//========== Sequence ========== // 1 5 10 15 20 25 30 // | | | | | | | sequence( r A1 GGAGGUAGUAGGUCGAAAGACCAUUCUGCCUCC ) //========== Relations ========== relation( A9 A10 { adjacent_5p } 75% A10 A23 { pairing } 75% A9 A25 { pairing } 75% A25 A24 { pairing } 75% ) //=========== Backtrack =========== // assemble the base triple structure = backtrack( // the triple ( A9 A25 A24 ) // next stage ( A9 A10 ) // the other base pair ( A10 A23 ) ) // ========= Constraints / Restraints ========= clash ( structure 2.0 !( pse || lp || hydrogen ) ) ribose_rst ( structure pucker = C3p_endo, glycosyl = anti, method = ccm, threshold = 1.0 ) backtrack_rst ( structure width_limit = 25%, height_limit = 100%, method = probabilistic ) // ========= Exploration Initialization ========= explore( structure option( model_limit = 100, time_limit = 1h, seed = 3210 ) rmsd( 0.5 sidechain && !( pse || lp || hydrogen ) ) pdb( "triple" zipped ) )