//============================== // 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 GGGCCAUACCUCUUGGGCCUGGUUAGUACCUCUUCGGUGGGAAUACCAGGUGCCC ) // ((((....(((..)))(((((((((.(((((((..)))))))))))))))))))) //========== Relations ========== relation( // coaxial stacking A16 A17 { adjacent_5p && stack } 10% // connect stems II and III A51 A52 { adjacent_5p && !stack } 20% ) //========== Cycles ========== ncm_01 = library( pdb( "MCSYM-DB/4/UCUU/*.pdb.gz" ) #1:#4 <- A11:A14 rmsd( 0.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_02 = library( pdb( "MCSYM-DB/2_2/CUUG/*_s.pdb.gz" ) #1:#2, #3:#4 <- A10:A11, A14:A15 rmsd( 1.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_03 = library( pdb( "MCSYM-DB/2_2/CCGG/*_t.pdb.gz" ) #1:#2, #3:#4 <- A9:A10, A15:A16 rmsd( 1.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_04 = library( pdb( "MCSYM-DB/4/UUCG/*_1.pdb.gz" ) #1:#4 <- A33:A36 rmsd( 0.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_05 = library( pdb( "MCSYM-DB/2_2/CUGG/*_s.pdb.gz" ) #1:#2, #3:#4 <- A32:A33, A36:A37 rmsd( 1.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_06 = library( pdb( "MCSYM-DB/2_2/UCGU/*_s.pdb.gz" ) #1:#2, #3:#4 <- A31:A32, A37:A38 rmsd( 1.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_07 = library( pdb( "MCSYM-DB/2_2/CUUG/*_s.pdb.gz" ) #1:#2, #3:#4 <- A30:A31, A38:A39 rmsd( 1.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_08 = library( pdb( "MCSYM-DB/2_2/CCGG/*_t.pdb.gz" ) #1:#2, #3:#4 <- A29:A30, A39:A40 rmsd( 1.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_09 = library( pdb( "MCSYM-DB/2_2/ACGG/*_s.pdb.gz" ) #1:#2, #3:#4 <- A28:A29, A40:A41 rmsd( 1.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_10 = library( pdb( "MCSYM-DB/2_2/UAGA/*_s.pdb.gz" ) #1:#2, #3:#4 <- A27:A28, A41:A42 rmsd( 1.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_11 = library( pdb( "MCSYM-DB/3_2/AGUAA/*_1.pdb.gz" ) #1:#3, #4:#5 <- A25:A27, A42:A43 rmsd( 1.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_12 = library( pdb( "MCSYM-DB/2_2/UAAU/*_s.pdb.gz" ) #1:#2, #3:#4 <- A24:A25, A43:A44 rmsd( 1.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_13 = library( pdb( "MCSYM-DB/2_2/UUUA/*_s.pdb.gz" ) #1:#2, #3:#4 <- A23:A24, A44:A45 rmsd( 1.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_14 = library( pdb( "MCSYM-DB/2_2/GUAC/*_t.pdb.gz" ) #1:#2, #3:#4 <- A22:A23, A45:A46 rmsd( 1.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_15 = library( pdb( "MCSYM-DB/2_2/GGCC/*_t.pdb.gz" ) #1:#2, #3:#4 <- A21:A22, A46:A47 rmsd( 1.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_16 = library( pdb( "MCSYM-DB/2_2/UGCA/*_t.pdb.gz" ) #1:#2, #3:#4 <- A20:A21, A47:A48 rmsd( 1.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_17 = library( pdb( "MCSYM-DB/2_2/CUAG/*_t.pdb.gz" ) #1:#2, #3:#4 <- A19:A20, A48:A49 rmsd( 1.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_18 = library( pdb( "MCSYM-DB/2_2/CCGG/*_t.pdb.gz" ) #1:#2, #3:#4 <- A18:A19, A49:A50 rmsd( 1.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_19 = library( pdb( "MCSYM-DB/2_2/GCGU/*_s.pdb.gz" ) #1:#2, #3:#4 <- A17:A18, A50:A51 rmsd( 1.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_20 = library( pdb( "MCSYM-DB/2_2/GCGC/*_t.pdb.gz" ) #1:#2, #3:#4 <- A3:A4, A52:A53 rmsd( 1.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_21 = library( pdb( "MCSYM-DB/2_2/GGCC/*_t.pdb.gz" ) #1:#2, #3:#4 <- A2:A3, A53:A54 rmsd( 1.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_22 = library( pdb( "MCSYM-DB/2_2/GGCC/*_t.pdb.gz" ) #1:#2, #3:#4 <- A1:A2, A54:A55 rmsd( 1.5 sidechain && !( pse || lp || hydrogen ) ) ) //=========== Backtrack =========== // assemble the whole structure: structure = backtrack( // stem_2 ncm_04 merge( ncm_05 2.0 ) merge( ncm_06 2.0 ) merge( ncm_07 2.0 ) merge( ncm_08 2.0 ) merge( ncm_09 2.0 ) merge( ncm_10 2.0 ) merge( ncm_11 2.0 ) merge( ncm_12 2.0 ) merge( ncm_13 2.0 ) merge( ncm_14 2.0 ) merge( ncm_15 2.0 ) merge( ncm_16 2.0 ) merge( ncm_17 2.0 ) merge( ncm_18 2.0 ) merge( ncm_19 2.0 ) // coax stacking place( A17 A16 ncm_03 ) // stem_1 merge( ncm_02 2.0 ) merge( ncm_01 2.0 ) // stem_3 place( A51 A52 ncm_20 ) merge( ncm_21 2.0 ) merge( ncm_22 2.0 ) ) // ========= Constraints / Restraints ========= clash ( structure 1.0 !( pse || lp || hydrogen ) ) ribose_rst ( structure method = estimate, threshold = 3.0, 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( "2HGH01.pdb" ) ) pdb( "2HGH" zipped ) )