Changes between Initial Version and Version 1 of Ticket #17089


Ignore:
Timestamp:
Mar 13, 2025, 2:55:31 PM (8 months ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #17089

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

  • Ticket #17089 – Description

    initial v1  
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    1573     "uuid" : "5576e4fd-aad2-3608-8c8f-4eec421236f9",
    1574     "path" : "\/usr\/lib\/system\/libdispatch.dylib",
    1575     "name" : "libdispatch.dylib"
    1576   },
    1577   {
    1578     "source" : "P",
    1579     "arch" : "arm64e",
    1580     "base" : 6975418368,
    1581     "CFBundleShortVersionString" : "6.9",
    1582     "CFBundleIdentifier" : "com.apple.CoreFoundation",
    1583     "size" : 5197824,
    1584     "uuid" : "190e6a36-fcaa-3ea3-94bb-7009c44653da",
    1585     "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
    1586     "name" : "CoreFoundation",
    1587     "CFBundleVersion" : "3302.1.400"
    1588   },
    1589   {
    1590     "source" : "P",
    1591     "arch" : "arm64e",
    1592     "base" : 7165075456,
    1593     "CFBundleShortVersionString" : "2.1.1",
    1594     "CFBundleIdentifier" : "com.apple.HIToolbox",
    1595     "size" : 3178496,
    1596     "uuid" : "950f1236-acaf-379d-819f-6c6b0b5deabd",
    1597     "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    1598     "name" : "HIToolbox"
    1599   },
    1600   {
    1601     "source" : "P",
    1602     "arch" : "arm64e",
    1603     "base" : 6971285504,
    1604     "size" : 532288,
    1605     "uuid" : "398a133c-9bcb-317f-a064-a40d3cea3c0f",
    1606     "path" : "\/usr\/lib\/dyld",
    1607     "name" : "dyld"
    1608   },
    1609   {
    1610     "size" : 0,
    1611     "source" : "A",
    1612     "base" : 0,
    1613     "uuid" : "00000000-0000-0000-0000-000000000000"
    1614   },
    1615   {
    1616     "source" : "P",
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    1620     "uuid" : "1480b446-99f7-3757-9d4e-5ba3014a2726",
    1621     "path" : "\/usr\/lib\/system\/libsystem_malloc.dylib",
    1622     "name" : "libsystem_malloc.dylib"
    1623   },
    1624   {
    1625     "source" : "P",
    1626     "arch" : "arm64e",
    1627     "base" : 6974017536,
    1628     "size" : 581628,
    1629     "uuid" : "bbab286c-2e51-3d64-9ae3-a4102935fe32",
    1630     "path" : "\/usr\/lib\/libc++.1.dylib",
    1631     "name" : "libc++.1.dylib"
    1632   },
    1633   {
    1634     "source" : "P",
    1635     "arch" : "arm64e",
    1636     "base" : 7086354432,
    1637     "CFBundleShortVersionString" : "1.22",
    1638     "CFBundleIdentifier" : "com.apple.HIServices",
    1639     "size" : 446464,
    1640     "uuid" : "5af090d7-4d2e-3263-9bec-687bc2058651",
    1641     "path" : "\/System\/Library\/Frameworks\/ApplicationServices.framework\/Versions\/A\/Frameworks\/HIServices.framework\/Versions\/A\/HIServices",
    1642     "name" : "HIServices"
    1643   },
    1644   {
    1645     "source" : "P",
    1646     "arch" : "arm64e",
    1647     "base" : 6994235392,
    1648     "CFBundleShortVersionString" : "6.9",
    1649     "CFBundleIdentifier" : "com.apple.Foundation",
    1650     "size" : 14974976,
    1651     "uuid" : "16d282d0-8b48-3e76-8036-fcb45dece518",
    1652     "path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
    1653     "name" : "Foundation",
    1654     "CFBundleVersion" : "3302.1.400"
    1655   }
     72[deleted to fit within ticket limits]
     73
    165674],
    165775  "sharedCache" : {
    … …  
    37722190> hide sel atoms
    37732191
    3774 > matchmaker #7/B to #2/B pairing ss
    3775 
    3776 Parameters 
    3777 --- 
    3778 Chain pairing | ss 
    3779 Alignment algorithm | Needleman-Wunsch 
    3780 Similarity matrix | BLOSUM-62 
    3781 SS fraction | 0.3 
    3782 Gap open (HH/SS/other) | 18/18/6 
    3783 Gap extend | 1 
    3784 SS matrix |  |  | H | S | O 
    3785 ---|---|---|--- 
    3786 H | 6 | -9 | -6 
    3787 S |  | 6 | -6 
    3788 O |  |  | 4 
    3789 Iteration cutoff | 2 
    3790  
    3791 Matchmaker 2ac0, chain B (#2) with 4mzr, chain B (#7), sequence alignment
    3792 score = 843.2 
    3793 RMSD between 190 pruned atom pairs is 0.842 angstroms; (across all 198 pairs:
    3794 1.070) 
    3795  
    3796 
    3797 > hide #!2 models
    3798 
    3799 > hide #!3 models
    3800 
    3801 > show #!2 models
    3802 
    3803 > matchmaker #7/C to #2/B pairing ss
    3804 
    3805 Parameters 
    3806 --- 
    3807 Chain pairing | ss 
    3808 Alignment algorithm | Needleman-Wunsch 
    3809 Similarity matrix | BLOSUM-62 
    3810 SS fraction | 0.3 
    3811 Gap open (HH/SS/other) | 18/18/6 
    3812 Gap extend | 1 
    3813 SS matrix |  |  | H | S | O 
    3814 ---|---|---|--- 
    3815 H | 6 | -9 | -6 
    3816 S |  | 6 | -6 
    3817 O |  |  | 4 
    3818 Iteration cutoff | 2 
    3819  
    3820 Matchmaker 2ac0, chain B (#2) with 4mzr, chain C (#7), sequence alignment
    3821 score = 933.2 
    3822 RMSD between 193 pruned atom pairs is 0.571 angstroms; (across all 198 pairs:
    3823 0.889) 
    3824  
    3825 
    3826 > matchmaker #7/D to #2/B pairing ss
    3827 
    3828 Parameters 
    3829 --- 
    3830 Chain pairing | ss 
    3831 Alignment algorithm | Needleman-Wunsch 
    3832 Similarity matrix | BLOSUM-62 
    3833 SS fraction | 0.3 
    3834 Gap open (HH/SS/other) | 18/18/6 
    3835 Gap extend | 1 
    3836 SS matrix |  |  | H | S | O 
    3837 ---|---|---|--- 
    3838 H | 6 | -9 | -6 
    3839 S |  | 6 | -6 
    3840 O |  |  | 4 
    3841 Iteration cutoff | 2 
    3842  
    3843 Matchmaker 2ac0, chain B (#2) with 4mzr, chain D (#7), sequence alignment
    3844 score = 948.8 
    3845 RMSD between 186 pruned atom pairs is 0.544 angstroms; (across all 198 pairs:
    3846 2.118) 
    3847  
    3848 
    3849 > matchmaker #7/A to #2/B pairing ss
    3850 
    3851 Parameters 
    3852 --- 
    3853 Chain pairing | ss 
    3854 Alignment algorithm | Needleman-Wunsch 
    3855 Similarity matrix | BLOSUM-62 
    3856 SS fraction | 0.3 
    3857 Gap open (HH/SS/other) | 18/18/6 
    3858 Gap extend | 1 
    3859 SS matrix |  |  | H | S | O 
    3860 ---|---|---|--- 
    3861 H | 6 | -9 | -6 
    3862 S |  | 6 | -6 
    3863 O |  |  | 4 
    3864 Iteration cutoff | 2 
    3865  
    3866 Matchmaker 2ac0, chain B (#2) with 4mzr, chain A (#7), sequence alignment
    3867 score = 948.8 
    3868 RMSD between 186 pruned atom pairs is 0.543 angstroms; (across all 198 pairs:
    3869 2.117) 
    3870  
    3871 
    3872 > select subtract #7
    3873 
    3874 Nothing selected 
    3875 
    3876 > matchmaker #7/C to #2/B pairing ss
    3877 
    3878 Parameters 
    3879 --- 
    3880 Chain pairing | ss 
    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 2ac0, chain B (#2) with 4mzr, chain C (#7), sequence alignment
    3894 score = 933.2 
    3895 RMSD between 193 pruned atom pairs is 0.571 angstroms; (across all 198 pairs:
    3896 0.889) 
    3897  
    3898 
    3899 > matchmaker #7/B to #2/B pairing ss
    3900 
    3901 Parameters 
    3902 --- 
    3903 Chain pairing | ss 
    3904 Alignment algorithm | Needleman-Wunsch 
    3905 Similarity matrix | BLOSUM-62 
    3906 SS fraction | 0.3 
    3907 Gap open (HH/SS/other) | 18/18/6 
    3908 Gap extend | 1 
    3909 SS matrix |  |  | H | S | O 
    3910 ---|---|---|--- 
    3911 H | 6 | -9 | -6 
    3912 S |  | 6 | -6 
    3913 O |  |  | 4 
    3914 Iteration cutoff | 2 
    3915  
    3916 Matchmaker 2ac0, chain B (#2) with 4mzr, chain B (#7), sequence alignment
    3917 score = 843.2 
    3918 RMSD between 190 pruned atom pairs is 0.842 angstroms; (across all 198 pairs:
    3919 1.070) 
    3920  
    3921 
    3922 > matchmaker #7/D to #2/B pairing ss
    3923 
    3924 Parameters 
    3925 --- 
    3926 Chain pairing | ss 
    3927 Alignment algorithm | Needleman-Wunsch 
    3928 Similarity matrix | BLOSUM-62 
    3929 SS fraction | 0.3 
    3930 Gap open (HH/SS/other) | 18/18/6 
    3931 Gap extend | 1 
    3932 SS matrix |  |  | H | S | O 
    3933 ---|---|---|--- 
    3934 H | 6 | -9 | -6 
    3935 S |  | 6 | -6 
    3936 O |  |  | 4 
    3937 Iteration cutoff | 2 
    3938  
    3939 Matchmaker 2ac0, chain B (#2) with 4mzr, chain D (#7), sequence alignment
    3940 score = 948.8 
    3941 RMSD between 186 pruned atom pairs is 0.544 angstroms; (across all 198 pairs:
    3942 2.118) 
    3943  
    3944 
    3945 > open 4ibu fromDatabase pdb format mmcif
    3946 
    3947 Summary of feedback from opening 4ibu fetched from pdb 
    3948 --- 
    3949 note | Fetching compressed mmCIF 4ibu from http://files.rcsb.org/download/4ibu.cif 
    3950  
    3951 4ibu title: 
    3952 Human p53 core domain with hot spot mutation R273C and second-site suppressor
    3953 mutation T284R in sequence-specific complex with DNA [more info...] 
    3954  
    3955 Chain information for 4ibu #8 
    3956 --- 
    3957 Chain | Description | UniProt 
    3958 A B C D | Cellular tumor antigen p53 | P53_HUMAN 94-293 
    3959 E F G H | DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3') |   
    3960  
    3961 Non-standard residues in 4ibu #8 
    3962 --- 
    3963 ACT — acetate ion 
    3964 EDO — 1,2-ethanediol (ethylene glycol) 
    3965 ZN — zinc ion 
    3966  
    3967 382 atoms have alternate locations. Control/examine alternate locations with
    3968 Altloc Explorer [start tool...] or the altlocs command. 
    3969 
    3970 > open 4ibv fromDatabase pdb format mmcif
    3971 
    3972 Summary of feedback from opening 4ibv fetched from pdb 
    3973 --- 
    3974 note | Fetching compressed mmCIF 4ibv from http://files.rcsb.org/download/4ibv.cif 
    3975  
    3976 4ibv title: 
    3977 Human p53 core domain with hot spot mutation R273C and second-site suppressor
    3978 mutation S240R in sequence-specific complex with DNA [more info...] 
    3979  
    3980 Chain information for 4ibv #9 
    3981 --- 
    3982 Chain | Description | UniProt 
    3983 A | Cellular tumor antigen p53 | P53_HUMAN 94-293 
    3984 B | DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3') |   
    3985  
    3986 Non-standard residues in 4ibv #9 
    3987 --- 
    3988 EDO — 1,2-ethanediol (ethylene glycol) 
    3989 ZN — zinc ion 
    3990  
    3991 4ibv mmCIF Assemblies 
    3992 --- 
    3993 1| author_and_software_defined_assembly 
    3994  
    3995 98 atoms have alternate locations. Control/examine alternate locations with
    3996 Altloc Explorer [start tool...] or the altlocs command. 
    3997 
    3998 > open 4ibw fromDatabase pdb format mmcif
    3999 
    4000 Summary of feedback from opening 4ibw fetched from pdb 
    4001 --- 
    4002 note | Fetching compressed mmCIF 4ibw from http://files.rcsb.org/download/4ibw.cif 
    4003  
    4004 4ibw title: 
    4005 Human p53 core domain with hot spot mutation R273H and second-site suppressor
    4006 mutation T284R in sequence-specific complex with DNA [more info...] 
    4007  
    4008 Chain information for 4ibw #10 
    4009 --- 
    4010 Chain | Description | UniProt 
    4011 A | Cellular tumor antigen p53 | P53_HUMAN 94-293 
    4012 B | DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3') |   
    4013  
    4014 Non-standard residues in 4ibw #10 
    4015 --- 
    4016 EDO — 1,2-ethanediol (ethylene glycol) 
    4017 ZN — zinc ion 
    4018  
    4019 4ibw mmCIF Assemblies 
    4020 --- 
    4021 1| author_defined_assembly 
    4022  
    4023 140 atoms have alternate locations. Control/examine alternate locations with
    4024 Altloc Explorer [start tool...] or the altlocs command. 
    4025 
    4026 > open 4hje fromDatabase pdb format mmcif
    4027 
    4028 Summary of feedback from opening 4hje fetched from pdb 
    4029 --- 
    4030 note | Fetching compressed mmCIF 4hje from http://files.rcsb.org/download/4hje.cif 
    4031  
    4032 4hje title: 
    4033 Crystal structure of p53 core domain in complex with DNA [more info...] 
    4034  
    4035 Chain information for 4hje #11 
    4036 --- 
    4037 Chain | Description | UniProt 
    4038 A B C D | Cellular tumor antigen p53 | P53_HUMAN 92-291 
    4039 E | DNA (5'-D(*TP*CP*AP*CP*AP*AP*GP*TP*TP*AP*GP*AP*GP*AP*CP*AP*AP*GP*CP*CP*T)-3') |   
    4040 F | DNA (5'-D(*AP*GP*GP*CP*TP*TP*GP*TP*CP*TP*CP*TP*AP*AP*CP*TP*TP*GP*TP*GP*A)-3') |   
    4041  
    4042 Non-standard residues in 4hje #11 
    4043 --- 
    4044 ZN — zinc ion 
    4045  
    4046 
    4047 > select add #11
    4048 
    4049 7975 atoms, 7386 bonds, 63 pseudobonds, 1678 residues, 3 models selected 
    4050 
    4051 > select add #10
    4052 
    4053 10147 atoms, 9266 bonds, 68 pseudobonds, 2240 residues, 6 models selected 
    4054 
    4055 > select add #9
    4056 
    4057 12096 atoms, 11103 bonds, 73 pseudobonds, 2620 residues, 9 models selected 
    4058 
    4059 > select add #8
    4060 
    4061 20184 atoms, 18460 bonds, 154 pseudobonds, 4433 residues, 12 models selected 
    4062 
    4063 > select add #7
    4064 
    4065 28777 atoms, 27272 bonds, 227 pseudobonds, 5494 residues, 15 models selected 
    4066 
    4067 > style sel stick
    4068 
    4069 Changed 28777 atom styles 
    4070 
    4071 > hide sel atoms
    4072 
    4073 > show sel cartoons
    4074 
    4075 > ui mousemode right select
    4076 
    4077 > select clear
    4078 
    4079 > matchmaker #11/B to #2/B pairing ss
    4080 
    4081 Parameters 
    4082 --- 
    4083 Chain pairing | ss 
    4084 Alignment algorithm | Needleman-Wunsch 
    4085 Similarity matrix | BLOSUM-62 
    4086 SS fraction | 0.3 
    4087 Gap open (HH/SS/other) | 18/18/6 
    4088 Gap extend | 1 
    4089 SS matrix |  |  | H | S | O 
    4090 ---|---|---|--- 
    4091 H | 6 | -9 | -6 
    4092 S |  | 6 | -6 
    4093 O |  |  | 4 
    4094 Iteration cutoff | 2 
    4095  
    4096 Matchmaker 2ac0, chain B (#2) with 4hje, chain B (#11), sequence alignment
    4097 score = 1018.3 
    4098 RMSD between 195 pruned atom pairs is 0.356 angstroms; (across all 198 pairs:
    4099 0.530) 
    4100  
    4101 
    4102 > matchmaker #10/B to #2/B pairing ss
    4103 
    4104 Match chain (4ibw (#10) chain B) not compatible with BLOSUM-62 similarity
    4105 matrix 
    4106 
    4107 > hide #!11 models
    4108 
    4109 > hide #!2 models
    4110 
    4111 > hide #!7 models
    4112 
    4113 > hide #!8 models
    4114 
    4115 > hide #!9 models
    4116 
    4117 > show #!2 models
    4118 
    4119 > matchmaker #10/A to #2/B pairing ss
    4120 
    4121 Parameters 
    4122 --- 
    4123 Chain pairing | ss 
    4124 Alignment algorithm | Needleman-Wunsch 
    4125 Similarity matrix | BLOSUM-62 
    4126 SS fraction | 0.3 
    4127 Gap open (HH/SS/other) | 18/18/6 
    4128 Gap extend | 1 
    4129 SS matrix |  |  | H | S | O 
    4130 ---|---|---|--- 
    4131 H | 6 | -9 | -6 
    4132 S |  | 6 | -6 
    4133 O |  |  | 4 
    4134 Iteration cutoff | 2 
    4135  
    4136 Matchmaker 2ac0, chain B (#2) with 4ibw, chain A (#10), sequence alignment
    4137 score = 1011.7 
    4138 RMSD between 188 pruned atom pairs is 0.497 angstroms; (across all 195 pairs:
    4139 0.717) 
    4140  
    4141 
    4142 > show #!1 models
    4143 
    4144 > show #!3 models
    4145 
    4146 > show #!4 models
    4147 
    4148 > show #!5 models
    4149 
    4150 > show #!6 models
    4151 
    4152 > show #!7 models
    4153 
    4154 > matchmaker #9/A to #2/B pairing ss
    4155 
    4156 Parameters 
    4157 --- 
    4158 Chain pairing | ss 
    4159 Alignment algorithm | Needleman-Wunsch 
    4160 Similarity matrix | BLOSUM-62 
    4161 SS fraction | 0.3 
    4162 Gap open (HH/SS/other) | 18/18/6 
    4163 Gap extend | 1 
    4164 SS matrix |  |  | H | S | O 
    4165 ---|---|---|--- 
    4166 H | 6 | -9 | -6 
    4167 S |  | 6 | -6 
    4168 O |  |  | 4 
    4169 Iteration cutoff | 2 
    4170  
    4171 Matchmaker 2ac0, chain B (#2) with 4ibv, chain A (#9), sequence alignment
    4172 score = 1000.1 
    4173 RMSD between 185 pruned atom pairs is 0.508 angstroms; (across all 195 pairs:
    4174 1.235) 
    4175  
    4176 
    4177 > show #!9 models
    4178 
    4179 > show #!8 models
    4180 
    4181 > hide #!9 models
    4182 
    4183 > show #!9 models
    4184 
    4185 > matchmaker #8/B to #2/B pairing ss
    4186 
    4187 Parameters 
    4188 --- 
    4189 Chain pairing | ss 
    4190 Alignment algorithm | Needleman-Wunsch 
    4191 Similarity matrix | BLOSUM-62 
    4192 SS fraction | 0.3 
    4193 Gap open (HH/SS/other) | 18/18/6 
    4194 Gap extend | 1 
    4195 SS matrix |  |  | H | S | O 
    4196 ---|---|---|--- 
    4197 H | 6 | -9 | -6 
    4198 S |  | 6 | -6 
    4199 O |  |  | 4 
    4200 Iteration cutoff | 2 
    4201  
    4202 Matchmaker 2ac0, chain B (#2) with 4ibu, chain B (#8), sequence alignment
    4203 score = 1018 
    4204 RMSD between 196 pruned atom pairs is 0.320 angstroms; (across all 198 pairs:
    4205 0.451) 
    4206  
    4207 
    4208 > select add #1
    4209 
    4210 5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected 
    4211 
    4212 > select subtract #1
    4213 
    4214 Nothing selected 
    4215 
    4216 > select add #10
    4217 
    4218 2172 atoms, 1880 bonds, 5 pseudobonds, 562 residues, 3 models selected 
    4219 
    4220 > select add #9
    4221 
    4222 4121 atoms, 3717 bonds, 10 pseudobonds, 942 residues, 6 models selected 
    4223 
    4224 > show #!11 models
    4225 
    4226 > matchmaker #11/B to #2/B pairing ss
    4227 
    4228 Parameters 
    4229 --- 
    4230 Chain pairing | ss 
    4231 Alignment algorithm | Needleman-Wunsch 
    4232 Similarity matrix | BLOSUM-62 
    4233 SS fraction | 0.3 
    4234 Gap open (HH/SS/other) | 18/18/6 
    4235 Gap extend | 1 
    4236 SS matrix |  |  | H | S | O 
    4237 ---|---|---|--- 
    4238 H | 6 | -9 | -6 
    4239 S |  | 6 | -6 
    4240 O |  |  | 4 
    4241 Iteration cutoff | 2 
    4242  
    4243 Matchmaker 2ac0, chain B (#2) with 4hje, chain B (#11), sequence alignment
    4244 score = 1018.3 
    4245 RMSD between 195 pruned atom pairs is 0.356 angstroms; (across all 198 pairs:
    4246 0.530) 
    4247  
    4248 
    4249 > matchmaker #11/A to #2/B pairing ss
    4250 
    4251 Parameters 
    4252 --- 
    4253 Chain pairing | ss 
    4254 Alignment algorithm | Needleman-Wunsch 
    4255 Similarity matrix | BLOSUM-62 
    4256 SS fraction | 0.3 
    4257 Gap open (HH/SS/other) | 18/18/6 
    4258 Gap extend | 1 
    4259 SS matrix |  |  | H | S | O 
    4260 ---|---|---|--- 
    4261 H | 6 | -9 | -6 
    4262 S |  | 6 | -6 
    4263 O |  |  | 4 
    4264 Iteration cutoff | 2 
    4265  
    4266 Matchmaker 2ac0, chain B (#2) with 4hje, chain A (#11), sequence alignment
    4267 score = 1018.3 
    4268 RMSD between 196 pruned atom pairs is 0.344 angstroms; (across all 198 pairs:
    4269 0.482) 
    4270  
    4271 
    4272 > select add #11
    4273 
    4274 12096 atoms, 11103 bonds, 73 pseudobonds, 2620 residues, 9 models selected 
    4275 
    4276 > select add #8
    4277 
    4278 20184 atoms, 18460 bonds, 154 pseudobonds, 4433 residues, 12 models selected 
    4279 
    4280 > select add #7
    4281 
    4282 28777 atoms, 27272 bonds, 227 pseudobonds, 5494 residues, 15 models selected 
    4283 
    4284 > select add #6
    4285 
    4286 30709 atoms, 29107 bonds, 231 pseudobonds, 5860 residues, 17 models selected 
    4287 
    4288 > select add #5
    4289 
    4290 38490 atoms, 36414 bonds, 301 pseudobonds, 7415 residues, 20 models selected 
    4291 
    4292 > select add #4
    4293 
    4294 46525 atoms, 43695 bonds, 375 pseudobonds, 9248 residues, 31 models selected 
    4295 
    4296 > select add #3
    4297 
    4298 53618 atoms, 51008 bonds, 432 pseudobonds, 10103 residues, 42 models selected 
    4299 
    4300 > select add #2
    4301 
    4302 61828 atoms, 58416 bonds, 510 pseudobonds, 11999 residues, 45 models selected 
    4303 
    4304 > select add #1
    4305 
    4306 67656 atoms, 64065 bonds, 565 pseudobonds, 13013 residues, 56 models selected 
    4307 
    4308 > style sel stick
    4309 
    4310 Changed 67656 atom styles 
    4311 
    4312 > hide sel atoms
    4313 
    4314 > show sel cartoons
    4315 
    4316 > select clear
    4317 
    4318 > select O
    4319 
    4320 18203 atoms, 12968 residues, 11 models selected 
    4321 
    4322 > show sel atoms
    4323 
    4324 > select clear
    4325 
    4326 > select add #1
    4327 
    4328 5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected 
    4329 
    4330 > select add #2
    4331 
    4332 14038 atoms, 13057 bonds, 133 pseudobonds, 2910 residues, 6 models selected 
    4333 
    4334 > select add #3
    4335 
    4336 21131 atoms, 20370 bonds, 190 pseudobonds, 3765 residues, 17 models selected 
    4337 
    4338 > select add #5
    4339 
    4340 28912 atoms, 27677 bonds, 260 pseudobonds, 5320 residues, 20 models selected 
    4341 
    4342 > select add #4
    4343 
    4344 36947 atoms, 34958 bonds, 334 pseudobonds, 7153 residues, 31 models selected 
    4345 
    4346 > select add #6
    4347 
    4348 38879 atoms, 36793 bonds, 338 pseudobonds, 7519 residues, 41 models selected 
    4349 
    4350 > select add #7
    4351 
    4352 47472 atoms, 45605 bonds, 411 pseudobonds, 8580 residues, 44 models selected 
    4353 
    4354 > select add #8
    4355 
    4356 55560 atoms, 52962 bonds, 492 pseudobonds, 10393 residues, 47 models selected 
    4357 
    4358 > select add #9
    4359 
    4360 57509 atoms, 54799 bonds, 497 pseudobonds, 10773 residues, 50 models selected 
    4361 
    4362 > select add #10
    4363 
    4364 59681 atoms, 56679 bonds, 502 pseudobonds, 11335 residues, 53 models selected 
    4365 
    4366 > select add #11
    4367 
    4368 67656 atoms, 64065 bonds, 565 pseudobonds, 13013 residues, 56 models selected 
    4369 
    4370 > hide sel atoms
    4371 
    4372 > show sel atoms
    4373 
    4374 > hide sel cartoons
    4375 
    4376 > select H
    4377 
    4378 Nothing selected 
    4379 
    4380 > show atoms
    4381 
    4382 > select hydroxyl
    4383 
    4384 1506 atoms, 1466 residues, 11 models selected 
    4385 
    4386 > show sel atoms
    4387 
    4388 > select add #1
    4389 
    4390 7211 atoms, 5649 bonds, 55 pseudobonds, 2357 residues, 37 models selected 
    4391 
    4392 > select subtract #1
    4393 
    4394 1383 atoms, 1343 residues, 34 models selected 
    4395 
    4396 > select clear
    4397 
    4398 > select add #1
    4399 
    4400 5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected 
    4401 
    4402 > select add #2
    4403 
    4404 14038 atoms, 13057 bonds, 133 pseudobonds, 2910 residues, 6 models selected 
    4405 
    4406 > select add #3
    4407 
    4408 21131 atoms, 20370 bonds, 190 pseudobonds, 3765 residues, 17 models selected 
    4409 
    4410 > select add #4
    4411 
    4412 29166 atoms, 27651 bonds, 264 pseudobonds, 5598 residues, 20 models selected 
    4413 
    4414 > select add #5
    4415 
    4416 36947 atoms, 34958 bonds, 334 pseudobonds, 7153 residues, 31 models selected 
    4417 
    4418 > select add #6
    4419 
    4420 38879 atoms, 36793 bonds, 338 pseudobonds, 7519 residues, 41 models selected 
    4421 
    4422 > select add #7
    4423 
    4424 47472 atoms, 45605 bonds, 411 pseudobonds, 8580 residues, 44 models selected 
    4425 
    4426 > select add #9
    4427 
    4428 49421 atoms, 47442 bonds, 416 pseudobonds, 8960 residues, 47 models selected 
    4429 
    4430 > select add #8
    4431 
    4432 57509 atoms, 54799 bonds, 497 pseudobonds, 10773 residues, 50 models selected 
    4433 
    4434 > select add #10
    4435 
    4436 59681 atoms, 56679 bonds, 502 pseudobonds, 11335 residues, 53 models selected 
    4437 
    4438 > select add #11
    4439 
    4440 67656 atoms, 64065 bonds, 565 pseudobonds, 13013 residues, 56 models selected 
    4441 
    4442 > show sel cartoons
    4443 
    4444 > hide sel atoms
    4445 
    4446 > open 3ts8 fromDatabase pdb format mmcif
    4447 
    4448 Summary of feedback from opening 3ts8 fetched from pdb 
    4449 --- 
    4450 note | Fetching compressed mmCIF 3ts8 from http://files.rcsb.org/download/3ts8.cif 
    4451  
    4452 3ts8 title: 
