# make sure you have the right last.1.pdb for this fitDefaultTolerance 1.0 integratorAccuracy .5 -PRIOR 0 globalCoulombScaleFactor 0 1 globalVdwScaleFactor 0 1 globalBondTorsionScaleFactor 0 globalBondStretchScaleFactor 1 globalBondBendScaleFactor 1 rigidifyFormedHelices 0 setChiBondMobility 1 firstStage 2 lastStage 17 reportingInterval .2 maxReportingIntervals 90 addSmallHuntCrossleySpheres 0 addHuntCrossleySpheres 0 weldToGround 1 # tetrahymena P5abc and P4 sequence A AAUUGCGGGAAAGGGGUCAACAGCCGUUCAGUACCAAGUCUCAGGGGAAACUUUGAGAUGGCCUUGCAAAGGGUAUGGUAAUAAGCUGACGGACAUGGUCCUAACCACGCA -FRN A 104 basePair A 104 Rigid A 214 Rigid Cis 1 #bangia P5abc sequence B AAUUGUCGGGAACGGCCUCACAAAAGACUUUUGUCUUUGAGAAACUCUGUCUACCGCGGUCCGCCGAGAGGUUAAAGCGAGCAAUCGCUUAGGACGCAGCAGUGCAUGUAACGAUGCACGGAUGGUAAAAACGACAGAAUUGGGCUAAUCCGCA #get rid of this later #basePair B 138 WatsonCrick B 149 WatsonCrick Cis 1 -FRN B 137 #resetBases B 1 basePair B 137 HardSphere B 140 HardSphere Cis 2 1 basePair B 137 HardSphere B 150 HardSphere Cis 3 1 basePair B 137 HardSphere B 160 HardSphere Cis 4 1 #basepair B 137 HardSphere B 170 HardSphere Cis 5 1 basePair B 137 HardSphere B 184 HardSphere Cis 6 1 basePair B 137 HardSphere B 196 HardSphere Cis 7 1 basePair B 137 HardSphere B 206 HardSphere Cis 8 1 basePair B 137 HardSphere B 235 HardSphere Cis 9 1 basePair B 137 HardSphere B 264 HardSphere Cis 10 1 basePair B 137 HardSphere B 274 HardSphere Cis 11 1 basePair B 137 HardSphere B 284 HardSphere Cis 12 1 basePair B 137 HardSphere B 290 HardSphere Cis 13 1 #mixing section #basePair A 104 Custom B 137 Custom Cis 1 #basePair A 105 Custom B 138 Custom Cis 1 #basePair A 106 Custom B 139 Custom Cis 1 basePair A 107 Custom B 140 Custom Cis 2 0 basePair A 108 Custom B 141 Custom Cis 3 0 basePair A 109 Custom B 143 Custom Cis 3 0 basePair A 110 Custom B 144 Custom Cis 3 0 basePair A 111 Custom B 145 Custom Cis 3 0 basePair A 112 Custom B 146 Custom Cis 3 0 basePair A 113 Custom B 147 Custom Cis 3 0 basePair A 114 Custom B 148 Custom Cis 3 0 basePair A 115 Custom B 149 Custom Cis 3 0 basePair A 116 Custom B 150 Custom Cis 3 0 basePair A 117 Custom B 151 Custom Cis 4 0 basePair A 118 Custom B 152 Custom Cis 4 0 basePair A 119 Custom B 153 Custom Cis 4 0 basePair A 120 Custom B 154 Custom Cis 4 0 basePair A 127 Custom B 182 Custom Cis 6 0 basePair A 128 Custom B 183 Custom Cis 6 0 basePair A 131 Custom B 184 Custom Cis 6 0 basePair A 132 Custom B 185 Custom Cis 7 0 basePair A 133 Custom B 186 Custom Cis 7 0 basePair A 134 Custom B 187 Custom Cis 7 0 basePair A 135 Custom B 188 Custom Cis 7 0 basePair A 136 Custom B 189 Custom Cis 7 0 basePair A 137 Custom B 190 Custom Cis 7 0 basePair A 138 Custom B 191 Custom Cis 7 0 basePair A 141 Custom B 192 Custom Cis 7 0 basePair