//==============================
// MC-Sym 4.2 script generated by MC-Fold 1.0
// Please cite: Parisien M, Major F. Nature. (2008) 452:51-55.


//========== Sequence ==========

sequence( r A26 GGGCGCUUGUCGCGUGCCA )
//              ((((((.......))))))



//========== Cycles ==========

ncm_01 = library(
	pdb( "MCSYM-DB/2_2/GCGU/*.pdb.gz" ) #1:#2, #3:#4 <- A30:A31, A39:A40
	rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) )

ncm_02 = library(
	pdb( "MCSYM-DB/2_2/CGUG/*.pdb.gz" ) #1:#2, #3:#4 <- A29:A30, A40:A41
	rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) )

ncm_03 = library(
	pdb( "MCSYM-DB/2_2/GCGC/*.pdb.gz" ) #1:#2, #3:#4 <- A28:A29, A41:A42
	rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) )

ncm_04 = library(
	pdb( "MCSYM-DB/2_2/GGCC/*.pdb.gz" ) #1:#2, #3:#4 <- A27:A28, A42:A43
	rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) )

ncm_05 = library(
	pdb( "MCSYM-DB/2_2/GGCA/*.pdb.gz" ) #1:#2, #3:#4 <- A26:A27, A43:A44
	rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) )

lnk_01 = library(
	pdb( "MCSYM-DB/ss3/CUU/*.pdb.gz" ) #1:#3 <- A31:A33
	rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) )

lnk_02 = library(
	pdb( "MCSYM-DB/ss4/CGCG/*.pdb.gz" ) #1:#4 <- A36:A39
	rmsd( 0.1 sidechain && !( pse || lp || hydrogen ) ) )

lnk_03 = library(
	pdb( "MCSYM-DB/ss3/GUC/*.pdb.gz" ) #1:#3 <- A34:A36
	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 )

	//----- loop -----
	merge( lnk_01 2.0 )
	merge( lnk_02 2.0 )
	merge( lnk_03 2.0 )
)



// ========= Constraints / Restraints =========

clash                 ( structure 1.5 !( pse || lp || hydrogen ) )

ribose_rst            ( structure
                        pucker = C3p_endo, glycosyl = anti,
                        method = ccm, threshold = 2.0 )

backtrack_rst         ( structure
                        width_limit = 25%, height_limit = 100%,
// for breadth-first-like search:
			method = probabilistic )
// for depth-first-like search:
//                      method = exhaustive )



// ========= Exploration Initialization =========
explore(
	structure
	option( model_limit = 100, time_limit = 1h, seed = 3210 )
	rmsd( 1.0 sidechain && !( pse || lp || hydrogen ) )
	pdb( "anticodon" zipped )
)