// ========== -*-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 GGAGGUAGUAGGUCGAAAGACCAUUCUGCCUCC ) // (((((((((((((((..)))))).))))))))) // AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA // 123456789012345678901234567890123 // ^^^^^^ ^^^^^^^ // ========== Library ========== ncm_01 = library( pdb( "MCSYM-DB/4/GAAA/*_1.pdb.gz" ) #1:#4 <- A15:A18 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_02 = library( pdb( "MCSYM-DB/2_2/CGAG/*_1.pdb.gz" ) #1:#2, #3:#4 <- A14:A15, A18:A19 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_03 = library( pdb( "MCSYM-DB/2_2/UCGA/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A13:A14, A19:A20 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_04 = library( pdb( "MCSYM-DB/2_2/GUAC/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A12:A13, A20:A21 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) intloop = library( pdb( "../{q9wHeQ3qeS,RI0nhTIxXS,1Q3ok01Zvx}/*.pdb.gz" ) //pdb( "../RI0nhTIxXS/H02-0000.pdb.gz" ) #1:#6, #7:#13 <- A7:A12, A21:A27 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_10 = library( pdb( "MCSYM-DB/2_2/UAUG/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A6:A7, A27:A28 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_11 = library( pdb( "MCSYM-DB/2_2/GUGC/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A5:A6, A28:A29 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_12 = library( pdb( "MCSYM-DB/2_2/GGCC/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A4:A5, A29:A30 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_13 = library( pdb( "MCSYM-DB/2_2/AGCU/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A3:A4, A30:A31 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_14 = library( pdb( "MCSYM-DB/2_2/GAUC/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A2:A3, A31:A32 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_15 = library( pdb( "MCSYM-DB/2_2/GGCC/*R20*.pdb.gz" ) #1:#2, #3:#4 <- A1:A2, A32:A33 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( intloop 1.5 ) merge( ncm_10 1.5 ) merge( ncm_11 1.5 ) merge( ncm_12 1.5 ) merge( ncm_13 1.5 ) merge( ncm_14 1.5 ) merge( ncm_15 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 = 1h, seed = 3210 ) rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) ) pdb( "2JXV" zipped ) )