
    10123 > swapaa #5/M:6 ile`
    10124 
    10125 Using Dunbrack library 
    10126 RAD54-J402_m1_real_space_refined_001.pdb #5/M VAL 6: phi -104.4, psi 112.3
    10127 trans 
    10128 Dunbrack rotamer library does not support ILE` 
    10129 
    10130 > swapaa #5/M:6 ile
    10131 
    10132 Using Dunbrack library 
    10133 RAD54-J402_m1_real_space_refined_001.pdb #5/M VAL 6: phi -104.4, psi 112.3
    10134 trans 
    10135 Density criteria with multiple volume models open; 
    10136 Need to specify one to use via 'density' keyword. 
    10137 
    10138 > swapaa #5/M:6 ile
    10139 
    10140 Using Dunbrack library 
    10141 RAD54-J402_m1_real_space_refined_001.pdb #5/M VAL 6: phi -104.4, psi 112.3
    10142 trans 
    10143 Density criteria with multiple volume models open; 
    10144 Need to specify one to use via 'density' keyword. 
    10145 
    10146 > swapaa #5/M:6 ile
    10147 
    10148 Using Dunbrack library 
    10149 RAD54-J402_m1_real_space_refined_001.pdb #5/M VAL 6: phi -104.4, psi 112.3
    10150 trans 
    10151 Density criteria with multiple volume models open; 
    10152 Need to specify one to use via 'density' keyword. 
    10153 
    10154 > swapaa #5/M:6 ile density #4
    10155 
    10156 Using Dunbrack library 
    10157 RAD54-J402_m1_real_space_refined_001.pdb #5/M VAL 6: phi -104.4, psi 112.3
    10158 trans 
    10159 Applying ILE rotamer (chi angles: 59.9 85.2) to
    10160 RAD54-J402_m1_real_space_refined_001.pdb #5/M ILE 6 
    10161 
    10162 > select #5/M
    10163 
    10164 69 atoms, 72 bonds, 8 residues, 1 model selected 
    10165 
    10166 > fitmap sel inMap #4 moveWholeMolecules false
    10167 
    10168 Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#5) to map
    10169 cryosparc_P26_J402_011_volume_map_sharp.mrc (#4) using 69 atoms 
    10170 average map value = 0.05783, steps = 44 
    10171 shifted from previous position = 1.34 
    10172 rotated from previous position = 1.09 degrees 
    10173 atoms outside contour = 26, contour level = 0.0343 
    10174  
    10175 
    10176 > select #5/A
    10177 
    10178 2471 atoms, 2510 bonds, 1 pseudobond, 317 residues, 2 models selected 
    10179 
    10180 > fitmap sel inMap #4 moveWholeMolecules false
    10181 
    10182 Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#5) to map
    10183 cryosparc_P26_J402_011_volume_map_sharp.mrc (#4) using 2471 atoms 
    10184 average map value = 0.1065, steps = 52 
    10185 shifted from previous position = 1.46 
    10186 rotated from previous position = 0.00296 degrees 
    10187 atoms outside contour = 426, contour level = 0.0343 
    10188  
    10189 
    10190 > select add #5
    10191 
    10192 15529 atoms, 15811 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    10193 
    10194 > select subtract #5
    10195 
    10196 Nothing selected 
    10197 
    10198 > swapaa #5/M:4 lys density #4
    10199 
    10200 Using Dunbrack library 
    10201 RAD54-J402_m1_real_space_refined_001.pdb #5/M VAL 4: phi -127.5, psi 139.0
    10202 trans 
    10203 Applying LYS rotamer (chi angles: -176.9 174.8 72.5 69.2) to
    10204 RAD54-J402_m1_real_space_refined_001.pdb #5/M LYS 4 
    10205 
    10206 > show #!5 atoms
    10207 
    10208 > hide #!5 atoms
    10209 
    10210 > select #5/M
    10211 
    10212 71 atoms, 74 bonds, 8 residues, 1 model selected 
    10213 
    10214 > show sel atoms
    10215 
    10216 > swapaa #5/M:3 pro density #4
    10217 
    10218 Using Dunbrack library 
    10219 RAD54-J402_m1_real_space_refined_001.pdb #5/M LYS 3: phi none, psi 134.6 trans 
    10220 Applying PRO rotamer (chi angles: 27.0 -34.6) to
    10221 RAD54-J402_m1_real_space_refined_001.pdb #5/M PRO 3 
    10222 
    10223 > swapaa #5/M:9 gly density #4
    10224 
    10225 Using Dunbrack library 
    10226 Swapping RAD54-J402_m1_real_space_refined_001.pdb #5/M PHE 9 to GLY 
    10227 
    10228 > swapaa #5/M:10 arg density #4
    10229 
    10230 Using Dunbrack library 
    10231 RAD54-J402_m1_real_space_refined_001.pdb #5/M LYS 10: phi -99.9, psi none
    10232 trans 
    10233 Applying ARG rotamer (chi angles: -83.1 81.9 69.8 -178.0) to
    10234 RAD54-J402_m1_real_space_refined_001.pdb #5/M ARG 10 
    10235 
    10236 > view matrix models #5,1,0,0,-0.47913,0,1,0,-1.925,0,0,1,-6.0718
    10237 
    10238 > select #A,M
    10239 
    10240 Expected an objects specifier or a keyword 
    10241 
    10242 > select #5/A,M
    10243 
    10244 2535 atoms, 2577 bonds, 1 pseudobond, 325 residues, 2 models selected 
    10245 
    10246 > fitmap sel inMap #4 moveWholeMolecules false
    10247 
    10248 Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#5) to map
    10249 cryosparc_P26_J402_011_volume_map_sharp.mrc (#4) using 2535 atoms 
    10250 average map value = 0.1055, steps = 64 
    10251 shifted from previous position = 0.574 
    10252 rotated from previous position = 0.016 degrees 
    10253 atoms outside contour = 440, contour level = 0.0343 
    10254  
    10255 
    10256 > select add #5
    10257 
    10258 15524 atoms, 15806 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    10259 
    10260 > select subtract #5
    10261 
    10262 Nothing selected 
    10263 
    10264 > ui tool show "Local EM Fitting"
    10265 
    10266 Populating font family aliases took 71 ms. Replace uses of missing font family
    10267 "Times" with one that exists to avoid this cost. 
    10268 
    10269 Must specify a resolution value for the full map 
    10270 
    10271 > select #5/M:3
    10272 
    10273 7 atoms, 7 bonds, 1 residue, 1 model selected 
    10274 
    10275 > show sel atoms
    10276 
    10277 > hide sel atoms
    10278 
    10279 > ui tool show Rotamers
    10280 
    10281 > select #5/M:10
    10282 
    10283 11 atoms, 10 bonds, 1 residue, 1 model selected 
    10284 
    10285 > ui tool show Rotamers
    10286 
    10287 > swapaa interactive sel ARG rotLib Dunbrack
    10288 
    10289 RAD54-J402_m1_real_space_refined_001.pdb #5/M ARG 10: phi -99.9, psi none
    10290 trans 
    10291 Changed 648 bond radii 
    10292 
    10293 > swapaa #!5/M:10 ARG criteria 5 rotLib Dunbrack retain false
    10294 
    10295 Using Dunbrack library 
    10296 RAD54-J402_m1_real_space_refined_001.pdb #!5/M ARG 10: phi -99.9, psi none
    10297 trans 
    10298 Applying ARG rotamer (chi angles: -176.9 176.3 178.8 -179.4) to
    10299 RAD54-J402_m1_real_space_refined_001.pdb #!5/M ARG 10 
    10300 
    10301 > swapaa interactive sel ARG rotLib Dunbrack
    10302 
    10303 RAD54-J402_m1_real_space_refined_001.pdb #5/M ARG 10: phi -99.9, psi none
    10304 trans 
    10305 Changed 648 bond radii 
    10306 
    10307 > select #5/M:4
    10308 
    10309 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10310 
    10311 > ui tool show Rotamers
    10312 
    10313 > swapaa interactive sel LYS rotLib Dunbrack
    10314 
    10315 RAD54-J402_m1_real_space_refined_001.pdb #5/M LYS 4: phi -127.5, psi 139.0
    10316 trans 
    10317 Changed 438 bond radii 
    10318 
    10319 > swapaa #!5/M:4 LYS criteria 1 rotLib Dunbrack retain false
    10320 
    10321 Using Dunbrack library 
    10322 RAD54-J402_m1_real_space_refined_001.pdb #!5/M LYS 4: phi -127.5, psi 139.0
    10323 trans 
    10324 Applying LYS rotamer (chi angles: -64.2 -177.9 -179.5 179.7) to
    10325 RAD54-J402_m1_real_space_refined_001.pdb #!5/M LYS 4 
    10326 
    10327 > select #5/M
    10328 
    10329 64 atoms, 67 bonds, 8 residues, 1 model selected 
    10330 
    10331 > fitmap sel inMap #4 moveWholeMolecules false
    10332 
    10333 Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#5) to map
    10334 cryosparc_P26_J402_011_volume_map_sharp.mrc (#4) using 64 atoms 
    10335 average map value = 0.06077, steps = 48 
    10336 shifted from previous position = 0.101 
    10337 rotated from previous position = 2.24 degrees 
    10338 atoms outside contour = 23, contour level = 0.0343 
    10339  
    10340 
    10341 > select #5/M:10
    10342 
    10343 11 atoms, 10 bonds, 1 residue, 1 model selected 
    10344 
    10345 > ui tool show Rotamers
    10346 
    10347 > swapaa interactive sel ARG rotLib Dunbrack
    10348 
    10349 RAD54-J402_m1_real_space_refined_001.pdb #5/M ARG 10: phi -99.9, psi none
    10350 trans 
    10351 Changed 648 bond radii 
    10352 
    10353 > view matrix models #5,1,0,0,-0.36351,0,1,0,-2.6595,0,0,1,-5.3788
    10354 
    10355 > select #5/A,M
    10356 
    10357 2535 atoms, 2577 bonds, 1 pseudobond, 325 residues, 2 models selected 
    10358 
    10359 > fitmap sel inMap #4 moveWholeMolecules false
    10360 
    10361 Fit molecule RAD54-J402_m1_real_space_refined_001.pdb (#5) to map
    10362 cryosparc_P26_J402_011_volume_map_sharp.mrc (#4) using 2535 atoms 
    10363 average map value = 0.1054, steps = 72 
    10364 shifted from previous position = 1.01 
    10365 rotated from previous position = 0.0195 degrees 
    10366 atoms outside contour = 446, contour level = 0.0343 
    10367  
    10368 
    10369 > select add #5
    10370 
    10371 15524 atoms, 15806 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    10372 
    10373 > select subtract #5
    10374 
    10375 Nothing selected 
    10376 
    10377 > select #5/M:10
    10378 
    10379 11 atoms, 10 bonds, 1 residue, 1 model selected 
    10380 
    10381 > ui tool show Rotamers
    10382 
    10383 > swapaa interactive sel ARG rotLib Dunbrack
    10384 
    10385 RAD54-J402_m1_real_space_refined_001.pdb #5/M ARG 10: phi -99.9, psi none
    10386 trans 
    10387 Changed 648 bond radii 
    10388 
    10389 > select add #5
    10390 
    10391 15524 atoms, 15806 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    10392 
    10393 > select subtract #5
    10394 
    10395 Nothing selected 
    10396 
    10397 > color zone #4 near #5 distance 4.38
    10398 
    10399 > transparency #4.1 0
    10400 
    10401 > transparency #4.1 50
    10402 
    10403 > hide #!5 models
    10404 
    10405 > hide #!4 models
    10406 
    10407 > show #!6 models
    10408 
    10409 > show #!2 models
    10410 
    10411 > hide #!2 models
    10412 
    10413 > show #!3 models
    10414 
    10415 > hide #!3 models
    10416 
    10417 > show #!3 models
    10418 
    10419 > hide #!3 surfaces
    10420 
    10421 > swapaa #3/P:3 lys density #6
    10422 
    10423 Using Dunbrack library 
    10424 newPDBfit-coot-10_real_space_refined_002.pdb #3/P LYS 3: phi none, psi -83.0
    10425 trans 
    10426 Applying LYS rotamer (chi angles: 69.5 85.2 -93.8 -177.2) to newPDBfit-
    10427 coot-10_real_space_refined_002.pdb #3/P LYS 3 
    10428 
    10429 > select #3/P:3
    10430 
    10431 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10432 
    10433 > ui tool show Rotamers
    10434 
    10435 > swapaa interactive sel LYS rotLib Dunbrack
    10436 
    10437 newPDBfit-coot-10_real_space_refined_002.pdb #3/P LYS 3: phi none, psi -83.0
    10438 trans 
    10439 Changed 486 bond radii 
    10440 
    10441 > swapaa #!3/P:3 LYS criteria 20 rotLib Dunbrack retain false
    10442 
    10443 Using Dunbrack library 
    10444 newPDBfit-coot-10_real_space_refined_002.pdb #!3/P LYS 3: phi none, psi -83.0
    10445 trans 
    10446 Applying LYS rotamer (chi angles: 65.9 -178.1 173.2 66.9) to newPDBfit-
    10447 coot-10_real_space_refined_002.pdb #!3/P LYS 3 
    10448 
    10449 > select add #3
    10450 
    10451 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected 
    10452 
    10453 > select subtract #3
    10454 
    10455 13 models selected 
    10456 
    10457 > ui tool show "Local EM Fitting"
    10458 
    10459 Must specify exactly two half maps for fitting 
    10460 [Repeated 1 time(s)]No part of model for specifying search center is displayed 
    10461 [Repeated 1 time(s)]
    10462 
    10463 > marker #8 position 123.064,92.5207,108.869 radius 82.2268 color 100,65,0,50
    10464 
    10465 > phenix emplaceLocal #3 mapData #6 resolution 2.5 center
    10466 > 123.064,92.5207,108.869 showSharpenedMap false applySymmetry false
    10467 
    10468 Could not find Phenix installation in /Users/sz140275local, /Applications. 
    10469 Use "phenix location" command to specify the location of your Phenix
    10470 installation. 
    10471 The value you give to 'phenix location' needs to be the full path to 
    10472 the top-level folder that Phenix created when it was installed. 
    10473 You can use 'phenix location browse' in order to use a file browser 
    10474 to specify the installation location. 
