//============================== // 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 GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUCUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGC ) // (((((((..(((((......)))))(((((((.....)))))))....((((((...)..)))))))))))) // DDDDDDD AAAAAAAAAAAAAAAABBBBBBBBBBBBBBBBBBB CCCCCCCCCCCCCCCCCDDDDDDD // 1 2 3 4 5 6 7 // 123456789012345678901234567890123456789012345678901234567890123456789012 // // http://www.major.iric.ca/MC-Sym/Work/MEZ5X7OSDn/ //========== Relations ========== relation( // anticodon's loop special conformation // Fuller W, Hodgson A. // Conformation of the anticodon loop in tRNA. // Nature. 1967 215:817-21. A33:A34 { adjacent_5p && !stack } 100 A34:A38 { file( "helixA_RNA" ) stack } 1 ) //========== Library ========== //---------- D stem/loop ---------- ncm_01 = library( pdb( "MCSYM-DB/2_2/CAAG/*_1.pdb.gz" ) #1:#2, #3:#4 <- A13:A14, A21:A22 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_02 = library( pdb( "MCSYM-DB/2_2/UCGA/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A12:A13, A22:A23 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_03 = library( pdb( "MCSYM-DB/2_2/CUAG/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A11:A12, A23:A24 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_04 = library( pdb( "MCSYM-DB/2_2/GCGC/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A10:A11, A24:A25 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) //---------- anticodon ---------- ncm_05 = library( pdb( "MCSYM-DB/2_2/ACAU/*_1.pdb.gz" ) #1:#2, #3:#4 <- A31:A32, A38:A39 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_06 = library( pdb( "MCSYM-DB/2_2/GAUC/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A30:A31, A39:A40 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_07 = library( pdb( "MCSYM-DB/2_2/AGCU/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A29:A30, A40:A41 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_08 = library( pdb( "MCSYM-DB/2_2/CAUG/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A28:A29, A41:A42 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_09 = library( pdb( "MCSYM-DB/2_2/CCGG/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A27:A28, A42:A43 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_10 = library( pdb( "MCSYM-DB/2_2/GCGA/*_1.pdb.gz" ) #1:#2, #3:#4 <- A26:A27, A43:A44 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) //---------- T stem/loop ---------- ncm_11 = library( pdb( "MCSYM-DB/5/UUCGA/*_1.pdb.gz" ) #1:#5 <- A54:A58 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_12 = library( pdb( "MCSYM-DB/2_4/GUAUCC/*_1.pdb.gz" ) #1:#2, #3:#6 <- A53:A54, A58:A61 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_13 = library( pdb( "MCSYM-DB/2_2/UGCA/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A52:A53, A61:A62 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_14 = library( pdb( "MCSYM-DB/2_2/GUAC/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A51:A52, A62:A63 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_15 = library( pdb( "MCSYM-DB/2_2/UGCA/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A50:A51, A63:A64 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_16 = library( pdb( "MCSYM-DB/2_2/CUAG/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A49:A50, A64:A65 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) //---------- acceptor ---------- ncm_17 = library( pdb( "MCSYM-DB/2_2/UUAA/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A6:A7, A66:A67 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_18 = library( pdb( "MCSYM-DB/2_2/AUAU/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A5:A6, A67:A68 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_19 = library( pdb( "MCSYM-DB/2_2/GAUU/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A4:A5, A68:A69 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_20 = library( pdb( "MCSYM-DB/2_2/GGUC/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A3:A4, A69:A70 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_21 = library( pdb( "MCSYM-DB/2_2/CGCG/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A2:A3, A70:A71 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_22 = library( pdb( "MCSYM-DB/2_2/GCGC/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A1:A2, A71:A72 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) //---------- single-stranded ---------- loop_D1 = library( pdb( "MCSYM-DB/ss4/GUUG/*.pdb.gz" ) #1:#4 <- A15:A18 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) loop_D2 = library( pdb( "MCSYM-DB/ss4/GGGA/*.pdb.gz" ) #1:#4 <- A18:A21 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) lnk_D_Acc = library( pdb( "MCSYM-DB/ss4/UUAG/*.pdb.gz" ) #1:#4 <- A7:A10 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) lnk_Xtra1 = library( pdb( "MCSYM-DB/ss3/GGU/*.pdb.gz" ) #1:#3 <- A45:A47 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) lnk_Xtra2 = library( pdb( "MCSYM-DB/ss3/UCC/*.pdb.gz" ) #1:#3 <- A47:A49 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) stk_D_Ant = library( pdb( "MCSYM-DB/ss2/CG/*.pdb.gz" ) #1:#2 <- A25:A26 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) stk_T_Acc = library( pdb( "MCSYM-DB/ss2/GA/*.pdb.gz" ) #1:#2 <- A65:A66 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) //=========== Backtrack =========== // assemble the whole structure: structure = backtrack( // <<<<<-------------------- // build the clover-leaf first //----- anticodon ----- ncm_10 merge( ncm_09 1.5 ) //----- D stem/loop ----- merge( stk_D_Ant 1.5 ) merge( ncm_04 1.5 ) merge( ncm_03 1.5 ) //----- acceptor ----- merge( lnk_D_Acc 1.5 ) merge( ncm_17 1.5 ) merge( ncm_18 1.5 ) //----- T stem/loop ----- merge( stk_T_Acc 1.5 ) merge( ncm_16 1.5 ) merge( ncm_15 1.5 ) // -------------------->>>>> // <<<<<-------------------- // extend the arms next //----- T stem/loop ----- merge( ncm_14 1.5 ) merge( ncm_13 1.5 ) merge( ncm_12 1.5 ) merge( ncm_11 1.5 ) //----- D stem/loop ----- // force it to build around T stem/loop merge( ncm_02 1.5 ) merge( ncm_01 1.5 ) merge( loop_D2 1.5 ) merge( loop_D1 1.5 ) //----- extra loop ----- merge( lnk_Xtra2 1.5 ) merge( lnk_Xtra1 1.5 ) //----- anticodon ----- merge( ncm_08 1.5 ) merge( ncm_07 1.5 ) merge( ncm_06 1.5 ) merge( ncm_05 1.5 ) ( A38 A37 A36 A35 A34 A33 ) //----- acceptor ----- merge( ncm_19 1.5 ) merge( ncm_20 1.5 ) merge( ncm_21 1.5 ) merge( ncm_22 1.5 ) // -------------------->>>>> ) // ========= Distance Restraints ========= // Levitt M. // Detailed model for transfer ribonucleic acid. // Nature. 1969 224:759-63. // coax stack between D and anticodon distance( A25:PSY A26:PSY 0.0 5.0 ) // coax stack between T and acceptor distance( A65:PSY A66:PSY 0.0 5.0 ) // ========= 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, //method = estimate, threshold = 1.5 ) // ========= Exploration Initialization ========= explore( structure option( model_limit = 9999, seed = 3210 ) rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) pdb( "tRNA_phe" zipped ) )