| 1 | help help:quickstart
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| 2 | lighting simple
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| 3 | lighting soft
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| 4 | lighting simple
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| 5 | set bgColor white
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| 6 | set bgColor black
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| 7 | help help:quickstart
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| 8 | show cartoons
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| 9 | style stick
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| 10 | style stick
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| 11 | style sphere
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| 12 | style ball
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| 13 | color bychain
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| 14 | color bypolymer
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| 15 | nucleotides atoms
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| 16 | style nucleic stick
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| 17 | ui mousemode right select
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| 18 | ui mousemode right rotate
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| 19 | open 8w6e fromDatabase pdb format mmcif
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| 20 | hide bonds
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| 21 | undo
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| 22 | hide /A
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| 23 | undo
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| 24 | hide /a
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| 25 | hide /b
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| 26 | hide /c
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| 27 | hide /d
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| 28 | select ~sel & ##selected
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| 29 | show /a
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| 30 | hide /a cartoons
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| 31 | select ~sel & ##selected
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| 32 | show /b
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| 33 | show /c
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| 34 | select ~sel & ##selected
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| 35 | select ~sel & ##selected
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| 36 | select ~sel & ##selected
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| 37 | hide /a cartoons
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| 38 | hide /b cartoons
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| 39 | hide /b
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| 40 | show /c
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| 41 | show /d
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| 42 | show /e
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| 43 | color bychain
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| 44 | ui mousemode right select
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| 45 | select /A:201@H071
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| 46 | select clear
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| 47 | ui mousemode right "rotate slab"
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| 48 | ui mousemode right "move planes"
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| 49 | ui mousemode right "rotate slab"
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| 50 | ui mousemode right "move planes"
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| 51 | #ui mousemode right "color key"
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| 52 | key delete
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| 53 | ui mousemode right "translate selected models"
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| 54 | preset "initial styles" cartoon
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| 55 | hide /a cartoons
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| 56 | select ~sel & ##selected
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| 57 | hide /a
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| 58 | hide target m
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| 59 | undo
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| 60 | save ~/rm/image1.png supersample 3
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| 61 | save ~/rm/image1.png supersample 3
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| 62 | ui tool show "Build Structure"
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| 63 | save ~/rm/image2.png supersample 3
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| 64 | ui tool show "Model Loops"
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| 65 | save ~/rm/image3.png supersample 3
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| 66 | ui windowfill toggle
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| 67 | select ~sel & ##selected
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| 68 | select ~sel & ##selected
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| 69 | view #1.1 clip false
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| 70 | sequence chain /A
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| 71 | select clear
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| 72 | ui mousemode right select
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| 73 | select clear
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| 74 | select /B:40
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| 75 | select clear
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| 76 | select /B:36
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| 77 | select /B:36
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| 78 | select /B:36
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| 79 | sequence chain /B
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| 80 | select /B:36
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| 81 | select /B:36
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| 82 | select /B:36
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| 83 | select /B:35
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| 84 | select clear
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| 85 | select /B:36
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| 86 | select /B:40
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| 87 | select clear
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| 88 | select /B:0
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| 89 | select /B:0-163
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| 90 | ui tool show "Model Loops"
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| 91 | modeller refine 1/B:1:all-missing numModels 1 fast false adjacentFlexible 1 protocol standard
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| 92 | select clear
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| 93 | ui mousemode right rotate
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| 94 | ui mousemode right select
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| 95 | select clear
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| 96 | undo
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| 97 | hide #!3 models
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| 98 | show #!3 models
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| 99 | hide #!3 models
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| 100 | show #!3 models
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| 101 | hide #!3 models
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| 102 | show #!3 models
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| 103 | hide #!3 models
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| 104 | hide #3.1 models
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| 105 | show #3.1 models
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| 106 | hide #3.1 models
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| 107 | show #3.1 models
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| 108 | hide #3.1 models
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| 109 | show #3.1 models
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| 110 | hide #3.1 models
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| 111 | show #3.1 models
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| 112 | hide #3.1 models
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| 113 | ui tool show "Model Loops"
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| 114 | select add #3
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| 115 | close #3
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| 116 | ui tool show "Model Loops"
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| 117 | select /B:36
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| 118 | select /B:36
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| 119 | select clear
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| 120 | select /B:40
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| 121 | ui tool show "Model Loops"
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| 122 | select /B:37-39
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| 123 | select /B:37-40
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| 124 | select clear
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| 125 | select /B:37-39
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| 126 | ui tool show "Model Loops"
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| 127 | select /B:36
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| 128 | select /B:40
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| 129 | ui tool show "Model Loops"
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| 130 | select /B:40
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| 131 | select clear
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| 132 | sequence chain /A
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| 133 | select /A:0-1
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| 134 | select /A:0-1
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| 135 | select /A:1-36,41-79,82-118,125-161
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| 136 | select clear
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| 137 | select /A:124