    4453 Crystal structure of a multidomain human p53 tetramer bound to the natural
    4454 CDKN1A(p21) p53-response element [more info...] 
    4455  
    4456 Chain information for 3ts8 #12 
    4457 --- 
    4458 Chain | Description | UniProt 
    4459 A B C D | Cellular tumor antigen p53 | P53_HUMAN 94-291 321-356 
    4460 K | CDKN1A(p21) sense strand |   
    4461 L | CDKN1A(p21) anti-sense strand |   
    4462  
    4463 Non-standard residues in 3ts8 #12 
    4464 --- 
    4465 ZN — zinc ion 
    4466  
    4467 
    4468 > select clear
    4469 
    4470 > select add #12
    4471 
    4472 8621 atoms, 8800 bonds, 71 pseudobonds, 1097 residues, 3 models selected 
    4473 
    4474 > style sel stick
    4475 
    4476 Changed 8621 atom styles 
    4477 
    4478 > show sel cartoons
    4479 
    4480 > hide sel atoms
    4481 
    4482 > matchmaker #12/B to #2/B pairing ss
    4483 
    4484 Parameters 
    4485 --- 
    4486 Chain pairing | ss 
    4487 Alignment algorithm | Needleman-Wunsch 
    4488 Similarity matrix | BLOSUM-62 
    4489 SS fraction | 0.3 
    4490 Gap open (HH/SS/other) | 18/18/6 
    4491 Gap extend | 1 
    4492 SS matrix |  |  | H | S | O 
    4493 ---|---|---|--- 
    4494 H | 6 | -9 | -6 
    4495 S |  | 6 | -6 
    4496 O |  |  | 4 
    4497 Iteration cutoff | 2 
    4498  
    4499 Matchmaker 2ac0, chain B (#2) with 3ts8, chain B (#12), sequence alignment
    4500 score = 893.7 
    4501 RMSD between 183 pruned atom pairs is 0.874 angstroms; (across all 198 pairs:
    4502 1.399) 
    4503  
    4504 
    4505 > matchmaker #12/A to #2/B pairing ss
    4506 
    4507 Parameters 
    4508 --- 
    4509 Chain pairing | ss 
    4510 Alignment algorithm | Needleman-Wunsch 
    4511 Similarity matrix | BLOSUM-62 
    4512 SS fraction | 0.3 
    4513 Gap open (HH/SS/other) | 18/18/6 
    4514 Gap extend | 1 
    4515 SS matrix |  |  | H | S | O 
    4516 ---|---|---|--- 
    4517 H | 6 | -9 | -6 
    4518 S |  | 6 | -6 
    4519 O |  |  | 4 
    4520 Iteration cutoff | 2 
    4521  
    4522 Matchmaker 2ac0, chain B (#2) with 3ts8, chain A (#12), sequence alignment
    4523 score = 947.1 
    4524 RMSD between 186 pruned atom pairs is 0.545 angstroms; (across all 198 pairs:
    4525 2.430) 
    4526  
    4527 
    4528 > matchmaker #11/C to #2/B pairing ss
    4529 
    4530 Parameters 
    4531 --- 
    4532 Chain pairing | ss 
    4533 Alignment algorithm | Needleman-Wunsch 
    4534 Similarity matrix | BLOSUM-62 
    4535 SS fraction | 0.3 
    4536 Gap open (HH/SS/other) | 18/18/6 
    4537 Gap extend | 1 
    4538 SS matrix |  |  | H | S | O 
    4539 ---|---|---|--- 
    4540 H | 6 | -9 | -6 
    4541 S |  | 6 | -6 
    4542 O |  |  | 4 
    4543 Iteration cutoff | 2 
    4544  
    4545 Matchmaker 2ac0, chain B (#2) with 4hje, chain C (#11), sequence alignment
    4546 score = 1018.3 
    4547 RMSD between 196 pruned atom pairs is 0.349 angstroms; (across all 198 pairs:
    4548 0.485) 
    4549  
    4550 
    4551 > matchmaker #12/D to #2/B pairing ss
    4552 
    4553 Parameters 
    4554 --- 
    4555 Chain pairing | ss 
    4556 Alignment algorithm | Needleman-Wunsch 
    4557 Similarity matrix | BLOSUM-62 
    4558 SS fraction | 0.3 
    4559 Gap open (HH/SS/other) | 18/18/6 
    4560 Gap extend | 1 
    4561 SS matrix |  |  | H | S | O 
    4562 ---|---|---|--- 
    4563 H | 6 | -9 | -6 
    4564 S |  | 6 | -6 
    4565 O |  |  | 4 
    4566 Iteration cutoff | 2 
    4567  
    4568 Matchmaker 2ac0, chain B (#2) with 3ts8, chain D (#12), sequence alignment
    4569 score = 950.1 
    4570 RMSD between 186 pruned atom pairs is 0.547 angstroms; (across all 198 pairs:
    4571 2.431) 
    4572  
    4573 
    4574 > hide #!11 models
    4575 
    4576 > hide #!10 models
    4577 
    4578 > hide #!9 models
    4579 
    4580 > hide #!8 models
    4581 
    4582 > hide #!7 models
    4583 
    4584 > hide #!6 models
    4585 
    4586 > hide #!5 models
    4587 
    4588 > hide #!4 models
    4589 
    4590 > hide #!3 models
    4591 
    4592 > hide #!2 models
    4593 
    4594 > hide #!1 models
    4595 
    4596 > show #!1 models
    4597 
    4598 > hide #!1 models
    4599 
    4600 > show #!1 models
    4601 
    4602 > hide #!1 models
    4603 
    4604 > show #!11 models
    4605 
    4606 > show #!2 models
    4607 
    4608 > hide #!11 models
    4609 
    4610 > matchmaker #12/A to #2/B pairing ss
    4611 
    4612 Parameters 
    4613 --- 
    4614 Chain pairing | ss 
    4615 Alignment algorithm | Needleman-Wunsch 
    4616 Similarity matrix | BLOSUM-62 
    4617 SS fraction | 0.3 
    4618 Gap open (HH/SS/other) | 18/18/6 
    4619 Gap extend | 1 
    4620 SS matrix |  |  | H | S | O 
    4621 ---|---|---|--- 
    4622 H | 6 | -9 | -6 
    4623 S |  | 6 | -6 
    4624 O |  |  | 4 
    4625 Iteration cutoff | 2 
    4626  
    4627 Matchmaker 2ac0, chain B (#2) with 3ts8, chain A (#12), sequence alignment
    4628 score = 947.1 
    4629 RMSD between 186 pruned atom pairs is 0.545 angstroms; (across all 198 pairs:
    4630 2.430) 
    4631  
    4632 
    4633 > matchmaker #12/B to #2/B pairing ss
    4634 
    4635 Parameters 
    4636 --- 
    4637 Chain pairing | ss 
    4638 Alignment algorithm | Needleman-Wunsch 
    4639 Similarity matrix | BLOSUM-62 
    4640 SS fraction | 0.3 
    4641 Gap open (HH/SS/other) | 18/18/6 
    4642 Gap extend | 1 
    4643 SS matrix |  |  | H | S | O 
    4644 ---|---|---|--- 
    4645 H | 6 | -9 | -6 
    4646 S |  | 6 | -6 
    4647 O |  |  | 4 
    4648 Iteration cutoff | 2 
    4649  
    4650 Matchmaker 2ac0, chain B (#2) with 3ts8, chain B (#12), sequence alignment
    4651 score = 893.7 
    4652 RMSD between 183 pruned atom pairs is 0.874 angstroms; (across all 198 pairs:
    4653 1.399) 
    4654  
    4655 
    4656 > matchmaker #12/C to #2/B pairing ss
    4657 
    4658 Parameters 
    4659 --- 
    4660 Chain pairing | ss 
    4661 Alignment algorithm | Needleman-Wunsch 
    4662 Similarity matrix | BLOSUM-62 
    4663 SS fraction | 0.3 
    4664 Gap open (HH/SS/other) | 18/18/6 
    4665 Gap extend | 1 
    4666 SS matrix |  |  | H | S | O 
    4667 ---|---|---|--- 
    4668 H | 6 | -9 | -6 
    4669 S |  | 6 | -6 
    4670 O |  |  | 4 
    4671 Iteration cutoff | 2 
    4672  
    4673 Matchmaker 2ac0, chain B (#2) with 3ts8, chain C (#12), sequence alignment
    4674 score = 939.3 
    4675 RMSD between 192 pruned atom pairs is 0.573 angstroms; (across all 198 pairs:
    4676 0.928) 
    4677  
    4678 
    4679 > matchmaker #12/D to #2/B pairing ss
    4680 
    4681 Parameters 
    4682 --- 
    4683 Chain pairing | ss 
    4684 Alignment algorithm | Needleman-Wunsch 
    4685 Similarity matrix | BLOSUM-62 
    4686 SS fraction | 0.3 
    4687 Gap open (HH/SS/other) | 18/18/6 
    4688 Gap extend | 1 
    4689 SS matrix |  |  | H | S | O 
    4690 ---|---|---|--- 
    4691 H | 6 | -9 | -6 
    4692 S |  | 6 | -6 
    4693 O |  |  | 4 
    4694 Iteration cutoff | 2 
    4695  
    4696 Matchmaker 2ac0, chain B (#2) with 3ts8, chain D (#12), sequence alignment
    4697 score = 950.1 
    4698 RMSD between 186 pruned atom pairs is 0.547 angstroms; (across all 198 pairs:
    4699 2.431) 
    4700  
    4701 
    4702 > hide #!12 models
    4703 
    4704 > show #!12 models
    4705 
    4706 > hide #!2 models
    4707 
    4708 > show #!2 models
    4709 
    4710 > matchmaker #12/L to #2/E pairing ss
    4711 
    4712 Using Nucleic matrix instead of BLOSUM-62 to match 3ts8 #12/L to 2ac0 #2/E 
    4713 Parameters 
    4714 --- 
    4715 Chain pairing | ss 
    4716 Alignment algorithm | Needleman-Wunsch 
    4717 Similarity matrix | Nucleic 
    4718 SS fraction | 0.3 
    4719 Gap open (HH/SS/other) | 18/18/6 
    4720 Gap extend | 1 
    4721 SS matrix |  |  | H | S | O 
    4722 ---|---|---|--- 
    4723 H | 6 | -9 | -6 
    4724 S |  | 6 | -6 
    4725 O |  |  | 4 
    4726 Iteration cutoff | 2 
    4727  
    4728 Matchmaker 2ac0, chain E (#2) with 3ts8, chain L (#12), sequence alignment
    4729 score = 23.5 
    4730 RMSD between 8 pruned atom pairs is 1.000 angstroms; (across all 12 pairs:
    4731 3.750) 
    4732  
    4733 
    4734 > matchmaker #12/K to #2/E pairing ss
    4735 
    4736 Using Nucleic matrix instead of BLOSUM-62 to match 3ts8 #12/K to 2ac0 #2/E 
    4737 Parameters 
    4738 --- 
    4739 Chain pairing | ss 
    4740 Alignment algorithm | Needleman-Wunsch 
    4741 Similarity matrix | Nucleic 
    4742 SS fraction | 0.3 
    4743 Gap open (HH/SS/other) | 18/18/6 
    4744 Gap extend | 1 
    4745 SS matrix |  |  | H | S | O 
    4746 ---|---|---|--- 
    4747 H | 6 | -9 | -6 
    4748 S |  | 6 | -6 
    4749 O |  |  | 4 
    4750 Iteration cutoff | 2 
    4751  
    4752 Matchmaker 2ac0, chain E (#2) with 3ts8, chain K (#12), sequence alignment
    4753 score = 23.5 
    4754 RMSD between 9 pruned atom pairs is 1.158 angstroms; (across all 12 pairs:
    4755 3.771) 
    4756  
    4757 
    4758 > matchmaker #12/L to #2/E pairing ss
    4759 
    4760 Using Nucleic matrix instead of BLOSUM-62 to match 3ts8 #12/L to 2ac0 #2/E 
    4761 Parameters 
    4762 --- 
    4763 Chain pairing | ss 
    4764 Alignment algorithm | Needleman-Wunsch 
    4765 Similarity matrix | Nucleic 
    4766 SS fraction | 0.3 
    4767 Gap open (HH/SS/other) | 18/18/6 
    4768 Gap extend | 1 
    4769 SS matrix |  |  | H | S | O 
    4770 ---|---|---|--- 
    4771 H | 6 | -9 | -6 
    4772 S |  | 6 | -6 
    4773 O |  |  | 4 
    4774 Iteration cutoff | 2 
    4775  
    4776 Matchmaker 2ac0, chain E (#2) with 3ts8, chain L (#12), sequence alignment
    4777 score = 23.5 
    4778 RMSD between 8 pruned atom pairs is 1.000 angstroms; (across all 12 pairs:
    4779 3.750) 
    4780  
    4781 
    4782 > hide #!2 models
    4783 
    4784 > select clear
    4785 
    4786 > show #!11 models
    4787 
    4788 > matchmaker #11/A to #12/A pairing ss
    4789 
    4790 Parameters 
    4791 --- 
    4792 Chain pairing | ss 
    4793 Alignment algorithm | Needleman-Wunsch 
    4794 Similarity matrix | BLOSUM-62 
    4795 SS fraction | 0.3 
    4796 Gap open (HH/SS/other) | 18/18/6 
    4797 Gap extend | 1 
    4798 SS matrix |  |  | H | S | O 
    4799 ---|---|---|--- 
    4800 H | 6 | -9 | -6 
    4801 S |  | 6 | -6 
    4802 O |  |  | 4 
    4803 Iteration cutoff | 2 
    4804  
    4805 Matchmaker 3ts8, chain A (#12) with 4hje, chain A (#11), sequence alignment
    4806 score = 941.4 
    4807 RMSD between 185 pruned atom pairs is 0.482 angstroms; (across all 198 pairs:
    4808 2.439) 
    4809  
    4810 
    4811 > matchmaker #11/B to #12/A pairing ss
    4812 
    4813 Parameters 
    4814 --- 
    4815 Chain pairing | ss 
    4816 Alignment algorithm | Needleman-Wunsch 
    4817 Similarity matrix | BLOSUM-62 
    4818 SS fraction | 0.3 
    4819 Gap open (HH/SS/other) | 18/18/6 
    4820 Gap extend | 1 
    4821 SS matrix |  |  | H | S | O 
    4822 ---|---|---|--- 
    4823 H | 6 | -9 | -6 
    4824 S |  | 6 | -6 
    4825 O |  |  | 4 
    4826 Iteration cutoff | 2 
    4827  
    4828 Matchmaker 3ts8, chain A (#12) with 4hje, chain B (#11), sequence alignment
    4829 score = 941.4 
    4830 RMSD between 183 pruned atom pairs is 0.461 angstroms; (across all 198 pairs:
    4831 2.441) 
    4832  
    4833 
    4834 > matchmaker #11/C to #12/A pairing ss
    4835 
    4836 Parameters 
    4837 --- 
    4838 Chain pairing | ss 
    4839 Alignment algorithm | Needleman-Wunsch 
    4840 Similarity matrix | BLOSUM-62 
    4841 SS fraction | 0.3 
    4842 Gap open (HH/SS/other) | 18/18/6 
    4843 Gap extend | 1 
    4844 SS matrix |  |  | H | S | O 
    4845 ---|---|---|--- 
    4846 H | 6 | -9 | -6 
    4847 S |  | 6 | -6 
    4848 O |  |  | 4 
    4849 Iteration cutoff | 2 
    4850  
    4851 Matchmaker 3ts8, chain A (#12) with 4hje, chain C (#11), sequence alignment
    4852 score = 941.4 
    4853 RMSD between 185 pruned atom pairs is 0.477 angstroms; (across all 198 pairs:
    4854 2.433) 
    4855  
    4856 
    4857 > matchmaker #11/D to #12/A pairing ss
    4858 
    4859 Parameters 
    4860 --- 
    4861 Chain pairing | ss 
    4862 Alignment algorithm | Needleman-Wunsch 
    4863 Similarity matrix | BLOSUM-62 
    4864 SS fraction | 0.3 
    4865 Gap open (HH/SS/other) | 18/18/6 
    4866 Gap extend | 1 
    4867 SS matrix |  |  | H | S | O 
    4868 ---|---|---|--- 
    4869 H | 6 | -9 | -6 
    4870 S |  | 6 | -6 
    4871 O |  |  | 4 
    4872 Iteration cutoff | 2 
    4873  
    4874 Matchmaker 3ts8, chain A (#12) with 4hje, chain D (#11), sequence alignment
    4875 score = 941.4 
    4876 RMSD between 183 pruned atom pairs is 0.466 angstroms; (across all 198 pairs:
    4877 2.450) 
    4878  
    4879 
    4880 > matchmaker #11/A to #12/A pairing ss
    4881 
    4882 Parameters 
    4883 --- 
    4884 Chain pairing | ss 
    4885 Alignment algorithm | Needleman-Wunsch 
    4886 Similarity matrix | BLOSUM-62 
    4887 SS fraction | 0.3 
    4888 Gap open (HH/SS/other) | 18/18/6 
    4889 Gap extend | 1 
    4890 SS matrix |  |  | H | S | O 
    4891 ---|---|---|--- 
    4892 H | 6 | -9 | -6 
    4893 S |  | 6 | -6 
    4894 O |  |  | 4 
    4895 Iteration cutoff | 2 
    4896  
    4897 Matchmaker 3ts8, chain A (#12) with 4hje, chain A (#11), sequence alignment
    4898 score = 941.4 
    4899 RMSD between 185 pruned atom pairs is 0.482 angstroms; (across all 198 pairs:
    4900 2.439) 
    4901  
    4902 
    4903 > hide #!11 models
    4904 
    4905 > show #!10 models
    4906 
    4907 > matchmaker #10/A to #12/A pairing ss
    4908 
    4909 Parameters 
    4910 --- 
    4911 Chain pairing | ss 
    4912 Alignment algorithm | Needleman-Wunsch 
    4913 Similarity matrix | BLOSUM-62 
    4914 SS fraction | 0.3 
    4915 Gap open (HH/SS/other) | 18/18/6 
    4916 Gap extend | 1 
    4917 SS matrix |  |  | H | S | O 
    4918 ---|---|---|--- 
    4919 H | 6 | -9 | -6 
    4920 S |  | 6 | -6 
    4921 O |  |  | 4 
    4922 Iteration cutoff | 2 
    4923  
    4924 Matchmaker 3ts8, chain A (#12) with 4ibw, chain A (#10), sequence alignment
    4925 score = 942.4 
    4926 RMSD between 184 pruned atom pairs is 0.577 angstroms; (across all 197 pairs:
    4927 2.357) 
    4928  
    4929 
    4930 > hide #!10 models
    4931 
    4932 > show #!9 models
    4933 
    4934 > matchmaker #9/A to #12/A pairing ss
    4935 
    4936 Parameters 
    4937 --- 
    4938 Chain pairing | ss 
    4939 Alignment algorithm | Needleman-Wunsch 
    4940 Similarity matrix | BLOSUM-62 
    4941 SS fraction | 0.3 
    4942 Gap open (HH/SS/other) | 18/18/6 
    4943 Gap extend | 1 
    4944 SS matrix |  |  | H | S | O 
    4945 ---|---|---|--- 
    4946 H | 6 | -9 | -6 
    4947 S |  | 6 | -6 
    4948 O |  |  | 4 
    4949 Iteration cutoff | 2 
    4950  
    4951 Matchmaker 3ts8, chain A (#12) with 4ibv, chain A (#9), sequence alignment
    4952 score = 944 
    4953 RMSD between 181 pruned atom pairs is 0.577 angstroms; (across all 197 pairs:
    4954 2.583) 
    4955  
    4956 
    4957 > hide #!9 models
    4958 
    4959 > show #!8 models
    4960 
    4961 > matchmaker #8/A to #12/A pairing ss
    4962 
    4963 Parameters 
    4964 --- 
    4965 Chain pairing | ss 
    4966 Alignment algorithm | Needleman-Wunsch 
    4967 Similarity matrix | BLOSUM-62 
    4968 SS fraction | 0.3 
    4969 Gap open (HH/SS/other) | 18/18/6 
    4970 Gap extend | 1 
    4971 SS matrix |  |  | H | S | O 
    4972 ---|---|---|--- 
    4973 H | 6 | -9 | -6 
    4974 S |  | 6 | -6 
    4975 O |  |  | 4 
    4976 Iteration cutoff | 2 
    4977  
    4978 Matchmaker 3ts8, chain A (#12) with 4ibu, chain A (#8), sequence alignment
    4979 score = 928.3 
    4980 RMSD between 184 pruned atom pairs is 0.578 angstroms; (across all 197 pairs:
    4981 2.491) 
    4982  
    4983 
    4984 > hide #!12 models
    4985 
    4986 > show #!12 models
    4987 
    4988 > matchmaker #8/B to #12/A pairing ss
    4989 
    4990 Parameters 
    4991 --- 
    4992 Chain pairing | ss 
    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 3ts8, chain A (#12) with 4ibu, chain B (#8), sequence alignment
    5006 score = 915.7 
    5007 RMSD between 185 pruned atom pairs is 0.556 angstroms; (across all 198 pairs:
    5008 2.406) 
    5009  
    5010 
    5011 > matchmaker #8/D to #12/A pairing ss
    5012 
    5013 Parameters 
    5014 --- 
    5015 Chain pairing | ss 
    5016 Alignment algorithm | Needleman-Wunsch 
    5017 Similarity matrix | BLOSUM-62 
    5018 SS fraction | 0.3 
    5019 Gap open (HH/SS/other) | 18/18/6 
    5020 Gap extend | 1 
    5021 SS matrix |  |  | H | S | O 
    5022 ---|---|---|--- 
    5023 H | 6 | -9 | -6 
    5024 S |  | 6 | -6 
    5025 O |  |  | 4 
    5026 Iteration cutoff | 2 
    5027  
    5028 Matchmaker 3ts8, chain A (#12) with 4ibu, chain D (#8), sequence alignment
    5029 score = 910.9 
    5030 RMSD between 187 pruned atom pairs is 0.556 angstroms; (across all 196 pairs:
    5031 2.334) 
    5032  
    5033 
    5034 > show #!9 models
    5035 
    5036 > hide #!9 models
    5037 
    5038 > matchmaker #8/B to #12/A pairing ss
    5039 
    5040 Parameters 
    5041 --- 
    5042 Chain pairing | ss 
    5043 Alignment algorithm | Needleman-Wunsch 
    5044 Similarity matrix | BLOSUM-62 
    5045 SS fraction | 0.3 
    5046 Gap open (HH/SS/other) | 18/18/6 
    5047 Gap extend | 1 
    5048 SS matrix |  |  | H | S | O 
    5049 ---|---|---|--- 
    5050 H | 6 | -9 | -6 
    5051 S |  | 6 | -6 
    5052 O |  |  | 4 
    5053 Iteration cutoff | 2 
    5054  
    5055 Matchmaker 3ts8, chain A (#12) with 4ibu, chain B (#8), sequence alignment
    5056 score = 915.7 
    5057 RMSD between 185 pruned atom pairs is 0.556 angstroms; (across all 198 pairs:
    5058 2.406) 
    5059  
    5060 
    5061 > matchmaker #8/A to #12/A pairing ss
    5062 
    5063 Parameters 
    5064 --- 
    5065 Chain pairing | ss 
    5066 Alignment algorithm | Needleman-Wunsch 
    5067 Similarity matrix | BLOSUM-62 
    5068 SS fraction | 0.3 
    5069 Gap open (HH/SS/other) | 18/18/6 
    5070 Gap extend | 1 
    5071 SS matrix |  |  | H | S | O 
    5072 ---|---|---|--- 
    5073 H | 6 | -9 | -6 
    5074 S |  | 6 | -6 
    5075 O |  |  | 4 
    5076 Iteration cutoff | 2 
    5077  
    5078 Matchmaker 3ts8, chain A (#12) with 4ibu, chain A (#8), sequence alignment
    5079 score = 928.3 
    5080 RMSD between 184 pruned atom pairs is 0.578 angstroms; (across all 197 pairs:
    5081 2.491) 
    5082  
    5083 
    5084 > hide #!12 models
    5085 
    5086 > show #!12 models
    5087 
    5088 > hide #!12 models
    5089 
    5090 > show #!12 models
    5091 
    5092 > hide #!12 models
    5093 
    5094 > show #!12 models
    5095 
    5096 > hide #!8 models
    5097 
    5098 > show #!7 models
    5099 
    5100 > matchmaker #7/A to #12/A pairing ss
    5101 
    5102 Parameters 
    5103 --- 
    5104 Chain pairing | ss 
    5105 Alignment algorithm | Needleman-Wunsch 
    5106 Similarity matrix | BLOSUM-62 
    5107 SS fraction | 0.3 
    5108 Gap open (HH/SS/other) | 18/18/6 
    5109 Gap extend | 1 
    5110 SS matrix |  |  | H | S | O 
    5111 ---|---|---|--- 
    5112 H | 6 | -9 | -6 
    5113 S |  | 6 | -6 
    5114 O |  |  | 4 
    5115 Iteration cutoff | 2 
    5116  
    5117 Matchmaker 3ts8, chain A (#12) with 4mzr, chain A (#7), sequence alignment
    5118 score = 1190.7 
    5119 RMSD between 226 pruned atom pairs is 0.355 angstroms; (across all 234 pairs:
    5120 0.747) 
    5121  
    5122 
    5123 > show #!6 models
    5124 
    5125 > hide #!7 models
    5126 
    5127 > matchmaker #6/A to #12/A pairing ss
    5128 
    5129 Parameters 
    5130 --- 
    5131 Chain pairing | ss 
    5132 Alignment algorithm | Needleman-Wunsch 
    5133 Similarity matrix | BLOSUM-62 
    5134 SS fraction | 0.3 
    5135 Gap open (HH/SS/other) | 18/18/6 
    5136 Gap extend | 1 
    5137 SS matrix |  |  | H | S | O 
    5138 ---|---|---|--- 
    5139 H | 6 | -9 | -6 
    5140 S |  | 6 | -6 
    5141 O |  |  | 4 
    5142 Iteration cutoff | 2 
    5143  
    5144 Matchmaker 3ts8, chain A (#12) with 5bua, chain A (#6), sequence alignment
    5145 score = 951.9 
    5146 RMSD between 184 pruned atom pairs is 0.599 angstroms; (across all 200 pairs:
    5147 2.577) 
    5148  
    5149 
    5150 > hide #!6 models
    5151 
    5152 > show #!5 models
    5153 
    5154 > matchmaker #5/A to #12/A pairing ss
    5155 
    5156 Parameters 
    5157 --- 
    5158 Chain pairing | ss 
    5159 Alignment algorithm | Needleman-Wunsch 
    5160 Similarity matrix | BLOSUM-62 
    5161 SS fraction | 0.3 
    5162 Gap open (HH/SS/other) | 18/18/6 
    5163 Gap extend | 1 
    5164 SS matrix |  |  | H | S | O 
    5165 ---|---|---|--- 
    5166 H | 6 | -9 | -6 
    5167 S |  | 6 | -6 
    5168 O |  |  | 4 
    5169 Iteration cutoff | 2 
    5170  