    10475 
    10476 > hide #!3 models
    10477 
    10478 > show #!2 models
    10479 
    10480 > hide #!6 models
    10481 
    10482 > select #2/D,P
    10483 
    10484 2539 atoms, 2580 bonds, 1 pseudobond, 325 residues, 2 models selected 
    10485 
    10486 > collor bfactor sel
    10487 
    10488 Unknown command: collor bfactor sel 
    10489 
    10490 > color bfactor sel
    10491 
    10492 2539 atoms, 325 residues, atom bfactor range 52.2 to 170 
    10493 
    10494 > select #2
    10495 
    10496 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    10497 
    10498 > color bfactor sel
    10499 
    10500 15528 atoms, 1962 residues, atom bfactor range 52.2 to 242 
    10501 
    10502 > view matrix models #2,1,0,0,12.319,0,1,0,-3.9459,0,0,1,4.8367
    10503 
    10504 > select #2
    10505 
    10506 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    10507 
    10508 > color sel wheat
    10509 
    10510 > select #2/D,P
    10511 
    10512 2539 atoms, 2580 bonds, 1 pseudobond, 325 residues, 2 models selected 
    10513 
    10514 > color bfactor sel
    10515 
    10516 2539 atoms, 325 residues, atom bfactor range 52.2 to 170 
    10517 
    10518 > select #2/D:ATP*
    10519 
    10520 31 atoms, 33 bonds, 1 residue, 1 model selected 
    10521 
    10522 > show sel atoms
    10523 
    10524 > select #2/D:Mg*
    10525 
    10526 2 atoms, 2 residues, 1 model selected 
    10527 
    10528 > show sel atoms
    10529 
    10530 [Repeated 1 time(s)]
    10531 
    10532 > select add #2
    10533 
    10534 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    10535 
    10536 > select subtract #2
    10537 
    10538 Nothing selected 
    10539 
    10540 > select #2/P
    10541 
    10542 68 atoms, 71 bonds, 8 residues, 1 model selected 
    10543 
    10544 > show sel atoms
    10545 
    10546 > select #2/P:3,10
    10547 
    10548 18 atoms, 16 bonds, 2 residues, 1 model selected 
    10549 
    10550 > hide sel atoms
    10551 
    10552 > select add #2
    10553 
    10554 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    10555 
    10556 > select subtract #2
    10557 
    10558 Nothing selected 
    10559 
    10560 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    10561 > RAD54/BRCA2bfactor.tif" width 841 height 750 supersample 3
    10562 
    10563 > show #!6 models
    10564 
    10565 > hide #!6 models
    10566 
    10567 > show #!6 models
    10568 
    10569 > hide #!6 models
    10570 
    10571 > show #!6 models
    10572 
    10573 > hide #!6 models
    10574 
    10575 > show #!3 models
    10576 
    10577 > hide #!3 models
    10578 
    10579 > show #!3 models
    10580 
    10581 > hide #!3 models
    10582 
    10583 > hide #!2 models
    10584 
    10585 > show #!3 models
    10586 
    10587 > select #3/D
    10588 
    10589 2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 2 models selected 
    10590 
    10591 > color sel royal blue
    10592 
    10593 > color sel dodger blue
    10594 
    10595 > color sel royal blue
    10596 
    10597 > select #3/P
    10598 
    10599 68 atoms, 71 bonds, 8 residues, 1 model selected 
    10600 
    10601 > color sel red
    10602 
    10603 > select #3/D:Mg*
    10604 
    10605 2 atoms, 2 residues, 1 model selected 
    10606 
    10607 > show sel atoms
    10608 
    10609 > color sel black
    10610 
    10611 > select #3/D:ATP*
    10612 
    10613 31 atoms, 33 bonds, 1 residue, 1 model selected 
    10614 
    10615 > color sel black
    10616 
    10617 > select #3/C:ATP*,MG*
    10618 
    10619 33 atoms, 33 bonds, 3 residues, 1 model selected 
    10620 
    10621 > color sel black
    10622 
    10623 > select #3/C:Mg*
    10624 
    10625 2 atoms, 2 residues, 1 model selected 
    10626 
    10627 > show sel atoms
    10628 
    10629 > select add #3
    10630 
    10631 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    10632 
    10633 > select subtract #3
    10634 
    10635 13 models selected 
    10636 
    10637 > select #3/E
    10638 
    10639 2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected 
    10640 
    10641 > show sel atoms
    10642 
    10643 > hide sel atoms
    10644 
    10645 > color sel wheat
    10646 
    10647 > select add #3
    10648 
    10649 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected 
    10650 
    10651 > select subtract #3
    10652 
    10653 13 models selected 
    10654 
    10655 > show #!6 models
    10656 
    10657 > hide #!6 models
    10658 
    10659 > show #!6 models
    10660 
    10661 > color zone #6 near #3 distance 4.38
    10662 
    10663 > transparency #3.2-14#6.1 0
    10664 
    10665 > transparency #3.2-14#6.1 50
    10666 
    10667 > volume #6 level 0.04563
    10668 
    10669 > color zone #6 near #3 distance 4.38
    10670 
    10671 > transparency #3.2-14#6.1 0
    10672 
    10673 > transparency #3.2-14#6.1 50
    10674 
    10675 > hide #!6 models
    10676 
    10677 Window position QRect(974,990 654x459) outside any known screen, using primary
    10678 screen 
    10679 
    10680 > show #!6 models
    10681 
    10682 > open "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
    10683 > structure BRCA2 07072025/cryosparc_P26_J362_012_volume_map.mrc"
    10684 
    10685 Opened cryosparc_P26_J362_012_volume_map.mrc as #8, grid size 336,336,336,
    10686 pixel 0.73, shown at level 0.0236, step 2, values float32 
    10687 
    10688 > hide #!6 models
    10689 
    10690 > color zone #8 near #3 distance 4.38
    10691 
    10692 > transparency #3.2-14#8.1 0
    10693 
    10694 > transparency #3.2-14#8.1 50
    10695 
    10696 > surface dust #8 size 7.3
    10697 
    10698 > swapaa #3/P:9 phe density #8
    10699 
    10700 Using Dunbrack library 
    10701 newPDBfit-coot-10_real_space_refined_002.pdb #3/P PHE 9: phi -81.6, psi 168.3
    10702 trans 
    10703 Applying PHE rotamer (chi angles: 60.6 108.6) to newPDBfit-
    10704 coot-10_real_space_refined_002.pdb #3/P PHE 9 
    10705 
    10706 > size sticksrad 0.7
    10707 
    10708 Expected a keyword 
    10709 
    10710 > size sticksrad 0.7
    10711 
    10712 Expected a keyword 
    10713 
    10714 > size stickRadius 0.7
    10715 
    10716 Changed 55012 bond radii 
    10717 
    10718 > size stickRadius 0.4
    10719 
    10720 Changed 55012 bond radii 
    10721 
    10722 > select #3/P
    10723 
    10724 68 atoms, 71 bonds, 8 residues, 1 model selected 
    10725 
    10726 > color bfactor sel
    10727 
    10728 68 atoms, 8 residues, 1 surfaces, atom bfactor range 104 to 145 
    10729 
    10730 > select add #3
    10731 
    10732 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected 
    10733 
    10734 > select subtract #3
    10735 
    10736 13 models selected 
    10737 
    10738 > color sel red
    10739 
    10740 > select #3/P
    10741 
    10742 68 atoms, 71 bonds, 8 residues, 1 model selected 
    10743 
    10744 > color sel red
    10745 
    10746 > select add #3
    10747 
    10748 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected 
    10749 
    10750 > select subtract #3
    10751 
    10752 13 models selected 
    10753 
    10754 > select #3/Q
    10755 
    10756 68 atoms, 71 bonds, 8 residues, 1 model selected 
    10757 
    10758 > color sel wheat
    10759 
    10760 > select add #3
    10761 
    10762 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected 
    10763 
    10764 > select subtract #3
    10765 
    10766 13 models selected 
    10767 
    10768 > color zone #8 near #3 distance 4.38
    10769 
    10770 > transparency #3.2-14#8.1 0
    10771 
    10772 > transparency #3.2-14#8.1 50
    10773 
    10774 > select #3/Q
    10775 
    10776 68 atoms, 71 bonds, 8 residues, 1 model selected 
    10777 
    10778 > hide sel atoms
    10779 
    10780 > select add #3
    10781 
    10782 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected 
    10783 
    10784 > select subtract #3
    10785 
    10786 13 models selected 
    10787 
    10788 > volume #6 style mesh
    10789 
    10790 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    10791 > RAD54/BRCA2bPeptide.tif" width 841 height 709 supersample 3
    10792 
    10793 > select #3/P:3,10
    10794 
    10795 18 atoms, 16 bonds, 2 residues, 1 model selected 
    10796 
    10797 > hide sel atoms
    10798 
    10799 > select add #3
    10800 
    10801 15528 atoms, 15810 bonds, 6 pseudobonds, 1962 residues, 3 models selected 
    10802 
    10803 > select subtract #3
    10804 
    10805 13 models selected 
    10806 
    10807 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    10808 > RAD54/BRCA2bPeptide.tif" width 841 height 709 supersample 3
    10809 
    10810 > open "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
    10811 > structure RAD54B 07072025/cryosparc_P26_J410_011_volume_map_sharp.mrc"
    10812 
    10813 Opened cryosparc_P26_J410_011_volume_map_sharp.mrc as #9, grid size
    10814 336,336,336, pixel 0.73, shown at level 0.032, step 2, values float32 
    10815 
    10816 > hide #!3 models
    10817 
    10818 > hide #!8 models
    10819 
    10820 > surface dust #9 size 7.3
    10821 
    10822 > open "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
    10823 > structure RAD54B 07072025/RAD54-J402_m4_real_space_refined_000.pdb"
    10824 
    10825 Chain information for RAD54-J402_m4_real_space_refined_000.pdb #10 
    10826 --- 
    10827 Chain | Description 
    10828 A B C D E F | No description available 
    10829 M | No description available 
    10830 N O P Q | No description available 
    10831 R | No description available 
    10832 X | No description available 
    10833  
    10834 
    10835 > style #!10 stick
    10836 
    10837 Changed 15512 atom styles 
    10838 
    10839 > hide #!10 atoms
    10840 
    10841 > show #!10 cartoons
    10842 
    10843 > transparency #9.1 50
    10844 
    10845 > open "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
    10846 > structure BRCA2 07072025/BRCA2_m4_real_space_refined_000.pdb"
    10847 
    10848 Chain information for BRCA2_m4_real_space_refined_000.pdb #11 
    10849 --- 
    10850 Chain | Description 
    10851 A B C D E F | No description available 
    10852 M N O P Q R | No description available 
    10853 X | No description available 
    10854  
    10855 
    10856 > hide #!11 models
    10857 
    10858 > select #9/X
    10859 
    10860 Nothing selected 
    10861 
    10862 > select #10/X
    10863 
    10864 360 atoms, 395 bonds, 18 residues, 1 model selected 
    10865 
    10866 > color sel lime
    10867 
    10868 > select #10/A,B,C,D,E,F,G:ATP*
    10869 
    10870 Nothing selected 
    10871 
    10872 > select #10/A,B,C,D,E,F,G:AMPPNP*
    10873 
    10874 Nothing selected 
    10875 
    10876 > select #10/A,B,C,D,E,F,G:ANP*
    10877 
    10878 155 atoms, 165 bonds, 5 residues, 1 model selected 
    10879 
    10880 > color sel blue
    10881 
    10882 > show sel atoms
    10883 
    10884 > select #10/A,B,C,D,E,F,G:Ca*
    10885 
    10886 10 atoms, 10 residues, 1 model selected 
    10887 
    10888 > color sel blue
    10889 
    10890 > show sel atoms
    10891 
    10892 [Repeated 1 time(s)]
    10893 
    10894 > select add #10
    10895 
    10896 15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    10897 
    10898 > select subtract #10
    10899 
    10900 Nothing selected 
    10901 
    10902 > select #10/M,N,O,P,Q,R,S
    10903 
    10904 359 atoms, 375 bonds, 45 residues, 1 model selected 
    10905 
    10906 > color sel red
    10907 
    10908 > show sel atoms
    10909 
    10910 > select #10/X
    10911 
    10912 360 atoms, 395 bonds, 18 residues, 1 model selected 
    10913 
    10914 > hide sel cartoons
    10915 
    10916 > show sel atoms
    10917 
    10918 > select add #10
    10919 
    10920 15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    10921 
    10922 > select subtract #10
    10923 
    10924 Nothing selected 
    10925 
    10926 > hide #!9 models
    10927 
    10928 > show #!9 models
    10929 
    10930 > color #10/C wheat
    10931 
    10932 > select add #10
    10933 
    10934 15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    10935 
    10936 > color zone #9 near sel & #10 distance 4.38
    10937 
    10938 > transparency #9.1 0
    10939 
    10940 > transparency #9.1 50
    10941 
    10942 > select subtract #10
    10943 
    10944 Nothing selected 
    10945 
    10946 > select #10/A,B,C,D,E,F,G
    10947 
    10948 14793 atoms, 15021 bonds, 6 pseudobonds, 1899 residues, 2 models selected 
    10949 
    10950 > hide sel cartoons
    10951 
    10952 > select add #10
    10953 
    10954 15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    10955 
    10956 > select subtract #10
    10957 
    10958 Nothing selected 
    10959 
    10960 > volume #6 level 0.05
    10961 
    10962 > volume #9 level 0.035
    10963 
    10964 > color zone #9 near #10 distance 4.38
    10965 
    10966 > transparency #9.1 0
    10967 
    10968 > transparency #9.1 50
    10969 
    10970 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    10971 > RAD54/RAD54SupB.tif" width 841 height 709 supersample 3
    10972 
    10973 > select #10/C
    10974 
    10975 2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 2 models selected 
    10976 
    10977 > hide #!9 models
    10978 
    10979 > select add #10
    10980 
    10981 15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    10982 
    10983 > select subtract #10
    10984 
    10985 Nothing selected 
    10986 
    10987 > select #10/A,B,C,D,E,F,G
    10988 
    10989 14793 atoms, 15021 bonds, 6 pseudobonds, 1899 residues, 2 models selected 
    10990 
    10991 > show sel cartoons
    10992 
    10993 > select #10/A,B,D,E,F,G
    10994 
    10995 12322 atoms, 12512 bonds, 5 pseudobonds, 1582 residues, 2 models selected 
    10996 
    10997 > show sel surfaces
    10998 
    10999 > select add #10
    11000 
    11001 15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 7 models selected 
    11002 
    11003 > select subtract #10
    11004 
    11005 5 models selected 
    11006 
    11007 > select #10/C:ANP*
    11008 
    11009 31 atoms, 33 bonds, 1 residue, 1 model selected 
    11010 
    11011 > color sel blue
    11012 
    11013 > select #10/C:Ca*
    11014 
    11015 2 atoms, 2 residues, 1 model selected 
    11016 
    11017 > color sel blue
    11018 
    11019 > size stickRadius 0.7
    11020 
    11021 Changed 86646 bond radii 
    11022 
    11023 > size stickRadius 0.4
    11024 
    11025 Changed 86646 bond radii 
    11026 
    11027 > size stickRadius 0.25
    11028 
    11029 Changed 86646 bond radii 
    11030 
    11031 > size atomRadius 0.25
    11032 
    11033 Changed 85392 atom radii 
    11034 
    11035 > size atomRadius 0.5
    11036 
    11037 Changed 85392 atom radii 
    11038 
    11039 > select #10/A,B,C:Ca*
    11040 
    11041 6 atoms, 6 residues, 1 model selected 
    11042 
    11043 > size atomRadius 0.5
    11044 
