CreatePredAlphaCost pred_alpha2k alpha11 T0252.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0252.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 T0252.t04.dssp-ehl2.constraints

HelixConstraint 	N5	F18	0.7035
StrandConstraint	A41	T47	0.7107
StrandConstraint	V52	S54	0.8034
StrandConstraint	R61	E65	0.6068
HelixConstraint 	K69	D79	0.6977
HelixConstraint 	P82	K88	0.8299
HelixConstraint 	A118	S125	0.617
HelixConstraint 	V132	L146	0.8656
HelixConstraint 	D155	Q159	0.6244
HelixConstraint 	F166	S177	0.806
HelixConstraint 	A185	C196	0.6219
HelixConstraint 	T202	A214	0.6061
HelixConstraint 	A228	N230	0.6198
HelixConstraint 	P232	M238	0.6162
StrandConstraint	G265	V270	0.6158
StrandConstraint	M274	F279	0.7294
HelixConstraint 	V290	Q302	0.7303


#from align1.sheets
SheetConstraint A41 T47  	S280 M274  	hbond A42
SheetConstraint A42 T47  	G56 N51  	hbond V43
SheetConstraint R61 L64  	N201 T198  	hbond F62
SheetConstraint G216 P219  	V225 H222  	hbond N218
SheetConstraint P257 G261  	V269 G265  	hbond K259
SheetConstraint G264 V270  	S280 M274  	hbond I266