CreatePredAlphaCost pred_alpha2k alpha11 T0242.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0242.t04.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 5 near_backbone 5 way_back 5 dry5 15 dry6.5 20 dry8 15 dry12 5 \
	phobic_fit 2 \
	sidechain 1 \
	bystroff 5 \
	soft_clashes 10  backbone_clashes 2 \
	break 20  \
	pred_alpha2k 3 \
	pred_alpha04 3 \
	constraints 35 \
	hbond_geom 1 \
	hbond_geom_backbone 1 \
	hbond_geom_beta 20 \
	hbond_geom_beta_pair 25

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

# from t2k.dssp-ehl2.constraints
# StrandConstraint	V4	T7	0.7616
# StrandConstraint	T20	T23	0.6506
# HelixConstraint 	E29	L34	0.6346
# HelixConstraint 	G43	I46	0.617
# HelixConstraint 	D52	C62	0.6396
# StrandConstraint	R70	M75	0.648
# StrandConstraint	E80	S87	0.7018
# HelixConstraint 	D98	R106	0.7949
# StrandConstraint	I110	E114	0.6163

HelixConstraint 	S11	K16
HelixConstraint 	E29	K35
# HelixConstraint 	E41	I49
HelixConstraint 	H51	G63
HelixConstraint 	S97	Q107

StrandConstraint	V4	T7	2.5	# s1
StrandConstraint	T21	I24	2.5	# s2
StrandConstraint	R70	M75	2.5	# s3
StrandConstraint	G78	I84	2.5	# s4
StrandConstraint	I110	V115	2.5	# s5


# from FUGMOD_SERVER_TS5
SheetConstraint R70 M75  I83  G78	hbond V71	20	# s3 ^v s4

# hope that these can work
SheetConstraint T20 I24 I84  E80 	hbond T21	18	# s2 ^v s4
SheetConstraint T20 I24 E114 I110	hbond T20	18	# s2 ^v s5
SheetConstraint V4  T7	Y113 I110	hbond V4 	16	# s1 ^v s5