    11045 Changed 85392 atom radii 
    11046 
    11047 > size atomRadius 1
    11048 
    11049 Changed 85392 atom radii 
    11050 
    11051 > size ballScale 1
    11052 
    11053 Changed 6 ball scales 
    11054 
    11055 > size ballScale 2
    11056 
    11057 Changed 6 ball scales 
    11058 
    11059 > size sel ballScale 2
    11060 
    11061 Changed 1 ball scales 
    11062 
    11063 > size sel atomRadius 1
    11064 
    11065 Changed 6 atom radii 
    11066 
    11067 > size sel atomRadius 3
    11068 
    11069 Changed 6 atom radii 
    11070 
    11071 > select #10/A,B,C:Ca*
    11072 
    11073 6 atoms, 6 residues, 1 model selected 
    11074 
    11075 > size sel atomRadius 1
    11076 
    11077 Changed 6 atom radii 
    11078 
    11079 > size sel atomRadius 10
    11080 
    11081 Changed 6 atom radii 
    11082 
    11083 > size sel ballScale 10
    11084 
    11085 Changed 1 ball scales 
    11086 
    11087 > style sel sphere
    11088 
    11089 Changed 6 atom styles 
    11090 
    11091 > size sel ballScale 1
    11092 
    11093 Changed 1 ball scales 
    11094 
    11095 > select #10/A,B,C:Ca*
    11096 
    11097 6 atoms, 6 residues, 1 model selected 
    11098 
    11099 > size sel ballScale 0.2
    11100 
    11101 Changed 1 ball scales 
    11102 
    11103 > size sel atomRadius 1
    11104 
    11105 Changed 6 atom radii 
    11106 
    11107 > select add #10
    11108 
    11109 15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    11110 
    11111 > select subtract #10
    11112 
    11113 5 models selected 
    11114 
    11115 > select #10/A,B,C:ATP*
    11116 
    11117 Nothing selected 
    11118 
    11119 > select #10/A,B,C:ANP*
    11120 
    11121 93 atoms, 99 bonds, 3 residues, 1 model selected 
    11122 
    11123 > size stickRadius 0.4
    11124 
    11125 Changed 86646 bond radii 
    11126 
    11127 > select add #10
    11128 
    11129 15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    11130 
    11131 > select subtract #10
    11132 
    11133 5 models selected 
    11134 
    11135 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    11136 > RAD54/RAD54SUPC.tif" width 841 height 709 supersample 3
    11137 
    11138 > ui tool show "Show Sequence Viewer"
    11139 
    11140 > sequence chain #11/O
    11141 
    11142 Alignment identifier is 11/O 
    11143 
    11144 > show #!9 models
    11145 
    11146 > ui mousemode right translate
    11147 
    11148 > hide #!9 models
    11149 
    11150 > select #11/O:3
    11151 
    11152 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11153 
    11154 > select #11/O:3
    11155 
    11156 9 atoms, 8 bonds, 1 residue, 1 model selected 
    11157 
    11158 > select up
    11159 
    11160 2 atoms, 1 bond, 1 residue, 1 model selected 
    11161 
    11162 > select up
    11163 
    11164 7 atoms, 7 bonds, 1 residue, 1 model selected 
    11165 
    11166 > select add #10
    11167 
    11168 15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    11169 
    11170 > select subtract #10
    11171 
    11172 5 models selected 
    11173 
    11174 > show #!9 models
    11175 
    11176 > select #9
    11177 
    11178 2 models selected 
    11179 
    11180 > select subtract #9
    11181 
    11182 Nothing selected 
    11183 
    11184 > hide #!9 models
    11185 
    11186 > select #10/O:10
    11187 
    11188 11 atoms, 10 bonds, 1 residue, 1 model selected 
    11189 
    11190 > select #10/O:9
    11191 
    11192 4 atoms, 3 bonds, 1 residue, 1 model selected 
    11193 
    11194 > ui tool show "Show Sequence Viewer"
    11195 
    11196 > sequence chain #10/O
    11197 
    11198 Alignment identifier is 10/O 
    11199 
    11200 > select add #10
    11201 
    11202 15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    11203 
    11204 > select subtract #10
    11205 
    11206 5 models selected 
    11207 
    11208 > show #!9 models
    11209 
    11210 > hide #!9 models
    11211 
    11212 > swapaa #10/O:10 arg density #9
    11213 
    11214 Using Dunbrack library 
    11215 RAD54-J402_m4_real_space_refined_000.pdb #10/O ARG 10: phi -128.2, psi none
    11216 trans 
    11217 Applying ARG rotamer (chi angles: -83.1 81.9 69.8 -178.0) to
    11218 RAD54-J402_m4_real_space_refined_000.pdb #10/O ARG 10 
    11219 
    11220 > show #!9 models
    11221 
    11222 > swapaa #10/O:10 arg density #9
    11223 
    11224 Using Dunbrack library 
    11225 RAD54-J402_m4_real_space_refined_000.pdb #10/O ARG 10: phi -128.2, psi none
    11226 trans 
    11227 Applying ARG rotamer (chi angles: -83.1 81.9 69.8 -178.0) to
    11228 RAD54-J402_m4_real_space_refined_000.pdb #10/O ARG 10 
    11229 
    11230 > swapaa #10/O:10 val density #9
    11231 
    11232 Using Dunbrack library 
    11233 RAD54-J402_m4_real_space_refined_000.pdb #10/O ARG 10: phi -128.2, psi none
    11234 trans 
    11235 Applying VAL rotamer (chi angles: 65.5) to
    11236 RAD54-J402_m4_real_space_refined_000.pdb #10/O VAL 10 
    11237 
    11238 > swapaa #10/O:10 val density #9
    11239 
    11240 Using Dunbrack library 
    11241 RAD54-J402_m4_real_space_refined_000.pdb #10/O VAL 10: phi -128.2, psi none
    11242 trans 
    11243 Applying VAL rotamer (chi angles: 65.5) to
    11244 RAD54-J402_m4_real_space_refined_000.pdb #10/O VAL 10 
    11245 
    11246 > swapaa #10/O:10 arg density #9
    11247 
    11248 Using Dunbrack library 
    11249 RAD54-J402_m4_real_space_refined_000.pdb #10/O VAL 10: phi -128.2, psi none
    11250 trans 
    11251 Applying ARG rotamer (chi angles: -78.6 73.8 -179.4 85.1) to
    11252 RAD54-J402_m4_real_space_refined_000.pdb #10/O ARG 10 
    11253 
    11254 > select #10/O:10
    11255 
    11256 11 atoms, 10 bonds, 1 residue, 1 model selected 
    11257 
    11258 > hide sel atoms
    11259 
    11260 > select add #10
    11261 
    11262 15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    11263 
    11264 > select subtract #10
    11265 
    11266 5 models selected 
    11267 
    11268 > ui mousemode right zoom
    11269 
    11270 > select #10/A,B,C,D,E,F,G:Ca*
    11271 
    11272 10 atoms, 10 residues, 1 model selected 
    11273 
    11274 > color sel black
    11275 
    11276 > select #10/A,B,C,D,E,F,G:ANP*
    11277 
    11278 155 atoms, 165 bonds, 5 residues, 1 model selected 
    11279 
    11280 > color sel black
    11281 
    11282 > select #10/A,C,E,F
    11283 
    11284 9851 atoms, 10003 bonds, 4 pseudobonds, 1265 residues, 2 models selected 
    11285 
    11286 > color sel wheat
    11287 
    11288 > select #10/B,D,F
    11289 
    11290 7380 atoms, 7494 bonds, 3 pseudobonds, 948 residues, 2 models selected 
    11291 
    11292 > color sel royal blue
    11293 
    11294 > select #10/A,C,E,G
    11295 
    11296 7413 atoms, 7527 bonds, 3 pseudobonds, 951 residues, 2 models selected 
    11297 
    11298 > color sel wheat
    11299 
    11300 > volume #9 color #feefdd80
    11301 
    11302 > volume #9 color #fef3d780
    11303 
    11304 > select add #10
    11305 
    11306 15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 4 models selected 
    11307 
    11308 > select subtract #10
    11309 
    11310 5 models selected 
    11311 
    11312 > select add #9
    11313 
    11314 2 models selected 
    11315 
    11316 > color sel misty rose
    11317 
    11318 > select subtract #9
    11319 
    11320 Nothing selected 
    11321 
    11322 > select add #9
    11323 
    11324 2 models selected 
    11325 
    11326 > select subtract #9
    11327 
    11328 Nothing selected 
    11329 
    11330 > hide #!10 models
    11331 
    11332 > show #!10 models
    11333 
    11334 > hide #!10 models
    11335 
    11336 > show #!10 models
    11337 
    11338 > select add #10
    11339 
    11340 15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    11341 
    11342 > hide sel surfaces
    11343 
    11344 > select subtract #10
    11345 
    11346 5 models selected 
    11347 
    11348 > select add #9
    11349 
    11350 2 models selected 
    11351 
    11352 > color zone #9 near #10 distance 4.38
    11353 
    11354 > select subtract #9
    11355 
    11356 Nothing selected 
    11357 
    11358 > hide #!10 models
    11359 
    11360 > show #!10 models
    11361 
    11362 > hide #!9 models
    11363 
    11364 > select #10/M,N,O,P,Q,R,S:1O
    11365 
    11366 Nothing selected 
    11367 
    11368 > select #10/M,N,O,P,Q,R,S:10
    11369 
    11370 55 atoms, 50 bonds, 5 residues, 1 model selected 
    11371 
    11372 > hide sel atoms
    11373 
    11374 > select add #10
    11375 
    11376 15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    11377 
    11378 > select subtract #10
    11379 
    11380 5 models selected 
    11381 
    11382 > show #!9 models
    11383 
    11384 > hide #!10 models
    11385 
    11386 > ui mousemode right translate
    11387 
    11388 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    11389 > RAD54/RAD54BfigA.tif" width 841 height 709 supersample 3
    11390 
    11391 > show #!10 models
    11392 
    11393 > transparency #9.1#10.2-6 0
    11394 
    11395 > transparency #9.1#10.2-6 50
    11396 
    11397 > ui mousemode right zoom
    11398 
    11399 > ui mousemode right translate
    11400 
    11401 > ui mousemode right zoom
    11402 
    11403 > ui mousemode right translate
    11404 
    11405 > select #10/D:85,89
    11406 
    11407 22 atoms, 22 bonds, 2 residues, 1 model selected 
    11408 
    11409 > show sel atoms
    11410 
    11411 > color sel orange
    11412 
    11413 > color zone #9 near sel & #10 distance 4.38
    11414 
    11415 > select add #10
    11416 
    11417 15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 3 models selected 
    11418 
    11419 > select subtract #10
    11420 
    11421 5 models selected 
    11422 
    11423 > color zone #9 near #10 distance 4.38
    11424 
    11425 > transparency #9.1#10.2-6 0
    11426 
    11427 > transparency #9.1#10.2-6 50
    11428 
    11429 > select #10/C:85,89
    11430 
    11431 22 atoms, 22 bonds, 2 residues, 1 model selected 
    11432 
    11433 > show sel atoms
    11434 
    11435 > select #10/D:85,89
    11436 
    11437 22 atoms, 22 bonds, 2 residues, 1 model selected 
    11438 
    11439 > select #10/E:85,89
    11440 
    11441 22 atoms, 22 bonds, 2 residues, 1 model selected 
    11442 
    11443 > show sel atoms
    11444 
    11445 > color sel orange
    11446 
    11447 > select add #10
    11448 
    11449 15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 3 models selected 
    11450 
    11451 > select subtract #10
    11452 
    11453 5 models selected 
    11454 
    11455 > color zone #9 near #10 distance 4.38
    11456 
    11457 > transparency #9.1#10.2-6 0
    11458 
    11459 > transparency #9.1#10.2-6 50
    11460 
    11461 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    11462 > RAD54/RAD54BfigB.tif" width 841 height 709 supersample 3
    11463 
    11464 > hide #!9 models
    11465 
    11466 > show #!9 models
    11467 
    11468 > ui mousemode right zoom
    11469 
    11470 > ui mousemode right translate
    11471 
    11472 > hide #!9 models
    11473 
    11474 > select #10/E
    11475 
    11476 2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 2 models selected 
    11477 
    11478 > color sel wheat
    11479 
    11480 > hide sel atoms
    11481 
    11482 > select add #10
    11483 
    11484 15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 3 models selected 
    11485 
    11486 > select subtract #10
    11487 
    11488 5 models selected 
    11489 
    11490 > show #!9 models
    11491 
    11492 > color zone #9 near #10 distance 4.38
    11493 
    11494 > transparency #9.1#10.2-6 0
    11495 
    11496 > transparency #9.1#10.2-6 50
    11497 
    11498 > cartoon style coil width 2 thickness 1
    11499 
    11500 > cartoon style coil width 2 thickness 0.5
    11501 
    11502 > hide #!9 models
    11503 
    11504 > select #10/Q
    11505 
    11506 64 atoms, 67 bonds, 8 residues, 1 model selected 
    11507 
    11508 > color sel wheat
    11509 
    11510 > select add #10
    11511 
    11512 15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    11513 
    11514 > select subtract #10
    11515 
    11516 5 models selected 
    11517 
    11518 > show #!9 models
    11519 
    11520 > color zone #9 near #10 distance 4.38
    11521 
    11522 > transparency #9.1#10.2-6 0
    11523 
    11524 > transparency #9.1#10.2-6 50
    11525 
    11526 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    11527 > RAD54/RAD54BfigD.tif" width 841 height 709 supersample 3
    11528 
    11529 > volume #9 level 0.02294
    11530 
    11531 > color zone #9 near #10 distance 4.38
    11532 
    11533 > transparency #9.1#10.2-6 0
    11534 
    11535 > transparency #9.1#10.2-6 50
    11536 
    11537 > hide #!9 models
    11538 
    11539 > select clear
    11540 
    11541 > select #10/P:9
    11542 
    11543 4 atoms, 3 bonds, 1 residue, 1 model selected 
    11544 
    11545 > select #10/P:8@CA
    11546 
    11547 1 atom, 1 residue, 1 model selected 
    11548 
    11549 > select #10/P:9
    11550 
    11551 4 atoms, 3 bonds, 1 residue, 1 model selected 
    11552 
    11553 > select #10/P:10
    11554 
    11555 11 atoms, 10 bonds, 1 residue, 1 model selected 
    11556 
    11557 > show #!9 models
    11558 
    11559 > select add #10
    11560 
    11561 15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    11562 
    11563 > select subtract #10
    11564 
    11565 5 models selected 
    11566 
    11567 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier FGLN1
    11568 > RAD54/RAD54B.cxs"
    11569 
    11570 ——— End of log from Thu Jul 10 10:47:21 2025 ———
    11571 
    11572 opened ChimeraX session 
    11573 
    11574 > close #2-3,5-11
    11575 
    11576 > open "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
    11577 > structure BRCA2 07072025/BRCA2_m4_real_space_refined_000.pdb"
    11578 > "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
    11579 > structure BRCA2 07072025/cryosparc_P26_J362_012_volume_map_sharp.mrc"
    11580 > "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
    11581 > structure BRCA2 07072025/cryosparc_P26_J362_012_volume_map.mrc"
    11582 
    11583 Chain information for BRCA2_m4_real_space_refined_000.pdb #1 
    11584 --- 
    11585 Chain | Description 
    11586 A B C D E F | No description available 
    11587 M N O P Q R | No description available 
    11588 X | No description available 
    11589  
    11590 Opened cryosparc_P26_J362_012_volume_map_sharp.mrc as #2, grid size
    11591 336,336,336, pixel 0.73, shown at level 0.0403, step 2, values float32 
    11592 Opened cryosparc_P26_J362_012_volume_map.mrc as #3, grid size 336,336,336,
    11593 pixel 0.73, shown at level 0.0236, step 2, values float32 
    11594 
    11595 > select add #2
    11596 
    11597 2 models selected 
    11598 
    11599 Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
    11600 models, 2 maps. 
