//============================== // MC-Sym 4.2 script generated by MC-Fold 1.0 // Please cite the following if you use MC-Sym: // 1) Major F et al. (1991) Science 253, 1255. // 2) Major F. (2003) Comp Sci Eng. 5, 44. //========== Sequence ========== sequence( r A1 AGUGGCGCCGACCACUUAAAAACAACGG ) // (((((..[[[[)))))........]]]] //========== Relations ========== relation( // coaxial stacking A11 A12 { adjacent_5p && stack } 10% // loop 1 A5:A8 { adjacent_5p && !stack } 10% ) //========== Cycles ========== ncm_02 = library( pdb( "MCSYM-DB/2_2/GGCC/*_s.pdb.gz" ) #1:#2, #3:#4 <- A4:A5, A12:A13 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) ncm_03 = library( pdb( "MCSYM-DB/2_2/UGCA/*_s.pdb.gz" ) #1:#2, #3:#4 <- A3:A4, A13:A14 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) ncm_04 = library( pdb( "MCSYM-DB/2_2/GUAC/*_s.pdb.gz" ) #1:#2, #3:#4 <- A2:A3, A14:A15 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) ncm_05 = library( pdb( "MCSYM-DB/2_2/AGCU/*_s.pdb.gz" ) #1:#2, #3:#4 <- A1:A2, A15:A16 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) ncm_06 = library( pdb( "MCSYM-DB/2_2/GAAC/*.pdb.gz" ) #1:#2, #3:#4 <- A10:A11, A25:A26 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) ncm_07 = library( pdb( "MCSYM-DB/2_2/CGCG/*_s.pdb.gz" ) #1:#2, #3:#4 <- A9:A10, A26:A27 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) ncm_08 = library( pdb( "MCSYM-DB/2_2/CCGG/*_s.pdb.gz" ) #1:#2, #3:#4 <- A8:A9, A27:A28 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) //=========== Backtrack =========== // assemble the whole structure: structure = backtrack( // coax between stems 1 and 2 ncm_02 place( A12 A11 ncm_06 ) // complete stem_2 merge( ncm_07 2.0 ) merge( ncm_08 2.0 ) // loop 1 ( A5 A6 ) ( A8 A7 ) // complete stem_1 merge( ncm_03 2.0 ) merge( ncm_04 2.0 ) merge( ncm_05 2.0 ) ) //=========== Feasible =========== // constraints on loop nucleotides `feasible`: // for 2 nucleotides i and i+k the 99th quantile // distance D on RNA select goes like D = 4.4 * k + 5.8 distance( A5:C1' A6:C1' 0.0 10.2 ) distance( A5:C1' A7:C1' 0.0 14.6 ) distance( A5:C1' A8:C1' 0.0 19.0 ) distance( A6:C1' A7:C1' 0.0 10.2 ) distance( A6:C1' A8:C1' 0.0 14.6 ) distance( A7:C1' A8:C1' 0.0 10.2 ) // ========= Constraints / Restraints ========= clash ( structure 1.0 !( pse || lp || hydrogen ) ) ribose_rst ( structure method = estimate, threshold = 2.0, pucker = C3p_endo, glycosyl = anti ) backtrack_rst ( structure method = probabilistic, width_limit = 25%, height_limit = 100% ) implicit_phosphate_rst( structure sampling = 90% ) // ========= Exploration Initialization ========= explore( structure option( time_limit = 12h, seed = 3210 ) reference( pdb( "2AP501.pdb" ) ) pdb( "2AP5" zipped ) )