A 142 Custom B 193 Custom Cis 7 0 basePair A 143 Custom B 194 Custom Cis 7 0 basePair A 144 Custom B 196 Custom Cis 7 0 basePair A 145 Custom B 197 Custom Cis 8 0 basePair A 146 Custom B 198 Custom Cis 8 0 basePair A 147 Custom B 199 Custom Cis 8 0 basePair A 148 Custom B 200 Custom Cis 8 0 basePair A 149 Custom B 201 Custom Cis 8 0 basePair A 150 Custom B 202 Custom Cis 8 0 basePair A 151 Custom B 203 Custom Cis 8 0 basePair A 152 Custom B 204 Custom Cis 8 0 basePair A 153 Custom B 205 Custom Cis 8 0 basePair A 154 Custom B 206 Custom Cis 8 0 basePair A 155 Custom B 207 Custom Cis 9 0 basePair A 156 Custom B 208 Custom Cis 9 0 basePair A 157 Custom B 228 Custom Cis 9 0 basePair A 158 Custom B 229 Custom Cis 9 0 basePair A 159 Custom B 230 Custom Cis 9 0 basePair A 160 Custom B 231 Custom Cis 9 0 basePair A 161 Custom B 232 Custom Cis 9 0 basePair A 162 Custom B 233 Custom Cis 9 0 basePair A 163 Custom B 234 Custom Cis 9 0 basePair A 164 Custom B 235 Custom Cis 9 0 basePair A 167 Custom B 238 Custom Cis 10 0 basePair A 173 Custom B 255 Custom Cis 10 0 basePair A 176 Custom B 257 Custom Cis 10 0 basePair A 177 Custom B 258 Custom Cis 10 0 basePair A 178 Custom B 259 Custom Cis 10 0 basePair A 180 Custom B 260 Custom Cis 10 0 basePair A 181 Custom B 261 Custom Cis 10 0 basePair A 182 Custom B 262 Custom Cis 10 0 basePair A 183 Custom B 263 Custom Cis 10 0 basePair A 184 Custom B 264 Custom Cis 10 0 basePair A 185 Custom B 265 Custom Cis 11 0 basePair A 186 Custom B 266 Custom Cis 11 0 basePair A 187 Custom B 267 Custom Cis 11 0 basePair A 188 Custom B 268 Custom Cis 11 0 basePair A 189 Custom B 269 Custom Cis 11 0 basePair A 190 Custom B 270 Custom Cis 11 0 basePair A 191 Custom B 271 Custom Cis 11 0 basePair A 192 Custom B 272 Custom Cis 11 0 basePair A 194 Custom B 273 Custom Cis 11 0 basePair A 195 Custom B 274 Custom Cis 11 0 basePair A 201 Custom B 278 Custom Cis 12 0 basePair A 202 Custom B 279 Custom Cis 12 0 basePair A 203 Custom B 280 Custom Cis 12 0 basePair A 204 Custom B 281 Custom Cis 12 0 basePair A 205 Custom B 282 Custom Cis 12 0 basePair A 206 Custom B 283 Custom Cis 12 0 basePair A 207 Custom B 284 Custom Cis 12 0 basePair A 208 Custom B 285 Custom Cis 13 0 basePair A 209 Custom B 286 Custom Cis 13 0 basePair A 211 Custom B 287 Custom Cis 13 0 basePair A 212 Custom B 288 Custom Cis 13 0 basePair A 213 Custom B 289 Custom Cis 13 0 basePair A 214 Custom B 290 Custom Cis 13 0 # sequence B rigidifyFormedHelices 0 basePair B 140 WatsonCrick B 290 WatsonCrick Cis 16 basePair B 141 WatsonCrick B 289 WatsonCrick Cis 16 basePair B 143 WatsonCrick B 288 WatsonCrick Cis 16 basePair B 144 WatsonCrick B 287 WatsonCrick Cis 15 basePair B 145 WatsonCrick B 286 WatsonCrick Cis 15 basePair B 146 WatsonCrick