//============================== // MC-Sym 4.2 script generated by MC-Fold 1.0 // Please cite: Parisien M, Major F. Nature. (2008) 452:51-55. //========== Sequence ========== sequence( r A1 GGCAGAUCUGAGCCUGGGAGCUCUCUGCC ) // ((((((...(((((...).)))))))))) //========== Cycles ========== ncm_01 = library( pdb( "MCSYM-DB/5/CUGGG/*.pdb.gz" ) #1:#5 <- A14:A18 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_02 = library( pdb( "MCSYM-DB/2_3/CCGAG/*.pdb.gz" ) #1:#2, #3:#5 <- A13:A14, A18:A20 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_03 = library( pdb( "MCSYM-DB/2_2/GCGC/*.pdb.gz" ) #1:#2, #3:#4 <- A12:A13, A20:A21 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_04 = library( pdb( "MCSYM-DB/2_2/AGCU/*.pdb.gz" ) #1:#2, #3:#4 <- A11:A12, A21:A22 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_05 = library( pdb( "MCSYM-DB/2_2/GAUC/*.pdb.gz" ) #1:#2, #3:#4 <- A10:A11, A22:A23 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_06 = library( pdb( "MCSYM-DB/2_2/GAUC/*.pdb.gz" ) #1:#2, #3:#4 <- A5:A6, A24:A25 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_07 = library( pdb( "MCSYM-DB/2_2/AGCU/*.pdb.gz" ) #1:#2, #3:#4 <- A4:A5, A25:A26 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_08 = library( pdb( "MCSYM-DB/2_2/CAUG/*.pdb.gz" ) #1:#2, #3:#4 <- A3:A4, A26:A27 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_09 = library( pdb( "MCSYM-DB/2_2/GCGC/*.pdb.gz" ) #1:#2, #3:#4 <- A2:A3, A27:A28 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_10 = library( pdb( "MCSYM-DB/2_2/GGCC/*.pdb.gz" ) #1:#2, #3:#4 <- A1:A2, A28:A29 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) lnk_01 = library( pdb( "MCSYM-DB/ss2/CU/*.pdb.gz" ) #1:#2 <- A23:A24 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) lnk_02 = library( pdb( "MCSYM-DB/ss4/AUCU/*.pdb.gz" ) #1:#4 <- A6:A9 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) //=========== Backtrack =========== // assemble the whole structure: structure = backtrack( //----- upper stem ----- ncm_01 merge( ncm_02 2.0 ) merge( ncm_03 2.0 ) merge( ncm_04 2.0 ) merge( ncm_05 2.0 ) //----- interior loop ----- merge( lnk_01 2.0 ) merge( ncm_06 2.0 ) merge( lnk_02 2.0 ) //----- lower stem ----- merge( ncm_07 2.0 ) merge( ncm_08 2.0 ) merge( ncm_09 2.0 ) merge( ncm_10 2.0 ) ) // ========= Constraints / Restraints ========= clash ( structure 1.5 !( pse || lp || hydrogen ) ) ribose_rst ( structure pucker = C3p_endo, glycosyl = anti, method = ccm, threshold = 2.0 ) backtrack_rst ( structure width_limit = 25%, height_limit = 100%, // for breadth-first-like search: method = probabilistic ) // for depth-first-like search: // method = exhaustive ) // ========= Exploration Initialization ========= explore( structure option( model_limit = 100, time_limit = 1h, seed = 3210 ) rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) pdb( "HIV_1_TAR" zipped ) )