    5171 Matchmaker 3ts8, chain A (#12) with 2ata, chain A (#5), sequence alignment
    5172 score = 945.3 
    5173 RMSD between 186 pruned atom pairs is 0.585 angstroms; (across all 197 pairs:
    5174 2.459) 
    5175  
    5176 
    5177 > show #!11 models
    5178 
    5179 > hide #!11 models
    5180 
    5181 > show #!10 models
    5182 
    5183 > hide #!10 models
    5184 
    5185 > show #!8 models
    5186 
    5187 > hide #!8 models
    5188 
    5189 > show #!8 models
    5190 
    5191 > hide #!8 models
    5192 
    5193 > show #!8 models
    5194 
    5195 > hide #!8 models
    5196 
    5197 > show #!4 models
    5198 
    5199 > hide #!5 models
    5200 
    5201 > matchmaker #4/A to #12/A pairing ss
    5202 
    5203 Parameters 
    5204 --- 
    5205 Chain pairing | ss 
    5206 Alignment algorithm | Needleman-Wunsch 
    5207 Similarity matrix | BLOSUM-62 
    5208 SS fraction | 0.3 
    5209 Gap open (HH/SS/other) | 18/18/6 
    5210 Gap extend | 1 
    5211 SS matrix |  |  | H | S | O 
    5212 ---|---|---|--- 
    5213 H | 6 | -9 | -6 
    5214 S |  | 6 | -6 
    5215 O |  |  | 4 
    5216 Iteration cutoff | 2 
    5217  
    5218 Matchmaker 3ts8, chain A (#12) with 2ahi, chain A (#4), sequence alignment
    5219 score = 947.7 
    5220 RMSD between 184 pruned atom pairs is 0.578 angstroms; (across all 197 pairs:
    5221 2.473) 
    5222  
    5223 
    5224 > show #!5 models
    5225 
    5226 > hide #!5 models
    5227 
    5228 > hide #!4 models
    5229 
    5230 > show #!3 models
    5231 
    5232 > matchmaker #3/A to #12/A pairing ss
    5233 
    5234 Parameters 
    5235 --- 
    5236 Chain pairing | ss 
    5237 Alignment algorithm | Needleman-Wunsch 
    5238 Similarity matrix | BLOSUM-62 
    5239 SS fraction | 0.3 
    5240 Gap open (HH/SS/other) | 18/18/6 
    5241 Gap extend | 1 
    5242 SS matrix |  |  | H | S | O 
    5243 ---|---|---|--- 
    5244 H | 6 | -9 | -6 
    5245 S |  | 6 | -6 
    5246 O |  |  | 4 
    5247 Iteration cutoff | 2 
    5248  
    5249 Matchmaker 3ts8, chain A (#12) with 5lgy, chain A (#3), sequence alignment
    5250 score = 944.4 
    5251 RMSD between 185 pruned atom pairs is 0.528 angstroms; (across all 197 pairs:
    5252 2.320) 
    5253  
    5254 
    5255 > hide #!3 models
    5256 
    5257 > show #!2 models
    5258 
    5259 > matchmaker #2/A to #12/A pairing ss
    5260 
    5261 Parameters 
    5262 --- 
    5263 Chain pairing | ss 
    5264 Alignment algorithm | Needleman-Wunsch 
    5265 Similarity matrix | BLOSUM-62 
    5266 SS fraction | 0.3 
    5267 Gap open (HH/SS/other) | 18/18/6 
    5268 Gap extend | 1 
    5269 SS matrix |  |  | H | S | O 
    5270 ---|---|---|--- 
    5271 H | 6 | -9 | -6 
    5272 S |  | 6 | -6 
    5273 O |  |  | 4 
    5274 Iteration cutoff | 2 
    5275  
    5276 Matchmaker 3ts8, chain A (#12) with 2ac0, chain A (#2), sequence alignment
    5277 score = 950.7 
    5278 RMSD between 187 pruned atom pairs is 0.618 angstroms; (across all 198 pairs:
    5279 2.423) 
    5280  
    5281 
    5282 > hide #!2 models
    5283 
    5284 > show #!1 models
    5285 
    5286 > matchmaker #1/A to #12/A pairing ss
    5287 
    5288 Parameters 
    5289 --- 
    5290 Chain pairing | ss 
    5291 Alignment algorithm | Needleman-Wunsch 
    5292 Similarity matrix | BLOSUM-62 
    5293 SS fraction | 0.3 
    5294 Gap open (HH/SS/other) | 18/18/6 
    5295 Gap extend | 1 
    5296 SS matrix |  |  | H | S | O 
    5297 ---|---|---|--- 
    5298 H | 6 | -9 | -6 
    5299 S |  | 6 | -6 
    5300 O |  |  | 4 
    5301 Iteration cutoff | 2 
    5302  
    5303 Matchmaker 3ts8, chain A (#12) with 1tup, chain A (#1), sequence alignment
    5304 score = 931.1 
    5305 RMSD between 184 pruned atom pairs is 0.596 angstroms; (across all 196 pairs:
    5306 2.426) 
    5307  
    5308 
    5309 > matchmaker #1/B to #12/A pairing ss
    5310 
    5311 Parameters 
    5312 --- 
    5313 Chain pairing | ss 
    5314 Alignment algorithm | Needleman-Wunsch 
    5315 Similarity matrix | BLOSUM-62 
    5316 SS fraction | 0.3 
    5317 Gap open (HH/SS/other) | 18/18/6 
    5318 Gap extend | 1 
    5319 SS matrix |  |  | H | S | O 
    5320 ---|---|---|--- 
    5321 H | 6 | -9 | -6 
    5322 S |  | 6 | -6 
    5323 O |  |  | 4 
    5324 Iteration cutoff | 2 
    5325  
    5326 Matchmaker 3ts8, chain A (#12) with 1tup, chain B (#1), sequence alignment
    5327 score = 919.1 
    5328 RMSD between 178 pruned atom pairs is 0.574 angstroms; (across all 194 pairs:
    5329 2.414) 
    5330  
    5331 
    5332 > select add #1
    5333 
    5334 5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected 
    5335 
    5336 > select subtract #1
    5337 
    5338 Nothing selected 
    5339 
    5340 > show #!11 models
    5341 
    5342 > hide #!11 models
    5343 
    5344 > show #!11 models
    5345 
    5346 > hide #!1 models
    5347 
    5348 > hide #!12 models
    5349 
    5350 > hide #!11 models
    5351 
    5352 > show #!12 models
    5353 
    5354 > show #!11 models
    5355 
    5356 > hide #!11 models
    5357 
    5358 > show #!1 models
    5359 
    5360 > matchmaker #1/C to #12/A pairing ss
    5361 
    5362 Parameters 
    5363 --- 
    5364 Chain pairing | ss 
    5365 Alignment algorithm | Needleman-Wunsch 
    5366 Similarity matrix | BLOSUM-62 
    5367 SS fraction | 0.3 
    5368 Gap open (HH/SS/other) | 18/18/6 
    5369 Gap extend | 1 
    5370 SS matrix |  |  | H | S | O 
    5371 ---|---|---|--- 
    5372 H | 6 | -9 | -6 
    5373 S |  | 6 | -6 
    5374 O |  |  | 4 
    5375 Iteration cutoff | 2 
    5376  
    5377 Matchmaker 3ts8, chain A (#12) with 1tup, chain C (#1), sequence alignment
    5378 score = 913.7 
    5379 RMSD between 182 pruned atom pairs is 0.634 angstroms; (across all 195 pairs:
    5380 2.442) 
    5381  
    5382 
    5383 > show #!2 models
    5384 
    5385 > hide #!2 models
    5386 
    5387 > show #!2 models
    5388 
    5389 > hide #!2 models
    5390 
    5391 > show #!2 models
    5392 
    5393 > hide #!2 models
    5394 
    5395 > show #!3 models
    5396 
    5397 > hide #!3 models
    5398 
    5399 > show #!4 models
    5400 
    5401 > hide #!4 models
    5402 
    5403 > show #!4 models
    5404 
    5405 > hide #!4 models
    5406 
    5407 > show #!4 models
    5408 
    5409 > hide #!4 models
    5410 
    5411 > hide #!12 models
    5412 
    5413 > show #!12 models
    5414 
    5415 > matchmaker #1/B to #12/A pairing ss
    5416 
    5417 Parameters 
    5418 --- 
    5419 Chain pairing | ss 
    5420 Alignment algorithm | Needleman-Wunsch 
    5421 Similarity matrix | BLOSUM-62 
    5422 SS fraction | 0.3 
    5423 Gap open (HH/SS/other) | 18/18/6 
    5424 Gap extend | 1 
    5425 SS matrix |  |  | H | S | O 
    5426 ---|---|---|--- 
    5427 H | 6 | -9 | -6 
    5428 S |  | 6 | -6 
    5429 O |  |  | 4 
    5430 Iteration cutoff | 2 
    5431  
    5432 Matchmaker 3ts8, chain A (#12) with 1tup, chain B (#1), sequence alignment
    5433 score = 919.1 
    5434 RMSD between 178 pruned atom pairs is 0.574 angstroms; (across all 194 pairs:
    5435 2.414) 
    5436  
    5437 
    5438 > hide #!1 models
    5439 
    5440 > show #!6 models
    5441 
    5442 > show #!3 models
    5443 
    5444 > hide #!12 models
    5445 
    5446 > show #!12 models
    5447 
    5448 > show #!11 models
    5449 
    5450 > show #!10 models
    5451 
    5452 > show #!9 models
    5453 
    5454 > show #!8 models
    5455 
    5456 > hide #!6 models
    5457 
    5458 > hide #!3 models
    5459 
    5460 > hide #!12 models
    5461 
    5462 > hide #!11 models
    5463 
    5464 > hide #!8 models
    5465 
    5466 > hide #!9 models
    5467 
    5468 > show #!9 models
    5469 
    5470 > show #!8 models
    5471 
    5472 > open /Users/kompa012/Desktop/P53/4ibv.pdb1
    5473 
    5474 4ibv.pdb1 title: 
    5475 Human P53 core domain with hot spot mutation R273C and second-site suppressor
    5476 mutation S240R In sequence-specific complex with DNA [more info...] 
    5477  
    5478 98 atoms have alternate locations. Control/examine alternate locations with
    5479 Altloc Explorer [start tool...] or the altlocs command. 
    5480 Chain information for 4ibv.pdb1 
    5481 --- 
    5482 Chain | Description 
    5483 13.1/A | No description available 
    5484 13.2/A | No description available 
    5485 13.1/B | No description available 
    5486 13.2/B | No description available 
    5487  
    5488 98 atoms have alternate locations. Control/examine alternate locations with
    5489 Altloc Explorer [start tool...] or the altlocs command. 
    5490 
    5491 > hide #!13 models
    5492 
    5493 > hide #!13.1 models
    5494 
    5495 > show #!13.1 models
    5496 
    5497 > hide #!10 models
    5498 
    5499 > hide #!9 models
    5500 
    5501 > hide #!8 models
    5502 
    5503 > hide #!13.2 models
    5504 
    5505 > show #!13.2 models
    5506 
    5507 > hide #!13.1 models
    5508 
    5509 > show #!13.1 models
    5510 
    5511 > hide #!13.2 models
    5512 
    5513 > show #!13.2 models
    5514 
    5515 > show #!12 models
    5516 
    5517 > matchmaker #13.1/A to #12/A pairing ss
    5518 
    5519 Parameters 
    5520 --- 
    5521 Chain pairing | ss 
    5522 Alignment algorithm | Needleman-Wunsch 
    5523 Similarity matrix | BLOSUM-62 
    5524 SS fraction | 0.3 
    5525 Gap open (HH/SS/other) | 18/18/6 
    5526 Gap extend | 1 
    5527 SS matrix |  |  | H | S | O 
    5528 ---|---|---|--- 
    5529 H | 6 | -9 | -6 
    5530 S |  | 6 | -6 
    5531 O |  |  | 4 
    5532 Iteration cutoff | 2 
    5533  
    5534 Matchmaker 3ts8, chain A (#12) with 4ibv.pdb1, chain A (#13.1), sequence
    5535 alignment score = 944 
    5536 RMSD between 181 pruned atom pairs is 0.577 angstroms; (across all 197 pairs:
    5537 2.583) 
    5538  
    5539 No reference and/or match structure/chain chosen 
    5540 
    5541 > hide #!13 models
    5542 
    5543 > matchmaker #13.2/B to #12/B pairing ss
    5544 
    5545 Match chain (4ibv.pdb1 (#13.2) chain B) not compatible with BLOSUM-62
    5546 similarity matrix 
    5547 
    5548 > show #!13 models
    5549 
    5550 > matchmaker #13.2/A to #12/A pairing ss
    5551 
    5552 Parameters 
    5553 --- 
    5554 Chain pairing | ss 
    5555 Alignment algorithm | Needleman-Wunsch 
    5556 Similarity matrix | BLOSUM-62 
    5557 SS fraction | 0.3 
    5558 Gap open (HH/SS/other) | 18/18/6 
    5559 Gap extend | 1 
    5560 SS matrix |  |  | H | S | O 
    5561 ---|---|---|--- 
    5562 H | 6 | -9 | -6 
    5563 S |  | 6 | -6 
    5564 O |  |  | 4 
    5565 Iteration cutoff | 2 
    5566  
    5567 Matchmaker 3ts8, chain A (#12) with 4ibv.pdb1, chain A (#13.2), sequence
    5568 alignment score = 923.8 
    5569 RMSD between 181 pruned atom pairs is 0.577 angstroms; (across all 197 pairs:
    5570 2.583) 
    5571  
    5572 No reference and/or match structure/chain chosen 
    5573 
    5574 > matchmaker #13.2/A to #12/B pairing ss
    5575 
    5576 Parameters 
    5577 --- 
    5578 Chain pairing | ss 
    5579 Alignment algorithm | Needleman-Wunsch 
    5580 Similarity matrix | BLOSUM-62 
    5581 SS fraction | 0.3 
    5582 Gap open (HH/SS/other) | 18/18/6 
    5583 Gap extend | 1 
    5584 SS matrix |  |  | H | S | O 
    5585 ---|---|---|--- 
    5586 H | 6 | -9 | -6 
    5587 S |  | 6 | -6 
    5588 O |  |  | 4 
    5589 Iteration cutoff | 2 
    5590  
    5591 Matchmaker 3ts8, chain B (#12) with 4ibv.pdb1, chain A (#13.2), sequence
    5592 alignment score = 889.6 
    5593 RMSD between 178 pruned atom pairs is 0.879 angstroms; (across all 197 pairs:
    5594 1.492) 
    5595  
    5596 
    5597 > hide #!12 models
    5598 
    5599 > close #13
    5600 
    5601 > show #!12 models
    5602 
    5603 > show #!11 models
    5604 
    5605 > show #!8 models
    5606 
    5607 > hide #!8 models
    5608 
    5609 > hide #!11 models
    5610 
    5611 > show #!7 models
    5612 
    5613 > hide #!7 models
    5614 
    5615 > open 3kmd fromDatabase pdb format mmcif
    5616 
    5617 Summary of feedback from opening 3kmd fetched from pdb 
    5618 --- 
    5619 note | Fetching compressed mmCIF 3kmd from http://files.rcsb.org/download/3kmd.cif 
    5620  
    5621 3kmd title: 
    5622 Crystal structure of the p53 core domain bound to a full consensus site as a
    5623 self-assembled tetramer [more info...] 
    5624  
    5625 Chain information for 3kmd #13 
    5626 --- 
    5627 Chain | Description | UniProt 
    5628 A B C D | Cellular tumor antigen p53 | P53_HUMAN 92-291 
    5629 E F | 5'-D(*GP*GP*GP*CP*AP*TP*GP*CP*CP*TP*AP*GP*GP*CP*AP*TP*GP*CP*C)-3' |   
    5630  
    5631 Non-standard residues in 3kmd #13 
    5632 --- 
    5633 ZN — zinc ion 
    5634  
    5635 
    5636 > select add #13
    5637 
    5638 7587 atoms, 7298 bonds, 64 pseudobonds, 1365 residues, 3 models selected 
    5639 
    5640 > style sel sphere
    5641 
    5642 Changed 7587 atom styles 
    5643 
    5644 > style sel stick
    5645 
    5646 Changed 7587 atom styles 
    5647 
    5648 > show sel cartoons
    5649 
    5650 > hide sel atoms
    5651 
    5652 > select clear
    5653 
    5654 > hide #!13 models
    5655 
    5656 > show #!13 models
    5657 
    5658 > hide #!13 models
    5659 
    5660 > show #!13 models
    5661 
    5662 > matchmaker #13/A to #12/A pairing ss
    5663 
    5664 Parameters 
    5665 --- 
    5666 Chain pairing | ss 
    5667 Alignment algorithm | Needleman-Wunsch 
    5668 Similarity matrix | BLOSUM-62 
    5669 SS fraction | 0.3 
    5670 Gap open (HH/SS/other) | 18/18/6 
    5671 Gap extend | 1 
    5672 SS matrix |  |  | H | S | O 
    5673 ---|---|---|--- 
    5674 H | 6 | -9 | -6 
    5675 S |  | 6 | -6 
    5676 O |  |  | 4 
    5677 Iteration cutoff | 2 
    5678  
    5679 Matchmaker 3ts8, chain A (#12) with 3kmd, chain A (#13), sequence alignment
    5680 score = 938.4 
    5681 RMSD between 185 pruned atom pairs is 0.477 angstroms; (across all 198 pairs:
    5682 2.352) 
    5683  
    5684 
    5685 > hide #!12 models
    5686 
    5687 > show #!12 models
    5688 
    5689 > hide #!13 models
    5690 
    5691 > open 3igk fromDatabase pdb format mmcif
    5692 
    5693 Summary of feedback from opening 3igk fetched from pdb 
    5694 --- 
    5695 note | Fetching compressed mmCIF 3igk from http://files.rcsb.org/download/3igk.cif 
    5696  
    5697 3igk title: 
    5698 Diversity in DNA recognition by p53 revealed by crystal structures with
    5699 Hoogsteen base pairs (p53-DNA complex 2) [more info...] 
    5700  
    5701 Chain information for 3igk #14 
    5702 --- 
    5703 Chain | Description | UniProt 
    5704 A | Cellular tumor antigen p53 | P53_HUMAN 94-293 
    5705 B | DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3') |   
    5706  
    5707 Non-standard residues in 3igk #14 
    5708 --- 
    5709 ZN — zinc ion 
    5710  
    5711 3igk mmCIF Assemblies 
    5712 --- 
    5713 1| author_and_software_defined_assembly 
    5714  
    5715 57 atoms have alternate locations. Control/examine alternate locations with
    5716 Altloc Explorer [start tool...] or the altlocs command. 
    5717 
    5718 > open 3igl fromDatabase pdb format mmcif
    5719 
    5720 Summary of feedback from opening 3igl fetched from pdb 
    5721 --- 
    5722 note | Fetching compressed mmCIF 3igl from http://files.rcsb.org/download/3igl.cif 
    5723  
    5724 3igl title: 
    5725 Diversity in DNA recognition by p53 revealed by crystal structures with
    5726 Hoogsteen base pairs (p53-DNA complex 1) [more info...] 
    5727  
    5728 Chain information for 3igl #15 
    5729 --- 
    5730 Chain | Description | UniProt 
    5731 A | Cellular tumor antigen p53 | P53_HUMAN 94-293 
    5732 B | DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3') |   
    5733  
    5734 Non-standard residues in 3igl #15 
    5735 --- 
    5736 EDO — 1,2-ethanediol (ethylene glycol) 
    5737 ZN — zinc ion 
    5738  
    5739 3igl mmCIF Assemblies 
    5740 --- 
    5741 1| author_and_software_defined_assembly 
    5742  
    5743 28 atoms have alternate locations. Control/examine alternate locations with
    5744 Altloc Explorer [start tool...] or the altlocs command. 
    5745 
    5746 > open 3kz8 fromDatabase pdb format mmcif
    5747 
    5748 Summary of feedback from opening 3kz8 fetched from pdb 
    5749 --- 
    5750 notes | Fetching compressed mmCIF 3kz8 from http://files.rcsb.org/download/3kz8.cif 
    5751 Fetching CCD IOD from
    5752 https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/IOD/IOD.cif 
    5753  
    5754 3kz8 title: 
    5755 Diversity in DNA recognition by p53 revealed by crystal structures with
    5756 Hoogsteen base pairs (p53-DNA complex 3) [more info...] 
    5757  
    5758 Chain information for 3kz8 #16 
    5759 --- 
    5760 Chain | Description | UniProt 
    5761 A B | Cellular tumor antigen p53 | P53_HUMAN 94-293 
    5762 C | DNA (5'-D(*TP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*C)-3') |   
    5763  
    5764 Non-standard residues in 3kz8 #16 
    5765 --- 
    5766 IOD — iodide ion 
    5767 ZN — zinc ion 
    5768  
    5769 3kz8 mmCIF Assemblies 
    5770 --- 
    5771 1| author_defined_assembly 
    5772  
    5773 87 atoms have alternate locations. Control/examine alternate locations with
    5774 Altloc Explorer [start tool...] or the altlocs command. 
    5775 
    5776 > matchmaker #14/A to #12/A pairing ss
    5777 
    5778 Parameters 
    5779 --- 
    5780 Chain pairing | ss 
    5781 Alignment algorithm | Needleman-Wunsch 
    5782 Similarity matrix | BLOSUM-62 
    5783 SS fraction | 0.3 
    5784 Gap open (HH/SS/other) | 18/18/6 
    5785 Gap extend | 1 
    5786 SS matrix |  |  | H | S | O 
    5787 ---|---|---|--- 
    5788 H | 6 | -9 | -6 
    5789 S |  | 6 | -6 
    5790 O |  |  | 4 
    5791 Iteration cutoff | 2 
    5792  
    5793 Matchmaker 3ts8, chain A (#12) with 3igk, chain A (#14), sequence alignment
    5794 score = 934.3 
    5795 RMSD between 181 pruned atom pairs is 0.672 angstroms; (across all 197 pairs:
    5796 2.601) 
    5797  
    5798 
    5799 > matchmaker #15/A to #12/A pairing ss
    5800 
    5801 Parameters 
    5802 --- 
    5803 Chain pairing | ss 
    5804 Alignment algorithm | Needleman-Wunsch 
    5805 Similarity matrix | BLOSUM-62 
    5806 SS fraction | 0.3 
    5807 Gap open (HH/SS/other) | 18/18/6 
    5808 Gap extend | 1 
    5809 SS matrix |  |  | H | S | O 
    5810 ---|---|---|--- 
    5811 H | 6 | -9 | -6 
    5812 S |  | 6 | -6 
    5813 O |  |  | 4 
    5814 Iteration cutoff | 2 
    5815  
    5816 Matchmaker 3ts8, chain A (#12) with 3igl, chain A (#15), sequence alignment
    5817 score = 944.1 
    5818 RMSD between 182 pruned atom pairs is 0.630 angstroms; (across all 197 pairs:
    5819 2.594) 
    5820  
    5821 
    5822 > matchmaker #16/A to #12/A pairing ss
    5823 
    5824 Parameters 
    5825 --- 
    5826 Chain pairing | ss 
    5827 Alignment algorithm | Needleman-Wunsch 
    5828 Similarity matrix | BLOSUM-62 
    5829 SS fraction | 0.3 
    5830 Gap open (HH/SS/other) | 18/18/6 
    5831 Gap extend | 1 
    5832 SS matrix |  |  | H | S | O 
    5833 ---|---|---|--- 
    5834 H | 6 | -9 | -6 
    5835 S |  | 6 | -6 
    5836 O |  |  | 4 
    5837 Iteration cutoff | 2 
    5838  
    5839 Matchmaker 3ts8, chain A (#12) with 3kz8, chain A (#16), sequence alignment
    5840 score = 948.3 
    5841 RMSD between 180 pruned atom pairs is 0.603 angstroms; (across all 195 pairs:
    5842 2.497) 
    5843  
    5844 
    5845 > hide #!14 models
    5846 
    5847 > hide #!15 models
    5848 
    5849 > hide #!12 models
    5850 
    5851 > show #!12 models
    5852 
    5853 > hide #!16 models
    5854 
    5855 > open 3q05 fromDatabase pdb format mmcif
    5856 
    5857 Summary of feedback from opening 3q05 fetched from pdb 
    5858 --- 
    5859 note | Fetching compressed mmCIF 3q05 from http://files.rcsb.org/download/3q05.cif 
    5860  
    5861 3q05 title: 
    5862 An induced fit mechanism regulates p53 DNA binding kinetics to confer sequence
    5863 specificity [more info...] 
    5864  
    5865 Chain information for 3q05 #17 
    5866 --- 
    5867 Chain | Description | UniProt 
    5868 A B C D | Cellular tumor antigen p53 | P53_HUMAN 94-291 321-356 
    5869 K | DNA (26-MER) |   
    5870 L | DNA (26-MER) |   
    5871  
    5872 Non-standard residues in 3q05 #17 
    5873 --- 
    5874 ZN — zinc ion 
    5875  
    5876 
    5877 > open 3q06 fromDatabase pdb format mmcif
    5878 
    5879 Summary of feedback from opening 3q06 fetched from pdb 
    5880 --- 
    5881 note | Fetching compressed mmCIF 3q06 from http://files.rcsb.org/download/3q06.cif 
    5882  
    5883 3q06 title: 
    5884 An induced fit mechanism regulates p53 DNA binding kinetics to confer sequence
    5885 specificity [more info...] 
