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 10 near_backbone 5 way_back 5 dry5 15 dry6.5 25 dry8 15 dry12 5 \
	phobic_fit 2 \
	sidechain 1 \
	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 1

// 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    10	##6.09
HelixConstraint         K350    Q360    7.94
StrandConstraint        R373    S382    10	##7.52
StrandConstraint        I388    P394    10	##6.41
StrandConstraint        I397    S398    10	##6.92
StrandConstraint        F404    C407    10	##6.91
HelixConstraint         N408    E418    6.62
StrandConstraint        Q421    I424    10	##7.16
HelixConstraint         E426    E433    6.7
StrandConstraint        K441    L445    10	##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