B 285 WatsonCrick Cis 15 basePair B 151 WatsonCrick B 281 WatsonCrick Cis 14 basePair B 152 WatsonCrick B 280 WatsonCrick Cis 14 basePair B 153 WatsonCrick B 279 WatsonCrick Cis 14 basePair B 154 WatsonCrick B 278 WatsonCrick Cis 14 basePair B 161 WatsonCrick B 172 WatsonCrick Cis 3 basePair B 162 WatsonCrick B 171 WatsonCrick Cis 3 basePair B 163 WatsonCrick B 170 WatsonCrick Cis 3 basePair B 164 WatsonCrick B 169 WatsonCrick Cis 3 basePair B 182 WatsonCrick B 274 WatsonCrick Cis 13 basePair B 183 WatsonCrick B 273 WatsonCrick Cis 13 basePair B 184 WatsonCrick B 272 WatsonCrick Cis 13 basePair B 185 WatsonCrick B 271 WatsonCrick Cis 13 basePair B 186 WatsonCrick B 270 WatsonCrick Cis 12 basePair B 187 WatsonCrick B 269 WatsonCrick Cis 12 basePair B 188 WatsonCrick B 267 WatsonCrick Cis 12 basePair B 189 WatsonCrick B 262 WatsonCrick Cis 11 basePair B 190 WatsonCrick B 261 WatsonCrick Cis 11 basePair B 191 WatsonCrick B 260 WatsonCrick Cis 11 basePair B 192 WatsonCrick B 233 WatsonCrick Cis 8 basePair B 193 WatsonCrick B 232 WatsonCrick Cis 8 basePair B 194 WatsonCrick B 231 WatsonCrick Cis 8 basePair B 196 WatsonCrick B 230 WatsonCrick Cis 7 basePair B 197 WatsonCrick B 229 WatsonCrick Cis 7 basePair B 198 WatsonCrick B 228 WatsonCrick Cis 7 basePair B 199 WatsonCrick B 208 WatsonCrick Cis 4 basePair B 200 WatsonCrick B 207 WatsonCrick Cis 4 basePair B 201 WatsonCrick B 206 WatsonCrick Cis 4 basePair B 211 WatsonCrick B 226 WatsonCrick Cis 6 basePair B 212 WatsonCrick B 225 WatsonCrick Cis 6 basePair B 213 WatsonCrick B 224 WatsonCrick Cis 6 basePair B 214 WatsonCrick B 223 WatsonCrick Cis 5 basePair B 215 WatsonCrick B 222 WatsonCrick Cis 5 basePair B 216 WatsonCrick B 221 WatsonCrick Cis 5 basePair B 238 WatsonCrick B 255 WatsonCrick Cis 10 basePair B 239 WatsonCrick B 254 WatsonCrick Cis 10 basePair B 240 WatsonCrick B 253 WatsonCrick Cis 10 basePair B 241 WatsonCrick B 252 WatsonCrick Cis 9 basePair B 242 WatsonCrick B 251 WatsonCrick Cis 9 basePair B 243 WatsonCrick B 250 WatsonCrick Cis 9 #basePair B 140 WatsonCrick B 290 WatsonCrick Cis 3 #basePair B 141 WatsonCrick B 289 WatsonCrick Cis 3 #basePair B 143 WatsonCrick B 288 WatsonCrick Cis 3 #basePair B 144 WatsonCrick B 287 WatsonCrick Cis 3 #basePair B 145 WatsonCrick B 286 WatsonCrick Cis 3 #basePair B 146 WatsonCrick B 285 WatsonCrick Cis 3 #basePair B 151 WatsonCrick B 281 WatsonCrick Cis 3 #basePair B 152 WatsonCrick B 280 WatsonCrick Cis 3 #basePair B 153 WatsonCrick B 279 WatsonCrick Cis 3 #basePair B 154 WatsonCrick B 278 WatsonCrick Cis 3 #basePair B 161 WatsonCrick B 172 WatsonCrick Cis 3 #basePair B 162 WatsonCrick B 171 WatsonCrick Cis 3 #basePair B 163 WatsonCrick B 170 WatsonCrick Cis 3 #basePair B 164 WatsonCrick B 169 WatsonCrick Cis 3