//============================== // MC-Sym 4.2 script generated by MC-Fold 1.0 //========== Sequence ========== sequence( r A1 UGACCAGCUAUGAGGUCAUACAUCGUCAUAGC ) // (((((.[[[[[[[))))).......]]]]]]] //not modeled: ^^^^^^^ //========== Cycles ========== ncm_01 = library( pdb( "MCSYM-DB/2_2/CCGG/*_t.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/*_t.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/*_t.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/*_t.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/*_t.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/*_t.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/*_t.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/*_t.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/*_t.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/*_t.pdb.gz" ) #1:#2, #3:#4 <- A7:A8, A31:A32 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) loop_01 = library( pdb( "MCSYM-DB/ss2/CA/*.pdb.gz" ) #1:#2 <- A5:A6 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) loop_02 = library( pdb( "MCSYM-DB/ss2/AG/*.pdb.gz" ) #1:#2 <- A13:A14 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 ) //----- loop 1/2 ----- merge( loop_02 2.0 ) merge( ncm_01 2.0 ) merge( loop_01 2.0 ) //----- stem 1 ----- merge( ncm_02 2.0 ) merge( ncm_03 2.0 ) merge( ncm_04 2.0 ) ) //========== Distance ========== // coaxial stacking between stems 1 and 2 distance( A13:PSY A14:PSY 0.0 5.0 ) // ========= Constraints / Restraints ========= clash ( structure 1.5 !( pse || lp || hydrogen ) ) ribose_rst ( structure method = ccm, threshold = 2.0, pucker = C3p_endo, glycosyl = anti ) backtrack_rst ( structure method = probabilistic, width_limit = 25%, height_limit = 100% ) // ========= Exploration Initialization ========= explore( structure option( model_limit = 100, time_limit = 1h, seed = 3210 ) rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) pdb( "PK" zipped ) )