    11601 
    11602 > surface dust #2 size 7.3
    11603 
    11604 > select add #3
    11605 
    11606 4 models selected 
    11607 
    11608 > select subtract #2
    11609 
    11610 2 models selected 
    11611 
    11612 > surface dust #3 size 7.3
    11613 
    11614 > hide #!2 models
    11615 
    11616 > hide #!3 models
    11617 
    11618 > select subtract #3
    11619 
    11620 Nothing selected 
    11621 
    11622 > select add #1
    11623 
    11624 15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected 
    11625 
    11626 > hide sel cartoons
    11627 
    11628 > hide sel atoms
    11629 
    11630 > show sel cartoons
    11631 
    11632 > select #1/A,C,E
    11633 
    11634 7413 atoms, 7528 bonds, 3 pseudobonds, 951 residues, 2 models selected 
    11635 
    11636 > color sel royal blue
    11637 
    11638 > select #1/B,D,F
    11639 
    11640 7380 atoms, 7494 bonds, 3 pseudobonds, 948 residues, 2 models selected 
    11641 
    11642 > color sel wheat
    11643 
    11644 > select #1/X
    11645 
    11646 360 atoms, 395 bonds, 18 residues, 1 model selected 
    11647 
    11648 > show sel atoms
    11649 
    11650 > hide sel cartoons
    11651 
    11652 > style sel stick
    11653 
    11654 Changed 360 atom styles 
    11655 
    11656 > color sel dark green
    11657 
    11658 > select add #1
    11659 
    11660 15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected 
    11661 
    11662 > select subtract #1
    11663 
    11664 Nothing selected 
    11665 
    11666 > color sel #1/M,N,O,P,Q,R,S
    11667 
    11668 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    11669 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    11670 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    11671 
    11672 > color sel #1/M,N,O,P,Q,R
    11673 
    11674 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    11675 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    11676 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    11677 
    11678 > color #1/M,N,O,P,Q,R red
    11679 
    11680 > show atoms
    11681 
    11682 > hide atoms
    11683 
    11684 > select #1/M,N,O,P,Q,R
    11685 
    11686 408 atoms, 426 bonds, 48 residues, 1 model selected 
    11687 
    11688 > show sel atoms
    11689 
    11690 > select #1/M,N,O,P,Q,R:3,10
    11691 
    11692 108 atoms, 96 bonds, 12 residues, 1 model selected 
    11693 
    11694 > hide sel atoms
    11695 
    11696 > select #1/A,C,E:ANP*
    11697 
    11698 93 atoms, 99 bonds, 3 residues, 1 model selected 
    11699 
    11700 > select #1/A,C,E:ANP*,Ca*
    11701 
    11702 99 atoms, 99 bonds, 9 residues, 1 model selected 
    11703 
    11704 > color sel black
    11705 
    11706 > color sel dark grey
    11707 
    11708 > show sel atoms
    11709 
    11710 > select #1/B,D,F:ANP*,Ca*
    11711 
    11712 66 atoms, 66 bonds, 6 residues, 1 model selected 
    11713 
    11714 > color sel dark grey
    11715 
    11716 > show sel atoms
    11717 
    11718 > select add #1
    11719 
    11720 15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected 
    11721 
    11722 > select subtract #1
    11723 
    11724 Nothing selected 
    11725 
    11726 > SEL #1/X
    11727 
    11728 Unknown command: SEL #1/X 
    11729 
    11730 > select #1/X
    11731 
    11732 360 atoms, 395 bonds, 18 residues, 1 model selected 
    11733 
    11734 > show sel atoms
    11735 
    11736 > select add #1
    11737 
    11738 15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected 
    11739 
    11740 > select subtract #1
    11741 
    11742 Nothing selected 
    11743 
    11744 > show #!2 models
    11745 
    11746 > hide #!2 models
    11747 
    11748 > show #!2 models
    11749 
    11750 > hide #!1 models
    11751 
    11752 > volume #2 level 0.05157
    11753 
    11754 > show #!1 models
    11755 
    11756 > color zone #2 near #1 distance 4.38
    11757 
    11758 > transparency #2.1 50
    11759 
    11760 > hide #!2 models
    11761 
    11762 > show #!2 models
    11763 
    11764 > hide #!2 models
    11765 
    11766 > show #!2 models
    11767 
    11768 > select add #1
    11769 
    11770 15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected 
    11771 
    11772 > color zone #2 near sel & #1 distance 4.38
    11773 
    11774 [Repeated 1 time(s)]
    11775 
    11776 > select subtract #1
    11777 
    11778 Nothing selected 
    11779 
    11780 > volume #2 level 0.04484
    11781 
    11782 > select #1/B,D,F
    11783 
    11784 7380 atoms, 7494 bonds, 3 pseudobonds, 948 residues, 2 models selected 
    11785 
    11786 > hide sel atoms
    11787 
    11788 [Repeated 2 time(s)]
    11789 
    11790 > select #1/B,D,F:ANP*,Ca*
    11791 
    11792 66 atoms, 66 bonds, 6 residues, 1 model selected 
    11793 
    11794 > show sel atoms
    11795 
    11796 > color zone #2 near sel & #1 distance 4.38
    11797 
    11798 [Repeated 1 time(s)]
    11799 
    11800 > select add #1
    11801 
    11802 15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected 
    11803 
    11804 > select subtract #1
    11805 
    11806 Nothing selected 
    11807 
    11808 > select add #1
    11809 
    11810 15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected 
    11811 
    11812 > color zone #2 near sel & #1 distance 4.38
    11813 
    11814 > select subtract #1
    11815 
    11816 Nothing selected 
    11817 
    11818 > color #2 #b7bfb9ff models
    11819 
    11820 > volume #2 level 0.0583
    11821 
    11822 > ui tool show "Color Zone"
    11823 
    11824 > color zone #2 near #1 distance 4
    11825 
    11826 > hide #!2 models
    11827 
    11828 > show #!2 models
    11829 
    11830 > hide #!2 models
    11831 
    11832 > show #!2 models
    11833 
    11834 > hide #!2 models
    11835 
    11836 > show #!2 models
    11837 
    11838 > hide #!2 models
    11839 
    11840 > select #1/A,B,C,D,E,F
    11841 
    11842 14793 atoms, 15022 bonds, 6 pseudobonds, 1899 residues, 2 models selected 
    11843 
    11844 > show sel atoms
    11845 
    11846 > style sel stick
    11847 
    11848 Changed 14793 atom styles 
    11849 
    11850 > hide sel atoms
    11851 
    11852 > color zone #2 near #1 distance 4
    11853 
    11854 > select add #1
    11855 
    11856 15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected 
    11857 
    11858 > select subtract #1
    11859 
    11860 Nothing selected 
    11861 
    11862 > show #!2 models
    11863 
    11864 > color zone #2 near #1 distance 4
    11865 
    11866 [Repeated 1 time(s)]
    11867 
    11868 > transparency #2.1 50
    11869 
    11870 > select #1/B,D,F
    11871 
    11872 7380 atoms, 7494 bonds, 3 pseudobonds, 948 residues, 2 models selected 
    11873 
    11874 > show sel atoms
    11875 
    11876 > select #1/A,C,E
    11877 
    11878 7413 atoms, 7528 bonds, 3 pseudobonds, 951 residues, 2 models selected 
    11879 
    11880 > show sel atoms
    11881 
    11882 > surface dust #2 size 7.3
    11883 
    11884 [Repeated 3 time(s)]
    11885 
    11886 > select add #1
    11887 
    11888 15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected 
    11889 
    11890 > select subtract #1
    11891 
    11892 Nothing selected 
    11893 
    11894 > hide #!2 models
    11895 
    11896 > show #!2 models
    11897 
    11898 > hide #!1 models
    11899 
    11900 > surface dust #2 size 7.3
    11901 
    11902 [Repeated 1 time(s)]
    11903 
    11904 > volume #2 level 0.06579
    11905 
    11906 > show #!1 models
    11907 
    11908 > transparency #2.1 50
    11909 
    11910 > volume #2 level 0.04183
    11911 
    11912 > color zone #2 near #1 distance 4
    11913 
    11914 > color single #2
    11915 
    11916 > color #2 light grey
    11917 
    11918 > color zone #2 near #1 distance 4
    11919 
    11920 > color single #2
    11921 
    11922 [Repeated 1 time(s)]
    11923 
    11924 > hide #!2 models
    11925 
    11926 > show #!2 models
    11927 
    11928 > hide #!2 models
    11929 
    11930 > show #!2 models
    11931 
    11932 > hide #!2 models
    11933 
    11934 > show #!3 models
    11935 
    11936 > color zone #3 near #1 distance 4.38
    11937 
    11938 > transparency #3.1 50
    11939 
    11940 > color #3 #b8bfb3ff models
    11941 
    11942 > color zone #3 near #1 distance 4.38
    11943 
    11944 > color single #3
    11945 
    11946 > color zone #3 near #1 distance 3.99
    11947 
    11948 [Repeated 1 time(s)]
    11949 
    11950 > color single #3
    11951 
    11952 > color zone #3 near #1 distance 3.99
    11953 
    11954 [Repeated 1 time(s)]
    11955 
    11956 > color single #3
    11957 
    11958 > color #3 light grey
    11959 
    11960 > color zone #3 near #1 distance 4.38
    11961 
    11962 [Repeated 1 time(s)]
    11963 
    11964 > color single #3
    11965 
    11966 > color zone #3 near #1 distance 3.99
    11967 
    11968 > color zone #2 near #1 distance 4
    11969 
    11970 > color single #3
    11971 
    11972 > color zone #2 near #1 distance 4
    11973 
    11974 > hide #!3 models
    11975 
    11976 > show #!2 models
    11977 
    11978 > color single #3
    11979 
    11980 > color single #2
    11981 
    11982 > color zone #2 near #1 distance 4
    11983 
    11984 > hide #!2 models
    11985 
    11986 > select #1
    11987 
    11988 15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected 
    11989 
    11990 > select #1/C
    11991 
    11992 2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 2 models selected 
    11993 
    11994 > select #1/C
    11995 
    11996 2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 2 models selected 
    11997 
    11998 > color sel royal blue
    11999 
    12000 > color zone #2 near sel distance 4
    12001 
    12002 > show #!2 models
    12003 
    12004 > select add #1
    12005 
    12006 15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected 
    12007 
    12008 > select subtract #1
    12009 
    12010 Nothing selected 
    12011 
    12012 > select #1/O
    12013 
    12014 68 atoms, 71 bonds, 8 residues, 1 model selected 
    12015 
    12016 > color zone #2 near sel distance 4
    12017 
    12018 > select #1/O,C
    12019 
    12020 2539 atoms, 2580 bonds, 1 pseudobond, 325 residues, 2 models selected 
    12021 
    12022 > color zone #2 near sel distance 4
    12023 
    12024 > select add #1
    12025 
    12026 15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected 
    12027 
    12028 > select subtract #1
    12029 
    12030 Nothing selected 
    12031 
    12032 > select #1/O
    12033 
    12034 68 atoms, 71 bonds, 8 residues, 1 model selected 
    12035 
    12036 > transparency #2.1 0
    12037 
    12038 > transparency #2.1 50
    12039 
    12040 > select #1/C
    12041 
    12042 2471 atoms, 2509 bonds, 1 pseudobond, 317 residues, 2 models selected 
    12043 
    12044 > transparency #2.1 0
    12045 
    12046 > select #1/O
    12047 
    12048 68 atoms, 71 bonds, 8 residues, 1 model selected 
    12049 
    12050 > transparency #2.1 50
    12051 
    12052 > select add #1
    12053 
    12054 15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected 
    12055 
    12056 > select subtract #1
    12057 
    12058 Nothing selected 
    12059 
    12060 > select #1/C:ANP*
    12061 
    12062 31 atoms, 33 bonds, 1 residue, 1 model selected 
    12063 
    12064 > color sel magenta
    12065 
    12066 > select #1/C:Ca*
    12067 
    12068 2 atoms, 2 residues, 1 model selected 
    12069 
    12070 > color sel magenta
    12071 
    12072 > select add #1
    12073 
    12074 15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected 
    12075 
    12076 > select subtract #1
    12077 
    12078 Nothing selected 
    12079 
    12080 > select #1/C:Ca*
    12081 
    12082 2 atoms, 2 residues, 1 model selected 
    12083 
    12084 > select #1/A,B,C,D,E,F:Ca*,ANP*
    12085 
    12086 165 atoms, 165 bonds, 15 residues, 1 model selected 
    12087 
    12088 > color sel magenta
    12089 
    12090 > color zone #2 near sel distance 4
    12091 
    12092 > select #1/A,B,C,D,E,F
    12093 
    12094 14793 atoms, 15022 bonds, 6 pseudobonds, 1899 residues, 2 models selected 
    12095 
    12096 > color zone #2 near sel distance 4
    12097 
    12098 > transparency #2.1 0
    12099 
    12100 > transparency #2.1 50
    12101 
    12102 > select add #1
    12103 
    12104 15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected 
    12105 
    12106 > select subtract #1
    12107 
    12108 Nothing selected 
    12109 
    12110 > select #1/A,B,C,D,E,F
    12111 
    12112 14793 atoms, 15022 bonds, 6 pseudobonds, 1899 residues, 2 models selected 
    12113 
    12114 > select #1/A,B,C,D,E,F:85,89
    12115 
    12116 132 atoms, 132 bonds, 12 residues, 1 model selected 
    12117 
    12118 > color sel orange
    12119 
    12120 > select add #1
    12121 
    12122 15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected 
    12123 
    12124 > select subtract #1
    12125 
    12126 Nothing selected 
    12127 
    12128 > open 8qqe
    12129 
    12130 8qqe title: 
    12131 Crystal structure of the complex between DMC1 and the PhePP domain of BRCA2
    12132 [more info...] 
