//---------------------------------------------------------------------- // Hypothesis #2 {1, 3} //========== Sequence ========== sequence( r B1 CCAUUCU ) sequence( r A1 AGUAGG ) //========== Library ========== //----- the 5' 2_2 capping NCM ----- ncm_5c = library( pdb( "MCSYM-DB/2_2/CCGG/*R20*.pdb.gz" ) #1:#2, #3:#4 <- B1:B2, A5:A6 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) //----- the 5' 2_2 transition NCM ----- ncm_5t = library( pdb( "MCSYM-DB/2_2/CAAG/*.pdb.gz" ) #1:#2, #3:#4 <- B2:B3, A4:A5 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) //----- the 3' 2_2 transition NCM ----- ncm_3t = library( pdb( "MCSYM-DB/2_2/UCGU/*.pdb.gz" ) #1:#2, #3:#4 <- B5:B6, A2:A3 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) //----- the 3' 2_2 capping NCM ----- ncm_3c = library( pdb( "MCSYM-DB/2_2/CUAG/*R20*.pdb.gz" ) #1:#2, #3:#4 <- B6:B7, A1:A2 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) //========== Relations ========== relation( B3:B5 { adjacent_5p } 100% ) //========== Backtrack ========== structure = backtrack( ncm_5c merge( ncm_5t 1.5 ) ( B3 B4 ) ( B4 B5 ) merge( ncm_3t 1.5 ) merge( ncm_3c 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( 0.5 sidechain && !( pse || lp || hydrogen ) ) pdb( "H02" zipped ) )