// ========== -*-Ruby-*- ========== // ========== Sequence ========== // P4-P6 domain of group I intron (PDB file 1GID) sequence( r A103 GAAUUGCGGGAAAGGGGUCAACAGCCGUUCAGUACCAAGUCUCAGGGGAAACUUUGAGAUGGCCUUGCAAAGGGUAUGGUAAUAAGCUGACGGACAUGGUCCUAACCACGCAGCCAAGUCCUAAGUCAACAGAUCUUCUGUUGAUAUGGAU ) // ========== Relations ========== relation ( A122:A126 { adjacent_5p } 90% A196:A199 { adjacent_5p } 90% ) // ========== Library ========== body = library( // make MC-Sym load partial fragments of the structure pdb( "../03JP146fZK/*-????.pdb.gz" ) ) // =========== Backtrack =========== // here we will add the loops structure = backtrack ( body //----- 122 - 126 loop ----- ( A126 A125 ) ( A122 A123 ) ( A125 A124 ) //----- 196 - 199 loop ----- ( A199 A198 ) ( A196 A197 ) ) // ========= Look-Ahead ========= //----- 122 - 126 loop ----- distance( A122:C1' A124:C1' 0.0 12.6 ) distance( A122:C1' A125:C1' 0.0 16.0 ) distance( A122:C1' A126:C1' 0.0 19.4 ) distance( A123:C1' A125:C1' 0.0 12.6 ) distance( A123:C1' A126:C1' 0.0 16.0 ) distance( A124:C1' A126:C1' 0.0 12.6 ) //----- 196 - 199 loop ----- distance( A196:C1' A198:C1' 0.0 12.6 ) distance( A196:C1' A199:C1' 0.0 16.0 ) distance( A197:C1' A199:C1' 0.0 12.6 ) // ========= Backtrack Restraints ========= clash ( structure 1.5 !( pse || lp || hydrogen ) ) backtrack_rst ( structure width_limit = 5%, height_limit = 5%, method = probabilistic ) // ========= Ribose Restraints ========= ribose_rst ( structure method = ccm, pucker = C3p_endo, glycosyl = anti, threshold = 3.0 ) // ========= Exploration Initialization ========= explore ( structure option( model_limit = 9999, seed = 3210 ) rmsd( 0.5 sidechain && !( pse || lp || hydrogen ) ) pdb( "p4p6" zipped ) )