//============================== // MC-Sym 4.2 script generated by MC-Fold 1.0 // Please cite the following if you use MC-Sym: // 1) Major F et al. (1991) Science 253, 1255. // 2) Major F. (2003) Comp Sci Eng. 5, 44. //========== Sequence ========== sequence( r A1 GGAAGUCCGGUCUUCGGACCGGCUUCC ) // (((((.(((((((..)))))))))))) //========== Cycles ========== ncm_01 = library( pdb( "MCSYM-DB/4/UUCG/*.pdb.gz" ) #1:#4 <- A13:A16 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_02 = library( pdb( "MCSYM-DB/2_2/CUGG/*.pdb.gz" ) #1:#2, #3:#4 <- A12:A13, A16:A17 rmsd( 0.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_03 = library( pdb( "MCSYM-DB/2_2/UCGA/*_s.pdb.gz" ) #1:#2, #3:#4 <- A11:A12, A17:A18 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) ncm_04 = library( pdb( "MCSYM-DB/2_2/GUAC/*_s.pdb.gz" ) #1:#2, #3:#4 <- A10:A11, A18:A19 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) ncm_05 = library( pdb( "MCSYM-DB/2_2/GGCC/*_s.pdb.gz" ) #1:#2, #3:#4 <- A9:A10, A19:A20 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) ncm_06 = library( pdb( "MCSYM-DB/2_2/CGCG/*_s.pdb.gz" ) #1:#2, #3:#4 <- A8:A9, A20:A21 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) ncm_07 = library( pdb( "MCSYM-DB/2_2/CCGG/*.pdb.gz" ) #1:#2, #3:#4 <- A7:A8, A21:A22 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) ncm_08 = library( pdb( "MCSYM-DB/3_2/GUCGC/*.pdb.gz" ) #1:#3, #4:#5 <- A5:A7, A22:A23 rmsd( 0.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_09 = library( pdb( "MCSYM-DB/2_2/AGCU/*.pdb.gz" ) #1:#2, #3:#4 <- A4:A5, A23:A24 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) ncm_10 = library( pdb( "MCSYM-DB/2_2/AAUU/*_s.pdb.gz" ) #1:#2, #3:#4 <- A3:A4, A24:A25 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) ncm_11 = library( pdb( "MCSYM-DB/2_2/GAUC/*_s.pdb.gz" ) #1:#2, #3:#4 <- A2:A3, A25:A26 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) ncm_12 = library( pdb( "MCSYM-DB/2_2/GGCC/*_s.pdb.gz" ) #1:#2, #3:#4 <- A1:A2, A26:A27 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) //=========== Backtrack =========== // assemble the whole structure: structure = backtrack( // stem_1 ncm_01 merge( ncm_02 2.0 ) merge( ncm_03 2.0 ) merge( ncm_04 2.0 ) merge( ncm_05 2.0 ) 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 ) merge( ncm_11 2.0 ) merge( ncm_12 2.0 ) ) // ========= Constraints / Restraints ========= clash ( structure 1.0 !( pse || lp || hydrogen ) ) ribose_rst ( structure method = estimate, threshold = 2.0, pucker = C3p_endo, glycosyl = anti ) backtrack_rst ( structure method = exhaustive, width_limit = 25%, height_limit = 100% ) implicit_phosphate_rst( structure sampling = 90% ) // ========= Exploration Initialization ========= explore( structure option( time_limit = 12h, seed = 3210 ) reference( pdb( "2CD101.pdb" ) ) pdb( "2CD1" zipped ) )