CreatePredAlphaCost pred_alpha2k alpha11 T0201.t2k.alpha.rdb 2 alpha alpha_prev sum 
CreatePredAlphaCost pred_alpha04 alpha11 T0201.t04.alpha.rdb 2 alpha alpha_prev sum 

#
# Need to adjust this part, not optimized yet
#
SetCost wet6.5 3 near_backbone 3 way_back 3 dry5 5 dry6.5 6 dry8 5 dry12 2 \
	phobic_fit 4 \
	sidechain 6 \
	bystroff 5 \
	soft_clashes 10  backbone_clashes 2 \
	break 10  \
	pred_alpha2k 5 \
	pred_alpha04 5 \
	constraints 10 \
	hbond_geom 0.1 \
	hbond_geom_backbone 0.1 \
	hbond_geom_beta 1 \
	hbond_geom_beta_pair 2

// 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,
//	ssbond, hbond, or just arbitrary pairs of atoms.

# From T0201.t04.dssp-ehl2.constraints
StrandConstraint	K3	V4	0.7391
StrandConstraint	F10	T14	0.6307
HelixConstraint 	C23	E40	0.6964
StrandConstraint	Y51	F56	0.6428
HelixConstraint 	N61	K80	0.6419
StrandConstraint	I85	I90	0.7018

# From T0204.t04.str2.constraints
StrandConstraint	K3	V4	0.795
StrandConstraint	F10	V13	0.709
HelixConstraint 	C23	A39	0.719
StrandConstraint	Y51	F56	0.713
HelixConstraint 	C62	K80	0.613
#StrandConstraint	R86	I90	0.624
# Increase strand constraint to try to form the sheet
StrandConstraint	R86	I90	0.824

#
# make his and cys close, to try to form metal-binding site. Also
#  try throwing in D19
#
Constraint      C23.SG  H16.NE2         3       4.5     7       2.0
Constraint      C23.SG  H32.NE2         3       4.5     7       2.0
Constraint      H16.NE2 H32.NE2         3       4.5     7       2.0
Constraint      D19.CG  H16.NE2         3       4.5     7       1.0 
Constraint      D19.CG  C23.SG          3       4.5     7       1.0
Constraint      D19.CG  H32.NE2         3.5     5.0     9       1.0