    5886  
    5887 Chain information for 3q06 #18 
    5888 --- 
    5889 Chain | Description | UniProt 
    5890 A B C D | Cellular tumor antigen p53 | P53_HUMAN 96-292 321-354 
    5891 K | DNA (26-MER) |   
    5892 L | DNA (26-MER) |   
    5893  
    5894 Non-standard residues in 3q06 #18 
    5895 --- 
    5896 ZN — zinc ion 
    5897  
    5898 
    5899 > select add #17
    5900 
    5901 8677 atoms, 8800 bonds, 77 pseudobonds, 1153 residues, 3 models selected 
    5902 
    5903 > select add #18
    5904 
    5905 17133 atoms, 17540 bonds, 136 pseudobonds, 2133 residues, 6 models selected 
    5906 
    5907 > style sel stick
    5908 
    5909 Changed 17133 atom styles 
    5910 
    5911 > hide sel atoms
    5912 
    5913 > show sel cartoons
    5914 
    5915 > matchmaker #17/A to #12/A pairing ss
    5916 
    5917 Parameters 
    5918 --- 
    5919 Chain pairing | ss 
    5920 Alignment algorithm | Needleman-Wunsch 
    5921 Similarity matrix | BLOSUM-62 
    5922 SS fraction | 0.3 
    5923 Gap open (HH/SS/other) | 18/18/6 
    5924 Gap extend | 1 
    5925 SS matrix |  |  | H | S | O 
    5926 ---|---|---|--- 
    5927 H | 6 | -9 | -6 
    5928 S |  | 6 | -6 
    5929 O |  |  | 4 
    5930 Iteration cutoff | 2 
    5931  
    5932 Matchmaker 3ts8, chain A (#12) with 3q05, chain A (#17), sequence alignment
    5933 score = 1171 
    5934 RMSD between 223 pruned atom pairs is 0.512 angstroms; (across all 234 pairs:
    5935 1.303) 
    5936  
    5937 
    5938 > matchmaker #18/A to #12/A pairing ss
    5939 
    5940 Parameters 
    5941 --- 
    5942 Chain pairing | ss 
    5943 Alignment algorithm | Needleman-Wunsch 
    5944 Similarity matrix | BLOSUM-62 
    5945 SS fraction | 0.3 
    5946 Gap open (HH/SS/other) | 18/18/6 
    5947 Gap extend | 1 
    5948 SS matrix |  |  | H | S | O 
    5949 ---|---|---|--- 
    5950 H | 6 | -9 | -6 
    5951 S |  | 6 | -6 
    5952 O |  |  | 4 
    5953 Iteration cutoff | 2 
    5954  
    5955 Matchmaker 3ts8, chain A (#12) with 3q06, chain A (#18), sequence alignment
    5956 score = 1133.5 
    5957 RMSD between 221 pruned atom pairs is 0.602 angstroms; (across all 230 pairs:
    5958 1.295) 
    5959  
    5960 
    5961 > select subtract #17
    5962 
    5963 8456 atoms, 8740 bonds, 59 pseudobonds, 980 residues, 3 models selected 
    5964 
    5965 > select subtract #18
    5966 
    5967 Nothing selected 
    5968 
    5969 > hide #!17 models
    5970 
    5971 > hide #!18 models
    5972 
    5973 > open 3d0a fromDatabase pdb format mmcif
    5974 
    5975 Summary of feedback from opening 3d0a fetched from pdb 
    5976 --- 
    5977 warnings | Atom P has no neighbors to form bonds with according to residue template for DG /F:3 
    5978 Atom CE has no neighbors to form bonds with according to residue template for
    5979 MET /B:243 
    5980 note | Fetching compressed mmCIF 3d0a from http://files.rcsb.org/download/3d0a.cif 
    5981  
    5982 3d0a title: 
    5983 Human p53 core domain with hot spot mutation R249S and second site suppressor
    5984 mutation H168R in sequence-specific complex with DNA [more info...] 
    5985  
    5986 Chain information for 3d0a #19 
    5987 --- 
    5988 Chain | Description | UniProt 
    5989 A B C D | Cellular tumor antigen p53 | P53_HUMAN 94-293 
    5990 E F G H | DNA (5'-D(*DCP*DGP*DGP*DGP*DCP*DAP*DTP*DGP*DCP*DCP*DCP*DG)-3') |   
    5991  
    5992 Non-standard residues in 3d0a #19 
    5993 --- 
    5994 ZN — zinc ion 
    5995  
    5996 3d0a mmCIF Assemblies 
    5997 --- 
    5998 1| author_and_software_defined_assembly 
    5999 2| author_and_software_defined_assembly 
    6000  
    6001 224 atoms have alternate locations. Control/examine alternate locations with
    6002 Altloc Explorer [start tool...] or the altlocs command. 
    6003 
    6004 > select add #19
    6005 
    6006 7633 atoms, 7112 bonds, 81 pseudobonds, 1578 residues, 4 models selected 
    6007 
    6008 > style sel stick
    6009 
    6010 Changed 7633 atom styles 
    6011 
    6012 > hide sel atoms
    6013 
    6014 > show sel cartoons
    6015 
    6016 > matchmaker #19/A to #12/A pairing ss
    6017 
    6018 Parameters 
    6019 --- 
    6020 Chain pairing | ss 
    6021 Alignment algorithm | Needleman-Wunsch 
    6022 Similarity matrix | BLOSUM-62 
    6023 SS fraction | 0.3 
    6024 Gap open (HH/SS/other) | 18/18/6 
    6025 Gap extend | 1 
    6026 SS matrix |  |  | H | S | O 
    6027 ---|---|---|--- 
    6028 H | 6 | -9 | -6 
    6029 S |  | 6 | -6 
    6030 O |  |  | 4 
    6031 Iteration cutoff | 2 
    6032  
    6033 Matchmaker 3ts8, chain A (#12) with 3d0a, chain A (#19), sequence alignment
    6034 score = 917.5 
    6035 RMSD between 185 pruned atom pairs is 0.571 angstroms; (across all 196 pairs:
    6036 2.397) 
    6037  
    6038 
    6039 > hide #!12 models
    6040 
    6041 > show #!12 models
    6042 
    6043 > show #!1 models
    6044 
    6045 > show #!2 models
    6046 
    6047 > show #!3 models
    6048 
    6049 > show #!4 models
    6050 
    6051 > show #!5 models
    6052 
    6053 > show #!6 models
    6054 
    6055 > show #!7 models
    6056 
    6057 > show #!8 models
    6058 
    6059 > show #!9 models
    6060 
    6061 > show #!10 models
    6062 
    6063 > show #!11 models
    6064 
    6065 > show #!13 models
    6066 
    6067 > show #!14 models
    6068 
    6069 > show #!16 models
    6070 
    6071 > show #!15 models
    6072 
    6073 > show #!17 models
    6074 
    6075 > show #!18 models
    6076 
    6077 > select clear
    6078 
    6079 > select add #1
    6080 
    6081 5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected 
    6082 
    6083 > select subtract #1
    6084 
    6085 Nothing selected 
    6086 
    6087 > hide #!3 models
    6088 
    6089 > hide #!2 models
    6090 
    6091 > hide #!4 models
    6092 
    6093 > hide #!5 models
    6094 
    6095 > hide #!6 models
    6096 
    6097 > hide #!7 models
    6098 
    6099 > hide #!8 models
    6100 
    6101 > hide #!9 models
    6102 
    6103 > hide #!10 models
    6104 
    6105 > hide #!11 models
    6106 
    6107 > hide #!12 models
    6108 
    6109 > hide #!13 models
    6110 
    6111 > hide #!14 models
    6112 
    6113 > hide #!15 models
    6114 
    6115 > hide #!16 models
    6116 
    6117 > hide #!17 models
    6118 
    6119 > hide #!18 models
    6120 
    6121 > hide #!19 models
    6122 
    6123 > show #!12 models
    6124 
    6125 > hide #!12 models
    6126 
    6127 > ui tool show "Show Sequence Viewer"
    6128 
    6129 > sequence chain #1/B
    6130 
    6131 Alignment identifier is 1/B 
    6132 
    6133 > select add #1
    6134 
    6135 5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected 
    6136 
    6137 > show sel surfaces
    6138 
    6139 Cell requested for row 12 is out of bounds for table with 21 rows! Resizing
    6140 table model. 
    6141 
    6142 > hide sel surfaces
    6143 
    6144 > select subtract #1.4
    6145 
    6146 4306 atoms, 4092 bonds, 51 pseudobonds, 820 residues, 8 models selected 
    6147 
    6148 > select subtract #1.7
    6149 
    6150 3871 atoms, 3602 bonds, 8 pseudobonds, 799 residues, 6 models selected 
    6151 
    6152 > select subtract #1.6
    6153 
    6154 3451 atoms, 3134 bonds, 8 pseudobonds, 778 residues, 5 models selected 
    6155 
    6156 > hide sel cartoons
    6157 
    6158 > select add #1
    6159 
    6160 5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 5 models selected 
    6161 
    6162 > select subtract #1
    6163 
    6164 5 models selected 
    6165 
    6166 > select add #1.7
    6167 
    6168 435 atoms, 21 residues, 1 model selected 
    6169 
    6170 > select add #1.6
    6171 
    6172 855 atoms, 42 residues, 2 models selected 
    6173 
    6174 > select add #1.4
    6175 
    6176 2377 atoms, 236 residues, 3 models selected 
    6177 
    6178 > hide sel cartoons
    6179 
    6180 > show sel atoms
    6181 
    6182 > select clear
    6183 
    6184 > select
    6185 > #1/B:110-112,124-127,132-135,141-146,156-163,195-197,204-207,214-219,230-236,251-258,264-274
    6186 
    6187 530 atoms, 532 bonds, 64 residues, 1 model selected 
    6188 
    6189 > select #1/B:220
    6190 
    6191 12 atoms, 12 bonds, 1 residue, 1 model selected 
    6192 
    6193 > select #1/B:220
    6194 
    6195 12 atoms, 12 bonds, 1 residue, 1 model selected 
    6196 
    6197 > save "/Users/kompa012/Desktop/P53/Before mutation.cxs"
    6198 
    6199 > ui tool show Rotamers
    6200 
    6201 > swapaa interactive sel SER rotLib Dunbrack
    6202 
    6203 1tup #1/B TYR 220: phi -77.3, psi 125.7 trans 
    6204 Changed 9 bond radii 
    6205 
    6206 > swapaa interactive sel SER rotLib Dynameomics
    6207 
    6208 1tup #!1/B TYR 220: phi -77.3, psi 125.7 trans 
    6209 Changed 9 bond radii 
    6210 
    6211 > hide sel atoms
    6212 
    6213 > show sel atoms
    6214 
    6215 > style sel stick
    6216 
    6217 Changed 12 atom styles 
    6218 
    6219 > style sel stick
    6220 
    6221 Changed 12 atom styles 
    6222 
    6223 > style sel ball
    6224 
    6225 Changed 12 atom styles 
    6226 
    6227 > style sel stick
    6228 
    6229 Changed 12 atom styles 
    6230 
    6231 > style (#!1 & sel) ringFill thin
    6232 
    6233 Changed 1 residue ring style 
    6234 
    6235 > style (#!1 & sel) stick
    6236 
    6237 Changed 12 atom styles 
    6238 
    6239 > style (#!1 & sel) ringFill off
    6240 
    6241 Changed 1 residue ring style 
    6242 
    6243 > color (#!1 & sel) byhetero
    6244 
    6245 > select add #1.8
    6246 
    6247 24 atoms, 21 bonds, 4 residues, 6 models selected 
    6248 
    6249 > select subtract #1.4
    6250 
    6251 12 atoms, 9 bonds, 3 residues, 5 models selected 
    6252 
    6253 > select add #1.9
    6254 
    6255 24 atoms, 18 bonds, 6 residues, 8 models selected 
    6256 
    6257 > close #1.8-9
    6258 
    6259 > select #1/B:220@CA
    6260 
    6261 1 atom, 1 residue, 1 model selected 
    6262 
    6263 > select #1/B:220@CA
    6264 
    6265 1 atom, 1 residue, 1 model selected 
    6266 
    6267 > select #1/B:220
    6268 
    6269 12 atoms, 12 bonds, 1 residue, 1 model selected 
    6270 
    6271 > select #1/B:220
    6272 
    6273 12 atoms, 12 bonds, 1 residue, 1 model selected 
    6274 
    6275 > swapaa interactive sel SER rotLib Richardson.common
    6276 
    6277 1tup #1/B TYR 220: phi -77.3, psi 125.7 trans 
    6278 Changed 9 bond radii 
    6279 
    6280 > hide sel atoms
    6281 
    6282 > select #!1/B:220
    6283 
    6284 12 atoms, 12 bonds, 1 residue, 1 model selected 
    6285 
    6286 > select #!1/B:220
    6287 
    6288 12 atoms, 12 bonds, 1 residue, 1 model selected 
    6289 
    6290 > select #!1/B:220
    6291 
    6292 12 atoms, 12 bonds, 1 residue, 1 model selected 
    6293 
    6294 > select #!1/B:220
    6295 
    6296 12 atoms, 12 bonds, 1 residue, 1 model selected 
    6297 
    6298 > select #!1/B:220
    6299 
    6300 12 atoms, 12 bonds, 1 residue, 1 model selected 
    6301 
    6302 > select #!1/B:220
    6303 
    6304 12 atoms, 12 bonds, 1 residue, 1 model selected 
    6305 
    6306 > swapaa interactive sel TYR rotLib Richardson.common
    6307 
    6308 1tup #!1/B TYR 220: phi -77.3, psi 125.7 trans 
    6309 Changed 40 bond radii 
    6310 
    6311 > select add #1.9
    6312 
    6313 52 atoms, 52 bonds, 5 residues, 7 models selected 
    6314 
    6315 > select add #1.8
    6316 
    6317 64 atoms, 61 bonds, 8 residues, 11 models selected 
    6318 
    6319 > close #1.8-9
    6320 
    6321 > select #1/B:220
    6322 
    6323 12 atoms, 12 bonds, 1 residue, 1 model selected 
    6324 
    6325 > select #1/B:220
    6326 
    6327 12 atoms, 12 bonds, 1 residue, 1 model selected 
    6328 
    6329 > swapaa interactive sel TYR rotLib Richardson.mode
    6330 
    6331 1tup #1/B TYR 220: phi -77.3, psi 125.7 trans 
    6332 Changed 40 bond radii 
    6333 
    6334 > close #1.8
    6335 
    6336 > swapaa interactive sel SER rotLib Richardson.mode
    6337 
    6338 1tup #1/B TYR 220: phi -77.3, psi 125.7 trans 
    6339 Changed 9 bond radii 
    6340 
    6341 > hide #1.8.3 models
    6342 
    6343 > hide #1.8.2 models
    6344 
    6345 > close #1.8
    6346 
    6347 > swapaa interactive sel SER rotLib Dunbrack
    6348 
    6349 1tup #1/B TYR 220: phi -77.3, psi 125.7 trans 
    6350 Changed 9 bond radii 
    6351 
    6352 > show sel atoms
    6353 
    6354 > hide sel atoms
    6355 
    6356 > show sel atoms
    6357 
    6358 > hide #1.8.3 models
    6359 
    6360 > hide #1.8.2 models
    6361 
    6362 > hide sel atoms
    6363 
    6364 [Repeated 1 time(s)]
    6365 
    6366 > show sel atoms
    6367 
    6368 > hide sel atoms
    6369 
    6370 [Repeated 1 time(s)]
    6371 
    6372 > select #!1/B:220@CD2
    6373 
    6374 1 atom, 1 residue, 1 model selected 
    6375 
    6376 > hide sel atoms
    6377 
    6378 [Repeated 1 time(s)]
    6379 
    6380 > select #!1/B:220@CG
    6381 
    6382 1 atom, 1 residue, 1 model selected 
    6383 
    6384 > hide sel atoms
    6385 
    6386 > select #!1/B:220@CZ
    6387 
    6388 1 atom, 1 residue, 1 model selected 
    6389 
    6390 > hide sel atoms
    6391 
    6392 > select #!1/B:220@CE2
    6393 
    6394 1 atom, 1 residue, 1 model selected 
    6395 
    6396 > hide sel atoms
    6397 
    6398 > select #!1/B:220@OH
    6399 
    6400 1 atom, 1 residue, 1 model selected 
    6401 
    6402 > hide sel atoms
    6403 
    6404 [Repeated 1 time(s)]
    6405 
    6406 > select #!1/B:220@CE1
    6407 
    6408 1 atom, 1 residue, 1 model selected 
    6409 
    6410 > hide sel atoms
    6411 
    6412 > select #!1/B:220@CD1
    6413 
    6414 1 atom, 1 residue, 1 model selected 
    6415 
    6416 > hide sel atoms
    6417 
    6418 > style sel ball
    6419 
    6420 Changed 0 atom styles 
    6421 
    6422 > style sel ball
    6423 
    6424 Changed 0 atom styles 
    6425 
    6426 > style sel sphere
    6427 
    6428 Changed 0 atom styles 
    6429 
    6430 > style sel sphere
    6431 
    6432 Changed 0 atom styles 
    6433 
    6434 > select add #1.8.1
    6435 
    6436 4 atoms, 3 bonds, 1 residue, 1 model selected 
    6437 
    6438 > style sel sphere
    6439 
    6440 Changed 4 atom styles 
    6441 
    6442 > style sel ball
    6443 
    6444 Changed 4 atom styles 
    6445 
    6446 > style sel stick
    6447 
    6448 Changed 4 atom styles 
    6449 
    6450 > select clear
    6451 
    6452 > select add #1.8.1
    6453 
    6454 4 atoms, 3 bonds, 1 residue, 1 model selected 
    6455 
    6456 > style sel sphere
    6457 
    6458 Changed 4 atom styles 
    6459 
    6460 > select subtract #1.8.1
    6461 
    6462 Nothing selected 
    6463 
    6464 > select add #1.8.1
    6465 
    6466 4 atoms, 3 bonds, 1 residue, 1 model selected 
    6467 
    6468 > show #1.8.2 models
    6469 
    6470 > select add #1.8.2
    6471 
    6472 8 atoms, 6 bonds, 2 residues, 2 models selected 
    6473 
    6474 > style sel stick
    6475 
    6476 Changed 8 atom styles 
    6477 
    6478 > show #1.8.3 models
    6479 
    6480 > select add #1.8
    6481 
    6482 12 atoms, 9 bonds, 3 residues, 4 models selected 
    6483 
    6484 > select subtract #1.8
    6485 
    6486 Nothing selected 
    6487 
    6488 > hide #!1.8 models
    6489 
    6490 > select #!1/B:220
    6491 
    6492 12 atoms, 12 bonds, 1 residue, 1 model selected 
    6493 
    6494 > select #!1/B:220
    6495 
    6496 12 atoms, 12 bonds, 1 residue, 1 model selected 
    6497 
    6498 > show sel atoms
    6499 
    6500 > select #1/B:282
    6501 
    6502 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6503 
    6504 > select #1/B:282
    6505 
    6506 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6507 
    6508 > color (#!1 & sel) byhetero
    6509 
    6510 > select #1/B:280-281
    6511 
    6512 19 atoms, 18 bonds, 2 residues, 1 model selected 
    6513 
    6514 > select #1/B:280-284
    6515 
    6516 48 atoms, 47 bonds, 5 residues, 1 model selected 
    6517 
    6518 > select subtract #1.4
    6519 
    6520 1 model selected 
    6521 
    6522 > select add #1.3
    6523 
    6524 1535 atoms, 196 residues, 1 model selected 
    6525 
    6526 > show sel cartoons
    6527 
    6528 > select #1/A:282
    6529 
    6530 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6531 
    6532 > show sel atoms
    6533 
    6534 > hide sel atoms
    6535 
    6536 > select subtract #1.3
    6537 
    6538 1 model selected 
    6539 
    6540 > select add #1.3
    6541 
    6542 1535 atoms, 196 residues, 1 model selected 
    6543 
    6544 > hide sel cartoons
    6545 
    6546 > select add #1.5
    6547 
    6548 3064 atoms, 391 residues, 2 models selected 
    6549 
    6550 > show sel cartoons
    6551 
    6552 > select subtract #1.5
    6553 
    6554 1535 atoms, 196 residues, 3 models selected 
    6555 
    6556 > hide sel cartoons
    6557 
    6558 > select #1/C:282
    6559 
    6560 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6561 
    6562 > show sel atoms
    6563 
    6564 > hide sel atoms
    6565 
    6566 > select subtract #1.5
    6567 
    6568 1 model selected 
    6569 
    6570 > select add #1.5
    6571 
    6572 1529 atoms, 195 residues, 1 model selected 
    6573 
    6574 > hide sel cartoons
    6575 
    6576 > select add #1.3
    6577 
    6578 3064 atoms, 391 residues, 2 models selected 
    6579 
    6580 > select subtract #1.3
    6581 
    6582 1529 atoms, 195 residues, 3 models selected 
    6583 
    6584 > select add #1.4
    6585 
    6586 3051 atoms, 389 residues, 2 models selected 
    6587 
    6588 > select subtract #1.5
    6589 
    6590 1522 atoms, 194 residues, 3 models selected 
    6591 
    6592 > show sel cartoons
    6593 
    6594 > select clear
    6595 
    6596 > select #1/B:282
    6597 
    6598 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6599 
    6600 > select #1/B:282
    6601 
    6602 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6603 
    6604 > swapaa interactive sel GLN rotLib Dunbrack
    6605 
    6606 1tup #1/B ARG 282: phi -80.7, psi -38.2 trans 
    6607 Changed 648 bond radii 
    6608 
    6609 > select add #1.8.108
    6610 
    6611 18 atoms, 16 bonds, 2 residues, 3 models selected 
    6612 
    6613 > select add #1.8.107
    6614 
    6615 25 atoms, 22 bonds, 3 residues, 4 models selected 
    6616 
    6617 > select add #1.8.106
    6618 
    6619 32 atoms, 28 bonds, 4 residues, 5 models selected 
    6620 
    6621 > select add #1.8.105
    6622 
    6623 39 atoms, 34 bonds, 5 residues, 6 models selected 
    6624 
    6625 > select add #1.8.104
    6626 
    6627 46 atoms, 40 bonds, 6 residues, 7 models selected 
    6628 
    6629 > select add #1.8.103
    6630 
    6631 53 atoms, 46 bonds, 7 residues, 8 models selected 
    6632 
    6633 > select add #1.8.102
    6634 
    6635 60 atoms, 52 bonds, 8 residues, 9 models selected 
    6636 
    6637 > select add #1.8.101
    6638 
    6639 67 atoms, 58 bonds, 9 residues, 10 models selected 
    6640 
    6641 > select add #1.8
    6642 
    6643 767 atoms, 658 bonds, 109 residues, 111 models selected 
    6644 
    6645 > select subtract #1.8
    6646 
    6647 11 atoms, 10 bonds, 1 residue, 2 models selected 
    6648 
    6649 > select add #1.8
    6650 
    6651 767 atoms, 658 bonds, 109 residues, 111 models selected 
    6652 
    6653 > select subtract #1.8.39
    6654 
    6655 760 atoms, 652 bonds, 108 residues, 110 models selected 
    6656 
    6657 > select subtract #1.8.38
    6658 
    6659 753 atoms, 646 bonds, 107 residues, 109 models selected 
    6660 
    6661 > select add #1.8.38
    6662 
    6663 760 atoms, 652 bonds, 108 residues, 110 models selected 
    6664 
    6665 > select subtract #1.8.40
    6666 
    6667 753 atoms, 646 bonds, 107 residues, 109 models selected 
    6668 
    6669 > select add #1.8.40
    6670 
    6671 760 atoms, 652 bonds, 108 residues, 110 models selected 
    6672 
    6673 > hide sel atoms
    6674 
    6675 > select #!1/B:282-283
    6676 
    6677 22 atoms, 21 bonds, 2 residues, 1 model selected 
    6678 
    6679 > select #!1/B:282-283
    6680 
    6681 22 atoms, 21 bonds, 2 residues, 1 model selected 
    6682 
    6683 > select #!1/B:282
    6684 
    6685 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6686 
    6687 > select #!1/B:282
    6688 
    6689 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6690 
    6691 > show sel atoms
    6692 
    6693 > select add #1.8.40
    6694 
    6695 18 atoms, 16 bonds, 2 residues, 3 models selected 
    6696 
    6697 > show sel atoms
    6698 
    6699 > select add #1.8.41
    6700 
    6701 25 atoms, 22 bonds, 3 residues, 4 models selected 
    6702 
    6703 > show sel atoms
    6704 
    6705 > select subtract #1.8.40
    6706 
    6707 18 atoms, 16 bonds, 2 residues, 3 models selected 
    6708 
    6709 > select add #1.8.40
    6710 
    6711 25 atoms, 22 bonds, 3 residues, 4 models selected 
    6712 
    6713 > select subtract #1.8.41
    6714 
    6715 18 atoms, 16 bonds, 2 residues, 3 models selected 
    6716 
    6717 > hide sel atoms
    6718 
    6719 > select add #1.8
    6720 
    6721 767 atoms, 658 bonds, 109 residues, 111 models selected 
    6722 
    6723 > hide sel atoms
    6724 
    6725 > select #!1/B:282-289
    6726 
    6727 72 atoms, 71 bonds, 8 residues, 1 model selected 
    6728 
    6729 > select #!1/B:282-289
    6730 
    6731 72 atoms, 71 bonds, 8 residues, 1 model selected 
    6732 
    6733 > select #!1/B:282
    6734 
    6735 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6736 
    6737 > select #!1/B:282
    6738 
    6739 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6740 
    6741 > show sel atoms
    6742 
    6743 > select #!1/B:220
    6744 
    6745 12 atoms, 12 bonds, 1 residue, 1 model selected 
    6746 
    6747 > select #!1/B:220
    6748 
    6749 12 atoms, 12 bonds, 1 residue, 1 model selected 
    6750 
    6751 > swapaa interactive sel CYS rotLib Dunbrack
    6752 
    6753 1tup #!1/B TYR 220: phi -77.3, psi 125.7 trans 
    6754 Changed 9 bond radii 
    6755 
    6756 > select add #1
    6757 
    6758 6596 atoms, 6306 bonds, 55 pseudobonds, 1125 residues, 117 models selected 
    6759 
    6760 > select subtract #1
    6761 
    6762 5 models selected 
    6763 
    6764 > hide #!1 models
    6765 
    6766 > show #!1 models
    6767 
    6768 > show #!2 models
    6769 
    6770 > select add #2
    6771 
    6772 8210 atoms, 7408 bonds, 78 pseudobonds, 1896 residues, 3 models selected 
    6773 
    6774 > show sel atoms
    6775 
    6776 > select clear
    6777 
    6778 > show #!3 models
    6779 
    6780 > show #!4 models
    6781 
    6782 > show #!5 models
    6783 
    6784 > show #!6 models
    6785 
    6786 > show #!7 models
    6787 
    6788 > show #!8 models
    6789 
    6790 > show #!9 models
    6791 
    6792 > show #!10 models
    6793 
    6794 > show #!12 models
    6795 
    6796 > show #!11 models
    6797 
    6798 > show #!19 models
    6799 
    6800 > show #!18 models
    6801 
    6802 > show #!17 models
    6803 
    6804 > show #!16 models
    6805 
    6806 > show #!15 models
    6807 
    6808 > show #!14 models
    6809 
    6810 > show #!13 models
    6811 
    6812 > select add #1
    6813 
    6814 6596 atoms, 6306 bonds, 55 pseudobonds, 1125 residues, 116 models selected 
    6815 
    6816 > select subtract #1
    6817 
    6818 5 models selected 
    6819 
    6820 > select add #3
    6821 
    6822 7093 atoms, 7313 bonds, 57 pseudobonds, 855 residues, 3 models selected 
    6823 
    6824 > select add #4
    6825 
    6826 15128 atoms, 14594 bonds, 131 pseudobonds, 2688 residues, 6 models selected 
    6827 
    6828 > select add #5
    6829 
    6830 22909 atoms, 21901 bonds, 201 pseudobonds, 4243 residues, 17 models selected 
    6831 
    6832 > select add #6
    6833 
    6834 24841 atoms, 23736 bonds, 205 pseudobonds, 4609 residues, 27 models selected 
    6835 
    6836 > select add #7
    6837 
    6838 33434 atoms, 32548 bonds, 278 pseudobonds, 5670 residues, 30 models selected 
    6839 
    6840 > select add #8
    6841 
    6842 41522 atoms, 39905 bonds, 359 pseudobonds, 7483 residues, 33 models selected 
    6843 
    6844 > select add #10
    6845 
    6846 43694 atoms, 41785 bonds, 364 pseudobonds, 8045 residues, 36 models selected 
    6847 
    6848 > select add #9
    6849 
    6850 45643 atoms, 43622 bonds, 369 pseudobonds, 8425 residues, 39 models selected 
    6851 
    6852 > select add #11
    6853 
