//============================== // 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 GGUUUGCCUUUUGGCUUACC ) // ((((((((....)))))))) //========== Cycles ========== ncm_01 = library( pdb( "MCSYM-DB/6/CUUUUG/*.pdb.gz" ) #1:#6 <- A8:A13 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_02 = library( pdb( "MCSYM-DB/2_2/CCGG/*.pdb.gz" ) #1:#2, #3:#4 <- A7:A8, A13:A14 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) ncm_03 = library( pdb( "MCSYM-DB/2_2/GCGC/*_s.pdb.gz" ) #1:#2, #3:#4 <- A6:A7, A14:A15 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) ncm_04 = library( pdb( "MCSYM-DB/2_2/UGCU/*.pdb.gz" ) #1:#2, #3:#4 <- A5:A6, A15:A16 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) ncm_05 = library( pdb( "MCSYM-DB/2_2/UUUU/*.pdb.gz" ) #1:#2, #3:#4 <- A4:A5, A16:A17 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) ncm_06 = library( pdb( "MCSYM-DB/2_2/UUUA/*.pdb.gz" ) #1:#2, #3:#4 <- A3:A4, A17:A18 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) ncm_07 = library( pdb( "MCSYM-DB/2_2/GUAC/*_s.pdb.gz" ) #1:#2, #3:#4 <- A2:A3, A18:A19 rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) ) ncm_08 = library( pdb( "MCSYM-DB/2_2/GGCC/*_s.pdb.gz" ) #1:#2, #3:#4 <- A1:A2, A19:A20 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 ) ) // ========= 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( "2O3301.pdb" ) ) pdb( "2O33" zipped ) )