// ============================== -*-Ruby-*- ============================== // ========== Sequence ========== sequence( r A1 GGUGACCUCCCGGGAGCGGGGGACCACU ) sequence( r B1 GGUGACCUCCCGGGAGCGGGGGACCACU ) // ========== Cycles ========== cycle_01 = library( pdb( "MCSYM-DB/2_2/GGCU/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A1:A2, B27:B28 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_02 = library( pdb( "MCSYM-DB/2_2/GUAC/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A2:A3, B26:B27 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_03 = library( pdb( "MCSYM-DB/2_2/UGCA/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A3:A4, B25:B26 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_04 = library( pdb( "MCSYM-DB/2_2/GACC/*_1.pdb.gz" ) #1:#2, #3:#4 <- A4:A5, B24:B25 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_05 = library( pdb( "MCSYM-DB/2_2/ACAC/*_1.pdb.gz" ) #1:#2, #3:#4 <- A5:A6, B23:B24 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_06 = library( pdb( "MCSYM-DB/2_2/CCGA/*_1.pdb.gz" ) #1:#2, #3:#4 <- A6:A7, B22:B23 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_07 = library( pdb( "MCSYM-DB/2_2/CUGG/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A7:A8, B21:B22 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_08 = library( pdb( "MCSYM-DB/2_2/UCGG/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A8:A9, B20:B21 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_09 = library( pdb( "MCSYM-DB/2_2/CCGG/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A9:A10, B19:B20 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_10 = library( pdb( "MCSYM-DB/2_2/CCGG/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A10:A11, B18:B19 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_11 = library( pdb( "MCSYM-DB/2_2/CGCG/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A11:A12, B17:B18 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_12 = library( pdb( "MCSYM-DB/2_2/GGGC/*_1.pdb.gz" ) #1:#2, #3:#4 <- A12:A13, B16:B17 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_13 = library( pdb( "MCSYM-DB/2_2/GGAG/*_1.pdb.gz" ) #1:#2, #3:#4 <- A13:A14, B15:B16 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_14 = library( pdb( "MCSYM-DB/2_2/GAGA/*_1.pdb.gz" ) #1:#2, #3:#4 <- A14:A15, B14:B15 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_15 = library( pdb( "MCSYM-DB/2_2/AGGG/*_1.pdb.gz" ) #1:#2, #3:#4 <- A15:A16, B13:B14 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_16 = library( pdb( "MCSYM-DB/2_2/GCGG/*_1.pdb.gz" ) #1:#2, #3:#4 <- A16:A17, B12:B13 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_17 = library( pdb( "MCSYM-DB/2_2/CGCG/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A17:A18, B11:B12 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_18 = library( pdb( "MCSYM-DB/2_2/GGCC/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A18:A19, B10:B11 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_19 = library( pdb( "MCSYM-DB/2_2/GGCC/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A19:A20, B9:B10 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_20 = library( pdb( "MCSYM-DB/2_2/GGUC/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A20:A21, B8:B9 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_21 = library( pdb( "MCSYM-DB/2_2/GGCU/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A21:A22, B7:B8 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_22 = library( pdb( "MCSYM-DB/2_2/GACC/*_1.pdb.gz" ) #1:#2, #3:#4 <- A22:A23, B6:B7 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_23 = library( pdb( "MCSYM-DB/2_2/ACAC/*_1.pdb.gz" ) #1:#2, #3:#4 <- A23:A24, B5:B6 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_24 = library( pdb( "MCSYM-DB/2_2/CCGA/*_1.pdb.gz" ) #1:#2, #3:#4 <- A24:A25, B4:B5 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_25 = library( pdb( "MCSYM-DB/2_2/CAUG/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A25:A26, B3:B4 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_26 = library( pdb( "MCSYM-DB/2_2/ACGU/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A26:A27, B2:B3 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_27 = library( pdb( "MCSYM-DB/2_2/CUGG/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A27:A28, B1:B2 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) // =========== Backtrack =========== structure = backtrack ( cycle_01 merge( cycle_02 1.5 ) merge( cycle_03 1.5 ) merge( cycle_04 1.5 ) merge( cycle_05 1.5 ) merge( cycle_06 1.5 ) merge( cycle_07 1.5 ) merge( cycle_08 1.5 ) merge( cycle_09 1.5 ) merge( cycle_10 1.5 ) merge( cycle_11 1.5 ) merge( cycle_12 1.5 ) merge( cycle_13 1.5 ) merge( cycle_14 1.5 ) merge( cycle_15 1.5 ) merge( cycle_16 1.5 ) merge( cycle_17 1.5 ) merge( cycle_18 1.5 ) merge( cycle_19 1.5 ) merge( cycle_20 1.5 ) merge( cycle_21 1.5 ) merge( cycle_22 1.5 ) merge( cycle_23 1.5 ) merge( cycle_24 1.5 ) merge( cycle_25 1.5 ) merge( cycle_26 1.5 ) merge( cycle_27 1.5 ) ) // ========= 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( "1D4R_o" zipped ) )