    6854 53618 atoms, 51008 bonds, 432 pseudobonds, 10103 residues, 42 models selected 
    6855 
    6856 > select add #12
    6857 
    6858 62239 atoms, 59808 bonds, 503 pseudobonds, 11200 residues, 45 models selected 
    6859 
    6860 > select add #13
    6861 
    6862 69826 atoms, 67106 bonds, 567 pseudobonds, 12565 residues, 48 models selected 
    6863 
    6864 > select add #14
    6865 
    6866 71919 atoms, 68920 bonds, 572 pseudobonds, 13112 residues, 51 models selected 
    6867 
    6868 > select add #15
    6869 
    6870 74028 atoms, 70747 bonds, 577 pseudobonds, 13663 residues, 54 models selected 
    6871 
    6872 > select add #16
    6873 
    6874 77725 atoms, 74246 bonds, 587 pseudobonds, 14388 residues, 57 models selected 
    6875 
    6876 > select add #17
    6877 
    6878 86402 atoms, 83046 bonds, 664 pseudobonds, 15541 residues, 60 models selected 
    6879 
    6880 > select add #18
    6881 
    6882 94858 atoms, 91786 bonds, 723 pseudobonds, 16521 residues, 63 models selected 
    6883 
    6884 > select add #19
    6885 
    6886 102491 atoms, 98898 bonds, 804 pseudobonds, 18099 residues, 67 models selected 
    6887 
    6888 > show sel atoms
    6889 
    6890 > select clear
    6891 
    6892 > select #!1/B:282
    6893 
    6894 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6895 
    6896 > select #!1/B:282
    6897 
    6898 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6899 
    6900 > select #!1/B:248
    6901 
    6902 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6903 
    6904 > select #!1/B:248
    6905 
    6906 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6907 
    6908 > hide #!13 models
    6909 
    6910 > hide #!14 models
    6911 
    6912 > hide #!15 models
    6913 
    6914 > hide #!16 models
    6915 
    6916 > hide #!17 models
    6917 
    6918 > hide #!18 models
    6919 
    6920 > hide #!19 models
    6921 
    6922 > hide #!11 models
    6923 
    6924 > hide #!10 models
    6925 
    6926 > hide #!9 models
    6927 
    6928 > hide #!8 models
    6929 
    6930 > hide #!7 models
    6931 
    6932 > hide #!6 models
    6933 
    6934 > hide #!5 models
    6935 
    6936 > hide #!4 models
    6937 
    6938 > hide #!3 models
    6939 
    6940 > hide #!2 models
    6941 
    6942 > hide #!12 models
    6943 
    6944 > show #!12 models
    6945 
    6946 > select add #12
    6947 
    6948 8632 atoms, 8810 bonds, 71 pseudobonds, 1098 residues, 5 models selected 
    6949 
    6950 > hide sel cartoons
    6951 
    6952 > select #!1/B:248
    6953 
    6954 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6955 
    6956 > select #!1/B:248
    6957 
    6958 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6959 
    6960 > ui mousemode right distance
    6961 
    6962 > distance #!1/B:248@NH2 #12/L:35@N2
    6963 
    6964 Distance between 1tup #!1/B ARG 248 NH2 and 3ts8 #12/L DG 35 N2: 5.304Å 
    6965 
    6966 > distance #12/A:248@NH2 #!1/F:1113@N2
    6967 
    6968 Distance between 3ts8 #12/A ARG 248 NH2 and 1tup #!1/F DG 1113 N2: 5.414Å 
    6969 
    6970 > hide #!12 models
    6971 
    6972 > select add #1
    6973 
    6974 6596 atoms, 6306 bonds, 55 pseudobonds, 1125 residues, 117 models selected 
    6975 
    6976 > select O
    6977 
    6978 30159 atoms, 21045 residues, 127 models selected 
    6979 
    6980 > show (#1.8.1-108#!1 & sel) target ab
    6981 
    6982 > ui mousemode right select
    6983 
    6984 > select clear
    6985 
    6986 > select #!1/B:248
    6987 
    6988 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6989 
    6990 > select #!1/B:248
    6991 
    6992 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6993 
    6994 > show #!12 models
    6995 
    6996 > hide #!1 models
    6997 
    6998 > select #12/A:248@CB
    6999 
    7000 1 atom, 1 residue, 1 model selected 
    7001 
    7002 > select #12/A:248@CA
    7003 
    7004 1 atom, 1 residue, 1 model selected 
    7005 
    7006 > select #12/A:248@CA
    7007 
    7008 1 atom, 1 residue, 1 model selected 
    7009 
    7010 > show #!1 models
    7011 
    7012 > hide #!1 models
    7013 
    7014 > select #12/A:248@CA
    7015 
    7016 1 atom, 1 residue, 1 model selected 
    7017 
    7018 > select #12/A:248@CA
    7019 
    7020 1 atom, 1 residue, 1 model selected 
    7021 
    7022 > select #12/C:283@NH2
    7023 
    7024 1 atom, 1 residue, 1 model selected 
    7025 Drag select of 1 atoms, 1 bonds 
    7026 
    7027 > ui tool show "Show Sequence Viewer"
    7028 
    7029 > sequence chain #12/A
    7030 
    7031 Alignment identifier is 12/A 
    7032 
    7033 > select #12/A:248-249
    7034 
    7035 22 atoms, 21 bonds, 2 residues, 1 model selected 
    7036 
    7037 > select #12/A:248-249
    7038 
    7039 22 atoms, 21 bonds, 2 residues, 1 model selected 
    7040 
    7041 > select #12/A:248
    7042 
    7043 11 atoms, 10 bonds, 1 residue, 1 model selected 
    7044 
    7045 > select #12/A:248
    7046 
    7047 11 atoms, 10 bonds, 1 residue, 1 model selected 
    7048 
    7049 > select add #12
    7050 
    7051 8621 atoms, 8800 bonds, 71 pseudobonds, 1097 residues, 3 models selected 
    7052 
    7053 > select clear
    7054 
    7055 > select O
    7056 
    7057 30159 atoms, 21045 residues, 127 models selected 
    7058 
    7059 > show (#!12 & sel) target ab
    7060 
    7061 > select clear
    7062 
    7063 > show #!1 models
    7064 
    7065 > select add #20
    7066 
    7067 2 pseudobonds, 2 models selected 
    7068 
    7069 > close #20
    7070 
    7071 > select #12/A:248
    7072 
    7073 11 atoms, 10 bonds, 1 residue, 1 model selected 
    7074 
    7075 > select #12/A:248
    7076 
    7077 11 atoms, 10 bonds, 1 residue, 1 model selected 
    7078 
    7079 > hide #!12 models
    7080 
    7081 > show #!12 models
    7082 
    7083 > hide #!1 models
    7084 
    7085 > hide #!12 models
    7086 
    7087 > show #!1 models
    7088 
    7089 > show #!12 models
    7090 
    7091 > hide #!1 models
    7092 
    7093 > show #!1 models
    7094 
    7095 > hide #!12 models
    7096 
    7097 > show #!2 models
    7098 
    7099 > show #!3 models
    7100 
    7101 > hide #!1 models
    7102 
    7103 > show #!1 models
    7104 
    7105 > hide #!2 models
    7106 
    7107 > hide #!3 models
    7108 
    7109 > select #!1/B:248
    7110 
    7111 11 atoms, 10 bonds, 1 residue, 1 model selected 
    7112 
    7113 > select #!1/B:248
    7114 
    7115 11 atoms, 10 bonds, 1 residue, 1 model selected 
    7116 
    7117 > show #!19 models
    7118 
    7119 > show #!18 models
    7120 
    7121 > show #!17 models
    7122 
    7123 > show #!16 models
    7124 
    7125 > show #!15 models
    7126 
    7127 > show #!14 models
    7128 
    7129 > show #!13 models
    7130 
    7131 > hide #!13 models
    7132 
    7133 > hide #!14 models
    7134 
    7135 > hide #!15 models
    7136 
    7137 > hide #!16 models
    7138 
    7139 > hide #!17 models
    7140 
    7141 > hide #!18 models
    7142 
    7143 > hide #!19 models
    7144 
    7145 > hide #!1 models
    7146 
    7147 > show #!1 models
    7148 
    7149 > select add #1
    7150 
    7151 6596 atoms, 6306 bonds, 55 pseudobonds, 1125 residues, 117 models selected 
    7152 
    7153 > show sel cartoons
    7154 
    7155 > show #!2 models
    7156 
    7157 > show #!3 models
    7158 
    7159 > hide #!2 models
    7160 
    7161 > select clear
    7162 
    7163 > select #!1/B:248
    7164 
    7165 11 atoms, 10 bonds, 1 residue, 1 model selected 
    7166 
    7167 > select #!1/B:248
    7168 
    7169 11 atoms, 10 bonds, 1 residue, 1 model selected 
    7170 
    7171 > show #!19 models
    7172 
    7173 > show #!18 models
    7174 
    7175 > hide #!1 models
    7176 
    7177 > hide #!18 models
    7178 
    7179 > hide #!19 models
    7180 
    7181 > show #!19 models
    7182 
    7183 > show #!18 models
    7184 
    7185 > show #!17 models
    7186 
    7187 > hide #!3 models
    7188 
    7189 > show #!16 models
    7190 
    7191 > hide #!17 models
    7192 
    7193 > hide #!18 models
    7194 
    7195 > hide #!19 models
    7196 
    7197 > select add #16
    7198 
    7199 3708 atoms, 3509 bonds, 10 pseudobonds, 726 residues, 5 models selected 
    7200 
    7201 > style sel & #!16 stick
    7202 
    7203 Changed 3697 atom styles 
    7204 
    7205 > hide sel & #!16 cartoons
    7206 
    7207 [Repeated 1 time(s)]
    7208 
    7209 > nucleotides sel & #!16 atoms
    7210 
    7211 > style nucleic & sel & #!16 stick
    7212 
    7213 Changed 410 atom styles 
    7214 
    7215 > show #!15 models
    7216 
    7217 > hide #!16 models
    7218 
    7219 > select add #15
    7220 
    7221 5817 atoms, 5336 bonds, 15 pseudobonds, 1277 residues, 8 models selected 
    7222 
    7223 > select subtract #16
    7224 
    7225 2120 atoms, 1837 bonds, 5 pseudobonds, 552 residues, 5 models selected 
    7226 
    7227 > nucleotides sel & #!15 atoms
    7228 
    7229 > style nucleic & sel & #!15 stick
    7230 
    7231 Changed 225 atom styles 
    7232 
    7233 > hide sel & #!15 cartoons
    7234 
    7235 > show #!16 models
    7236 
    7237 > show #!14 models
    7238 
    7239 > select add #14
    7240 
    7241 4213 atoms, 3651 bonds, 10 pseudobonds, 1099 residues, 8 models selected 
    7242 
    7243 > select subtract #15
    7244 
    7245 2104 atoms, 1824 bonds, 5 pseudobonds, 548 residues, 5 models selected 
    7246 
    7247 > nucleotides sel & #!14 atoms
    7248 
    7249 > style nucleic & sel & #!14 stick
    7250 
    7251 Changed 225 atom styles 
    7252 
    7253 > hide sel & #!14 cartoons
    7254 
    7255 > show #!13 models
    7256 
    7257 > select subtract #14
    7258 
    7259 11 atoms, 10 bonds, 1 residue, 2 models selected 
    7260 
    7261 > select add #13
    7262 
    7263 7598 atoms, 7308 bonds, 64 pseudobonds, 1366 residues, 5 models selected 
    7264 
    7265 > hide sel & #!13 cartoons
    7266 
    7267 > hide #!14 models
    7268 
    7269 > hide #!15 models
    7270 
    7271 > hide #!16 models
    7272 
    7273 > show #!12 models
    7274 
    7275 > hide #!13 models
    7276 
    7277 > show #!11 models
    7278 
    7279 > show #!10 models
    7280 
    7281 > show #!9 models
    7282 
    7283 > show #!8 models
    7284 
    7285 > show #!7 models
    7286 
    7287 > show #!6 models
    7288 
    7289 > select add #12
    7290 
    7291 16219 atoms, 16108 bonds, 135 pseudobonds, 2463 residues, 8 models selected 
    7292 
    7293 > select subtract #13
    7294 
    7295 8632 atoms, 8810 bonds, 71 pseudobonds, 1098 residues, 5 models selected 
    7296 
    7297 > select add #11
    7298 
    7299 16607 atoms, 16196 bonds, 134 pseudobonds, 2776 residues, 8 models selected 
    7300 
    7301 > select add #10
    7302 
    7303 18779 atoms, 18076 bonds, 139 pseudobonds, 3338 residues, 11 models selected 
    7304 
    7305 > select add #9
    7306 
    7307 20728 atoms, 19913 bonds, 144 pseudobonds, 3718 residues, 14 models selected 
    7308 
    7309 > select add #8
    7310 
    7311 28816 atoms, 27270 bonds, 225 pseudobonds, 5531 residues, 17 models selected 
    7312 
    7313 > select add #6
    7314 
    7315 30748 atoms, 29105 bonds, 229 pseudobonds, 5897 residues, 19 models selected 
    7316 
    7317 > select add #7
    7318 
    7319 39341 atoms, 37917 bonds, 302 pseudobonds, 6958 residues, 22 models selected 
    7320 
    7321 > nucleotides sel & #!6-12 atoms
    7322 
    7323 > style nucleic & sel & #!6-12 stick
    7324 
    7325 Changed 4560 atom styles 
    7326 
    7327 > hide sel & #!6-12 cartoons
    7328 
    7329 > hide #!6 models
    7330 
    7331 > show #!19 models
    7332 
    7333 > show #!18 models
    7334 
    7335 > show #!17 models
    7336 
    7337 > show #!16 models
    7338 
    7339 > show #!15 models
    7340 
    7341 > show #!14 models
    7342 
    7343 > show #!13 models
    7344 
    7345 > select add #13
    7346 
    7347 46928 atoms, 45215 bonds, 366 pseudobonds, 8323 residues, 25 models selected 
    7348 
    7349 > select add #14
    7350 
    7351 49021 atoms, 47029 bonds, 371 pseudobonds, 8870 residues, 28 models selected 
    7352 
    7353 > select add #15
    7354 
    7355 51130 atoms, 48856 bonds, 376 pseudobonds, 9421 residues, 31 models selected 
    7356 
    7357 > select add #16
    7358 
    7359 54827 atoms, 52355 bonds, 386 pseudobonds, 10146 residues, 34 models selected 
    7360 
    7361 > select add #17
    7362 
    7363 63504 atoms, 61155 bonds, 463 pseudobonds, 11299 residues, 37 models selected 
    7364 
    7365 > select add #18
    7366 
    7367 71960 atoms, 69895 bonds, 522 pseudobonds, 12279 residues, 40 models selected 
    7368 
    7369 > select add #19
    7370 
    7371 79593 atoms, 77007 bonds, 603 pseudobonds, 13857 residues, 44 models selected 
    7372 
    7373 > hide sel & #!7-19 cartoons
    7374 
    7375 > nucleotides sel & #!7-19 atoms
    7376 
    7377 > style nucleic & sel & #!7-19 stick
    7378 
    7379 Changed 9010 atom styles 
    7380 
    7381 > show #!6 models
    7382 
    7383 > select subtract #6
    7384 
    7385 77661 atoms, 75172 bonds, 599 pseudobonds, 13491 residues, 42 models selected 
    7386 
    7387 > show #!5 models
    7388 
    7389 > show #!4 models
    7390 
    7391 > show #!3 models
    7392 
    7393 > show #!2 models
    7394 
    7395 > show #!1 models
    7396 
    7397 > select add #2
    7398 
    7399 85871 atoms, 82580 bonds, 677 pseudobonds, 15387 residues, 45 models selected 
    7400 
    7401 > select add #1
    7402 
    7403 92456 atoms, 88876 bonds, 732 pseudobonds, 16511 residues, 168 models selected 
    7404 
    7405 > select add #3
    7406 
    7407 99549 atoms, 96189 bonds, 789 pseudobonds, 17366 residues, 175 models selected 
    7408 
    7409 > select add #4
    7410 
    7411 107584 atoms, 103470 bonds, 863 pseudobonds, 19199 residues, 178 models
    7412 selected 
    7413 
    7414 > select add #5
    7415 
    7416 115365 atoms, 110777 bonds, 933 pseudobonds, 20754 residues, 189 models
    7417 selected 
    7418 
    7419 > select add #6
    7420 
    7421 117297 atoms, 112612 bonds, 937 pseudobonds, 21120 residues, 199 models
    7422 selected 
    7423 
    7424 > select subtract #7
    7425 
    7426 108704 atoms, 103800 bonds, 864 pseudobonds, 20059 residues, 196 models
    7427 selected 
    7428 
    7429 > select add #7
    7430 
    7431 117297 atoms, 112612 bonds, 937 pseudobonds, 21120 residues, 199 models
    7432 selected 
    7433 
    7434 > hide #!7 models
    7435 
    7436 > select subtract #7
    7437 
    7438 108704 atoms, 103800 bonds, 864 pseudobonds, 20059 residues, 196 models
    7439 selected 
    7440 
    7441 > hide #!8 models
    7442 
    7443 > show #!8 models
    7444 
    7445 > show #!7 models
    7446 
    7447 > select add #7
    7448 
    7449 117297 atoms, 112612 bonds, 937 pseudobonds, 21120 residues, 199 models
    7450 selected 
    7451 
    7452 > hide sel cartoons
    7453 
    7454 > nucleotides sel atoms
    7455 
    7456 > style nucleic & sel stick
    7457 
    7458 Changed 13700 atom styles 
    7459 
    7460 > hide #!10 models
    7461 
    7462 > hide #!8 models
    7463 
    7464 > show #!8 models
    7465 
    7466 > hide #!8 models
    7467 
    7468 > show #!10 models
    7469 
    7470 > hide #!10 models
    7471 
    7472 > hide #!1 models
    7473 
    7474 > hide #!4 models
    7475 
    7476 > hide #!11 models
    7477 
    7478 > hide #!5 models
    7479 
    7480 > hide #!7 models
    7481 
    7482 > hide #!17 models
    7483 
    7484 > hide #!9 models
    7485 
    7486 > hide #!12 models
    7487 
    7488 > show sel & #!2-3,6,13-16,18-19 surfaces
    7489 
    7490 > hide sel & #!2-3,6,13-16,18-19 surfaces
    7491 
    7492 > hide #!19 models
    7493 
    7494 > show #!19 models
    7495 
    7496 > hide #!19 models
    7497 
    7498 > hide #!18 models
    7499 
    7500 > hide #!16 models
    7501 
    7502 > hide #!15 models
    7503 
    7504 > hide #!14 models
    7505 
    7506 > hide #!13 models
    7507 
    7508 > hide #!6 models
    7509 
    7510 > hide #!3 models
    7511 
    7512 > select clear
    7513 
    7514 > select add #2
    7515 
    7516 8210 atoms, 7408 bonds, 78 pseudobonds, 1896 residues, 3 models selected 
    7517 
    7518 > select subtract #2.10
    7519 
    7520 7967 atoms, 7136 bonds, 44 pseudobonds, 1884 residues, 11 models selected 
    7521 
    7522 > select subtract #2.9
    7523 
    7524 7724 atoms, 6864 bonds, 44 pseudobonds, 1872 residues, 10 models selected 
    7525 
    7526 > select subtract #2.8
    7527 
    7528 7481 atoms, 6592 bonds, 16 pseudobonds, 1860 residues, 8 models selected 
    7529 
    7530 > select subtract #2.7
    7531 
    7532 7238 atoms, 6320 bonds, 16 pseudobonds, 1848 residues, 7 models selected 
    7533 
    7534 > select add #2.9
    7535 
    7536 7481 atoms, 6320 bonds, 16 pseudobonds, 1860 residues, 6 models selected 
    7537 
    7538 > select subtract #2.9
    7539 
    7540 7238 atoms, 6320 bonds, 16 pseudobonds, 1848 residues, 7 models selected 
    7541 
    7542 > select subtract #2.5
    7543 
    7544 5709 atoms, 4756 bonds, 12 pseudobonds, 1653 residues, 6 models selected 
    7545 
    7546 > select add #2.5
    7547 
    7548 7238 atoms, 4756 bonds, 12 pseudobonds, 1848 residues, 5 models selected 
    7549 
    7550 > select subtract #2.3
    7551 
    7552 5686 atoms, 3169 bonds, 8 pseudobonds, 1649 residues, 6 models selected 
    7553 
    7554 > hide sel atoms
    7555 
    7556 > select add #2.10
    7557 
    7558 5929 atoms, 3169 bonds, 8 pseudobonds, 1661 residues, 5 models selected 
    7559 
    7560 > select add #2.9
    7561 
    7562 6172 atoms, 3169 bonds, 8 pseudobonds, 1673 residues, 6 models selected 
    7563 
    7564 > select subtract #2.6
    7565 
    7566 4618 atoms, 1580 bonds, 4 pseudobonds, 1475 residues, 7 models selected 
    7567 
    7568 > select subtract #2.5
    7569 
    7570 3089 atoms, 1580 bonds, 4 pseudobonds, 1280 residues, 6 models selected 
    7571 
    7572 > select subtract #2.4
    7573 
    7574 1544 atoms, 1082 residues, 4 models selected 
    7575 
    7576 > hide sel atoms
    7577 
    7578 > select add #1
    7579 
    7580 8140 atoms, 6306 bonds, 55 pseudobonds, 2207 residues, 119 models selected 
    7581 
    7582 > select subtract #1
    7583 
    7584 1544 atoms, 1082 residues, 8 models selected 
    7585 
    7586 > show #!1 models
    7587 
    7588 > hide #!1 models
    7589 
    7590 > hide #!2 models
    7591 
    7592 > select add #2
    7593 
    7594 8210 atoms, 7408 bonds, 78 pseudobonds, 1896 residues, 5 models selected 
    7595 
    7596 > select subtract #2
    7597 
    7598 8 models selected 
    7599 
    7600 > show #!3 models
    7601 
    7602 > select add #3
    7603 
    7604 7093 atoms, 7313 bonds, 57 pseudobonds, 855 residues, 3 models selected 
    7605 
    7606 > show #!1 models
    7607 
    7608 > hide #!1 models
    7609 
    7610 > select subtract #3.8
    7611 
    7612 6666 atoms, 6835 bonds, 16 pseudobonds, 834 residues, 8 models selected 
    7613 
    7614 > select subtract #3.7
    7615 
    7616 6238 atoms, 6354 bonds, 16 pseudobonds, 813 residues, 7 models selected 
    7617 
    7618 > select subtract #3.3
    7619 
    7620 4686 atoms, 4767 bonds, 12 pseudobonds, 616 residues, 6 models selected 
    7621 
    7622 > hide sel atoms
    7623 
    7624 > show #!2 models
    7625 
    7626 > hide #!3 models
    7627 
    7628 > hide #!2 models
    7629 
    7630 > show #!3 models
    7631 
    7632 > hide #!3 models
    7633 
    7634 > select add #3
    7635 
    7636 7093 atoms, 7313 bonds, 57 pseudobonds, 855 residues, 6 models selected 
    7637 
    7638 > select subtract #3
    7639 
    7640 6 models selected 
    7641 
    7642 Cell requested for row 3 is out of bounds for table with 27 rows! Resizing
    7643 table model. 
    7644 
    7645 > show #!4 models
    7646 
    7647 > select add #4
    7648 
    7649 8035 atoms, 7281 bonds, 74 pseudobonds, 1833 residues, 3 models selected 
    7650 
    7651 > select subtract #4.10
    7652 
    7653 7792 atoms, 7009 bonds, 42 pseudobonds, 1821 residues, 11 models selected 
    7654 
    7655 > select add #4.10
    7656 
    7657 8035 atoms, 7009 bonds, 42 pseudobonds, 1833 residues, 10 models selected 
    7658 
    7659 > select subtract #4.10
    7660 
    7661 7792 atoms, 7009 bonds, 42 pseudobonds, 1821 residues, 11 models selected 
    7662 
    7663 > select subtract #4.9
    7664 
    7665 7549 atoms, 6737 bonds, 42 pseudobonds, 1809 residues, 10 models selected 
    7666 
    7667 > select subtract #4.8
    7668 
    7669 7325 atoms, 6486 bonds, 16 pseudobonds, 1798 residues, 8 models selected 
    7670 
    7671 > select subtract #4.7
    7672 
    7673 7123 atoms, 6260 bonds, 16 pseudobonds, 1788 residues, 7 models selected 
    7674 
    7675 > select subtract #4.3
    7676 
    7677 5572 atoms, 4674 bonds, 12 pseudobonds, 1589 residues, 6 models selected 
    7678 
    7679 > hide sel atoms
    7680 
    7681 > show #!3 models
    7682 
    7683 > hide #!3 models
    7684 
    7685 > show #!2 models
    7686 
    7687 > hide #!2 models
    7688 
    7689 > show #!1 models
    7690 
    7691 > hide #!1 models
    7692 
    7693 > show #!1 models
    7694 
    7695 > show #!2 models
    7696 
    7697 > show #!3 models
    7698 
    7699 > select add #4
    7700 
    7701 8035 atoms, 7281 bonds, 74 pseudobonds, 1833 residues, 6 models selected 
    7702 
    7703 > select subtract #4
    7704 
    7705 8 models selected 
    7706 
    7707 > select add #4.10
    7708 
    7709 243 atoms, 12 residues, 1 model selected 
    7710 
    7711 > select add #4.9
    7712 
    7713 486 atoms, 24 residues, 2 models selected 
    7714 
    7715 > hide sel atoms
    7716 
    7717 > select add #4
    7718 
    7719 8035 atoms, 7281 bonds, 74 pseudobonds, 1833 residues, 5 models selected 
    7720 
    7721 > select subtract #4
    7722 
    7723 8 models selected 
    7724 
    7725 > hide #!3 models
    7726 
    7727 > hide #!2 models
    7728 
    7729 > hide #!1 models
    7730 
    7731 > show #!5 models
    7732 
    7733 > hide #!4 models
    7734 
    7735 > select add #5.10
    7736 
    7737 223 atoms, 11 residues, 1 model selected 
    7738 
    7739 > select add #5.9
    7740 
    7741 466 atoms, 23 residues, 2 models selected 
    7742 
    7743 > select add #5.6
    7744 
    7745 2002 atoms, 221 residues, 3 models selected 
    7746 
    7747 > select add #5.5
    7748 
    7749 3537 atoms, 417 residues, 4 models selected 
    7750 
    7751 > select add #5.4
    7752 
    7753 5089 atoms, 616 residues, 5 models selected 
    7754 
    7755 > hide sel atoms
    7756 
    7757 > show #!4 models
    7758 
    7759 > hide #!4 models
    7760 
    7761 > select add #5
    7762 
    7763 7781 atoms, 7307 bonds, 70 pseudobonds, 1555 residues, 8 models selected 
    7764 
    7765 > select subtract #5
    7766 
    7767 8 models selected 
    7768 
    7769 > show #!6 models
    7770 
    7771 > hide #!5 models
    7772 
    7773 > show #!7 models
    7774 
    7775 > hide #!6 models
    7776 
    7777 > select add #7
    7778 
    7779 8593 atoms, 8812 bonds, 73 pseudobonds, 1061 residues, 3 models selected 
    7780 
    7781 > show sel surfaces
    7782 
    7783 > hide sel surfaces
    7784 
    7785 > select subtract #7
    7786 
    7787 6 models selected 
    7788 
    7789 > select add #7.8
    7790 
    7791 535 atoms, 26 residues, 1 model selected 
    7792 
    7793 > select add #7.7
    7794 
    7795 1060 atoms, 52 residues, 2 models selected 
    7796 
    7797 > select subtract #7.7
    7798 
    7799 535 atoms, 26 residues, 3 models selected 
    7800 
    7801 > select subtract #7.8
    7802 
    7803 1 model selected 
    7804 
    7805 > select add #7.6
    7806 
    7807 1865 atoms, 234 residues, 1 model selected 
    7808 
    7809 > select add #7.5
    7810 
    7811 3730 atoms, 468 residues, 2 models selected 
    7812 
    7813 > select add #7.4
    7814 
    7815 5595 atoms, 702 residues, 3 models selected 
    7816 
    7817 > hide sel atoms
    7818 
    7819 > show #!6 models
    7820 
    7821 > hide #!6 models
    7822 
    7823 > select add #7
    7824 
    7825 8593 atoms, 8812 bonds, 73 pseudobonds, 1061 residues, 6 models selected 
    7826 
    7827 > select subtract #7
    7828 
    7829 6 models selected 
    7830 
    7831 Cell requested for row 7 is out of bounds for table with 27 rows! Resizing
    7832 table model. 