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| 138 | select /A:162
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| 139 | select /A:162-163
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| 140 | select /A:119
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| 141 | select /A:119-121
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| 142 | select /A:0
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| 143 | select /A:0-163
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| 144 | select /A:42
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| 145 | select /A:42-77
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| 146 | select /A:36
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| 147 | select /A:36-41
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| 148 | ui tool show "Model Loops"
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| 149 | modeller refine 1/A:1:internal-missing numModels 1 fast false adjacentFlexible 1 protocol standard
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| 150 | select #1/B:140
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| 151 | undo
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| 152 | select #2.1/A:56
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| 153 | close #2
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| 154 | sequence chain /B
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| 155 | ui tool show "Model Loops"
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| 156 | select /B:5
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| 157 | select /B:5-47
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| 158 | modeller refine 1/B:1:internal-missing numModels 1 fast false adjacentFlexible 1 protocol standard
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| 159 | select /B:5-47
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| 160 | select clear
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| 161 | rename #2 8w6e
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| 162 | close #1
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| 163 | rename #2 id #1
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| 164 | preset "initial styles" cartoon
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| 165 | open 8w6e fromDatabase pdb format mmcif
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| 166 | select clear
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| 167 | select clear
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| 168 | ui mousemode right rotate
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| 169 | delete all
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| 170 | open 8w6e fromDatabase pdb format mmcif
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| 171 | ui mousemode right select
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| 172 | select /B:82
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| 173 | select clear
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| 174 | select /B:24
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| 175 | select clear
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| 176 | ui mousemode right select
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| 177 | select ::name="ALA"::name="ARG"::name="ASP"::name="GLU"::name="GLY"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
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| 178 | hide sel surfaces
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| 179 | hide sel cartoons
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| 180 | hide sel atoms
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| 181 | delete /a
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| 182 | show sel surfaces
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| 183 | hide sel surfaces
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| 184 | show sel cartoons
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| 185 | show sel atoms
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| 186 | hide sel atoms
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| 187 | select clear
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| 188 | delete all
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| 189 | open 8w6e fromDatabase pdb format mmcif
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| 190 | delete /b
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| 191 | select clear
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| 192 | save ~/rm/image4.png supersample 3
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| 193 | save ~/rm/image1.png supersample 3
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| 194 | select clear
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| 195 | close #1
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| 196 | ui tool show "Model Loops"
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| 197 | sequence chain /a
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| 198 | ui tool show "Model Loops"
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| 199 | modeller refine 2/A:1:internal-missing numModels 1 fast false adjacentFlexible 1 protocol standard
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| 200 | select clear
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| 201 | select clear
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| 202 | ui tool show "Model Loops"
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| 203 | close #2
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| 204 | save "C:\Users\moham\Downloads\Chimera Testing Grounds\image1.png" supersample 3
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| 205 | open 8w6e fromDatabase pdb format mmcif
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| 206 | delete /b
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| 207 | close #1
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| 208 | save ~/rm/image2.png supersample 3
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| 209 | select ::name="KY6"
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| 210 | color red
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| 211 | select clear
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| 212 | select ~sel & ##selected
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| 213 | select ~sel & ##selected
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| 214 | select ~sel & ##selected
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| 215 | select ~sel & ##selected
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| 216 | color sel red
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| 217 | select ::name="KY6"
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| 218 | color sel red
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| 219 | select clear
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| 220 | select ::name="KY6"
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| 221 | color sel byatom
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| 222 | select ::name="ALA"::name="ARG"::name="ASP"::name="GLU"::name="GLY"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
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| 223 | color sel red
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| 224 | color sel white
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| 225 | preset "initial styles" cartoon
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| 226 | preset "initial styles" cartoon
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| 227 | preset "initial styles" sticks
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| 228 | preset "initial styles" cartoon
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| 229 | preset "initial styles" "original look"
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| 230 | preset "initial styles" "space-filling (chain colors)"
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| 231 | preset "initial styles" cartoon
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| 232 | select clear
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| 233 | select ::name="KY6"
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| 234 | color sel byelement
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| 235 | select clear
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| 236 | select ::name="ALA"::name="ARG"::name="ASP"::name="GLU"::name="GLY"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
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| 237 | color (#!2 & sel) magenta
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| 238 | color (#!2 & sel) medium blue
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| 239 | color (#!2 & sel) cyan
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| 240 | color (#!2 & sel) yellow
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| 241 | select clear
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| 242 | save ~/rm/image3.png supersample 3
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| 243 | surface
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| 244 | save ~/rm/image3.png supersample 3
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| 245 | hide target a
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| 246 | surface hidePatches
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| 247 | hide #2.2 models
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| 248 | show #2.2 models
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| 249 | hide #!2.1 models
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| 250 | show #!2.1 models
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| 251 | hide #!2 models
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| 252 | show #!2 models
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| 253 | select ::name="KY6"
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| 254 | select ::name="KY6"
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| 255 | show sel cartoons
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| 256 | show sel atoms
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| 257 | color sel bynucleotide
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| 258 | color sel byhetero
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| 259 | color sel bychain
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| 260 | color sel bypolymer
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| 261 | rainbow sel
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| 262 | coulombic sel