    12133  
    12134 Chain information for 8qqe #4 
    12135 --- 
    12136 Chain | Description | UniProt 
    12137 A B | Meiotic recombination protein DMC1/LIM15 homolog | DMC1_HUMAN 2-340 
    12138 C D | Breast cancer type 2 susceptibility protein | BRCA2_HUMAN 1398-1417 2398-2417 
    12139  
    12140 Non-standard residues in 8qqe #4 
    12141 --- 
    12142 CL — chloride ion 
    12143 MG — magnesium ion 
    12144  
    12145 8qqe mmCIF Assemblies 
    12146 --- 
    12147 1| author_defined_assembly 
    12148  
    12149 39 atoms have alternate locations. Control/examine alternate locations with
    12150 Altloc Explorer [start tool...] or the altlocs command. 
    12151 
    12152 > mmaker #4/B to #1/D
    12153 
    12154 Computing secondary structure 
    12155 [Repeated 1 time(s)]  Parameters 
    12156 --- 
    12157 Chain pairing | bb 
    12158 Alignment algorithm | Needleman-Wunsch 
    12159 Similarity matrix | BLOSUM-62 
    12160 SS fraction | 0.3 
    12161 Gap open (HH/SS/other) | 18/18/6 
    12162 Gap extend | 1 
    12163 SS matrix |  |  | H | S | O 
    12164 ---|---|---|--- 
    12165 H | 6 | -9 | -6 
    12166 S |  | 6 | -6 
    12167 O |  |  | 4 
    12168 Iteration cutoff | 2 
    12169  
    12170 Matchmaker BRCA2_m4_real_space_refined_000.pdb, chain D (#1) with 8qqe, chain
    12171 B (#4), sequence alignment score = 1439.4 
    12172 RMSD between 221 pruned atom pairs is 0.588 angstroms; (across all 247 pairs:
    12173 2.519) 
    12174  
    12175 
    12176 > hide #!2 models
    12177 
    12178 > select #1/A,B,C,D,E,F
    12179 
    12180 14793 atoms, 15022 bonds, 6 pseudobonds, 1899 residues, 2 models selected 
    12181 
    12182 > hide sel atoms
    12183 
    12184 > select #1/A,B,C,D,E,F:ANP*,Ca*
    12185 
    12186 165 atoms, 165 bonds, 15 residues, 1 model selected 
    12187 
    12188 > show sel atoms
    12189 
    12190 > select add #1
    12191 
    12192 15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected 
    12193 
    12194 > select subtract #1
    12195 
    12196 Nothing selected 
    12197 
    12198 > open "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
    12199 > structure RAD54B 07072025/RAD54-J402_m4_real_space_refined_000.pdb"
    12200 
    12201 Chain information for RAD54-J402_m4_real_space_refined_000.pdb #5 
    12202 --- 
    12203 Chain | Description 
    12204 A B C D E F | No description available 
    12205 M | No description available 
    12206 N O P Q | No description available 
    12207 R | No description available 
    12208 X | No description available 
    12209  
    12210 
    12211 > mmaker #5 to #1
    12212 
    12213 Computing secondary structure 
    12214 [Repeated 1 time(s)]  Parameters 
    12215 --- 
    12216 Chain pairing | bb 
    12217 Alignment algorithm | Needleman-Wunsch 
    12218 Similarity matrix | BLOSUM-62 
    12219 SS fraction | 0.3 
    12220 Gap open (HH/SS/other) | 18/18/6 
    12221 Gap extend | 1 
    12222 SS matrix |  |  | H | S | O 
    12223 ---|---|---|--- 
    12224 H | 6 | -9 | -6 
    12225 S |  | 6 | -6 
    12226 O |  |  | 4 
    12227 Iteration cutoff | 2 
    12228  
    12229 Matchmaker BRCA2_m4_real_space_refined_000.pdb, chain D (#1) with
    12230 RAD54-J402_m4_real_space_refined_000.pdb, chain B (#5), sequence alignment
    12231 score = 1612.8 
    12232 RMSD between 314 pruned atom pairs is 0.198 angstroms; (across all 314 pairs:
    12233 0.198) 
    12234  
    12235 
    12236 > hide #!4 models
    12237 
    12238 > hide #!1 models
    12239 
    12240 > hide #!5 atoms
    12241 
    12242 > select add #5
    12243 
    12244 15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    12245 
    12246 > show sel atoms
    12247 
    12248 > hide sel atoms
    12249 
    12250 > show sel cartoons
    12251 
    12252 > select subtract #5
    12253 
    12254 Nothing selected 
    12255 
    12256 > show #!1 models
    12257 
    12258 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
    12259 > structure BRCA2 07072025/ForAlexPhePP.cxs"
    12260 
    12261 > hide #!5 models
    12262 
    12263 > show #!4 models
    12264 
    12265 > select #1/A,B,C
    12266 
    12267 7413 atoms, 7528 bonds, 3 pseudobonds, 951 residues, 2 models selected 
    12268 
    12269 > hide sel cartoons
    12270 
    12271 > select #1/M,N,O
    12272 
    12273 204 atoms, 213 bonds, 24 residues, 1 model selected 
    12274 
    12275 > hide sel cartoons
    12276 
    12277 > select #1/A,B,C
    12278 
    12279 7413 atoms, 7528 bonds, 3 pseudobonds, 951 residues, 2 models selected 
    12280 
    12281 > hide sel atoms
    12282 
    12283 [Repeated 1 time(s)]
    12284 
    12285 > select #1/M,N,O
    12286 
    12287 204 atoms, 213 bonds, 24 residues, 1 model selected 
    12288 
    12289 > hide sel atoms
    12290 
    12291 > select #1/X
    12292 
    12293 360 atoms, 395 bonds, 18 residues, 1 model selected 
    12294 
    12295 > hide sel atoms
    12296 
    12297 > select #1/F,R
    12298 
    12299 2506 atoms, 2547 bonds, 1 pseudobond, 322 residues, 2 models selected 
    12300 
    12301 > hide sel cartoons
    12302 
    12303 > hide sel atoms
    12304 
    12305 > select #4
    12306 
    12307 4377 atoms, 4448 bonds, 5 pseudobonds, 564 residues, 4 models selected 
    12308 
    12309 > ~label (#!4 & sel) residues
    12310 
    12311 > ~label (#!4 & sel) atoms
    12312 
    12313 > select #4
    12314 
    12315 4377 atoms, 4448 bonds, 5 pseudobonds, 564 residues, 4 models selected 
    12316 
    12317 > label offset
    12318 
    12319 Missing "offset" keyword's argument 
    12320 
    12321 > label
    12322 
    12323 > label #4
    12324 
    12325 > label #4 offset
    12326 
    12327 Missing "offset" keyword's argument 
    12328 
    12329 > ~label (#!4 & sel) residues
    12330 
    12331 > label chain
    12332 
    12333 Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
    12334 keyword 
    12335 
    12336 > label models
    12337 
    12338 > label models offset
    12339 
    12340 Missing "offset" keyword's argument 
    12341 
    12342 > label models
    12343 
    12344 > cartoon hide (#!4 & sel)
    12345 
    12346 > cartoon (#!4 & sel)
    12347 
    12348 > select subtract #4
    12349 
    12350 Nothing selected 
    12351 
    12352 > select add #4
    12353 
    12354 4377 atoms, 4448 bonds, 5 pseudobonds, 564 residues, 4 models selected 
    12355 
    12356 > select subtract #4
    12357 
    12358 Nothing selected 
    12359 
    12360 > select #1/E:89
    12361 
    12362 11 atoms, 11 bonds, 1 residue, 1 model selected 
    12363 
    12364 > show sel atoms
    12365 
    12366 > select #1/E:85
    12367 
    12368 11 atoms, 11 bonds, 1 residue, 1 model selected 
    12369 
    12370 > show sel atoms
    12371 
    12372 > select add #1
    12373 
    12374 15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected 
    12375 
    12376 > select subtract #1
    12377 
    12378 Nothing selected 
    12379 
    12380 > select clear
    12381 
    12382 [Repeated 1 time(s)]
    12383 
    12384 > select #4/C:2403
    12385 
    12386 7 atoms, 6 bonds, 1 residue, 1 model selected 
    12387 
    12388 > select add #4
    12389 
    12390 4377 atoms, 4448 bonds, 5 pseudobonds, 564 residues, 4 models selected 
    12391 
    12392 > select subtract #4
    12393 
    12394 Nothing selected 
    12395 
    12396 > select #4/C,D
    12397 
    12398 141 atoms, 146 bonds, 18 residues, 1 model selected 
    12399 
    12400 > color sel purple
    12401 
    12402 > select add #4
    12403 
    12404 4377 atoms, 4448 bonds, 5 pseudobonds, 564 residues, 4 models selected 
    12405 
    12406 > select subtract #4
    12407 
    12408 Nothing selected 
    12409 
    12410 > select #4/A:100-390
    12411 
    12412 1756 atoms, 1785 bonds, 1 pseudobond, 226 residues, 2 models selected 
    12413 
    12414 > show sel surfaces
    12415 
    12416 > hide sel surfaces
    12417 
    12418 > select #4/B:100-390
    12419 
    12420 1768 atoms, 1798 bonds, 1 pseudobond, 228 residues, 2 models selected 
    12421 
    12422 > show sel surfaces
    12423 
    12424 > select add #4
    12425 
    12426 4377 atoms, 4448 bonds, 5 pseudobonds, 564 residues, 5 models selected 
    12427 
    12428 > select subtract #4
    12429 
    12430 2 models selected 
    12431 
    12432 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
    12433 > structure BRCA2 07072025/Brca2 xray vs cryo.cxs"
    12434 
    12435 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
    12436 > structure BRCA2 07072025/BRCA2xrayVScryoEM.tif" width 786 height 694
    12437 > supersample 3
    12438 
    12439 Alignment identifier is 1 
    12440 Alignment identifier is 2 
    12441 Alignment identifier is 3 
    12442 Alignment identifier is 4 
    12443 Alignment identifier is 5 
    12444 Alignment identifier is 5/M 
    12445 Alignment identifier is 6 
    12446 Alignment identifier is 5/R 
    12447 
    12448 > select #4/C,D
    12449 
    12450 141 atoms, 146 bonds, 18 residues, 1 model selected 
    12451 
    12452 > select #4/C,D
    12453 
    12454 141 atoms, 146 bonds, 18 residues, 1 model selected 
    12455 
    12456 > show sel atoms
    12457 
    12458 > select add #4
    12459 
    12460 4377 atoms, 4448 bonds, 5 pseudobonds, 564 residues, 4 models selected 
    12461 
    12462 > select subtract #4
    12463 
    12464 2 models selected 
    12465 
    12466 > show #!3 models
    12467 
    12468 > hide #!3 models
    12469 
    12470 > show #!3 models
    12471 
    12472 > transparency #3.1#4.3-4 50
    12473 
    12474 > hide #!3 models
    12475 
    12476 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
    12477 > structure BRCA2 07072025/Brca2 xray vs cryo.cxs"
    12478 
    12479 > select #4/A:290:299
    12480 
    12481 11 atoms, 9 bonds, 2 residues, 1 model selected 
    12482 
    12483 > select #1/X
    12484 
    12485 360 atoms, 395 bonds, 18 residues, 1 model selected 
    12486 
    12487 > show sel cartoons
    12488 
    12489 > color sel black
    12490 
    12491 > select add #1
    12492 
    12493 15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected 
    12494 
    12495 > select subtract #1
    12496 
    12497 Nothing selected 
    12498 
    12499 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
    12500 > structure BRCA2 07072025/BRCA2xrayVScryoEM2.tif" width 786 height 694
    12501 > supersample 3
    12502 
    12503 > select #4/A:317:327
    12504 
    12505 15 atoms, 13 bonds, 2 residues, 1 model selected 
    12506 
    12507 > select #4/A:317-327
    12508 
    12509 83 atoms, 84 bonds, 11 residues, 1 model selected 
    12510 
    12511 > hide sel surfaces
    12512 
    12513 [Repeated 1 time(s)]
    12514 
    12515 > select add #4
    12516 
    12517 4377 atoms, 4448 bonds, 5 pseudobonds, 564 residues, 5 models selected 
    12518 
    12519 > select subtract #4
    12520 
    12521 2 models selected 
    12522 
    12523 > select add #4
    12524 
    12525 4377 atoms, 4448 bonds, 5 pseudobonds, 564 residues, 4 models selected 
    12526 
    12527 > hide sel surfaces
    12528 
    12529 > select subtract #4
    12530 
    12531 2 models selected 
    12532 
    12533 > select add #4
    12534 
    12535 4377 atoms, 4448 bonds, 5 pseudobonds, 564 residues, 4 models selected 
    12536 
    12537 > select subtract #4
    12538 
    12539 2 models selected 
    12540 
    12541 > select #4/A
    12542 
    12543 2306 atoms, 2338 bonds, 4 pseudobonds, 298 residues, 3 models selected 
    12544 
    12545 > select #4/A
    12546 
    12547 2306 atoms, 2338 bonds, 4 pseudobonds, 298 residues, 3 models selected 
    12548 
    12549 > color sel aquamarine
    12550 
    12551 > select add #4
    12552 
    12553 4377 atoms, 4448 bonds, 5 pseudobonds, 564 residues, 5 models selected 
    12554 
    12555 > select subtract #4
    12556 
    12557 2 models selected 
    12558 
    12559 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
    12560 > structure BRCA2 07072025/Brca2 xray vs cryo.cxs"
    12561 
    12562 > close #5
    12563 
    12564 > close #2-3
    12565 
    12566 > open "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
    12567 > structure RAD54B 07072025/cryosparc_P26_J410_011_volume_map_sharp.mrc"
    12568 > "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
    12569 > structure RAD54B 07072025/cryosparc_P26_J410_011_volume_map.mrc"
    12570 
    12571 Opened cryosparc_P26_J410_011_volume_map_sharp.mrc as #2.1, grid size
    12572 336,336,336, pixel 0.73, shown at level 0.032, step 2, values float32 
    12573 Opened cryosparc_P26_J410_011_volume_map.mrc as #2.2, grid size 336,336,336,
    12574 pixel 0.73, shown at level 0.0225, step 2, values float32 
    12575 
    12576 > surface dust #2.1 size 7.3
    12577 
    12578 > surface dust #2.2 size 7.3
    12579 
    12580 > open "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
    12581 > structure RAD54B 07072025/RAD54-J402_m4_real_space_refined_000.pdb"
    12582 
    12583 Chain information for RAD54-J402_m4_real_space_refined_000.pdb #3 
    12584 --- 
    12585 Chain | Description 
    12586 A B C D E F | No description available 
    12587 M | No description available 
    12588 N O P Q | No description available 
    12589 R | No description available 
    12590 X | No description available 
    12591  
    12592 
    12593 > mmaker #1 to #3
    12594 
    12595 Computing secondary structure 
    12596 [Repeated 1 time(s)]  Parameters 
    12597 --- 
    12598 Chain pairing | bb 
    12599 Alignment algorithm | Needleman-Wunsch 
    12600 Similarity matrix | BLOSUM-62 
    12601 SS fraction | 0.3 
    12602 Gap open (HH/SS/other) | 18/18/6 
    12603 Gap extend | 1 
    12604 SS matrix |  |  | H | S | O 
    12605 ---|---|---|--- 
    12606 H | 6 | -9 | -6 
    12607 S |  | 6 | -6 
    12608 O |  |  | 4 
    12609 Iteration cutoff | 2 
    12610  