    7833 
    7834 > show #!8 models
    7835 
    7836 > hide #!7 models
    7837 
    7838 > select add #8
    7839 
    7840 8088 atoms, 7357 bonds, 81 pseudobonds, 1813 residues, 3 models selected 
    7841 
    7842 > select add #9
    7843 
    7844 10037 atoms, 9194 bonds, 86 pseudobonds, 2193 residues, 6 models selected 
    7845 
    7846 > select add #10
    7847 
    7848 12209 atoms, 11074 bonds, 91 pseudobonds, 2755 residues, 9 models selected 
    7849 
    7850 > select add #11
    7851 
    7852 20184 atoms, 18460 bonds, 154 pseudobonds, 4433 residues, 12 models selected 
    7853 
    7854 > show sel & #!8 surfaces
    7855 
    7856 > hide sel & #!8 surfaces
    7857 
    7858 > select subtract #9
    7859 
    7860 18235 atoms, 16623 bonds, 149 pseudobonds, 4053 residues, 17 models selected 
    7861 
    7862 > select subtract #10
    7863 
    7864 16063 atoms, 14743 bonds, 144 pseudobonds, 3491 residues, 14 models selected 
    7865 
    7866 > select subtract #11
    7867 
    7868 8088 atoms, 7357 bonds, 81 pseudobonds, 1813 residues, 11 models selected 
    7869 
    7870 > select subtract #8.10
    7871 
    7872 7845 atoms, 7085 bonds, 47 pseudobonds, 1801 residues, 11 models selected 
    7873 
    7874 > select subtract #8.9
    7875 
    7876 7602 atoms, 6813 bonds, 47 pseudobonds, 1789 residues, 10 models selected 
    7877 
    7878 > select subtract #8.6
    7879 
    7880 6083 atoms, 5260 bonds, 43 pseudobonds, 1593 residues, 9 models selected 
    7881 
    7882 > select subtract #8.5
    7883 
    7884 4569 atoms, 3711 bonds, 39 pseudobonds, 1398 residues, 8 models selected 
    7885 
    7886 > select subtract #8.4
    7887 
    7888 3028 atoms, 2135 bonds, 35 pseudobonds, 1200 residues, 7 models selected 
    7889 
    7890 > hide sel atoms
    7891 
    7892 > select subtract #8.3
    7893 
    7894 1483 atoms, 555 bonds, 31 pseudobonds, 1003 residues, 5 models selected 
    7895 
    7896 > select add #8.4
    7897 
    7898 3024 atoms, 555 bonds, 31 pseudobonds, 1201 residues, 4 models selected 
    7899 
    7900 > select add #8.5
    7901 
    7902 4538 atoms, 555 bonds, 31 pseudobonds, 1396 residues, 5 models selected 
    7903 
    7904 > select add #8.6
    7905 
    7906 6057 atoms, 555 bonds, 31 pseudobonds, 1592 residues, 6 models selected 
    7907 
    7908 > hide sel atoms
    7909 
    7910 > select add #8.3
    7911 
    7912 7602 atoms, 555 bonds, 31 pseudobonds, 1789 residues, 7 models selected 
    7913 
    7914 > select subtract #8.4
    7915 
    7916 6061 atoms, 555 bonds, 31 pseudobonds, 1591 residues, 8 models selected 
    7917 
    7918 > select subtract #8.5
    7919 
    7920 4547 atoms, 555 bonds, 31 pseudobonds, 1396 residues, 7 models selected 
    7921 
    7922 > select subtract #8.6
    7923 
    7924 3028 atoms, 555 bonds, 31 pseudobonds, 1200 residues, 6 models selected 
    7925 
    7926 > select subtract #8.7
    7927 
    7928 2807 atoms, 308 bonds, 1189 residues, 4 models selected 
    7929 
    7930 > select subtract #8.8
    7931 
    7932 2580 atoms, 54 bonds, 1178 residues, 3 models selected 
    7933 
    7934 > show sel atoms
    7935 
    7936 > show #!7 models
    7937 
    7938 > hide #!7 models
    7939 
    7940 > select add #8.10
    7941 
    7942 2823 atoms, 54 bonds, 1190 residues, 2 models selected 
    7943 
    7944 > select add #8.9
    7945 
    7946 3066 atoms, 54 bonds, 1202 residues, 3 models selected 
    7947 
    7948 > select subtract #8.3
    7949 
    7950 1521 atoms, 54 bonds, 1005 residues, 4 models selected 
    7951 
    7952 > hide sel atoms
    7953 
    7954 > select add #8.8
    7955 
    7956 1748 atoms, 54 bonds, 1016 residues, 3 models selected 
    7957 
    7958 > select add #8.7
    7959 
    7960 1969 atoms, 54 bonds, 1027 residues, 4 models selected 
    7961 
    7962 > select subtract #8.9
    7963 
    7964 1726 atoms, 54 bonds, 1015 residues, 5 models selected 
    7965 
    7966 > select subtract #8.10
    7967 
    7968 1483 atoms, 54 bonds, 1003 residues, 4 models selected 
    7969 
    7970 > show sel atoms
    7971 
    7972 > select clear
    7973 
    7974 > hide #!8 models
    7975 
    7976 > show #!10 models
    7977 
    7978 > show #!9 models
    7979 
    7980 > show #!8 models
    7981 
    7982 > hide #!8 models
    7983 
    7984 > hide #!9 models
    7985 
    7986 > hide #!10 models
    7987 
    7988 > show #!11 models
    7989 
    7990 > select add #11
    7991 
    7992 7975 atoms, 7386 bonds, 63 pseudobonds, 1678 residues, 3 models selected 
    7993 
    7994 > show sel surfaces
    7995 
    7996 > hide sel surfaces
    7997 
    7998 > show sel surfaces
    7999 
    8000 > hide sel surfaces
    8001 
    8002 > select subtract #11.8
    8003 
    8004 7548 atoms, 6909 bonds, 16 pseudobonds, 1657 residues, 8 models selected 
    8005 
    8006 > select add #11.8
    8007 
    8008 7975 atoms, 6909 bonds, 16 pseudobonds, 1678 residues, 7 models selected 
    8009 
    8010 > select subtract #11.3
    8011 
    8012 6404 atoms, 5302 bonds, 12 pseudobonds, 1478 residues, 8 models selected 
    8013 
    8014 > select add #11.3
    8015 
    8016 7975 atoms, 5302 bonds, 12 pseudobonds, 1678 residues, 7 models selected 
    8017 
    8018 > select subtract #11.3
    8019 
    8020 6404 atoms, 5302 bonds, 12 pseudobonds, 1478 residues, 8 models selected 
    8021 
    8022 > select subtract #11.8
    8023 
    8024 5977 atoms, 5302 bonds, 12 pseudobonds, 1457 residues, 7 models selected 
    8025 
    8026 > select subtract #11.7
    8027 
    8028 5549 atoms, 4821 bonds, 12 pseudobonds, 1436 residues, 6 models selected 
    8029 
    8030 > hide sel atoms
    8031 
    8032 > show #!10 models
    8033 
    8034 > hide #!10 models
    8035 
    8036 > select add #11
    8037 
    8038 7975 atoms, 7386 bonds, 63 pseudobonds, 1678 residues, 6 models selected 
    8039 
    8040 > select subtract #11
    8041 
    8042 6 models selected 
    8043 
    8044 > show #!12 models
    8045 
    8046 > hide #!11 models
    8047 
    8048 > select add #12
    8049 
    8050 8621 atoms, 8800 bonds, 71 pseudobonds, 1097 residues, 3 models selected 
    8051 
    8052 > show sel surfaces
    8053 
    8054 > hide sel surfaces
    8055 
    8056 > select subtract #12.3
    8057 
    8058 6758 atoms, 6897 bonds, 67 pseudobonds, 863 residues, 9 models selected 
    8059 
    8060 > select subtract #12.8
    8061 
    8062 6232 atoms, 6310 bonds, 12 pseudobonds, 837 residues, 7 models selected 
    8063 
    8064 > select subtract #12.7
    8065 
    8066 5698 atoms, 5709 bonds, 12 pseudobonds, 811 residues, 6 models selected 
    8067 
    8068 > hide sel atoms
    8069 
    8070 > show #!11 models
    8071 
    8072 > hide #!11 models
    8073 
    8074 > show #!11 models
    8075 
    8076 > hide #!11 models
    8077 
    8078 > hide #!12 models
    8079 
    8080 > show #!13 models
    8081 
    8082 > select add #12
    8083 
    8084 8621 atoms, 8800 bonds, 71 pseudobonds, 1097 residues, 6 models selected 
    8085 
    8086 > select subtract #12
    8087 
    8088 6 models selected 
    8089 
    8090 > select add #13
    8091 
    8092 7587 atoms, 7298 bonds, 64 pseudobonds, 1365 residues, 3 models selected 
    8093 
    8094 > select subtract #13.3
    8095 
    8096 6016 atoms, 5691 bonds, 60 pseudobonds, 1165 residues, 9 models selected 
    8097 
    8098 > select subtract #13.8
    8099 
    8100 5628 atoms, 5256 bonds, 12 pseudobonds, 1146 residues, 7 models selected 
    8101 
    8102 > select subtract #13.7
    8103 
    8104 5240 atoms, 4821 bonds, 12 pseudobonds, 1127 residues, 6 models selected 
    8105 
    8106 > hide sel atoms
    8107 
    8108 > select add #13
    8109 
    8110 7587 atoms, 7298 bonds, 64 pseudobonds, 1365 residues, 6 models selected 
    8111 
    8112 > select subtract #13
    8113 
    8114 6 models selected 
    8115 
    8116 > show #!14 models
    8117 
    8118 > hide #!13 models
    8119 
    8120 > show #!15 models
    8121 
    8122 > hide #!14 models
    8123 
    8124 > show #!16 models
    8125 
    8126 > hide #!15 models
    8127 
    8128 > select add #16
    8129 
    8130 3697 atoms, 3499 bonds, 10 pseudobonds, 725 residues, 3 models selected 
    8131 
    8132 > select subtract #16.3
    8133 
    8134 2211 atoms, 1979 bonds, 5 pseudobonds, 530 residues, 6 models selected 
    8135 
    8136 > select subtract #16.5
    8137 
    8138 1801 atoms, 1520 bonds, 5 pseudobonds, 510 residues, 5 models selected 
    8139 
    8140 > hide sel atoms
    8141 
    8142 > select add #16
    8143 
    8144 3697 atoms, 3499 bonds, 10 pseudobonds, 725 residues, 4 models selected 
    8145 
    8146 > select subtract #16
    8147 
    8148 3 models selected 
    8149 
    8150 > show #!17 models
    8151 
    8152 > hide #!16 models
    8153 
    8154 > select add #17
    8155 
    8156 8677 atoms, 8800 bonds, 77 pseudobonds, 1153 residues, 3 models selected 
    8157 
    8158 > show sel surfaces
    8159 
    8160 > hide sel surfaces
    8161 
    8162 > select subtract #17.3
    8163 
    8164 6814 atoms, 6897 bonds, 73 pseudobonds, 919 residues, 9 models selected 
    8165 
    8166 > select subtract #17.8
    8167 
    8168 6281 atoms, 6299 bonds, 12 pseudobonds, 893 residues, 7 models selected 
    8169 
    8170 > select subtract #17.7
    8171 
    8172 5754 atoms, 5709 bonds, 12 pseudobonds, 867 residues, 6 models selected 
    8173 
    8174 > hide sel atoms
    8175 
    8176 > select add #17
    8177 
    8178 8677 atoms, 8800 bonds, 77 pseudobonds, 1153 residues, 6 models selected 
    8179 
    8180 > select subtract #17
    8181 
    8182 6 models selected 
    8183 
    8184 Cell requested for row 17 is out of bounds for table with 27 rows! Resizing
    8185 table model. 
    8186 
    8187 > show #!18 models
    8188 
    8189 > hide #!17 models
    8190 
    8191 > select add #18
    8192 
    8193 8456 atoms, 8740 bonds, 59 pseudobonds, 980 residues, 3 models selected 
    8194 
    8195 > select subtract #18.3
    8196 
    8197 6608 atoms, 6852 bonds, 55 pseudobonds, 749 residues, 9 models selected 
    8198 
    8199 > select subtract #18.8
    8200 
    8201 6075 atoms, 6254 bonds, 12 pseudobonds, 723 residues, 7 models selected 
    8202 
    8203 > select subtract #18.7
    8204 
    8205 5548 atoms, 5664 bonds, 12 pseudobonds, 697 residues, 6 models selected 
    8206 
    8207 > hide sel atoms
    8208 
    8209 > hide #!18 models
    8210 
    8211 > select add #18
    8212 
    8213 8456 atoms, 8740 bonds, 59 pseudobonds, 980 residues, 6 models selected 
    8214 
    8215 > select subtract #18
    8216 
    8217 6 models selected 
    8218 
    8219 > show #!19 models
    8220 
    8221 > select add #19
    8222 
    8223 7633 atoms, 7112 bonds, 81 pseudobonds, 1578 residues, 4 models selected 
    8224 
    8225 > select subtract #19.11
    8226 
    8227 7406 atoms, 6860 bonds, 46 pseudobonds, 1566 residues, 12 models selected 
    8228 
    8229 > select subtract #19.10
    8230 
    8231 7163 atoms, 6588 bonds, 46 pseudobonds, 1554 residues, 11 models selected 
    8232 
    8233 > select subtract #19.4
    8234 
    8235 5649 atoms, 5040 bonds, 42 pseudobonds, 1358 residues, 10 models selected 
    8236 
    8237 > select add #19.10
    8238 
    8239 5892 atoms, 5040 bonds, 42 pseudobonds, 1370 residues, 9 models selected 
    8240 
    8241 > select add #19.11
    8242 
    8243 6119 atoms, 5040 bonds, 42 pseudobonds, 1382 residues, 10 models selected 
    8244 
    8245 > select subtract #19.9
    8246 
    8247 5903 atoms, 4802 bonds, 12 pseudobonds, 1371 residues, 9 models selected 
    8248 
    8249 > select subtract #19.8
    8250 
    8251 5690 atoms, 4566 bonds, 12 pseudobonds, 1359 residues, 8 models selected 
    8252 
    8253 > hide sel atoms
    8254 
    8255 > select add #19
    8256 
    8257 7633 atoms, 7112 bonds, 81 pseudobonds, 1578 residues, 9 models selected 
    8258 
    8259 > select subtract #19
    8260 
    8261 8 models selected 
    8262 
    8263 > show #!1 models
    8264 
    8265 > show #!2 models
    8266 
    8267 > show #!3 models
    8268 
    8269 > show #!4 models
    8270 
    8271 > show #!5 models
    8272 
    8273 > show #!6 models
    8274 
    8275 > show #!8 models
    8276 
    8277 > show #!7 models
    8278 
    8279 > show #!9 models
    8280 
    8281 > show #!10 models
    8282 
    8283 > show #!11 models
    8284 
    8285 > show #!12 models
    8286 
    8287 > show #!13 models
    8288 
    8289 > show #!14 models
    8290 
    8291 > show #!15 models
    8292 
    8293 > show #!16 models
    8294 
    8295 > show #!17 models
    8296 
    8297 > show #!18 models
    8298 
    8299 > select
    8300 > #!1/B:110-112,124-127,132-135,141-146,156-163,195-197,204-207,214-219,230-236,251-258,264-274
    8301 
    8302 530 atoms, 532 bonds, 64 residues, 1 model selected 
    8303 
    8304 > select #!1/B:220
    8305 
    8306 12 atoms, 12 bonds, 1 residue, 1 model selected 
    8307 
    8308 > select #!1/B:220
    8309 
    8310 12 atoms, 12 bonds, 1 residue, 1 model selected 
    8311 
    8312 > select O
    8313 
    8314 30159 atoms, 21045 residues, 127 models selected 
    8315 
    8316 > hide sel atoms
    8317 
    8318 > show sel atoms
    8319 
    8320 [Repeated 1 time(s)]
    8321 
    8322 > select add #1
    8323 
    8324 35149 atoms, 6306 bonds, 55 pseudobonds, 21051 residues, 230 models selected 
    8325 
    8326 > select add #2
    8327 
    8328 40862 atoms, 13714 bonds, 133 pseudobonds, 21058 residues, 232 models selected 
    8329 
    8330 > select add #3
    8331 
    8332 46517 atoms, 21027 bonds, 190 pseudobonds, 21062 residues, 234 models selected 
    8333 
    8334 > select add #4
    8335 
    8336 52139 atoms, 28308 bonds, 264 pseudobonds, 21070 residues, 236 models selected 
    8337 
    8338 > select add #5
    8339 
    8340 57787 atoms, 35615 bonds, 334 pseudobonds, 21078 residues, 238 models selected 
    8341 
    8342 > select add #6
    8343 
    8344 59208 atoms, 37450 bonds, 338 pseudobonds, 21079 residues, 239 models selected 
    8345 
    8346 > select add #7
    8347 
    8348 66012 atoms, 46262 bonds, 411 pseudobonds, 21083 residues, 241 models selected 
    8349 
    8350 > select add #8
    8351 
    8352 71687 atoms, 53619 bonds, 492 pseudobonds, 21087 residues, 243 models selected 
    8353 
    8354 > select add #9
    8355 
    8356 73111 atoms, 55456 bonds, 497 pseudobonds, 21088 residues, 245 models selected 
    8357 
    8358 > select add #10
    8359 
    8360 74561 atoms, 57336 bonds, 502 pseudobonds, 21089 residues, 247 models selected 
    8361 
    8362 > select add #11
    8363 
    8364 80272 atoms, 64722 bonds, 565 pseudobonds, 21093 residues, 249 models selected 
    8365 
    8366 > select add #12
    8367 
    8368 87064 atoms, 73522 bonds, 636 pseudobonds, 21097 residues, 251 models selected 
    8369 
    8370 > select add #13
    8371 
    8372 92720 atoms, 80820 bonds, 700 pseudobonds, 21101 residues, 253 models selected 
    8373 
    8374 > select add #14
    8375 
    8376 94122 atoms, 82634 bonds, 705 pseudobonds, 21102 residues, 255 models selected 
    8377 
    8378 > select add #15
    8379 
    8380 95535 atoms, 84461 bonds, 710 pseudobonds, 21104 residues, 257 models selected 
    8381 
    8382 > select add #16
    8383 
    8384 98255 atoms, 87960 bonds, 720 pseudobonds, 21108 residues, 259 models selected 
    8385 
    8386 > select add #17
    8387 
    8388 105047 atoms, 96760 bonds, 797 pseudobonds, 21112 residues, 261 models
    8389 selected 
    8390 
    8391 > select add #18
    8392 
    8393 111803 atoms, 105500 bonds, 856 pseudobonds, 21116 residues, 263 models
    8394 selected 
    8395 
    8396 > select add #19
    8397 
    8398 117297 atoms, 112612 bonds, 937 pseudobonds, 21120 residues, 266 models
    8399 selected 
    8400 
    8401 > show sel atoms
    8402 
    8403 > select subtract #1
    8404 
    8405 110701 atoms, 106306 bonds, 882 pseudobonds, 19995 residues, 150 models
    8406 selected 
    8407 
    8408 > select subtract #2
    8409 
    8410 102491 atoms, 98898 bonds, 804 pseudobonds, 18099 residues, 142 models
    8411 selected 
    8412 
    8413 > select subtract #3
    8414 
    8415 95398 atoms, 91585 bonds, 747 pseudobonds, 17244 residues, 131 models selected 
    8416 
    8417 > select subtract #4
    8418 
    8419 87363 atoms, 84304 bonds, 673 pseudobonds, 15411 residues, 122 models selected 
    8420 
    8421 > select subtract #5
    8422 
    8423 79582 atoms, 76997 bonds, 603 pseudobonds, 13856 residues, 111 models selected 
    8424 
    8425 > select subtract #6
    8426 
    8427 77650 atoms, 75162 bonds, 599 pseudobonds, 13490 residues, 101 models selected 
    8428 
    8429 > select subtract #7
    8430 
    8431 69057 atoms, 66350 bonds, 526 pseudobonds, 12429 residues, 96 models selected 
    8432 
    8433 > select subtract #8
    8434 
    8435 60969 atoms, 58993 bonds, 445 pseudobonds, 10616 residues, 87 models selected 
    8436 
    8437 > select subtract #9
    8438 
    8439 59020 atoms, 57156 bonds, 440 pseudobonds, 10236 residues, 76 models selected 
    8440 
    8441 > select subtract #10
    8442 
    8443 56848 atoms, 55276 bonds, 435 pseudobonds, 9674 residues, 73 models selected 
    8444 
    8445 > select subtract #11
    8446 
    8447 48873 atoms, 47890 bonds, 372 pseudobonds, 7996 residues, 70 models selected 
    8448 
    8449 > select subtract #12
    8450 
    8451 40252 atoms, 39090 bonds, 301 pseudobonds, 6899 residues, 61 models selected 
    8452 
    8453 > select subtract #13
    8454 
    8455 32665 atoms, 31792 bonds, 237 pseudobonds, 5534 residues, 52 models selected 
    8456 
    8457 > select subtract #14
    8458 
    8459 30572 atoms, 29978 bonds, 232 pseudobonds, 4987 residues, 43 models selected 
    8460 
    8461 > select subtract #15
    8462 
    8463 28463 atoms, 28151 bonds, 227 pseudobonds, 4436 residues, 38 models selected 
    8464 
    8465 > select subtract #16
    8466 
    8467 24766 atoms, 24652 bonds, 217 pseudobonds, 3711 residues, 33 models selected 
    8468 
    8469 > select subtract #17
    8470 
    8471 16089 atoms, 15852 bonds, 140 pseudobonds, 2558 residues, 27 models selected 
    8472 
    8473 > select subtract #18
    8474 
    8475 7633 atoms, 7112 bonds, 81 pseudobonds, 1578 residues, 18 models selected 
    8476 
    8477 > select subtract #19
    8478 
    8479 8 models selected 
    8480 
    8481 > select add #1.2
    8482 
    8483 12 pseudobonds, 1 model selected 
    8484 
    8485 > select subtract #1.2
    8486 
    8487 Nothing selected 
    8488 
    8489 > select add #1.1
    8490 
    8491 43 pseudobonds, 1 model selected 
    8492 
    8493 > select add #2.3
    8494 
    8495 1552 atoms, 43 pseudobonds, 199 residues, 2 models selected 
    8496 
    8497 > select subtract #2.3
    8498 
    8499 43 pseudobonds, 2 models selected 
    8500 
    8501 > hide #!1 models
    8502 
    8503 > select add #1
    8504 
    8505 6596 atoms, 6306 bonds, 55 pseudobonds, 1125 residues, 116 models selected 
    8506 
    8507 > select subtract #1
    8508 
    8509 5 models selected 
    8510 
    8511 > hide #!19 models
    8512 
    8513 > hide #!18 models
    8514 
    8515 > hide #!17 models
    8516 
    8517 > hide #!16 models
    8518 
    8519 > hide #!15 models
    8520 
    8521 > hide #!13 models
    8522 
    8523 > hide #!12 models
    8524 
    8525 > hide #!11 models
    8526 
    8527 > hide #!14 models
    8528 
    8529 > hide #!10 models
    8530 
    8531 > hide #!9 models
    8532 
    8533 > hide #!8 models
    8534 
    8535 > hide #!7 models
    8536 
    8537 > hide #!6 models
    8538 
    8539 > hide #!5 models
    8540 
    8541 > hide #!4 models
    8542 
    8543 > hide #!3 models
    8544 
    8545 > show #!1 models
    8546 
    8547 > hide #!2 models
    8548 
    8549 > show #!2 models
    8550 
    8551 > hide #!2 models
    8552 
    8553 > select add #1.2
    8554 
    8555 12 pseudobonds, 1 model selected 
    8556 
    8557 > select subtract #1.2
    8558 
    8559 Nothing selected 
    8560 
    8561 > select add #1.1
    8562 
    8563 43 pseudobonds, 1 model selected 
    8564 
    8565 > select subtract #1.1
    8566 
    8567 Nothing selected 
    8568 
    8569 > select add #1.3
    8570 
    8571 1535 atoms, 196 residues, 1 model selected 
    8572 
    8573 > select add #1.5
    8574 
    8575 3064 atoms, 391 residues, 2 models selected 
    8576 
    8577 > select add #1.6
    8578 
    8579 3484 atoms, 412 residues, 3 models selected 
    8580 
    8581 > select add #1.7
    8582 
    8583 3919 atoms, 433 residues, 4 models selected 
    8584 
    8585 > select subtract #1.7
    8586 
    8587 3484 atoms, 412 residues, 5 models selected 
    8588 
    8589 > select subtract #1.6
    8590 
    8591 3064 atoms, 391 residues, 4 models selected 
    8592 
    8593 > hide sel atoms
    8594 
    8595 Drag select of 46 atoms 
    8596 Drag select of 72 atoms 
    8597 
    8598 > hide sel atoms
    8599 
    8600 Drag select of 2 atoms 
    8601 
    8602 > hide sel atoms
    8603 
    8604 Drag select of 1 atoms 
    8605 
    8606 > hide sel atoms
    8607 
    8608 Drag select of 2 atoms 
    8609 
    8610 > hide sel atoms
    8611 
    8612 Drag select of 81 atoms 
    8613 
    8614 > hide sel atoms
    8615 
    8616 Drag select of 35 atoms 
    8617 
    8618 > hide sel atoms
    8619 
    8620 Drag select of 1 atoms 
    8621 
    8622 > hide sel atoms
    8623 
    8624 > select add #1
    8625 
    8626 6596 atoms, 6306 bonds, 55 pseudobonds, 1125 residues, 116 models selected 
    8627 
    8628 > select subtract #1
    8629 
    8630 5 models selected 
    8631 
    8632 Cell requested for row 0 is out of bounds for table with 28 rows! Resizing
    8633 table model. 
