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 40  \
	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 	2.0
SheetConstraint (T0251)V2 (T0251)A6	(T0251)Y41 (T0251)D45	hbond (T0251)Y4 	2.0
SheetConstraint (T0251)L73 (T0251)I74	(T0251)D83 (T0251)A82	hbond (T0251)I74	2.0
SheetConstraint (T0251)I74 (T0251)M76	(T0251)V81 (T0251)E79	hbond (T0251)M76	2.0

# is this redundant with SSbond command?
Constraint C10.SG C13.SG	-10 3.5 7	2.0

# from try4-opt2
HelixConstraint (T0251)C10	(T0251)N15
HelixConstraint (T0251)K20	(T0251)Q27
HelixConstraint (T0251)W25	(T0251)K31
HelixConstraint (T0251)D49	(T0251)D55
HelixConstraint (T0251)H56	(T0251)E65
HelixConstraint (T0251)I86	(T0251)R93
HelixConstraint (T0251)F94	(T0251)E102

# 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