CreatePredAlphaCost pred_alpha2k alpha11 T0249.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0249.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  T0249.t04.dssp-ehl2.constraints
HelixConstraint 	R5	F17	6.743
HelixConstraint 	L25	I31	8.473
HelixConstraint 	P38	E53	6.526
HelixConstraint 	P74	L84	6.914
HelixConstraint 	R94	W105	7.871
HelixConstraint 	K111	I117	6.861
HelixConstraint 	D123	A131	7.734
HelixConstraint 	E154	L159	7.985
HelixConstraint 	L171	L187	6.978

StrandConstraint	T58	I64	6.922
StrandConstraint	Y68	L71	7.73
StrandConstraint	I135	V137	6.648

# from align5.sheets

SheetConstraint P22 N24	R69 G67	hbond V23	10
SheetConstraint I61 I64	F70 G67	hbond H62	10