CreatePredAlphaCost pred_alpha2k alpha11 T0234.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0234.t04.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 3 near_backbone 3 way_back 3 dry5 10 dry6.5 20 dry8 15 dry12 2 \
	phobic_fit 2 \
	sidechain 6 \
	bystroff 5 \
	soft_clashes 30  backbone_clashes 2 \
	break 80  \
	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.

# from the first alignment:
HelixConstraint L4  	G13
HelixConstraint A55  	N64
HelixConstraint E97  	V106
HelixConstraint Q109  	Q116
HelixConstraint G144  	I149
SheetConstraint Q19 S27  	F39 I31  	hbond A21
SheetConstraint A21 T25  	F71 V67  	hbond I22
SheetConstraint I41 D43  	Y48 N46  	hbond D43
SheetConstraint N46 S52  	T133 F127  	hbond I47
SheetConstraint P65 F71  	A93 L87  	hbond V67
SheetConstraint R85 C91  	I141 K135  	hbond R86
SheetConstraint D90 I96  	K135 I129  	hbond T94


Constraint F14.CZ	L87.CG	3 4 6		8