CreatePredAlphaCost pred_alpha2k alpha11 T0363.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0363.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0363.t06.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 15 dry6.5 20 dry8 15 dry12 5 \
	phobic_fit 2 \
	sidechain 4 \
	n_ca_c	5 bad_peptide 10 \
	bystroff 5 \
	soft_clashes 60  backbone_clashes 2 \
	break 50  \
	pred_alpha2k 2 \
	pred_alpha04 2 \
	pred_alpha06 2 \
	constraints 20 \
	hbond_geom 5 \
	hbond_geom_backbone 10 \
	hbond_geom_beta 50 \
	hbond_geom_beta_pair 100 \
	missing_atoms 1 \
	maybe_metal 0 \
	maybe_ssbond 0

// remove maybe_ssbond weight if protein known to be in reducing environment.
// remove maybe_metal weight if protein known to have disulfides or
//	known not to bind metal ions.

// Add the following for extra-cellular proteins:
#	known_ssbond 0.5	# and put ssbond command in constraints file

// For comparative modeling, increase weight of break and hbond_geom...

// put any constraints here, such as helix constraints, strand constraints,
//	sheet constraints, ssbonds, hbonds, or just arbitrary pairs of atoms.

include T0363.dssp-ehl2.constraints
//include T0363.undertaker-align.sheets
include rr.constraints

//from try2-op2.sheets
SheetConstraint (T0363)Q12 (T0363)Y19	(T0363)D33 (T0363)Y25	hbond (T0363)I13	5


//from try3-opt2.helices (but modified)
HelixConstraint (T0363)M1	(T0363)H6	1
HelixConstraint (T0363)A18	(T0363)L27 	1.5 // will force the helix to turn inward, burying certain regions.
HelixConstraint (T0363)V38	(T0363)S57 	3// combines two helices currently separated
HelixConstraint (T0363)D89	(T0363)G97	1