CreatePredAlphaCost pred_alpha2k alpha11 T0251.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0251.t04.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 3 near_backbone 3 way_back 3 dry5 5 dry6.5 6 dry8 5 dry12 2 \
	phobic_fit 2 \
	sidechain 6 \
	bystroff 5 \
	soft_clashes 10  backbone_clashes 2 \
	break 20  \
	pred_alpha2k 3 \
	pred_alpha04 3 \
	constraints 10 \
	hbond_geom 1 \
	hbond_geom_backbone 1 \
	hbond_geom_beta 5 \
	hbond_geom_beta_pair 10

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

// 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.

# from t04.dssp-ehl2
StrandConstraint	V2	Y4	0.7157
StrandConstraint	V8	I9	0.6778
HelixConstraint 	S19	R32	0.6327
StrandConstraint	F39	D45	0.773
HelixConstraint 	D57	E65	0.6137
StrandConstraint	L73	M76	0.7471
HelixConstraint 	K89	L99	0.6494


SheetConstraint K31 K33	T42 K40	hbond T42

# from try2-opt2
SheetConstraint (T0251)M1 (T0251)A6	(T0251)F39 (T0251)I44	hbond (T0251)M1
SheetConstraint (T0251)M1 (T0251)G5	(T0251)M76 (T0251)P72	hbond (T0251)V2
SheetConstraint (T0251)T75 (T0251)M76	(T0251)Y80 (T0251)E79	hbond (T0251)M76

SheetConstraint L73 M76	A82 E79	hbond M76

# Constraint C10.SG C13.SG	-10 3.5 7	1.0