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 20 \
	known_ssbond 0.5 \
	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

SSBond C10 C13	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

# From Kevin, prior to try4.
# SheetConstraint K31 K33	T42 K40	hbond T42

# from try3-opt2
SheetConstraint (T0251)V2 (T0251)G5	(T0251)M76 (T0251)L73	hbond (T0251)V3
SheetConstraint (T0251)V2 (T0251)A6	(T0251)Y41 (T0251)D45	hbond (T0251)Y4
SheetConstraint (T0251)L73 (T0251)I74	(T0251)D83 (T0251)A82	hbond (T0251)I74
SheetConstraint (T0251)I74 (T0251)M76	(T0251)V81 (T0251)E79	hbond (T0251)M76

# is this redundant with SSbond command?
Constraint C10.SG C13.SG	-10 3.5 7	1.0

# include the SSbonding cysteine C13 in a helix found in try3
HelixConstraint 	A11	V14	1.0

# from try3-opt2
HelixConstraint (T0251)V14	(T0251)Q27
HelixConstraint (T0251)W25	(T0251)K31
HelixConstraint (T0251)D57	(T0251)E65
# HelixConstraint (T0251)Q87	(T0251)N101   # starts too early?

# attempt to bury hydrophobics in the sheet using helices on either side
Constraint I22.CD1  A6.CB	-10 3.5 7	1.0
#onstraint L26.CD1  ??
Constraint L29.CD1  V2.CG2	-10 3.5 7	1.0

Constraint I91.CD1  I74.CD1	-10 3.5 7	1.0
Constraint I95.CD1  V81.CG1	-10 3.5 7	1.0
Constraint L99.CD1  I37.CD1	-10 3.5 7	0.5 #  ??

Constraint L58.CD1  I44.CD1	-10 3.5 7	1.0
Constraint I61.CD1  V2.CG1 	-10 3.5 7	1.0
Constraint I64.CD1  L73.CD1	-10 3.5 7	1.0