// ========== -*-Ruby-*- ========== // // MC-Sym 4.2 script generated by Dot2Sym.pl // (c) Jean-Christophe Grenier, University of Montreal // Please cite: Parisien M, Major F. Nature. (2008) 452:51-55. // // web site FAQ: www.major.iric.ca/MC-Sym/faq.html // advanced features: commands.html file of your working directory // // ========== Sequence ========== sequence( r A1 GGAGUGCUUCAACAGUGCUUGGACGCUCC ) // ((((((.((((((...).))))))))))) // AAAAAAAAAAAAAAAAAAAAAAAAAAAAA // 12345678901234567890123456789 // ========== Library ========== ncm_01 = library( pdb( "MCSYM-DB/5/CAGUG/*_1.pdb.gz" ) #1:#5 <- A13:A17 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_02 = library( pdb( "MCSYM-DB/2_3/ACGCU/*_1.pdb.gz" ) #1:#2, #3:#5 <- A12:A13, A17:A19 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_03 = library( pdb( "MCSYM-DB/2_2/AAUU/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A11:A12, A19:A20 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_04 = library( pdb( "MCSYM-DB/2_2/CAUG/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A10:A11, A20:A21 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_05 = library( pdb( "MCSYM-DB/2_2/UCGG/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A9:A10, A21:A22 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_06 = library( pdb( "MCSYM-DB/2_2/UUGA/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A8:A9, A22:A23 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_07 = library( pdb( "MCSYM-DB/3_2/GCUAC/*_1.pdb.gz" ) #1:#3, #4:#5 <- A6:A8, A23:A24 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_08 = library( pdb( "MCSYM-DB/2_2/UGCG/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A5:A6, A24:A25 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_09 = library( pdb( "MCSYM-DB/2_2/GUGC/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A4:A5, A25:A26 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_10 = library( pdb( "MCSYM-DB/2_2/AGCU/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A3:A4, A26:A27 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_11 = library( pdb( "MCSYM-DB/2_2/GAUC/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A2:A3, A27:A28 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_12 = library( pdb( "MCSYM-DB/2_2/GGCC/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A1:A2, A28:A29 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) // =========== Backtrack =========== // assemble the whole structure: structure = backtrack ( //Stem 01 ncm_01 merge( ncm_02 1.5 ) merge( ncm_03 1.5 ) merge( ncm_04 1.5 ) merge( ncm_05 1.5 ) merge( ncm_06 1.5 ) merge( ncm_07 1.5 ) merge( ncm_08 1.5 ) merge( ncm_09 1.5 ) merge( ncm_10 1.5 ) merge( ncm_11 1.5 ) merge( ncm_12 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 = 12h, seed = 3210 ) rmsd( 0.5 sidechain && !( pse || lp || hydrogen ) ) pdb( "1NBR_o" zipped ) )