// ============================== -*-Ruby-*- ============================== // ========== Sequence ========== sequence( r A1 CGCGAAUUAGCG ) sequence( r B1 CGCGAAUUAGCG ) // ========== Cycles ========== cycle_01 = library( pdb( "MCSYM-DB/2_2/CGCG/*_1.pdb.gz" ) #1:#2, #3:#4 <- A1:A2, B11:B12 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_02 = library( pdb( "MCSYM-DB/2_2/GCGC/*_1.pdb.gz" ) #1:#2, #3:#4 <- A2:A3, B10:B11 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_03 = library( pdb( "MCSYM-DB/2_2/CGAG/*.pdb.gz" ) #1:#2, #3:#4 <- A3:A4, B9:B10 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_04 = library( pdb( "MCSYM-DB/2_2/GAUA/*.pdb.gz" ) #1:#2, #3:#4 <- A4:A5, B8:B9 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_05 = library( pdb( "MCSYM-DB/2_2/AAUU/*_1.pdb.gz" ) #1:#2, #3:#4 <- A5:A6, B7:B8 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_06 = library( pdb( "MCSYM-DB/2_2/AUAU/*_1.pdb.gz" ) #1:#2, #3:#4 <- A6:A7, B6:B7 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_07 = library( pdb( "MCSYM-DB/2_2/UUAA/*_1.pdb.gz" ) #1:#2, #3:#4 <- A7:A8, B5:B6 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_08 = library( pdb( "MCSYM-DB/2_2/UAGA/*.pdb.gz" ) #1:#2, #3:#4 <- A8:A9, B4:B5 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_09 = library( pdb( "MCSYM-DB/2_2/AGCG/*.pdb.gz" ) #1:#2, #3:#4 <- A9:A10, B3:B4 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_10 = library( pdb( "MCSYM-DB/2_2/GCGC/*_1.pdb.gz" ) #1:#2, #3:#4 <- A10:A11, B2:B3 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) cycle_11 = library( pdb( "MCSYM-DB/2_2/CGCG/*_1.pdb.gz" ) #1:#2, #3:#4 <- A11:A12, 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 ) ) // ========= 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 = 1h, seed = 3210 ) rmsd( 0.5 sidechain && !( pse || lp || hydrogen ) ) pdb( "2Q1R_a" zipped ) )