    8634 
    8635 > show #!2 models
    8636 
    8637 > hide #!1 models
    8638 
    8639 > select add #2
    8640 
    8641 8210 atoms, 7408 bonds, 78 pseudobonds, 1896 residues, 3 models selected 
    8642 
    8643 > select subtract #2.10
    8644 
    8645 7967 atoms, 7136 bonds, 44 pseudobonds, 1884 residues, 11 models selected 
    8646 
    8647 > select add #2.10
    8648 
    8649 8210 atoms, 7136 bonds, 44 pseudobonds, 1896 residues, 10 models selected 
    8650 
    8651 > select subtract #2.8
    8652 
    8653 7967 atoms, 6864 bonds, 16 pseudobonds, 1884 residues, 10 models selected 
    8654 
    8655 > select subtract #2.7
    8656 
    8657 7724 atoms, 6592 bonds, 16 pseudobonds, 1872 residues, 9 models selected 
    8658 
    8659 > select subtract #2.6
    8660 
    8661 6170 atoms, 5003 bonds, 12 pseudobonds, 1674 residues, 8 models selected 
    8662 
    8663 > select subtract #2.5
    8664 
    8665 4641 atoms, 3439 bonds, 8 pseudobonds, 1479 residues, 7 models selected 
    8666 
    8667 > select subtract #2.4
    8668 
    8669 3096 atoms, 1859 bonds, 4 pseudobonds, 1281 residues, 6 models selected 
    8670 
    8671 > hide sel atoms
    8672 
    8673 > select add #2.8
    8674 
    8675 3339 atoms, 1859 bonds, 4 pseudobonds, 1293 residues, 5 models selected 
    8676 
    8677 > select add #2.7
    8678 
    8679 3582 atoms, 1859 bonds, 4 pseudobonds, 1305 residues, 6 models selected 
    8680 
    8681 > select add #2.6
    8682 
    8683 5136 atoms, 1859 bonds, 4 pseudobonds, 1503 residues, 7 models selected 
    8684 
    8685 > select add #2.5
    8686 
    8687 6665 atoms, 1859 bonds, 4 pseudobonds, 1698 residues, 8 models selected 
    8688 
    8689 > select add #2.4
    8690 
    8691 8210 atoms, 1859 bonds, 4 pseudobonds, 1896 residues, 9 models selected 
    8692 
    8693 > show #!1 models
    8694 
    8695 > select subtract #2.3
    8696 
    8697 6658 atoms, 272 bonds, 1697 residues, 9 models selected 
    8698 
    8699 > select add #2.3
    8700 
    8701 8210 atoms, 272 bonds, 1896 residues, 8 models selected 
    8702 
    8703 > select subtract #2.4
    8704 
    8705 6665 atoms, 272 bonds, 1698 residues, 9 models selected 
    8706 
    8707 > select add #2.4
    8708 
    8709 8210 atoms, 272 bonds, 1896 residues, 8 models selected 
    8710 
    8711 > select subtract #2.3
    8712 
    8713 6658 atoms, 272 bonds, 1697 residues, 9 models selected 
    8714 
    8715 > select subtract #2.8
    8716 
    8717 6415 atoms, 272 bonds, 1685 residues, 8 models selected 
    8718 
    8719 > select add #2.8
    8720 
    8721 6658 atoms, 272 bonds, 1697 residues, 7 models selected 
    8722 
    8723 > hide sel atoms
    8724 
    8725 > select add #2.3
    8726 
    8727 8210 atoms, 272 bonds, 1896 residues, 8 models selected 
    8728 
    8729 > select subtract #2.4
    8730 
    8731 6665 atoms, 272 bonds, 1698 residues, 9 models selected 
    8732 
    8733 > select subtract #2.5
    8734 
    8735 5136 atoms, 272 bonds, 1503 residues, 8 models selected 
    8736 
    8737 > select subtract #2.6
    8738 
    8739 3582 atoms, 272 bonds, 1305 residues, 7 models selected 
    8740 
    8741 > select subtract #2.7
    8742 
    8743 3339 atoms, 272 bonds, 1293 residues, 6 models selected 
    8744 
    8745 > select subtract #2.8
    8746 
    8747 3096 atoms, 272 bonds, 1281 residues, 5 models selected 
    8748 
    8749 > select subtract #2.9
    8750 
    8751 2853 atoms, 1269 residues, 4 models selected 
    8752 
    8753 > select subtract #2.10
    8754 
    8755 2610 atoms, 1257 residues, 3 models selected 
    8756 
    8757 > show sel atoms
    8758 
    8759 > select clear
    8760 
    8761 > hide #!1 models
    8762 
    8763 > select add #1.8
    8764 
    8765 756 atoms, 648 bonds, 108 residues, 109 models selected 
    8766 
    8767 > select subtract #1.8
    8768 
    8769 Nothing selected 
    8770 
    8771 > select add #1.7
    8772 
    8773 435 atoms, 21 residues, 1 model selected 
    8774 
    8775 > select subtract #1.7
    8776 
    8777 1 model selected 
    8778 
    8779 > show #!1 models
    8780 
    8781 > hide #!1 models
    8782 
    8783 > select add #2.9
    8784 
    8785 243 atoms, 12 residues, 1 model selected 
    8786 
    8787 > select add #2.10
    8788 
    8789 486 atoms, 24 residues, 2 models selected 
    8790 
    8791 > show sel atoms
    8792 
    8793 > hide sel atoms
    8794 
    8795 > select add #2.8
    8796 
    8797 729 atoms, 36 residues, 3 models selected 
    8798 
    8799 > select add #2.7
    8800 
    8801 972 atoms, 48 residues, 4 models selected 
    8802 
    8803 > select subtract #2.9
    8804 
    8805 729 atoms, 36 residues, 5 models selected 
    8806 
    8807 > select subtract #2.10
    8808 
    8809 486 atoms, 24 residues, 4 models selected 
    8810 
    8811 > show sel atoms
    8812 
    8813 > show #!1 models
    8814 
    8815 > hide #!1 models
    8816 
    8817 > show #!1 models
    8818 
    8819 > hide #!1 models
    8820 
    8821 > show #!1 models
    8822 
    8823 > select add #2
    8824 
    8825 8210 atoms, 7408 bonds, 78 pseudobonds, 1896 residues, 5 models selected 
    8826 
    8827 > select subtract #2
    8828 
    8829 8 models selected 
    8830 
    8831 > hide #!2 models
    8832 
    8833 > hide #!1 models
    8834 
    8835 > show #!3 models
    8836 
    8837 > select add #3.4
    8838 
    8839 1558 atoms, 198 residues, 1 model selected 
    8840 
    8841 > select add #3.5
    8842 
    8843 3110 atoms, 395 residues, 2 models selected 
    8844 
    8845 > select add #3.6
    8846 
    8847 4662 atoms, 592 residues, 3 models selected 
    8848 
    8849 > select add #3.7
    8850 
    8851 5090 atoms, 613 residues, 4 models selected 
    8852 
    8853 > select subtract #3.7
    8854 
    8855 4662 atoms, 592 residues, 5 models selected 
    8856 
    8857 > hide sel atoms
    8858 
    8859 > show #!2 models
    8860 
    8861 > hide #!2 models
    8862 
    8863 > select add #3
    8864 
    8865 7093 atoms, 7313 bonds, 57 pseudobonds, 855 residues, 6 models selected 
    8866 
    8867 > select subtract #3
    8868 
    8869 6 models selected 
    8870 
    8871 > show #!4 models
    8872 
    8873 > hide #!3 models
    8874 
    8875 > select add #4.10
    8876 
    8877 243 atoms, 12 residues, 1 model selected 
    8878 
    8879 > select subtract #4.10
    8880 
    8881 1 model selected 
    8882 
    8883 > select add #4.10
    8884 
    8885 243 atoms, 12 residues, 1 model selected 
    8886 
    8887 > select add #4.9
    8888 
    8889 486 atoms, 24 residues, 2 models selected 
    8890 
    8891 > select add #4.6
    8892 
    8893 2010 atoms, 220 residues, 3 models selected 
    8894 
    8895 > select add #4.5
    8896 
    8897 3518 atoms, 413 residues, 4 models selected 
    8898 
    8899 > select add #4.4
    8900 
    8901 5056 atoms, 611 residues, 5 models selected 
    8902 
    8903 > hide sel atoms
    8904 
    8905 > show #!3 models
    8906 
    8907 > hide #!3 models
    8908 
    8909 > select add #4
    8910 
    8911 8035 atoms, 7281 bonds, 74 pseudobonds, 1833 residues, 8 models selected 
    8912 
    8913 > select subtract #4
    8914 
    8915 8 models selected 
    8916 
    8917 > show #!19 models
    8918 
    8919 > select add #19.11
    8920 
    8921 227 atoms, 12 residues, 1 model selected 
    8922 
    8923 > select add #19.10
    8924 
    8925 470 atoms, 24 residues, 2 models selected 
    8926 
    8927 > select add #19.7
    8928 
    8929 1954 atoms, 218 residues, 3 models selected 
    8930 
    8931 > select add #19.6
    8932 
    8933 3450 atoms, 411 residues, 4 models selected 
    8934 
    8935 > select add #19.5
    8936 
    8937 4939 atoms, 608 residues, 5 models selected 
    8938 
    8939 > hide sel atoms
    8940 
    8941 > select add #19
    8942 
    8943 7633 atoms, 7112 bonds, 81 pseudobonds, 1578 residues, 9 models selected 
    8944 
    8945 > select subtract #19
    8946 
    8947 8 models selected 
    8948 
    8949 Cell requested for row 17 is out of bounds for table with 30 rows! Resizing
    8950 table model. 
    8951 
    8952 > show #!18 models
    8953 
    8954 > hide #!19 models
    8955 
    8956 > select add #18.6
    8957 
    8958 1848 atoms, 231 residues, 1 model selected 
    8959 
    8960 > select add #18.5
    8961 
    8962 3696 atoms, 462 residues, 2 models selected 
    8963 
    8964 > select add #18.4
    8965 
    8966 5544 atoms, 693 residues, 3 models selected 
    8967 
    8968 > hide sel atoms
    8969 
    8970 > select add #18.7
    8971 
    8972 6071 atoms, 719 residues, 4 models selected 
    8973 
    8974 > select subtract #18.7
    8975 
    8976 5544 atoms, 693 residues, 5 models selected 
    8977 
    8978 > hide #!18 models
    8979 
    8980 > show #!17 models
    8981 
    8982 > select add #18
    8983 
    8984 8456 atoms, 8740 bonds, 59 pseudobonds, 980 residues, 6 models selected 
    8985 
    8986 > select subtract #18
    8987 
    8988 6 models selected 
    8989 
    8990 > select add #17.6
    8991 
    8992 1863 atoms, 234 residues, 1 model selected 
    8993 
    8994 > select add #17.5
    8995 
    8996 3726 atoms, 468 residues, 2 models selected 
    8997 
    8998 > select add #17.4
    8999 
    9000 5589 atoms, 702 residues, 3 models selected 
    9001 
    9002 > hide sel atoms
    9003 
    9004 > select add #17
    9005 
    9006 8677 atoms, 8800 bonds, 77 pseudobonds, 1153 residues, 6 models selected 
    9007 
    9008 > select subtract #17
    9009 
    9010 6 models selected 
    9011 
    9012 Cell requested for row 15 is out of bounds for table with 27 rows! Resizing
    9013 table model. 
    9014 
    9015 > show #!16 models
    9016 
    9017 > hide #!17 models
    9018 
    9019 > select add #16.5
    9020 
    9021 410 atoms, 20 residues, 1 model selected 
    9022 
    9023 > select subtract #16.5
    9024 
    9025 1 model selected 
    9026 
    9027 > select add #16.4
    9028 
    9029 1486 atoms, 195 residues, 1 model selected 
    9030 
    9031 > hide sel atoms
    9032 
    9033 > select add #16.1
    9034 
    9035 1486 atoms, 8 pseudobonds, 195 residues, 3 models selected 
    9036 
    9037 > select subtract #16.1
    9038 
    9039 1486 atoms, 195 residues, 2 models selected 
    9040 
    9041 > select add #16.2
    9042 
    9043 1486 atoms, 2 pseudobonds, 195 residues, 3 models selected 
    9044 
    9045 > select subtract #16.2
    9046 
    9047 1486 atoms, 195 residues, 2 models selected 
    9048 
    9049 > select add #16.3
    9050 
    9051 2972 atoms, 390 residues, 2 models selected 
    9052 
    9053 > select subtract #16.3
    9054 
    9055 1486 atoms, 195 residues, 3 models selected 
    9056 
    9057 > select add #16
    9058 
    9059 3697 atoms, 3499 bonds, 10 pseudobonds, 725 residues, 4 models selected 
    9060 
    9061 > select subtract #16
    9062 
    9063 3 models selected 
    9064 
    9065 > hide #!16 models
    9066 
    9067 > show #!16 models
    9068 
    9069 > show #!15 models
    9070 
    9071 > hide #!16 models
    9072 
    9073 > show #!14 models
    9074 
    9075 > show #!13 models
    9076 
    9077 > hide #!14 models
    9078 
    9079 > hide #!15 models
    9080 
    9081 > hide #15.1 models
    9082 
    9083 > show #15.1 models
    9084 
    9085 > hide #!15 models
    9086 
    9087 > select add #13.8
    9088 
    9089 388 atoms, 19 residues, 1 model selected 
    9090 
    9091 > select subtract #13.8
    9092 
    9093 1 model selected 
    9094 
    9095 > select add #13.6
    9096 
    9097 1571 atoms, 200 residues, 1 model selected 
    9098 
    9099 > select add #13.5
    9100 
    9101 3142 atoms, 400 residues, 2 models selected 
    9102 
    9103 > select add #13.4
    9104 
    9105 4713 atoms, 600 residues, 3 models selected 
    9106 
    9107 > hide sel atoms
    9108 
    9109 > select add #13
    9110 
    9111 7587 atoms, 7298 bonds, 64 pseudobonds, 1365 residues, 6 models selected 
    9112 
    9113 > select subtract #13
    9114 
    9115 6 models selected 
    9116 
    9117 > show #!12 models
    9118 
    9119 > hide #!13 models
    9120 
    9121 > select add #12.8
    9122 
    9123 526 atoms, 26 residues, 1 model selected 
    9124 
    9125 > select subtract #12.8
    9126 
    9127 1 model selected 
    9128 
    9129 > select add #12.6
    9130 
    9131 1863 atoms, 234 residues, 1 model selected 
    9132 
    9133 > select add #12.5
    9134 
    9135 3726 atoms, 468 residues, 2 models selected 
    9136 
    9137 > select add #12.4
    9138 
    9139 5589 atoms, 702 residues, 3 models selected 
    9140 
    9141 > hide sel atoms
    9142 
    9143 > select add #12
    9144 
    9145 8621 atoms, 8800 bonds, 71 pseudobonds, 1097 residues, 6 models selected 
    9146 
    9147 > select subtract #12
    9148 
    9149 6 models selected 
    9150 
    9151 > show #!11 models
    9152 
    9153 > hide #!12 models
    9154 
    9155 > select add #11.6
    9156 
    9157 1571 atoms, 200 residues, 1 model selected 
    9158 
    9159 > select add #11.5
    9160 
    9161 3142 atoms, 400 residues, 2 models selected 
    9162 
    9163 > select add #11.4
    9164 
    9165 4713 atoms, 600 residues, 3 models selected 
    9166 
    9167 > hide sel atoms
    9168 
    9169 > select add #11.7
    9170 
    9171 5141 atoms, 621 residues, 4 models selected 
    9172 
    9173 > select subtract #11.7
    9174 
    9175 4713 atoms, 600 residues, 5 models selected 
    9176 
    9177 > select subtract #11.6
    9178 
    9179 3142 atoms, 400 residues, 4 models selected 
    9180 
    9181 > select subtract #11.5
    9182 
    9183 1571 atoms, 200 residues, 3 models selected 
    9184 
    9185 > select subtract #11.4
    9186 
    9187 1 model selected 
    9188 
    9189 > show #!10 models
    9190 
    9191 > hide #!11 models
    9192 
    9193 > hide #!10 models
    9194 
    9195 > show #!10 models
    9196 
    9197 > hide #!4 models
    9198 
    9199 > show #!9 models
    9200 
    9201 > hide #!10 models
    9202 
    9203 > show #!10 models
    9204 
    9205 > hide #!10 models
    9206 
    9207 > show #!8 models
    9208 
    9209 > hide #!9 models
    9210 
    9211 > select add #8.10
    9212 
    9213 243 atoms, 12 residues, 1 model selected 
    9214 
    9215 > select add #8.9
    9216 
    9217 486 atoms, 24 residues, 2 models selected 
    9218 
    9219 > select add #8.6
    9220 
    9221 2005 atoms, 220 residues, 3 models selected 
    9222 
    9223 > select add #8.5
    9224 
    9225 3519 atoms, 415 residues, 4 models selected 
    9226 
    9227 > select add #8.4
    9228 
    9229 5060 atoms, 613 residues, 5 models selected 
    9230 
    9231 > hide sel atoms
    9232 
    9233 > select add #8
    9234 
    9235 8088 atoms, 7357 bonds, 81 pseudobonds, 1813 residues, 8 models selected 
    9236 
    9237 > select subtract #8
    9238 
    9239 8 models selected 
    9240 
    9241 > hide #!8 models
    9242 
    9243 > show #!8 models
    9244 
    9245 > hide #!8 models
    9246 
    9247 > show #!7 models
    9248 
    9249 > select add #7.6
    9250 
    9251 1865 atoms, 234 residues, 1 model selected 
    9252 
    9253 > select add #7.5
    9254 
    9255 3730 atoms, 468 residues, 2 models selected 
    9256 
    9257 > select add #7.4
    9258 
    9259 5595 atoms, 702 residues, 3 models selected 
    9260 
    9261 > hide sel atoms
    9262 
    9263 > select add #7
    9264 
    9265 8593 atoms, 8812 bonds, 73 pseudobonds, 1061 residues, 6 models selected 
    9266 
    9267 > select subtract #7
    9268 
    9269 6 models selected 
    9270 
    9271 > show #!6 models
    9272 
    9273 > hide #!7 models
    9274 
    9275 > hide #!6 models
    9276 
    9277 > show #!6 models
    9278 
    9279 > show #!5 models
    9280 
    9281 > hide #!6 models
    9282 
    9283 > select add #5.9
    9284 
    9285 243 atoms, 12 residues, 1 model selected 
    9286 
    9287 > select add #5.10
    9288 
    9289 466 atoms, 23 residues, 2 models selected 
    9290 
    9291 > select add #5.6
    9292 
    9293 2002 atoms, 221 residues, 3 models selected 
    9294 
    9295 > select add #5.5
    9296 
    9297 3537 atoms, 417 residues, 4 models selected 
    9298 
    9299 > select add #5.4
    9300 
    9301 5089 atoms, 616 residues, 5 models selected 
    9302 
    9303 > hide sel atoms
    9304 
    9305 > select add #5
    9306 
    9307 7781 atoms, 7307 bonds, 70 pseudobonds, 1555 residues, 8 models selected 
    9308 
    9309 > select subtract #5
    9310 
    9311 8 models selected 
    9312 
    9313 > show #!4 models
    9314 
    9315 > hide #!5 models
    9316 
    9317 > show #!3 models
    9318 
    9319 > hide #!4 models
    9320 
    9321 > show #!1 models
    9322 
    9323 > show #!2 models
    9324 
    9325 > show #!4 models
    9326 
    9327 > show #!5 models
    9328 
    9329 > show #!6 models
    9330 
    9331 > show #!7 models
    9332 
    9333 > show #!8 models
    9334 
    9335 > show #!9 models
    9336 
    9337 > show #!10 models
    9338 
    9339 > show #!11 models
    9340 
    9341 > show #!12 models
    9342 
    9343 > show #!13 models
    9344 
    9345 > show #!14 models
    9346 
    9347 > show #!15 models
    9348 
    9349 > show #!19 models
    9350 
    9351 > show #!18 models
    9352 
    9353 > show #!17 models
    9354 
    9355 > show #!16 models
    9356 
    9357 Drag select of 883 atoms, 15 bonds 
    9358 
    9359 > hide sel atoms
    9360 
    9361 Drag select of 560 atoms, 6 bonds 
    9362 
    9363 > hide sel atoms
    9364 
    9365 Drag select of 49 atoms 
    9366 
    9367 > hide sel atoms
    9368 
    9369 Drag select of 358 atoms, 3 bonds 
    9370 
    9371 > hide sel atoms
    9372 
    9373 Drag select of 604 atoms 
    9374 
    9375 > hide sel atoms
    9376 
    9377 Drag select of 106 atoms 
    9378 
    9379 > hide sel atoms
    9380 
    9381 Drag select of 22 atoms 
    9382 
    9383 > hide sel atoms
    9384 
    9385 Drag select of 610 atoms, 3 bonds 
    9386 
    9387 > hide sel atoms
    9388 
    9389 Drag select of 112 atoms 
    9390 
    9391 > hide sel atoms
    9392 
    9393 Drag select of 252 atoms, 1 bonds 
    9394 
    9395 > hide sel atoms
    9396 
    9397 Drag select of 4 atoms 
    9398 
    9399 > hide sel atoms
    9400 
    9401 Drag select of 3 atoms 
    9402 
    9403 > hide sel atoms
    9404 
    9405 Drag select of 47 atoms, 8 bonds 
    9406 
    9407 > hide sel atoms
    9408 
    9409 Drag select of 77 atoms 
    9410 
    9411 > hide sel atoms
    9412 
    9413 Drag select of 15 atoms 
    9414 
    9415 > hide sel atoms
    9416 
    9417 > select ions
    9418 
    9419 61 atoms, 61 residues, 19 models selected 
    9420 
    9421 > select solvent
    9422 
    9423 8211 atoms, 8211 residues, 18 models selected 
    9424 
    9425 > hide sel atoms
    9426 
    9427 > save "/Users/kompa012/Desktop/P53/Before mutation 1.cxs"
    9428 
    9429 > hide #!2 models
    9430 
    9431 > show #!2 models
    9432 
    9433 > hide #!2 models
    9434 
    9435 > select #!1/B:220
    9436 
    9437 12 atoms, 12 bonds, 1 residue, 1 model selected 
    9438 
    9439 > select #!1/B:220
    9440 
    9441 12 atoms, 12 bonds, 1 residue, 1 model selected 
    9442 
    9443 > style sel sphere
    9444 
    9445 Changed 12 atom styles 
    9446 
    9447 > style sel stick
    9448 
    9449 Changed 12 atom styles 
    9450 
    9451 > show #!2 models
    9452 
    9453 > select Y220
    9454 
    9455 Expected an objects specifier or a keyword 
    9456 
    9457 > select #1 Y220
    9458 
    9459 Expected a keyword 
    9460 
    9461 > select #1, Y220
    9462 
    9463 Expected an objects specifier or a keyword 
    9464 
    9465 > select #1 :Y220
    9466 
    9467 Nothing selected 
    9468 
    9469 > select #1-19 :Y220
    9470 
    9471 Nothing selected 
    9472 
    9473 > select #1-19 :220
    9474 
    9475 698 atoms, 696 bonds, 60 residues, 19 models selected 
    9476 
    9477 > select #1-19 /A :220
    9478 
    9479 228 atoms, 228 bonds, 19 residues, 19 models selected 
    9480 
    9481 > style sel sphere
    9482 
    9483 Changed 228 atom styles 
    9484 
    9485 > style sel stick
    9486 
    9487 Changed 228 atom styles 
    9488 
    9489 > hide #!9 models
    9490 
    9491 > show #!9 models
    9492 
    9493 > hide #!9 models
    9494 
    9495 > show #!9 models
    9496 
    9497 > hide #!9 models
    9498 
    9499 > hide #!10 models
    9500 
    9501 > show #!9 models
    9502 
    9503 > show #!10 models
    9504 
    9505 > select add #9.2
    9506 
    9507 228 atoms, 228 bonds, 1 pseudobond, 19 residues, 37 models selected 
    9508 
    9509 > select subtract #9.2
    9510 
    9511 228 atoms, 228 bonds, 19 residues, 36 models selected 
    9512 
    9513 > select add #9.1
    9514 
    9515 228 atoms, 228 bonds, 4 pseudobonds, 19 residues, 37 models selected 
    9516 
    9517 > select subtract #9.1
    9518 
    9519 228 atoms, 228 bonds, 19 residues, 36 models selected 
    9520 
    9521 > select clear
    9522 
    9523 > select ligand
    9524 
    9525 172 atoms, 129 bonds, 43 residues, 4 models selected 
    9526 
    9527 > hide sel atoms
    9528 
    9529 > select add #8
    9530 
    9531 8188 atoms, 7432 bonds, 81 pseudobonds, 1838 residues, 6 models selected 
    9532 
    9533 > select subtract #8
    9534 
    9535 100 atoms, 75 bonds, 25 residues, 11 models selected 
    9536 
    9537 > select add #9
    9538 
    9539 2021 atoms, 1891 bonds, 5 pseudobonds, 398 residues, 5 models selected 
    9540 
    9541 > select subtract #9
    9542 
    9543 72 atoms, 54 bonds, 18 residues, 2 models selected 
    9544 
    9545 > select add #10
    9546 
    9547 2176 atoms, 1883 bonds, 5 pseudobonds, 563 residues, 4 models selected 
    9548 
    9549 > select subtract #10
    9550 
    9551 4 atoms, 3 bonds, 1 residue, 1 model selected 
    9552 
    9553 > select #1-19 /A :220
    9554 
    9555 228 atoms, 228 bonds, 19 residues, 19 models selected 
    9556 
    9557 > select subtract #1.3
    9558 
    9559 216 atoms, 216 bonds, 18 residues, 35 models selected 
    9560 
    9561 > lighting full
    9562 
    9563 > lighting simple
    9564 
    9565 > lighting soft
    9566 
    9567 Cell requested for row 8 is out of bounds for table with 28 rows! Resizing
    9568 table model. 
