CreatePredAlphaCost pred_alpha2k alpha11 T0231.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0231.t04.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 3 near_backbone 3 way_back 3 dry5 10 dry6.5 20 dry8 10 dry12 2 \
	phobic_fit 2 \
	sidechain 6 \
	bystroff 5 \
	soft_clashes 30  backbone_clashes 2 \
	break 50  \
	pred_alpha2k 3 \
	pred_alpha04 3 \
	constraints 10 \
	hbond_geom 0.1 \
	hbond_geom_backbone 0.1 \
	hbond_geom_beta 0.4 \
	hbond_geom_beta_pair 1

// 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.

# helices and sheets from try1-opt2

HelixConstraint D11  	E16
HelixConstraint L14  	F23
HelixConstraint S53  	E60
HelixConstraint K97  	M102
HelixConstraint Q100  	K108
HelixConstraint S107  	A115
HelixConstraint T130  	R142

SheetConstraint A30 I33  	Q50 D47  	hbond A31
SheetConstraint A31 M34  	Y71 F68  	hbond I32
SheetConstraint I33 K38  	E46 Q41  	hbond K35
SheetConstraint M42 V43  	E9 V10  	hbond V43
SheetConstraint P66 S72  	S92 L86  	hbond R67
SheetConstraint K74 H77  	Y84 R81  	hbond Y75
SheetConstraint C87 S92  	K119 R124  	hbond F88