CreatePredAlphaCost pred_alpha2k alpha11 T0250.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0250.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.

# Conserved H173, H175, and H186  may be part of a metal-binding site.
# and should probaby be clustered

Constraint H173.NE2 H175.NE2    -10 6 9 1.0
Constraint H173.NE2 H186.NE2    -10 6 9 1.0
Constraint H175.NE2 H186.NE2    -10 6 9 1.0

# The secondary structure patterns seems fairly clear in the t04 predictions:

HelixConstraint         T10     L18     6.018
HelixConstraint         I25     E30     8.218
HelixConstraint         Q92     M103    6.218
HelixConstraint         T134    R141    6.726
HelixConstraint         E162    L163    6.32
HelixConstraint         E214    K218    6.588
HelixConstraint         Y223    A233    7.254

StrandConstraint        L5      Y6      6.084
StrandConstraint        E45     L49     7.068
StrandConstraint        K52     A56     6.802
StrandConstraint        F62     L65     6.814
StrandConstraint        Y73     T77     7.021
StrandConstraint        S110    F118    6.565
StrandConstraint        H120    M125    7.165
StrandConstraint        G153    F158    6.785
StrandConstraint        I174    F176    6.246
StrandConstraint        H186    V192    6.438
StrandConstraint        V195    Q200    6.065
StrandConstraint        Q206    H208    6.913