    12611 Matchmaker RAD54-J402_m4_real_space_refined_000.pdb, chain B (#3) with
    12612 BRCA2_m4_real_space_refined_000.pdb, chain D (#1), sequence alignment score =
    12613 1612.8 
    12614 RMSD between 314 pruned atom pairs is 0.198 angstroms; (across all 314 pairs:
    12615 0.198) 
    12616  
    12617 
    12618 > select add #1
    12619 
    12620 15848 atoms, 15843 bonds, 6 pseudobonds, 2252 residues, 2 models selected 
    12621 
    12622 > select subtract #1
    12623 
    12624 Nothing selected 
    12625 
    12626 > select add #3
    12627 
    12628 15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    12629 
    12630 > hide sel atoms
    12631 
    12632 > show sel atoms
    12633 
    12634 > hide sel atoms
    12635 
    12636 > show sel cartoons
    12637 
    12638 [Repeated 1 time(s)]
    12639 
    12640 > mmaker #4/B to #3/D
    12641 
    12642 Computing secondary structure 
    12643 [Repeated 1 time(s)]  Parameters 
    12644 --- 
    12645 Chain pairing | bb 
    12646 Alignment algorithm | Needleman-Wunsch 
    12647 Similarity matrix | BLOSUM-62 
    12648 SS fraction | 0.3 
    12649 Gap open (HH/SS/other) | 18/18/6 
    12650 Gap extend | 1 
    12651 SS matrix |  |  | H | S | O 
    12652 ---|---|---|--- 
    12653 H | 6 | -9 | -6 
    12654 S |  | 6 | -6 
    12655 O |  |  | 4 
    12656 Iteration cutoff | 2 
    12657  
    12658 Matchmaker RAD54-J402_m4_real_space_refined_000.pdb, chain D (#3) with 8qqe,
    12659 chain B (#4), sequence alignment score = 1439.4 
    12660 RMSD between 222 pruned atom pairs is 0.604 angstroms; (across all 247 pairs:
    12661 2.534) 
    12662  
    12663 
    12664 > select add #2.1
    12665 
    12666 15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 4 models selected 
    12667 
    12668 > hide #!1 models
    12669 
    12670 > hide #!2 models
    12671 
    12672 > hide #!2.2 models
    12673 
    12674 > hide #!3 models
    12675 
    12676 > hide #!4 models
    12677 
    12678 > select add #2
    12679 
    12680 15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 7 models selected 
    12681 
    12682 > select subtract #2
    12683 
    12684 15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    12685 
    12686 > show #!3 models
    12687 
    12688 > show #!2 models
    12689 
    12690 > color zone #2.1 near sel & #3 distance 4.38
    12691 
    12692 > color #8/X drak green
    12693 
    12694 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    12695 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    12696 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    12697 
    12698 > color #3/X drak green
    12699 
    12700 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    12701 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    12702 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    12703 
    12704 > color #3/X dark green
    12705 
    12706 > hide sel atoms
    12707 
    12708 > show sel atoms
    12709 
    12710 > hide sel cartoons
    12711 
    12712 [Repeated 1 time(s)]
    12713 
    12714 > hide sel atoms
    12715 
    12716 > show sel atoms
    12717 
    12718 > select #3/X
    12719 
    12720 360 atoms, 395 bonds, 18 residues, 1 model selected 
    12721 
    12722 > style sel stick
    12723 
    12724 Changed 360 atom styles 
    12725 
    12726 > show sel atoms
    12727 
    12728 > color zone #2.1 near sel distance 4.38
    12729 
    12730 > select #3/A,B,C,D,E,F
    12731 
    12732 14793 atoms, 15021 bonds, 6 pseudobonds, 1899 residues, 2 models selected 
    12733 
    12734 > hide sel atoms
    12735 
    12736 > select #3/A,B,C,D,E,F
    12737 
    12738 14793 atoms, 15021 bonds, 6 pseudobonds, 1899 residues, 2 models selected 
    12739 
    12740 > show sel cartoons
    12741 
    12742 > hide sel atoms
    12743 
    12744 [Repeated 1 time(s)]
    12745 
    12746 > select #3/A,C,E
    12747 
    12748 7413 atoms, 7527 bonds, 3 pseudobonds, 951 residues, 2 models selected 
    12749 
    12750 > color sel royalblue bluie
    12751 
    12752 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
    12753 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword 
    12754 
    12755 > color sel royal blue
    12756 
    12757 > select #3/A,C,E:ANP*,Ca*
    12758 
    12759 99 atoms, 99 bonds, 9 residues, 1 model selected 
    12760 
    12761 > color sel royal blue
    12762 
    12763 > show sel atoms
    12764 
    12765 > style sel stick
    12766 
    12767 Changed 99 atom styles 
    12768 
    12769 > select #3/B,D,F
    12770 
    12771 7380 atoms, 7494 bonds, 3 pseudobonds, 948 residues, 2 models selected 
    12772 
    12773 > color sel wheat
    12774 
    12775 > select #3/B,D,F:Ca*,ANP*
    12776 
    12777 66 atoms, 66 bonds, 6 residues, 1 model selected 
    12778 
    12779 > show sel atoms
    12780 
    12781 > select #3/M,N,O,P,Q,R,S
    12782 
    12783 359 atoms, 375 bonds, 45 residues, 1 model selected 
    12784 
    12785 > color sel red
    12786 
    12787 > show sel cartoons
    12788 
    12789 > show sel atoms
    12790 
    12791 > select #3/M,N,O,P,Q,R,S:18,25
    12792 
    12793 Nothing selected 
    12794 
    12795 > select #3/M,N,O,P,Q,R,S:3,10
    12796 
    12797 83 atoms, 78 bonds, 9 residues, 1 model selected 
    12798 
    12799 > hide sel atoms
    12800 
    12801 > select #3
    12802 
    12803 15512 atoms, 15791 bonds, 6 pseudobonds, 1962 residues, 2 models selected 
    12804 
    12805 > color zone #2.1 near sel distance 4.38
    12806 
    12807 > transparency #2.1.1 50
    12808 
    12809 > select subtract #3
    12810 
    12811 Nothing selected 
    12812 
    12813 > show #!1 models
    12814 
    12815 > hide #!1 models
    12816 
    12817 > save "/Users/sz140275local/Documents/Simona/DMC1/Papier EM DMC1/Meilleure
    12818 > structure RAD54B 07072025/ForAlexRAD54B.cxs"
    12819 
    12820 ——— End of log from Fri Jul 11 19:20:58 2025 ———
    12821 
    12822 > view name session-start
    12823 
    12824 opened ChimeraX session 
    12825 
    12826 > transparency 0.2
    12827 
    12828 > transparency 0.9
    12829 
    12830 > hide #!2 models
    12831 
    12832 > show #!2 models
    12833 
    12834 > hide #!3 models
    12835 
    12836 > view p1
    12837 
    12838 Expected an objects specifier or a view name or a keyword 
    12839 
    12840 > view name p1
    12841 
    12842 > view name p2
    12843 
    12844 > fly p1 p2
    12845 
    12846 > fly p1 p2 p1
    12847 
    12848 > save "/Users/anz/Desktop/P-motifs/2025 RAD54B paper/data/250712 CryoEM
    12849 > structures RAD54B PhePP from Sophie/ForAlexRAD54B movies TMM.cxs"
    12850 
    12851 ——— End of log from Wed Sep 3 19:35:27 2025 ———
    12852 
    12853 > view name session-start
    12854 
    12855 opened ChimeraX session 
    12856 
    12857 > split #4
    12858 
    12859 Split 8qqe (#4) into 4 models 
    12860 Chain information for 8qqe A #4.1 
    12861 --- 
    12862 Chain | Description 
    12863 A | No description available 
    12864  
    12865 Chain information for 8qqe B #4.2 
    12866 --- 
    12867 Chain | Description 
    12868 B | No description available 
    12869  
    12870 Chain information for 8qqe C #4.3 
    12871 --- 
    12872 Chain | Description 
    12873 C | No description available 
    12874  
    12875 Chain information for 8qqe D #4.4 
    12876 --- 
    12877 Chain | Description 
    12878 D | No description available 
    12879  
    12880 
    12881 > split #1
    12882 
    12883 Split BRCA2_m4_real_space_refined_000.pdb (#1) into 14 models 
    12884 Chain information for BRCA2_m4_real_space_refined_000.pdb A #1.1 
    12885 --- 
    12886 Chain | Description 
    12887 A | No description available 
    12888  
    12889 Chain information for BRCA2_m4_real_space_refined_000.pdb B #1.2 
    12890 --- 
    12891 Chain | Description 
    12892 B | No description available 
    12893  
    12894 Chain information for BRCA2_m4_real_space_refined_000.pdb C #1.3 
    12895 --- 
    12896 Chain | Description 
    12897 C | No description available 
    12898  
    12899 Chain information for BRCA2_m4_real_space_refined_000.pdb D #1.4 
    12900 --- 
    12901 Chain | Description 
    12902 D | No description available 
    12903  
    12904 Chain information for BRCA2_m4_real_space_refined_000.pdb E #1.5 
    12905 --- 
    12906 Chain | Description 
    12907 E | No description available 
    12908  
    12909 Chain information for BRCA2_m4_real_space_refined_000.pdb F #1.6 
    12910 --- 
    12911 Chain | Description 
    12912 F | No description available 
    12913  
    12914 Chain information for BRCA2_m4_real_space_refined_000.pdb M #1.8 
    12915 --- 
    12916 Chain | Description 
    12917 M | No description available 
    12918  
    12919 Chain information for BRCA2_m4_real_space_refined_000.pdb N #1.9 
    12920 --- 
    12921 Chain | Description 
    12922 N | No description available 
    12923  
    12924 Chain information for BRCA2_m4_real_space_refined_000.pdb O #1.10 
    12925 --- 
    12926 Chain | Description 
    12927 O | No description available 
    12928  
    12929 Chain information for BRCA2_m4_real_space_refined_000.pdb P #1.11 
    12930 --- 
    12931 Chain | Description 
    12932 P | No description available 
    12933  
    12934 Chain information for BRCA2_m4_real_space_refined_000.pdb Q #1.12 
    12935 --- 
    12936 Chain | Description 
    12937 Q | No description available 
    12938  
    12939 Chain information for BRCA2_m4_real_space_refined_000.pdb R #1.13 
    12940 --- 
    12941 Chain | Description 
    12942 R | No description available 
    12943  
    12944 Chain information for BRCA2_m4_real_space_refined_000.pdb X #1.14 
    12945 --- 
    12946 Chain | Description 
    12947 X | No description available 
    12948  
    12949 
    12950 > split #3
    12951 
    12952 Split RAD54-J402_m4_real_space_refined_000.pdb (#3) into 13 models 
    12953 Chain information for RAD54-J402_m4_real_space_refined_000.pdb A #3.1 
    12954 --- 
    12955 Chain | Description 
    12956 A | No description available 
    12957  
    12958 Chain information for RAD54-J402_m4_real_space_refined_000.pdb B #3.2 
    12959 --- 
    12960 Chain | Description 
    12961 B | No description available 
    12962  
    12963 Chain information for RAD54-J402_m4_real_space_refined_000.pdb C #3.3 
    12964 --- 
    12965 Chain | Description 
    12966 C | No description available 
    12967  
    12968 Chain information for RAD54-J402_m4_real_space_refined_000.pdb D #3.4 
    12969 --- 
    12970 Chain | Description 
    12971 D | No description available 
    12972  
    12973 Chain information for RAD54-J402_m4_real_space_refined_000.pdb E #3.5 
    12974 --- 
    12975 Chain | Description 
    12976 E | No description available 
    12977  
    12978 Chain information for RAD54-J402_m4_real_space_refined_000.pdb F #3.6 
    12979 --- 
    12980 Chain | Description 
    12981 F | No description available 
    12982  
    12983 Chain information for RAD54-J402_m4_real_space_refined_000.pdb M #3.7 
    12984 --- 
    12985 Chain | Description 
    12986 M | No description available 
    12987  
    12988 Chain information for RAD54-J402_m4_real_space_refined_000.pdb N #3.8 
    12989 --- 
    12990 Chain | Description 
    12991 N | No description available 
    12992  
    12993 Chain information for RAD54-J402_m4_real_space_refined_000.pdb O #3.9 
    12994 --- 
    12995 Chain | Description 
    12996 O | No description available 
    12997  
    12998 Chain information for RAD54-J402_m4_real_space_refined_000.pdb P #3.10 
    12999 --- 
    13000 Chain | Description 
    13001 P | No description available 
    13002  
    13003 Chain information for RAD54-J402_m4_real_space_refined_000.pdb Q #3.11 
    13004 --- 
    13005 Chain | Description 
    13006 Q | No description available 
    13007  
    13008 Chain information for RAD54-J402_m4_real_space_refined_000.pdb R #3.12 
    13009 --- 
    13010 Chain | Description 
    13011 R | No description available 
    13012  
    13013 Chain information for RAD54-J402_m4_real_space_refined_000.pdb X #3.13 
    13014 --- 
    13015 Chain | Description 
    13016 X | No description available 
    13017  
    13018 
    13019 > hide #!2.1 models
    13020 
    13021 > hide #!3 models
    13022 
    13023 > show #!3 models
    13024 
    13025 > cartoon #3
    13026 
    13027 > cartoon #3.1
    13028 
    13029 > view #3.1 clip false
    13030 
    13031 > show #3.7-13#!3.1-6 target m
    13032 
    13033 > hide #!3 models
    13034 
    13035 > show #!3 models
    13036 
    13037 > hide #!1 models
    13038 
    13039 > show #!1.1 models
    13040 
    13041 > hide #!1.1 models
    13042 
    13043 > show #1.11 models
    13044 
    13045 > hide #1.11 models
    13046 
    13047 > show #1.12 models
    13048 
    13049 > hide #1.12 models
    13050 
    13051 > show #1.12 models
    13052 
    13053 > show #1.11 models
    13054 
    13055 > hide #1.12 models
    13056 
    13057 > show #1.12 models
    13058 
    13059 > hide #1.12 models
    13060 
    13061 > show #1.12 models
    13062 
    13063 > hide #1.12 models
    13064 
    13065 > hide #1.11 models
    13066 
    13067 > show #1.11 models
    13068 
    13069 > hide #1.11 models
    13070 
    13071 > show #1.11 models
    13072 
    13073 > hide #1.11 models
    13074 
    13075 > show #1.11 models
    13076 
    13077 > show #!4.1 models
    13078 
    13079 > hide #!4.1 models
    13080 
    13081 > show #!4.2 models
    13082 
    13083 > hide #!4.2 models
    13084 
    13085 > show #!4.1 models
    13086 
    13087 > show #!4.2 models
    13088 
    13089 > hide #!4.2 models
    13090 
    13091 > hide #!4.1 models
    13092 
    13093 > save "/Users/anz/Desktop/P-motifs/2025 RAD54B paper/data/250712 CryoEM
    13094 > structures RAD54B PhePP from Sophie/ForAlexRAD54B movies TMM peptide 2.cxs"