    9569 
    9570 > select add #1.9
    9571 
    9572 228 atoms, 225 bonds, 21 residues, 38 models selected 
    9573 
    9574 > select add #1.8
    9575 
    9576 984 atoms, 873 bonds, 129 residues, 147 models selected 
    9577 
    9578 > select clear
    9579 
    9580 > select add #1.8
    9581 
    9582 756 atoms, 648 bonds, 108 residues, 109 models selected 
    9583 
    9584 > select add #1.9
    9585 
    9586 768 atoms, 657 bonds, 111 residues, 113 models selected 
    9587 
    9588 > hide sel atoms
    9589 
    9590 > select add #1
    9591 
    9592 6596 atoms, 6306 bonds, 55 pseudobonds, 1125 residues, 116 models selected 
    9593 
    9594 > select subtract #1
    9595 
    9596 5 models selected 
    9597 
    9598 > select #1-19 /A :220
    9599 
    9600 228 atoms, 228 bonds, 19 residues, 19 models selected 
    9601 
    9602 > color (#!1-19 & sel) black
    9603 
    9604 > style sel sphere
    9605 
    9606 Changed 228 atom styles 
    9607 
    9608 > select #1-19 /A :248
    9609 
    9610 207 atoms, 188 bonds, 19 residues, 19 models selected 
    9611 
    9612 > select add #1
    9613 
    9614 6792 atoms, 6484 bonds, 55 pseudobonds, 1143 residues, 151 models selected 
    9615 
    9616 > select subtract #1
    9617 
    9618 196 atoms, 178 bonds, 18 residues, 39 models selected 
    9619 
    9620 > color (#!2-19 & sel) black
    9621 
    9622 > style sel sphere
    9623 
    9624 Changed 196 atom styles 
    9625 
    9626 > select #1-19 /A :282
    9627 
    9628 209 atoms, 190 bonds, 19 residues, 19 models selected 
    9629 
    9630 > color (#!1-19 & sel) black
    9631 
    9632 > style sel sphere
    9633 
    9634 Changed 209 atom styles 
    9635 
    9636 > ui tool show "Color Actions"
    9637 
    9638 > select clear
    9639 
    9640 > set bgColor white
    9641 
    9642 > set bgColor #ffffff00
    9643 
    9644 > lighting flat
    9645 
    9646 > select #1-19 /A :282
    9647 
    9648 209 atoms, 190 bonds, 19 residues, 19 models selected 
    9649 
    9650 > lighting full
    9651 
    9652 > graphics silhouettes false
    9653 
    9654 > lighting flat
    9655 
    9656 > graphics silhouettes false
    9657 
    9658 > graphics silhouettes true
    9659 
    9660 > select clear
    9661 
    9662 > color #1 #0009d1ff
    9663 
    9664 > color #1 #0017d1ff
    9665 
    9666 > color #1 #00d1c3ff
    9667 
    9668 > color #1 #00d1b9ff
    9669 
    9670 > color #1 #74d100ff
    9671 
    9672 > color #1 #70d100ff
    9673 
    9674 > color #1 #5bd100ff
    9675 
    9676 > color #1 #60d100ff
    9677 
    9678 > color #2 #85d406ff
    9679 
    9680 > color #2 #87d401ff
    9681 
    9682 > color #3 #b1dc05ff
    9683 
    9684 > color #4 #d0d405ff
    9685 
    9686 > color #5 #d4ba04ff
    9687 
    9688 > color #6 #db9704ff
    9689 
    9690 > color #7 #d16404ff
    9691 
    9692 > color #8 #f4520cff
    9693 
    9694 > color #9 #ff2f10ff
    9695 
    9696 > color #10 #940907ff
    9697 
    9698 > color #9 #ff1f1aff
    9699 
    9700 > color #10 #a71728ff
    9701 
    9702 > color #11 #fc1a3dff
    9703 
    9704 > color #10 #ff3b4cff
    9705 
    9706 > color #10 #ff1ed9ff
    9707 
    9708 > color #10 #ff08ceff
    9709 
    9710 > color #10 #ff00efff
    9711 
    9712 > color #9 #ff00adff
    9713 
    9714 > color #11 #e406ffff
    9715 
    9716 > color #12 #ce02fcff
    9717 
    9718 > color #13 #b700fcff
    9719 
    9720 > color #14 #826cffff
    9721 
    9722 > color #14 #b000ffff
    9723 
    9724 > color #14 #ad00ffff
    9725 
    9726 > color #15 #ff7c70ff
    9727 
    9728 > color #15 #8308ffff
    9729 
    9730 > color #16 #edff78ff
    9731 
    9732 > color #16 #3907ffff
    9733 
    9734 > color #16 #4a11ffff
    9735 
    9736 > color #17 #0d00fcff
    9737 
    9738 > color #18 #0040e1ff
    9739 
    9740 > color #19 #008afaff
    9741 
    9742 > select #1-19 /A :282
    9743 
    9744 209 atoms, 190 bonds, 19 residues, 19 models selected 
    9745 
    9746 > color (#!1-19 & sel) black
    9747 
    9748 > select #1-19 /A :248
    9749 
    9750 207 atoms, 188 bonds, 19 residues, 19 models selected 
    9751 
    9752 > color (#!1-19 & sel) black
    9753 
    9754 > select #1-19 /A :220
    9755 
    9756 228 atoms, 228 bonds, 19 residues, 19 models selected 
    9757 
    9758 > color (#!1-19 & sel) black
    9759 
    9760 > select clear
    9761 
    9762 > select #!1/B:220
    9763 
    9764 12 atoms, 12 bonds, 1 residue, 1 model selected 
    9765 
    9766 > select #!1/B:220
    9767 
    9768 12 atoms, 12 bonds, 1 residue, 1 model selected 
    9769 
    9770 > style sel sphere
    9771 
    9772 Changed 12 atom styles 
    9773 
    9774 > color (#!1 & sel) black
    9775 
    9776 > select #!1/B:282
    9777 
    9778 11 atoms, 10 bonds, 1 residue, 1 model selected 
    9779 
    9780 > select #!1/B:282
    9781 
    9782 11 atoms, 10 bonds, 1 residue, 1 model selected 
    9783 
    9784 > style sel sphere
    9785 
    9786 Changed 11 atom styles 
    9787 
    9788 > color (#!1 & sel) black
    9789 
    9790 > select #!1/B:220
    9791 
    9792 12 atoms, 12 bonds, 1 residue, 1 model selected 
    9793 
    9794 > select #!1/B:220
    9795 
    9796 12 atoms, 12 bonds, 1 residue, 1 model selected 
    9797 
    9798 > select #!1/B:248
    9799 
    9800 11 atoms, 10 bonds, 1 residue, 1 model selected 
    9801 
    9802 > select #!1/B:248
    9803 
    9804 11 atoms, 10 bonds, 1 residue, 1 model selected 
    9805 
    9806 > style sel sphere
    9807 
    9808 Changed 11 atom styles 
    9809 
    9810 > color (#!1 & sel) black
    9811 
    9812 > select clear
    9813 
    9814 [Repeated 1 time(s)]
    9815 
    9816 > lighting flat
    9817 
    9818 > lighting simple
    9819 
    9820 > lighting shadows true
    9821 
    9822 > lighting shadows false
    9823 
    9824 > ui tool show "Side View"
    9825 
    9826 > select add #8
    9827 
    9828 8088 atoms, 7357 bonds, 81 pseudobonds, 1813 residues, 3 models selected 
    9829 
    9830 > select add #9
    9831 
    9832 10037 atoms, 9194 bonds, 86 pseudobonds, 2193 residues, 14 models selected 
    9833 
    9834 > select add #10
    9835 
    9836 12209 atoms, 11074 bonds, 91 pseudobonds, 2755 residues, 17 models selected 
    9837 
    9838 > select add #11
    9839 
    9840 20184 atoms, 18460 bonds, 154 pseudobonds, 4433 residues, 20 models selected 
    9841 
    9842 > select add #12
    9843 
    9844 28805 atoms, 27260 bonds, 225 pseudobonds, 5530 residues, 29 models selected 
    9845 
    9846 > select add #13
    9847 
    9848 36392 atoms, 34558 bonds, 289 pseudobonds, 6895 residues, 38 models selected 
    9849 
    9850 > select add #14
    9851 
    9852 38485 atoms, 36372 bonds, 294 pseudobonds, 7442 residues, 47 models selected 
    9853 
    9854 > select add #15
    9855 
    9856 40594 atoms, 38199 bonds, 299 pseudobonds, 7993 residues, 52 models selected 
    9857 
    9858 > select add #16
    9859 
    9860 44291 atoms, 41698 bonds, 309 pseudobonds, 8718 residues, 57 models selected 
    9861 
    9862 > select add #17
    9863 
    9864 52968 atoms, 50498 bonds, 386 pseudobonds, 9871 residues, 63 models selected 
    9865 
    9866 > select add #18
    9867 
    9868 61424 atoms, 59238 bonds, 445 pseudobonds, 10851 residues, 72 models selected 
    9869 
    9870 > select add #19
    9871 
    9872 69057 atoms, 66350 bonds, 526 pseudobonds, 12429 residues, 82 models selected 
    9873 
    9874 > select add #7
    9875 
    9876 77650 atoms, 75162 bonds, 599 pseudobonds, 13490 residues, 93 models selected 
    9877 
    9878 > select add #6
    9879 
    9880 79582 atoms, 76997 bonds, 603 pseudobonds, 13856 residues, 101 models selected 
    9881 
    9882 > select add #5
    9883 
    9884 87363 atoms, 84304 bonds, 673 pseudobonds, 15411 residues, 106 models selected 
    9885 
    9886 > select add #4
    9887 
    9888 95398 atoms, 91585 bonds, 747 pseudobonds, 17244 residues, 117 models selected 
    9889 
    9890 > select add #3
    9891 
    9892 102491 atoms, 98898 bonds, 804 pseudobonds, 18099 residues, 128 models
    9893 selected 
    9894 
    9895 > select add #2
    9896 
    9897 110701 atoms, 106306 bonds, 882 pseudobonds, 19995 residues, 137 models
    9898 selected 
    9899 
    9900 > select add #1
    9901 
    9902 117297 atoms, 112612 bonds, 937 pseudobonds, 21120 residues, 261 models
    9903 selected 
    9904 
    9905 > color (#1.8.1-108#1.9.1-3#!1-19 & sel) dark gray
    9906 
    9907 > select #1-19 /A :220
    9908 
    9909 228 atoms, 228 bonds, 19 residues, 19 models selected 
    9910 
    9911 > color (#!1-19 & sel) black
    9912 
    9913 > select #1-19 /A :248
    9914 
    9915 207 atoms, 188 bonds, 19 residues, 19 models selected 
    9916 
    9917 > color (#!1-19 & sel) black
    9918 
    9919 > select #1-19 /A :282
    9920 
    9921 209 atoms, 190 bonds, 19 residues, 19 models selected 
    9922 
    9923 > color (#!1-19 & sel) black
    9924 
    9925 > select #!1/B:248
    9926 
    9927 11 atoms, 10 bonds, 1 residue, 1 model selected 
    9928 
    9929 > select #!1/B:248
    9930 
    9931 11 atoms, 10 bonds, 1 residue, 1 model selected 
    9932 
    9933 > color (#!1 & sel) black
    9934 
    9935 > select #!1/B:167-170,177-181,278-287
    9936 
    9937 167 atoms, 169 bonds, 19 residues, 1 model selected 
    9938 
    9939 > select #!1/B:282
    9940 
    9941 11 atoms, 10 bonds, 1 residue, 1 model selected 
    9942 
    9943 > select #!1/B:282
    9944 
    9945 11 atoms, 10 bonds, 1 residue, 1 model selected 
    9946 
    9947 > color (#!1 & sel) black
    9948 
    9949 > select #!1/B:220
    9950 
    9951 12 atoms, 12 bonds, 1 residue, 1 model selected 
    9952 
    9953 > select #!1/B:220
    9954 
    9955 12 atoms, 12 bonds, 1 residue, 1 model selected 
    9956 
    9957 > color (#!1 & sel) black
    9958 
    9959 > select clear
    9960 
    9961 Cell requested for row 15 is out of bounds for table with 28 rows! Resizing
    9962 table model. 
    9963 
    9964 > select #1-19 :AP, TP, GP, CP
    9965 
    9966 Nothing selected 
    9967 
    9968 > select #1-19 :AP
    9969 
    9970 Nothing selected 
    9971 
    9972 > select add #3
    9973 
    9974 7093 atoms, 7313 bonds, 57 pseudobonds, 855 residues, 3 models selected 
    9975 
    9976 > select add #4
    9977 
    9978 15128 atoms, 14594 bonds, 131 pseudobonds, 2688 residues, 12 models selected 
    9979 
    9980 > select add #5
    9981 
    9982 22909 atoms, 21901 bonds, 201 pseudobonds, 4243 residues, 23 models selected 
    9983 
    9984 > select add #6
    9985 
    9986 24841 atoms, 23736 bonds, 205 pseudobonds, 4609 residues, 33 models selected 
    9987 
    9988 > select add #7
    9989 
    9990 33434 atoms, 32548 bonds, 278 pseudobonds, 5670 residues, 38 models selected 
    9991 
    9992 > select add #8
    9993 
    9994 41522 atoms, 39905 bonds, 359 pseudobonds, 7483 residues, 47 models selected 
    9995 
    9996 > select add #9
    9997 
    9998 43471 atoms, 41742 bonds, 364 pseudobonds, 7863 residues, 58 models selected 
    9999 
    10000 > select add #10
    10001 
    10002 45643 atoms, 43622 bonds, 369 pseudobonds, 8425 residues, 61 models selected 
    10003 
    10004 > select add #11
    10005 
    10006 53618 atoms, 51008 bonds, 432 pseudobonds, 10103 residues, 64 models selected 
    10007 
    10008 > select add #12
    10009 
    10010 62239 atoms, 59808 bonds, 503 pseudobonds, 11200 residues, 73 models selected 
    10011 
    10012 > select add #13
    10013 
    10014 69826 atoms, 67106 bonds, 567 pseudobonds, 12565 residues, 82 models selected 
    10015 
    10016 > select add #14
    10017 
    10018 71919 atoms, 68920 bonds, 572 pseudobonds, 13112 residues, 91 models selected 
    10019 
    10020 > select add #15
    10021 
    10022 74028 atoms, 70747 bonds, 577 pseudobonds, 13663 residues, 96 models selected 
    10023 
    10024 > select add #16
    10025 
    10026 77725 atoms, 74246 bonds, 587 pseudobonds, 14388 residues, 101 models selected 
    10027 
    10028 > select add #17
    10029 
    10030 86402 atoms, 83046 bonds, 664 pseudobonds, 15541 residues, 107 models selected 
    10031 
    10032 > select add #18
    10033 
    10034 94858 atoms, 91786 bonds, 723 pseudobonds, 16521 residues, 116 models selected 
    10035 
    10036 > select add #19
    10037 
    10038 102491 atoms, 98898 bonds, 804 pseudobonds, 18099 residues, 126 models
    10039 selected 
    10040 
    10041 > show sel cartoons
    10042 
    10043 > select add #1
    10044 
    10045 109087 atoms, 105204 bonds, 859 pseudobonds, 19224 residues, 250 models
    10046 selected 
    10047 
    10048 > select add #2
    10049 
    10050 117297 atoms, 112612 bonds, 937 pseudobonds, 21120 residues, 258 models
    10051 selected 
    10052 
    10053 > select subtract #19.4
    10054 
    10055 115783 atoms, 111064 bonds, 933 pseudobonds, 20924 residues, 266 models
    10056 selected 
    10057 
    10058 > select subtract #19.11
    10059 
    10060 115556 atoms, 110812 bonds, 898 pseudobonds, 20912 residues, 265 models
    10061 selected 
    10062 
    10063 > select subtract #19.10
    10064 
    10065 115313 atoms, 110540 bonds, 898 pseudobonds, 20900 residues, 264 models
    10066 selected 
    10067 
    10068 > hide #!18 models
    10069 
    10070 > hide #!17 models
    10071 
    10072 > hide #!16 models
    10073 
    10074 > hide #!15 models
    10075 
    10076 > hide #!14 models
    10077 
    10078 > hide #!13 models
    10079 
    10080 > hide #!12 models
    10081 
    10082 > hide #!11 models
    10083 
    10084 > hide #!10 models
    10085 
    10086 > hide #!9 models
    10087 
    10088 > hide #!8 models
    10089 
    10090 > hide #!7 models
    10091 
    10092 > hide #!6 models
    10093 
    10094 > hide #!5 models
    10095 
    10096 > hide #!4 models
    10097 
    10098 > hide #!3 models
    10099 
    10100 > hide #!2 models
    10101 
    10102 > hide #!1 models
    10103 
    10104 > select subtract #1
    10105 
    10106 108717 atoms, 104234 bonds, 843 pseudobonds, 19775 residues, 147 models
    10107 selected 
    10108 
    10109 > select subtract #2
    10110 
    10111 100507 atoms, 96826 bonds, 765 pseudobonds, 17879 residues, 139 models
    10112 selected 
    10113 
    10114 > select subtract #3
    10115 
    10116 93414 atoms, 89513 bonds, 708 pseudobonds, 17024 residues, 128 models selected 
    10117 
    10118 > select subtract #4
    10119 
    10120 85379 atoms, 82232 bonds, 634 pseudobonds, 15191 residues, 119 models selected 
    10121 
    10122 > select subtract #5
    10123 
    10124 77598 atoms, 74925 bonds, 564 pseudobonds, 13636 residues, 108 models selected 
    10125 
    10126 > select subtract #6
    10127 
    10128 75666 atoms, 73090 bonds, 560 pseudobonds, 13270 residues, 98 models selected 
    10129 
    10130 > select subtract #7
    10131 
    10132 67073 atoms, 64278 bonds, 487 pseudobonds, 12209 residues, 93 models selected 
    10133 
    10134 > select subtract #9
    10135 
    10136 65124 atoms, 62441 bonds, 482 pseudobonds, 11829 residues, 84 models selected 
    10137 
    10138 > select subtract #8
    10139 
    10140 57036 atoms, 55084 bonds, 401 pseudobonds, 10016 residues, 81 models selected 
    10141 
    10142 > select subtract #10
    10143 
    10144 54864 atoms, 53204 bonds, 396 pseudobonds, 9454 residues, 70 models selected 
    10145 
    10146 > select subtract #11
    10147 
    10148 46889 atoms, 45818 bonds, 333 pseudobonds, 7776 residues, 67 models selected 
    10149 
    10150 > select subtract #12
    10151 
    10152 38268 atoms, 37018 bonds, 262 pseudobonds, 6679 residues, 58 models selected 
    10153 
    10154 > select subtract #13
    10155 
    10156 30681 atoms, 29720 bonds, 198 pseudobonds, 5314 residues, 49 models selected 
    10157 
    10158 > select subtract #14
    10159 
    10160 28588 atoms, 27906 bonds, 193 pseudobonds, 4767 residues, 40 models selected 
    10161 
    10162 > select subtract #15
    10163 
    10164 26479 atoms, 26079 bonds, 188 pseudobonds, 4216 residues, 35 models selected 
    10165 
    10166 > select subtract #16
    10167 
    10168 22782 atoms, 22580 bonds, 178 pseudobonds, 3491 residues, 30 models selected 
    10169 
    10170 > select subtract #17
    10171 
    10172 14105 atoms, 13780 bonds, 101 pseudobonds, 2338 residues, 24 models selected 
    10173 
    10174 > select subtract #18
    10175 
    10176 5649 atoms, 5040 bonds, 42 pseudobonds, 1358 residues, 15 models selected 
    10177 
    10178 > select add #19.10
    10179 
    10180 5892 atoms, 5040 bonds, 42 pseudobonds, 1370 residues, 9 models selected 
    10181 
    10182 > select add #19.11
    10183 
    10184 6119 atoms, 5040 bonds, 42 pseudobonds, 1382 residues, 10 models selected 
    10185 
    10186 > select subtract #19.9
    10187 
    10188 5903 atoms, 4802 bonds, 12 pseudobonds, 1371 residues, 9 models selected 
    10189 
    10190 > select subtract #19.8
    10191 
    10192 5690 atoms, 4566 bonds, 12 pseudobonds, 1359 residues, 8 models selected 
    10193 
    10194 > hide sel atoms
    10195 
    10196 > hide sel cartoons
    10197 
    10198 > select add #8
    10199 
    10200 13778 atoms, 11923 bonds, 93 pseudobonds, 3172 residues, 10 models selected 
    10201 
    10202 > select subtract #8
    10203 
    10204 5690 atoms, 4566 bonds, 12 pseudobonds, 1359 residues, 15 models selected 
    10205 
    10206 > select add #19
    10207 
    10208 7633 atoms, 7112 bonds, 81 pseudobonds, 1578 residues, 9 models selected 
    10209 
    10210 > select subtract #19
    10211 
    10212 8 models selected 
    10213 
    10214 > hide #!19 models
    10215 
    10216 > show #!19 models
    10217 
    10218 > show #!18 models
    10219 
    10220 > show #!17 models
    10221 
    10222 > show #!16 models
    10223 
    10224 > show #!15 models
    10225 
    10226 > show #!14 models
    10227 
    10228 > show #!13 models
    10229 
    10230 > show #!12 models
    10231 
    10232 > show #!11 models
    10233 
    10234 > show #!10 models
    10235 
    10236 > show #!9 models
    10237 
    10238 > show #!8 models
    10239 
    10240 > show #!7 models
    10241 
    10242 > show #!6 models
    10243 
    10244 > show #!5 models
    10245 
    10246 > show #!4 models
    10247 
    10248 > show #!3 models
    10249 
    10250 > show #!2 models
    10251 
    10252 > show #!1 models
    10253 
    10254 > select add #1
    10255 
    10256 6596 atoms, 6306 bonds, 55 pseudobonds, 1125 residues, 116 models selected 
    10257 
    10258 > select add #2
    10259 
    10260 14806 atoms, 13714 bonds, 133 pseudobonds, 3021 residues, 124 models selected 
    10261 
    10262 > select add #3
    10263 
    10264 21899 atoms, 21027 bonds, 190 pseudobonds, 3876 residues, 135 models selected 
    10265 
    10266 > select add #4
    10267 
    10268 29934 atoms, 28308 bonds, 264 pseudobonds, 5709 residues, 144 models selected 
    10269 
    10270 > select add #5
    10271 
    10272 37715 atoms, 35615 bonds, 334 pseudobonds, 7264 residues, 155 models selected 
    10273 
    10274 > select add #6
    10275 
    10276 39647 atoms, 37450 bonds, 338 pseudobonds, 7630 residues, 165 models selected 
    10277 
    10278 > select add #7
    10279 
    10280 48240 atoms, 46262 bonds, 411 pseudobonds, 8691 residues, 170 models selected 
    10281 
    10282 > select add #9
    10283 
    10284 50189 atoms, 48099 bonds, 416 pseudobonds, 9071 residues, 179 models selected 
    10285 
    10286 > select add #8
    10287 
    10288 58277 atoms, 55456 bonds, 497 pseudobonds, 10884 residues, 182 models selected 
    10289 
    10290 > select add #10
    10291 
    10292 60449 atoms, 57336 bonds, 502 pseudobonds, 11446 residues, 193 models selected 
    10293 
    10294 > select add #11
    10295 
    10296 68424 atoms, 64722 bonds, 565 pseudobonds, 13124 residues, 196 models selected 
    10297 
    10298 > select add #12
    10299 
    10300 77045 atoms, 73522 bonds, 636 pseudobonds, 14221 residues, 205 models selected 
    10301 
    10302 > select add #13
    10303 
    10304 84632 atoms, 80820 bonds, 700 pseudobonds, 15586 residues, 214 models selected 
    10305 
    10306 > select add #14
    10307 
    10308 86725 atoms, 82634 bonds, 705 pseudobonds, 16133 residues, 223 models selected 
    10309 
    10310 > select add #15
    10311 
    10312 88834 atoms, 84461 bonds, 710 pseudobonds, 16684 residues, 228 models selected 
    10313 
    10314 > select add #16
    10315 
    10316 92531 atoms, 87960 bonds, 720 pseudobonds, 17409 residues, 233 models selected 
    10317 
    10318 > select add #17
    10319 
    10320 101208 atoms, 96760 bonds, 797 pseudobonds, 18562 residues, 239 models
    10321 selected 
    10322 
    10323 > select add #18
    10324 
    10325 109664 atoms, 105500 bonds, 856 pseudobonds, 19542 residues, 248 models
    10326 selected 
    10327 
    10328 > select add #19
    10329 
    10330 117297 atoms, 112612 bonds, 937 pseudobonds, 21120 residues, 258 models
    10331 selected 
    10332 
    10333 > hide sel cartoons
    10334 
    10335 > nucleotides sel atoms
    10336 
    10337 > style nucleic & sel stick
    10338 
    10339 Changed 13700 atom styles 
    10340 
    10341 > nucleotides sel tube/slab shape box
    10342 
    10343 > select subtract #1
    10344 
    10345 110701 atoms, 106306 bonds, 882 pseudobonds, 19995 residues, 150 models
    10346 selected 
    10347 
    10348 > select add #1.7
    10349 
    10350 111136 atoms, 106306 bonds, 882 pseudobonds, 20016 residues, 146 models
    10351 selected 
    10352 
    10353 > select subtract #1.7
    10354 
    10355 110701 atoms, 106306 bonds, 882 pseudobonds, 19995 residues, 146 models
    10356 selected 
    10357 
    10358 > select add #1.7
    10359 
    10360 111136 atoms, 106306 bonds, 882 pseudobonds, 20016 residues, 146 models
    10361 selected 
    10362 
    10363 > select add #1.6
    10364 
    10365 111556 atoms, 106306 bonds, 882 pseudobonds, 20037 residues, 147 models
    10366 selected 
    10367 
    10368 > select add #1
    10369 
    10370 117297 atoms, 112612 bonds, 937 pseudobonds, 21120 residues, 263 models
    10371 selected 
    10372 
    10373 > select subtract #1
    10374 
    10375 110701 atoms, 106306 bonds, 882 pseudobonds, 19995 residues, 150 models
    10376 selected 
    10377 
    10378 > select subtract #2
    10379 
    10380 102491 atoms, 98898 bonds, 804 pseudobonds, 18099 residues, 142 models
    10381 selected 
    10382 
    10383 > select subtract #3
    10384 
    10385 95398 atoms, 91585 bonds, 747 pseudobonds, 17244 residues, 131 models selected 
    10386 
    10387 > select subtract #4
    10388 
    10389 87363 atoms, 84304 bonds, 673 pseudobonds, 15411 residues, 122 models selected 
    10390 
    10391 > select subtract #5
    10392 
    10393 79582 atoms, 76997 bonds, 603 pseudobonds, 13856 residues, 111 models selected 
    10394 
    10395 > select subtract #6
    10396 
    10397 77650 atoms, 75162 bonds, 599 pseudobonds, 13490 residues, 101 models selected 
    10398 
    10399 > select subtract #7
    10400 
    10401 69057 atoms, 66350 bonds, 526 pseudobonds, 12429 residues, 96 models selected 
    10402 
    10403 > select subtract #8
    10404 
    10405 60969 atoms, 58993 bonds, 445 pseudobonds, 10616 residues, 87 models selected 
    10406 
    10407 > select subtract #9
    10408 
    10409 59020 atoms, 57156 bonds, 440 pseudobonds, 10236 residues, 76 models selected 
    10410 
    10411 > select subtract #10
    10412 
    10413 56848 atoms, 55276 bonds, 435 pseudobonds, 9674 residues, 73 models selected 
     2192[deleted to fit within ticket limits]
    104142193
    104152194> select subtract #12