//============================== // MC-Sym 4.2 script generated by MC-Fold 1.0 //========== Sequence ========== sequence( r A1 UGACCAGCUAUGAGGUCAUACAUCGUCAUAGC ) // (((((.[[[[[[[))))).......]]]]]]] //not modeled: ^^^^^^^ //========== Relations ========== relation( // the coaxial stacking between the 2 pseudo-knotted stem: A13 A14 { adjacent_5p && stack } 50% // loop 1: A6 A7 { adjacent_5p && !stack } 50% ) //========== Cycles ========== ncm_01 = library( pdb( "MCSYM-DB/2_2/CCGG/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A4:A5, A14:A15 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_02 = library( pdb( "MCSYM-DB/2_2/ACGU/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A3:A4, A15:A16 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_03 = library( pdb( "MCSYM-DB/2_2/GAUC/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A2:A3, A16:A17 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_04 = library( pdb( "MCSYM-DB/2_2/UGCA/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A1:A2, A17:A18 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_05 = library( pdb( "MCSYM-DB/2_2/GAUC/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A12:A13, A26:A27 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_06 = library( pdb( "MCSYM-DB/2_2/UGCA/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A11:A12, A27:A28 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_07 = library( pdb( "MCSYM-DB/2_2/AUAU/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A10:A11, A28:A29 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_08 = library( pdb( "MCSYM-DB/2_2/UAUA/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A9:A10, A29:A30 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_09 = library( pdb( "MCSYM-DB/2_2/CUAG/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A8:A9, A30:A31 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_10 = library( pdb( "MCSYM-DB/2_2/GCGC/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A7:A8, A31:A32 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) // =========== Backtrack =========== // assemble the whole structure: structure = backtrack( //----- stem_2 ----- ncm_05 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 ) //----- stem_1 ----- place( A13 A14 ncm_01 ) ( A7 A6 ) merge( ncm_02 2.0 ) merge( ncm_03 2.0 ) merge( ncm_04 2.0 ) ) // ========= Backtrack Restraints ========= clash ( structure 1.5 !( pse || lp || hydrogen ) ) backtrack_rst ( structure width_limit = 25%, height_limit = 100%, method = probabilistic ) // ========= Ribose Restraints ========= ribose_rst ( structure method = ccm, pucker = C3p_endo, glycosyl = anti, threshold = 1.5 ) // ========= Exploration Initialization ========= explore ( structure option( model_limit = 9999, time_limit = 12h, seed = 3210 ) rmsd( 0.5 sidechain && !( pse || lp || hydrogen ) ) pdb( "2TPK_o" zipped ) )