    13095 
    13096 > show #!1.1 models
    13097 
    13098 > hide #!1.1 models
    13099 
    13100 > hide #1.11 models
    13101 
    13102 > show #1.11 models
    13103 
    13104 > color #1.11 #941751ff
    13105 
    13106 > color #1.11 #fffb00ff
    13107 
    13108 > color #1.7 #fffc79ff
    13109 
    13110 > show #1.7 models
    13111 
    13112 > show #1.8 models
    13113 
    13114 > show #1.9 models
    13115 
    13116 > show #1.10 models
    13117 
    13118 > color #1.10 #fffb00ff
    13119 
    13120 > view #1.10 clip false
    13121 
    13122 No displayed objects specified. 
    13123 
    13124 > select add #1.10
    13125 
    13126 68 atoms, 71 bonds, 8 residues, 1 model selected 
    13127 
    13128 > select subtract #1.10
    13129 
    13130 Nothing selected 
    13131 
    13132 > show #1.7-11#3.7-13#!3.1-6 atoms
    13133 
    13134 > hide #1.7-11#3.7-13#!3.1-6 atoms
    13135 
    13136 > show #!1.6 models
    13137 
    13138 > hide #!1.6 models
    13139 
    13140 > hide #!3 models
    13141 
    13142 > show #!1.6 models
    13143 
    13144 > show #!1.5 models
    13145 
    13146 > show #!1.3 models
    13147 
    13148 > show #!1.2 models
    13149 
    13150 > show #!1.4 models
    13151 
    13152 > show #!1.1 models
    13153 
    13154 > show #!3 models
    13155 
    13156 > show #!4.1 models
    13157 
    13158 > show #!4.2 models
    13159 
    13160 > show #4.3 models
    13161 
    13162 > show #4.4 models
    13163 
    13164 > hide #!1.5 models
    13165 
    13166 > hide #!1 models
    13167 
    13168 > show #!1 models
    13169 
    13170 > style #1.7-11#3.7-13#4.3-4#!1.1-4,6#!3.1-6#!4.1-2 ball
    13171 
    13172 Changed 32770 atom styles 
    13173 
    13174 > style #1.7-11#3.7-13#4.3-4#!1.1-4,6#!3.1-6#!4.1-2 ball
    13175 
    13176 Changed 32770 atom styles 
    13177 
    13178 > hide #1.11 models
    13179 
    13180 > show #1.11 models
    13181 
    13182 > style #1.7-11#3.7-13#4.3-4#!1.1-4,6#!3.1-6#!4.1-2 ball
    13183 
    13184 Changed 32770 atom styles 
    13185 
    13186 > show #1.7-11#3.7-13#4.3-4#!1.1-4,6#!3.1-6#!4.1-2 atoms
    13187 
    13188 > hide #1.7-11#3.7-13#4.3-4#!1.1-4,6#!3.1-6#!4.1-2 atoms
    13189 
    13190 > select add #1.11
    13191 
    13192 68 atoms, 71 bonds, 8 residues, 1 model selected 
    13193 
    13194 > style sel ball
    13195 
    13196 Changed 68 atom styles 
    13197 
    13198 > show sel atoms
    13199 
    13200 > select subtract #1.11
    13201 
    13202 Nothing selected 
    13203 
    13204 > open
    13205 > /Users/anz/Downloads/fold_rad54_nterm_rad51/fold_rad54_nterm_rad51_model_0.cif
    13206 
    13207 Chain information for fold_rad54_nterm_rad51_model_0.cif #5 
    13208 --- 
    13209 Chain | Description 
    13210 A | . 
    13211 B | . 
    13212  
    13213 Computing secondary structure 
    13214 
    13215 > view #5 clip false
    13216 
    13217 > split #5
    13218 
    13219 Split fold_rad54_nterm_rad51_model_0.cif (#5) into 2 models 
    13220 Chain information for fold_rad54_nterm_rad51_model_0.cif A #5.1 
    13221 --- 
    13222 Chain | Description 
    13223 A | No description available 
    13224  
    13225 Chain information for fold_rad54_nterm_rad51_model_0.cif B #5.2 
    13226 --- 
    13227 Chain | Description 
    13228 B | No description available 
    13229  
    13230 
    13231 > color #5.1 #0096ffff
    13232 
    13233 > select #5.1:82
    13234 
    13235 11 atoms, 11 bonds, 1 residue, 1 model selected 
    13236 
    13237 > show #5.1:82
    13238 
    13239 > view #5 clip false
    13240 
    13241 > view #4 clip false
    13242 
    13243 > matchmaker #5.2 to #3.2 bring #5.1
    13244 
    13245 Parameters 
    13246 --- 
    13247 Chain pairing | bb 
    13248 Alignment algorithm | Needleman-Wunsch 
    13249 Similarity matrix | BLOSUM-62 
    13250 SS fraction | 0.3 
    13251 Gap open (HH/SS/other) | 18/18/6 
    13252 Gap extend | 1 
    13253 SS matrix |  |  | H | S | O 
    13254 ---|---|---|--- 
    13255 H | 6 | -9 | -6 
    13256 S |  | 6 | -6 
    13257 O |  |  | 4 
    13258 Iteration cutoff | 2 
    13259  
    13260 Matchmaker RAD54-J402_m4_real_space_refined_000.pdb B, chain B (#3.2) with
    13261 fold_rad54_nterm_rad51_model_0.cif B, chain B (#5.2), sequence alignment score
    13262 = 1025.4 
    13263 RMSD between 260 pruned atom pairs is 0.874 angstroms; (across all 309 pairs:
    13264 1.756) 
    13265  
    13266 
    13267 > color #5.1 #ff40ffff
    13268 
    13269 > show #5.1:85
    13270 
    13271 > hide #!5 models
    13272 
    13273 > hide #!4.1 models
    13274 
    13275 > show #!4.1 models
    13276 
    13277 > mmaker #4.2 to #3.2 bring #4.1,3,4
    13278 
    13279 Parameters 
    13280 --- 
    13281 Chain pairing | bb 
    13282 Alignment algorithm | Needleman-Wunsch 
    13283 Similarity matrix | BLOSUM-62 
    13284 SS fraction | 0.3 
    13285 Gap open (HH/SS/other) | 18/18/6 
    13286 Gap extend | 1 
    13287 SS matrix |  |  | H | S | O 
    13288 ---|---|---|--- 
    13289 H | 6 | -9 | -6 
    13290 S |  | 6 | -6 
    13291 O |  |  | 4 
    13292 Iteration cutoff | 2 
    13293  
    13294 Matchmaker RAD54-J402_m4_real_space_refined_000.pdb B, chain B (#3.2) with
    13295 8qqe B, chain B (#4.2), sequence alignment score = 1204.2 
    13296 RMSD between 223 pruned atom pairs is 0.621 angstroms; (across all 247 pairs:
    13297 2.554) 
    13298  
    13299 
    13300 > hide #!4.1 models
    13301 
    13302 > hide #!4.2 models
    13303 
    13304 > hide #4.4 models
    13305 
    13306 > open 8pbc
    13307 
    13308 8pbc title: 
    13309 RAD51 filament on ssDNA bound by the BRCA2 c-terminus [more info...] 
    13310  
    13311 Chain information for 8pbc #6 
    13312 --- 
    13313 Chain | Description | UniProt 
    13314 A B C D E F G H I J K | DNA repair protein RAD51 homolog 1 | RAD51_HUMAN 1-339 
    13315 L M N O P Q R S T U | Breast cancer type 2 susceptibility protein | BRCA2_HUMAN 3260-3308 
    13316 V | DNA (30-MER) |   
    13317  
    13318 Non-standard residues in 8pbc #6 
    13319 --- 
    13320 ATP — adenosine-5'-triphosphate 
    13321 CA — calcium ion 
    13322  
    13323 
    13324 > split #6
    13325 
    13326 Split 8pbc (#6) into 22 models 
    13327 Chain information for 8pbc A #6.1 
    13328 --- 
    13329 Chain | Description 
    13330 A | No description available 
    13331  
    13332 Chain information for 8pbc B #6.2 
    13333 --- 
    13334 Chain | Description 
    13335 B | No description available 
    13336  
    13337 Chain information for 8pbc C #6.3 
    13338 --- 
    13339 Chain | Description 
    13340 C | No description available 
    13341  
    13342 Chain information for 8pbc D #6.4 
    13343 --- 
    13344 Chain | Description 
    13345 D | No description available 
    13346  
    13347 Chain information for 8pbc E #6.5 
    13348 --- 
    13349 Chain | Description 
    13350 E | No description available 
    13351  
    13352 Chain information for 8pbc F #6.6 
    13353 --- 
    13354 Chain | Description 
    13355 F | No description available 
    13356  
    13357 Chain information for 8pbc G #6.7 
    13358 --- 
    13359 Chain | Description 
    13360 G | No description available 
    13361  
    13362 Chain information for 8pbc H #6.8 
    13363 --- 
    13364 Chain | Description 
    13365 H | No description available 
    13366  
    13367 Chain information for 8pbc I #6.9 
    13368 --- 
    13369 Chain | Description 
    13370 I | No description available 
    13371  
    13372 Chain information for 8pbc J #6.10 
    13373 --- 
    13374 Chain | Description 
    13375 J | No description available 
    13376  
    13377 Chain information for 8pbc K #6.11 
    13378 --- 
    13379 Chain | Description 
    13380 K | No description available 
    13381  
    13382 Chain information for 8pbc L #6.12 
    13383 --- 
    13384 Chain | Description 
    13385 L | No description available 
    13386  
    13387 Chain information for 8pbc M #6.13 
    13388 --- 
    13389 Chain | Description 
    13390 M | No description available 
    13391  
    13392 Chain information for 8pbc N #6.14 
    13393 --- 
    13394 Chain | Description 
    13395 N | No description available 
    13396  
    13397 Chain information for 8pbc O #6.15 
    13398 --- 
    13399 Chain | Description 
    13400 O | No description available 
    13401  
    13402 Chain information for 8pbc P #6.16 
    13403 --- 
    13404 Chain | Description 
    13405 P | No description available 
    13406  
    13407 Chain information for 8pbc Q #6.17 
    13408 --- 
    13409 Chain | Description 
    13410 Q | No description available 
    13411  
    13412 Chain information for 8pbc R #6.18 
    13413 --- 
    13414 Chain | Description 
    13415 R | No description available 
    13416  
    13417 Chain information for 8pbc S #6.19 
    13418 --- 
    13419 Chain | Description 
    13420 S | No description available 
    13421  
    13422 Chain information for 8pbc T #6.20 
    13423 --- 
    13424 Chain | Description 
    13425 T | No description available 
    13426  
    13427 Chain information for 8pbc U #6.21 
    13428 --- 
    13429 Chain | Description 
    13430 U | No description available 
    13431  
    13432 Chain information for 8pbc V #6.22 
    13433 --- 
    13434 Chain | Description 
    13435 V | No description available 
    13436  
    13437 
    13438 > hide #6
    13439 
    13440 > cartoon #6
    13441 
    13442 > hide #!6.1 models
    13443 
    13444 > hide #!6.2 models
    13445 
    13446 > show #!6.1 models
    13447 
    13448 > show #!6.2 models
    13449 
    13450 > hide #!6.2 models
    13451 
    13452 > hide #!6.1 models
    13453 
    13454 > hide #!6.3 models
    13455 
    13456 > hide #!6.5 models
    13457 
    13458 > hide #!6.6 models
    13459 
    13460 > hide #!6.7 models
    13461 
    13462 > hide #!6.8 models
    13463 
    13464 > hide #!6.9 models
    13465 
    13466 > hide #!6.10 models
    13467 
    13468 > hide #!6.11 models
    13469 
    13470 > show #!6.11 models
    13471 
    13472 > hide #!6.11 models
    13473 
    13474 > show #!6.11 models
    13475 
    13476 > mmaker #6.11 to #3.2 bring #6
    13477 
    13478 Cannot 'bring' parent model of match structure 
    13479 
    13480 > mmaker #6.11 to #3.2 bring #6.12
    13481 
    13482 Parameters 
    13483 --- 
    13484 Chain pairing | bb 
    13485 Alignment algorithm | Needleman-Wunsch 
    13486 Similarity matrix | BLOSUM-62 
    13487 SS fraction | 0.3 
    13488 Gap open (HH/SS/other) | 18/18/6 
    13489 Gap extend | 1 
    13490 SS matrix |  |  | H | S | O 
    13491 ---|---|---|--- 
    13492 H | 6 | -9 | -6 
    13493 S |  | 6 | -6 
    13494 O |  |  | 4 
    13495 Iteration cutoff | 2 
    13496  
    13497 Matchmaker RAD54-J402_m4_real_space_refined_000.pdb B, chain B (#3.2) with
    13498 8pbc K, chain K (#6.11), sequence alignment score = 1011.4 
    13499 RMSD between 275 pruned atom pairs is 0.914 angstroms; (across all 307 pairs:
    13500 1.554) 
    13501  
    13502 
    13503 > ~cartoon #6.11
    13504 
    13505 > color #6.12 orange
    13506 
    13507 > show #!6.10 models
    13508 
    13509 > hide #!6.10 models
    13510 
    13511 > hide #6.13 models
    13512 
    13513 > show #6.13 models
    13514 
    13515 > show #!6.10 models
    13516 
    13517 > show #!6.9 models
    13518 
    13519 > hide #6.14 models
    13520 
    13521 > show #6.14 models
    13522 
    13523 > hide #6.14 models
    13524 
    13525 > show #6.14 models
    13526 
    13527 > close #6
    13528 
    13529 > open 8pbc
    13530 
    13531 8pbc title: 
