CreatePredAlphaCost pred_alpha2k alpha11 T0237.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0237.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 10 \
	hbond_geom 1 \
	hbond_geom_backbone 1 \
	hbond_geom_beta 4 \
	hbond_geom_beta_pair 10 \
	known_ssbond 5

// 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.


# T0237.t2k.bys.constraints
HelixConstraint         Q338    L342    6.07
StrandConstraint        F344    P345    6.09
HelixConstraint         K350    Q360    7.94
StrandConstraint        R373    S382    7.52
StrandConstraint        I388    P394    6.41
StrandConstraint        I397    S398    6.92
StrandConstraint        F404    C407    6.91
HelixConstraint         N408    E418    6.62
StrandConstraint        Q421    I424    7.16
HelixConstraint         E426    E433    6.7
StrandConstraint        K441    L445    7.5

# from main structure, try8-opt2.sheets
SheetConstraint E395 S398	V406 N403	hbond E395	7

# previously discovered disulphide bonds
SSbond  C346    C402    1.0
SSBond  C390    C407    1.0
SSBond  C392    C409    1.0