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| 263 | color sel bynucleotide
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| 264 | color sel byhetero
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| 265 | rainbow sel
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| 266 | coulombic sel
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| 267 | coulombic sel
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| 268 | color sel bychain
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| 269 | hide sel surfaces
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| 270 | color sel bynucleotide
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| 271 | color sel byhetero
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| 272 | select ~sel & ##selected
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| 273 | select ~sel & ##selected
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| 274 | color sel byatom
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| 275 | show sel surfaces
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| 276 | hide sel surfaces
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| 277 | select /A:25
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| 278 | select /A:25
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| 279 | select clear
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| 280 | select ::name="ALA"::name="ARG"::name="ASP"::name="GLU"::name="GLY"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
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| 281 | show sel surfaces
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| 282 | hide sel surfaces
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| 283 | show sel surfaces
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| 284 | hide sel surfaces
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| 285 | show sel surfaces
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| 286 | hide sel surfaces
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| 287 | select ::name="KY6"
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| 288 | select clear
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| 289 | ui mousemode right select
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| 290 | split
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| 291 | select ::name="KY6"
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| 292 | split
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| 293 | split
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| 294 | select clear
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| 295 | split #2
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| 296 | select ::name="KY6"
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| 297 | split #2 atoms sel
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| 298 | hide #2.1 models
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| 299 | show #2.1 models
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| 300 | hide #!2.2 models
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| 301 | show #!2.2 models
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| 302 | select clear
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| 303 | hide #2.1 models
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| 304 | show #2.1 models
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| 305 | hide #2.1 models
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| 306 | show #2.1 models
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| 307 | hide #2.2.1 models
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| 308 | show #2.2.1 models
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| 309 | hide #!2.2 models
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| 310 | show #!2.2 models
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| 311 | rename #2.1 ligand
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| 312 | rename #2.2 protein
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| 313 | select clear
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| 314 | show surfaces
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| 315 | select clear
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| 316 | ui mousemode right clip
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| 317 | ui mousemode right "clip rotate"
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| 318 | ui mousemode right zone
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| 319 | ui mousemode right rotate
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| 320 | ui mousemode right "clip rotate"
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| 321 | ui mousemode right clip
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| 322 | ui mousemode right "clip rotate"
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| 323 | ui mousemode right clip
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| 324 | save ~/rm/image4.png supersample 3
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| 325 | save ~/rm/image5.png supersample 3
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| 326 | select add #2.1
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| 327 | hide sel surfaces
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| 328 | select add #2.2
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| 329 | select subtract #2.1
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| 330 | select subtract #2.2
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| 331 | select add #2.2
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| 332 | hide sel surfaces
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| 333 | ui tool show H-Bonds
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| 334 | ui tool show H-Bonds
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| 335 | hbonds reveal true
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| 336 | show sel cartoons
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| 337 | hide sel atoms
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| 338 | show sel atoms
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| 339 | hide sel atoms
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| 340 | show sel surfaces
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| 341 | ui mousemode right clip
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| 342 | ui mousemode right select
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| 343 | select clear
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| 344 | clip model #2.2 true
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| 345 | select clear
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| 346 | ui mousemode right clip
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| 347 | clip model #2.2 true
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| 348 | clip model #2.2
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| 349 | select ~sel & ##selected
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| 350 | select ~sel & ##selected
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| 351 | clip model #2
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| 352 | clip model #2.1 false
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| 353 | ui mousemode right clip
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| 354 | ui mousemode right select
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| 355 | ui mousemode right clip
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| 356 | ui mousemode right select
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| 357 | ui mousemode right clip
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| 358 | clip
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| 359 | ui mousemode right "clip rotate"
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| 360 | ui mousemode right clip
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| 361 | ui mousemode right "clip rotate"
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| 362 | ui mousemode right clip
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| 363 | ui mousemode right "clip rotate"
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| 364 | ui mousemode right clip
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| 365 | ui mousemode right translate
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| 366 | ui mousemode right zoom
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| 367 | ui mousemode right translate
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| 368 | ui mousemode right select
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| 369 | select clear
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| 370 | select add #2.1
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| 371 | ui mousemode right zoom
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| 372 | view sel
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| 373 | ui mousemode right "clip rotate"
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| 374 | ui mousemode right translate
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| 375 | color #2.2 #140cffff
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| 376 | color #2.2 #ff2aadff
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| 377 | select clear
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| 378 | set bgColor white
|
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| 379 | set bgColor #ffffff00
|
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| 380 | set bgColor black
|
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| 381 | set bgColor transparent
|
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| 382 | lighting soft
|
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| 383 | lighting full
|
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| 384 | lighting simple
|
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| 385 | lighting full
|
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| 386 | lighting soft
|
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| 387 | lighting simple
|
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| 388 | lighting soft
|
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| 389 | lighting full
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| 390 | save ~/rm/image6.png supersample 3
|
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| 391 | lighting simple
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| 392 | save ~/rm/wFAP.cxs
|
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![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
