// ========== -*-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 CCAUGGGGAGCCGCACGGAGGCGAUGAACCAUGG ) // ((((((((((((((...)))))...))))))))) // AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA // 1234567890123456789012345678901234 // 1 2 3 // ^^^^^ ^^^^^^^^ // ========== Library ========== ncm_01 = library( pdb( "MCSYM-DB/5/CACGG/*.pdb.gz" ) #1:#5 <- A14:A18 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_02 = library( pdb( "MCSYM-DB/2_2/GCGA/*_1.pdb.gz" ) #1:#2, #3:#4 <- A13:A14, A18:A19 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_03 = library( pdb( "MCSYM-DB/2_2/CGAG/*_1.pdb.gz" ) #1:#2, #3:#4 <- A12:A13, A19:A20 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_04 = library( pdb( "MCSYM-DB/2_2/CCGG/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A11:A12, A20:A21 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_05 = library( pdb( "MCSYM-DB/2_2/GCGC/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A10:A11, A21:A22 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) // not used: //ncm_06 = library( // pdb( "MCSYM-DB/2_2/GAGA/*.pdb.gz" ) // #1:#2, #3:#4 <- A8:A9, A26:A27 // rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) // not used: //ncm_07 = library( // pdb( "MCSYM-DB/2_2/GGAA/*.pdb.gz" ) // #1:#2, #3:#4 <- A7:A8, A27:A28 // rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) // not used: //ncm_08 = library( // pdb( "MCSYM-DB/2_2/GGAC/*_1.pdb.gz" ) // #1:#2, #3:#4 <- A6:A7, A28:A29 // rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_09 = library( pdb( "MCSYM-DB/2_2/GGCC/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A5:A6, A29:A30 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_10 = library( pdb( "MCSYM-DB/2_2/UGCA/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A4:A5, A30:A31 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_11 = library( pdb( "MCSYM-DB/2_2/AUAU/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A3:A4, A31:A32 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_12 = library( pdb( "MCSYM-DB/2_2/CAUG/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A2:A3, A32:A33 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_13 = library( pdb( "MCSYM-DB/2_2/CCGG/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A1:A2, A33:A34 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) // ============Internal loop(s)============ // not used: //lnk_01 = library( // pdb( "MCSYM-DB/ss4/CGAU/*.pdb.gz" ) // #1:#4 <- A22:A25 // rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) // not used: //lnk_02 = library( // pdb( "MCSYM-DB/ss2/AG/*.pdb.gz" ) // #1:#2 <- A9:A10 // rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) k_turn = library( pdb( "../BINuPWoBcT/results.pdb" ) #1:#5, #6:#13 <- A6:A10, A22:A29 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) // =========== Backtrack =========== // assemble the whole structure: structure = backtrack ( ncm_01 merge( ncm_02 1.5 ) merge( ncm_03 1.5 ) merge( ncm_04 1.5 ) merge( ncm_05 1.5 ) //merge( lnk_01 1.5 ) //merge( lnk_02 1.5 ) //merge( ncm_06 1.5 ) //merge( ncm_07 1.5 ) //merge( ncm_08 1.5 ) merge( k_turn 1.5 ) merge( ncm_09 1.5 ) merge( ncm_10 1.5 ) merge( ncm_11 1.5 ) merge( ncm_12 1.5 ) merge( ncm_13 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 = 1000, time_limit = 30m, seed = 3210 ) rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) pdb( "hairpin" zipped ) )