//============================== // MC-Sym 4.2 script generated by MC-Fold 1.0 // Please cite the following if you use MC-Sym: // 1) Major F et al. (1991) Science 253, 1255. // 2) Major F. (2003) Comp Sci Eng. 5, 44. //========== Sequence ========== sequence( r A1 GAGACUAUCGACAUUUGAUACACUAUUUAUCAAUGGAUGUCUC ) // (((((.(((..((((.((((((...)))))))))))))))))) //========== Cycles ========== ncm_01 = library( pdb( "MCSYM-DB/5/ACUAU/*.pdb.gz" ) #1:#5 <- A22:A26 rmsd( 0.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_02 = library( pdb( "MCSYM-DB/2_2/CAUU/*.pdb.gz" ) #1:#2, #3:#4 <- A21:A22, A26:A27 rmsd( 0.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_03 = library( pdb( "MCSYM-DB/2_2/ACUU/*.pdb.gz" ) #1:#2, #3:#4 <- A20:A21, A27:A28 rmsd( 0.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_04 = library( pdb( "MCSYM-DB/2_2/UAUA/*_x.pdb.gz" ) #1:#2, #3:#4 <- A19:A20, A28:A29 rmsd( 0.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_05 = library( pdb( "MCSYM-DB/2_2/AUAU/*_x.pdb.gz" ) #1:#2, #3:#4 <- A18:A19, A29:A30 rmsd( 0.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_06 = library( pdb( "MCSYM-DB/2_2/GAUC/*.pdb.gz" ) #1:#2, #3:#4 <- A17:A18, A30:A31 rmsd( 0.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_07 = library( pdb( "MCSYM-DB/3_2/UUGCA/*.pdb.gz" ) #1:#3, #4:#5 <- A15:A17, A31:A32 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_08 = library( pdb( "MCSYM-DB/2_2/UUAA/*.pdb.gz" ) #1:#2, #3:#4 <- A14:A15, A32:A33 rmsd( 0.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_09 = library( pdb( "MCSYM-DB/2_2/AUAU/*_x.pdb.gz" ) #1:#2, #3:#4 <- A13:A14, A33:A34 rmsd( 0.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_10 = library( pdb( "MCSYM-DB/2_2/CAUG/*.pdb.gz" ) #1:#2, #3:#4 <- A12:A13, A34:A35 rmsd( 0.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_11 = library( pdb( "MCSYM-DB/2_2/UCGA/*.pdb.gz" ) #1:#2, #3:#4 <- A8:A9, A36:A37 rmsd( 0.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_12 = library( pdb( "MCSYM-DB/2_2/AUAU/*.pdb.gz" ) #1:#2, #3:#4 <- A7:A8, A37:A38 rmsd( 0.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_13 = library( pdb( "MCSYM-DB/2_2/ACGU/*.pdb.gz" ) #1:#2, #3:#4 <- A4:A5, A39:A40 rmsd( 0.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_14 = library( pdb( "MCSYM-DB/2_2/GAUC/*_x.pdb.gz" ) #1:#2, #3:#4 <- A3:A4, A40:A41 rmsd( 0.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_15 = library( pdb( "MCSYM-DB/2_2/AGCU/*_x.pdb.gz" ) #1:#2, #3:#4 <- A2:A3, A41:A42 rmsd( 0.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_16 = library( pdb( "MCSYM-DB/2_2/GAUC/*_x.pdb.gz" ) #1:#2, #3:#4 <- A1:A2, A42:A43 rmsd( 0.5 sidechain && !( pse || lp || hydrogen ) ) ) ncm_22 = library( pdb( "MCSYM-DB/4_2/CGACGG/*.pdb.gz" ) #1:#4, #5:#6 <- A9:A12, A35:A36 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) ncm_33 = library( pdb( "MCSYM-DB/3_2/CUAUG/*.pdb.gz" ) #1:#3, #4:#5 <- A5:A7, A38:A39 rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) ) //=========== Backtrack =========== // assemble the whole structure: structure = backtrack( // stem_1 ncm_01 merge( ncm_02 2.0 ) merge( ncm_03 2.0 ) merge( ncm_04 2.0 ) merge( ncm_05 2.0 ) merge( ncm_06 2.0 ) merge( ncm_07 2.0 ) merge( ncm_08 2.0 ) merge( ncm_09 2.0 ) merge( ncm_10 2.0 ) merge( ncm_22 2.0 ) merge( ncm_11 2.0 ) merge( ncm_12 2.0 ) merge( ncm_33 2.0 ) merge( ncm_13 2.0 ) merge( ncm_14 2.0 ) merge( ncm_15 2.0 ) merge( ncm_16 2.0 ) ) // ========= Constraints / Restraints ========= clash ( structure 1.0 !( pse || lp || hydrogen ) ) ribose_rst ( structure method = estimate, threshold = 3.0, pucker = C3p_endo, glycosyl = anti ) backtrack_rst ( structure method = probabilistic, width_limit = 25%, height_limit = 100% ) implicit_phosphate_rst( structure sampling = 90% ) // ========= Exploration Initialization ========= explore( structure option( time_limit = 12h, seed = 3210 ) reference( pdb( "2FEY01.pdb" ) ) pdb( "2FEY" zipped ) )