    13532 RAD51 filament on ssDNA bound by the BRCA2 c-terminus [more info...] 
    13533  
    13534 Chain information for 8pbc #6 
    13535 --- 
    13536 Chain | Description | UniProt 
    13537 A B C D E F G H I J K | DNA repair protein RAD51 homolog 1 | RAD51_HUMAN 1-339 
    13538 L M N O P Q R S T U | Breast cancer type 2 susceptibility protein | BRCA2_HUMAN 3260-3308 
    13539 V | DNA (30-MER) |   
    13540  
    13541 Non-standard residues in 8pbc #6 
    13542 --- 
    13543 ATP — adenosine-5'-triphosphate 
    13544 CA — calcium ion 
    13545  
    13546 
    13547 > hide #6
    13548 
    13549 > cartoon #6
    13550 
    13551 > ~cartoon #6
    13552 
    13553 > cartoon #6.9,10,11,12
    13554 
    13555 > split #6
    13556 
    13557 Split 8pbc (#6) into 22 models 
    13558 Chain information for 8pbc A #6.1 
    13559 --- 
    13560 Chain | Description 
    13561 A | No description available 
    13562  
    13563 Chain information for 8pbc B #6.2 
    13564 --- 
    13565 Chain | Description 
    13566 B | No description available 
    13567  
    13568 Chain information for 8pbc C #6.3 
    13569 --- 
    13570 Chain | Description 
    13571 C | No description available 
    13572  
    13573 Chain information for 8pbc D #6.4 
    13574 --- 
    13575 Chain | Description 
    13576 D | No description available 
    13577  
    13578 Chain information for 8pbc E #6.5 
    13579 --- 
    13580 Chain | Description 
    13581 E | No description available 
    13582  
    13583 Chain information for 8pbc F #6.6 
    13584 --- 
    13585 Chain | Description 
    13586 F | No description available 
    13587  
    13588 Chain information for 8pbc G #6.7 
    13589 --- 
    13590 Chain | Description 
    13591 G | No description available 
    13592  
    13593 Chain information for 8pbc H #6.8 
    13594 --- 
    13595 Chain | Description 
    13596 H | No description available 
    13597  
    13598 Chain information for 8pbc I #6.9 
    13599 --- 
    13600 Chain | Description 
    13601 I | No description available 
    13602  
    13603 Chain information for 8pbc J #6.10 
    13604 --- 
    13605 Chain | Description 
    13606 J | No description available 
    13607  
    13608 Chain information for 8pbc K #6.11 
    13609 --- 
    13610 Chain | Description 
    13611 K | No description available 
    13612  
    13613 Chain information for 8pbc L #6.12 
    13614 --- 
    13615 Chain | Description 
    13616 L | No description available 
    13617  
    13618 Chain information for 8pbc M #6.13 
    13619 --- 
    13620 Chain | Description 
    13621 M | No description available 
    13622  
    13623 Chain information for 8pbc N #6.14 
    13624 --- 
    13625 Chain | Description 
    13626 N | No description available 
    13627  
    13628 Chain information for 8pbc O #6.15 
    13629 --- 
    13630 Chain | Description 
    13631 O | No description available 
    13632  
    13633 Chain information for 8pbc P #6.16 
    13634 --- 
    13635 Chain | Description 
    13636 P | No description available 
    13637  
    13638 Chain information for 8pbc Q #6.17 
    13639 --- 
    13640 Chain | Description 
    13641 Q | No description available 
    13642  
    13643 Chain information for 8pbc R #6.18 
    13644 --- 
    13645 Chain | Description 
    13646 R | No description available 
    13647  
    13648 Chain information for 8pbc S #6.19 
    13649 --- 
    13650 Chain | Description 
    13651 S | No description available 
    13652  
    13653 Chain information for 8pbc T #6.20 
    13654 --- 
    13655 Chain | Description 
    13656 T | No description available 
    13657  
    13658 Chain information for 8pbc U #6.21 
    13659 --- 
    13660 Chain | Description 
    13661 U | No description available 
    13662  
    13663 Chain information for 8pbc V #6.22 
    13664 --- 
    13665 Chain | Description 
    13666 V | No description available 
    13667  
    13668 
    13669 > cartoon #6.9,10,11,12
    13670 
    13671 > mmaker #6.10 to #3.2 bring #6
    13672 
    13673 Cannot 'bring' parent model of match structure 
    13674 
    13675 > mmaker #6.10 to #3.2 bring #6.9,11,12
    13676 
    13677 Parameters 
    13678 --- 
    13679 Chain pairing | bb 
    13680 Alignment algorithm | Needleman-Wunsch 
    13681 Similarity matrix | BLOSUM-62 
    13682 SS fraction | 0.3 
    13683 Gap open (HH/SS/other) | 18/18/6 
    13684 Gap extend | 1 
    13685 SS matrix |  |  | H | S | O 
    13686 ---|---|---|--- 
    13687 H | 6 | -9 | -6 
    13688 S |  | 6 | -6 
    13689 O |  |  | 4 
    13690 Iteration cutoff | 2 
    13691  
    13692 Matchmaker RAD54-J402_m4_real_space_refined_000.pdb B, chain B (#3.2) with
    13693 8pbc J, chain J (#6.10), sequence alignment score = 1011.4 
    13694 RMSD between 275 pruned atom pairs is 0.914 angstroms; (across all 307 pairs:
    13695 1.554) 
    13696  
    13697 
    13698 > color #6.9-12 orange
    13699 
    13700 > close #6
    13701 
    13702 > open 8pbc
    13703 
    13704 8pbc title: 
    13705 RAD51 filament on ssDNA bound by the BRCA2 c-terminus [more info...] 
    13706  
    13707 Chain information for 8pbc #6 
    13708 --- 
    13709 Chain | Description | UniProt 
    13710 A B C D E F G H I J K | DNA repair protein RAD51 homolog 1 | RAD51_HUMAN 1-339 
    13711 L M N O P Q R S T U | Breast cancer type 2 susceptibility protein | BRCA2_HUMAN 3260-3308 
    13712 V | DNA (30-MER) |   
    13713  
    13714 Non-standard residues in 8pbc #6 
    13715 --- 
    13716 ATP — adenosine-5'-triphosphate 
    13717 CA — calcium ion 
    13718  
    13719 
    13720 > hide #6
    13721 
    13722 > split #6
    13723 
    13724 Split 8pbc (#6) into 22 models 
    13725 Chain information for 8pbc A #6.1 
    13726 --- 
    13727 Chain | Description 
    13728 A | No description available 
    13729  
    13730 Chain information for 8pbc B #6.2 
    13731 --- 
    13732 Chain | Description 
    13733 B | No description available 
    13734  
    13735 Chain information for 8pbc C #6.3 
    13736 --- 
    13737 Chain | Description 
    13738 C | No description available 
    13739  
    13740 Chain information for 8pbc D #6.4 
    13741 --- 
    13742 Chain | Description 
    13743 D | No description available 
    13744  
    13745 Chain information for 8pbc E #6.5 
    13746 --- 
    13747 Chain | Description 
    13748 E | No description available 
    13749  
    13750 Chain information for 8pbc F #6.6 
    13751 --- 
    13752 Chain | Description 
    13753 F | No description available 
    13754  
    13755 Chain information for 8pbc G #6.7 
    13756 --- 
    13757 Chain | Description 
    13758 G | No description available 
    13759  
    13760 Chain information for 8pbc H #6.8 
    13761 --- 
    13762 Chain | Description 
    13763 H | No description available 
    13764  
    13765 Chain information for 8pbc I #6.9 
    13766 --- 
    13767 Chain | Description 
    13768 I | No description available 
    13769  
    13770 Chain information for 8pbc J #6.10 
    13771 --- 
    13772 Chain | Description 
    13773 J | No description available 
    13774  
    13775 Chain information for 8pbc K #6.11 
    13776 --- 
    13777 Chain | Description 
    13778 K | No description available 
    13779  
    13780 Chain information for 8pbc L #6.12 
    13781 --- 
    13782 Chain | Description 
    13783 L | No description available 
    13784  
    13785 Chain information for 8pbc M #6.13 
    13786 --- 
    13787 Chain | Description 
    13788 M | No description available 
    13789  
    13790 Chain information for 8pbc N #6.14 
    13791 --- 
    13792 Chain | Description 
    13793 N | No description available 
    13794  
    13795 Chain information for 8pbc O #6.15 
    13796 --- 
    13797 Chain | Description 
    13798 O | No description available 
    13799  
    13800 Chain information for 8pbc P #6.16 
    13801 --- 
    13802 Chain | Description 
    13803 P | No description available 
    13804  
    13805 Chain information for 8pbc Q #6.17 
    13806 --- 
    13807 Chain | Description 
    13808 Q | No description available 
    13809  
    13810 Chain information for 8pbc R #6.18 
    13811 --- 
    13812 Chain | Description 
    13813 R | No description available 
    13814  
    13815 Chain information for 8pbc S #6.19 
    13816 --- 
    13817 Chain | Description 
    13818 S | No description available 
    13819  
    13820 Chain information for 8pbc T #6.20 
    13821 --- 
    13822 Chain | Description 
    13823 T | No description available 
    13824  
    13825 Chain information for 8pbc U #6.21 
    13826 --- 
    13827 Chain | Description 
    13828 U | No description available 
    13829  
    13830 Chain information for 8pbc V #6.22 
    13831 --- 
    13832 Chain | Description 
    13833 V | No description available 
    13834  
    13835 
    13836 > color #6 orange
    13837 
    13838 > cartoon #6
    13839 
    13840 > ~cartoon #6
    13841 
    13842 > cartoon #6.10-13
    13843 
    13844 > mmaker #6.11 to #3.2 bring #6.10,12,13
    13845 
    13846 Parameters 
    13847 --- 
    13848 Chain pairing | bb 
    13849 Alignment algorithm | Needleman-Wunsch 
    13850 Similarity matrix | BLOSUM-62 
    13851 SS fraction | 0.3 
    13852 Gap open (HH/SS/other) | 18/18/6 
    13853 Gap extend | 1 
    13854 SS matrix |  |  | H | S | O 
    13855 ---|---|---|--- 
    13856 H | 6 | -9 | -6 
    13857 S |  | 6 | -6 
    13858 O |  |  | 4 
    13859 Iteration cutoff | 2 
    13860  
    13861 Matchmaker RAD54-J402_m4_real_space_refined_000.pdb B, chain B (#3.2) with
    13862 8pbc K, chain K (#6.11), sequence alignment score = 1011.4 
    13863 RMSD between 275 pruned atom pairs is 0.914 angstroms; (across all 307 pairs:
    13864 1.554) 
    13865  
    13866 
    13867 > ~cartoon #6
    13868 
    13869 > show #6.13
    13870 
    13871 > hide #6.13
    13872 
    13873 > hide #6.12
    13874 
    13875 > show #6.12 stick
    13876 
    13877 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
    13878 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword 
    13879 
    13880 > show #6.12 atoms
    13881 
    13882 > select #6.12
    13883 
    13884 121 atoms, 125 bonds, 16 residues, 1 model selected 
    13885 
    13886 > style sel ball
    13887 
    13888 Changed 121 atom styles 
    13889 
    13890 > ~select
    13891 
    13892 Nothing selected 
    13893 
    13894 > name peptides #6.12 | #3.8 | #1.11 | #4.3
    13895 
    13896 > style peptides sticks
    13897 
    13898 Expected a keyword 
    13899 
    13900 > style peptides stick
    13901 
    13902 Changed 355 atom styles 
    13903 
    13904 > style peptides ball
    13905 
    13906 Changed 355 atom styles 
    13907 
    13908 > show peptides
    13909 
    13910 > name apple #6.10-13
    13911 
    13912 > cartoon apple
    13913 
    13914 > log metadata #6.12
    13915 
    13916 The model has no metadata
    13917 
    13918 > log chains #6.12
    13919 
    13920 Chain information for 8pbc L #6.12 
    13921 --- 
    13922 Chain | Description 
    13923 L | No description available 
    13924  
    13925 
    13926 > select #6.12/L:3289-3304
    13927 
    13928 121 atoms, 125 bonds, 16 residues, 1 model selected 
    13929 
    13930 > sequence chain #6.12/L
    13931 
    13932 Alignment identifier is 6.12/L 
    13933 
    13934 > select #6.12/L:3298
    13935 
    13936 11 atoms, 11 bonds, 1 residue, 1 model selected 
    13937 
    13938 > select #6.12/L:3298-3301
    13939 
    13940 34 atoms, 36 bonds, 4 residues, 1 model selected 
    13941 
    13942 > color #6.12 lightGrey
    13943 
    13944 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    13945 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
    13946 'fromcartoons', 'fromribbons', or 'random' or a keyword 
    13947 
    13948 > color #6.12 azure
    13949 
    13950 > color #6.12 byatom
    13951 
    13952 > select up
    13953 
    13954 121 atoms, 125 bonds, 16 residues, 1 model selected 
    13955 
    13956 > color #6.12 azure
    13957 
    13958 > color #6.12 byhetero
    13959 
    13960 > ~cartoon #6.10,11,13
    13961 
    13962 > ~select
    13963 
    13964 Nothing selected 
    13965 
    13966 > surface #3.2
    13967 
    13968 > surface #3.2 transparency 80
    13969 
    13970 > surface #3.2 transparency 30
    13971 
    13972 > show #3.3:89
    13973 
    13974 > color #3.3:89 byhetero
    13975 
    13976 > select #6.12/L:3289
    13977 
    13978 11 atoms, 11 bonds, 1 residue, 1 model selected 
    13979 
    13980 > select #6.12/L
    13981 
    13982 121 atoms, 125 bonds, 16 residues, 1 model selected 
    13983 
    13984 > select #6.12/L:3298
    13985 
    13986 11 atoms, 11 bonds, 1 residue, 1 model selected 
    13987 
    13988 > select #6.12/L:3298-3301
    13989 
    13990 34 atoms, 36 bonds, 4 residues, 1 model selected 
    13991 
    13992 > hide #6.12 & ! :3298-3301
    13993 
    13994 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
    13995 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword 
    13996 
    13997 > hide (#6.12 & ! :3298-3301)
    13998 
    13999 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
    14000 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword 
    14001 
    14002 > hide (#6.12 & ! :3298-3301) atoms
    14003 
    14004 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
    14005 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword 
    14006 
    14007 > hide #6.12 & ~:3298-3301 atoms
    14008 
    14009 > ~cartoon #6.12
    14010 
    14011 > select ~sel & ##selected
    14012 
    14013 87 atoms, 89 bonds, 12 residues, 1 model selected 
    14014 
    14015 > ~cartoon #1.11
    14016 
    14017 > ~cartoon #3.8
    14018 
    14019 > ~cartoon #4.3
    14020 
    14021 > save "/Users/anz/Desktop/P-motifs/2025 RAD54B paper/data/250712 CryoEM
    14022 > structures RAD54B PhePP from Sophie/ForAlexRAD54B movies TMM peptide 2.cxs"
    14023 
    14024 > hide #6.12 models
    14025 
    14026 > select add #6.12
    14027 
    14028 121 atoms, 125 bonds, 16 residues, 1 model selected 
    14029 
    14030 > select subtract #6.12
    14031 
    14032 Nothing selected 
    14033 
    14034 > show #6.12 models
    14035 
    14036 > hide #6.12 models
    14037 
    14038 > show #6.12 models
    14039 
    14040 > hide #6.12 models
    14041 
    14042 > color #4.3 thistle
    14043 
    14044 > view #4.4 clip false
    14045 
    14046 No displayed objects specified. 
    14047 
    14048 > view #4.3 clip false
    14049 
    14050 > color #4.3 byhetero
    14051 
    14052 > name FPP #6.12:3298,3230,3231 | #3.8:5,7,8 | #1.11:5,7,8 | #4.3:2406,2408,2409
    14053 
    14054 > select FPP
    14055 
    14056 86 atoms, 89 bonds, 10 residues, 4 models selected 
    14057 
    14058 > name list
    14059 
    14060 ANP #3:ANP 
    14061 FPP #6.12:3298,3230,3231 | #3.8:5,7,8 | #1.11:5,7,8 | #4.3:2406,2408,2409 
    14062 R54B #3/M-R 
    14063 apple #6.10-13 
    14064 peptides #6.12 | #3.8 | #1.11 | #4.3 
    14065 phe85 #3:85 
    14066 
    14067 > hide peptides
    14068 
    14069 > show FPP
    14070 
    14071 > view name core1
    14072 
    14073 > select ~sel & ##selected
    14074 
    14075 269 atoms, 279 bonds, 35 residues, 4 models selected 
    14076 
    14077 > view name core2
    14078 
    14079 > view name core3
    14080 
    14081 > view core1
    14082 
    14083 > move record
    14084 
    14085 Missing or invalid "axis" argument: Expected 3 floats or "x", or "y", or "z"
    14086 or two atoms 
    14087 
    14088 > movie record
    14089 
    14090 > fly core1 core2 core3 core1
    14091 
    14092 > movie encode FPP.mp4
    14093 
    14094 Movie saved to FPP.mp4 
    14095  
     2193[deleted to fit within ticket limits]
    140962194
    140972195> movie encode /Users/anz/Desktop/FPP.mp4