CreatePredAlphaCost pred_alpha2k alpha11 T0354.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0354.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0354.t06.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 15 dry6.5 20 dry8 15 dry12 5 \
	phobic_fit 2 \
	sidechain 5 \
	n_ca_c	5 bad_peptide 10 \
	bystroff 5 \
	soft_clashes 20  backbone_clashes 2 \
	break 100  \
	pred_alpha2k 2 \
	pred_alpha04 2 \
	pred_alpha06 2 \
	constraints 10 \
	hbond_geom 5 \
	hbond_geom_backbone 10 \
	hbond_geom_beta 50 \
	hbond_geom_beta_pair 100 \
	missing_atoms 1 \
	maybe_metal 0.5 \
	maybe_ssbond 1

// remove maybe_ssbond weight if protein known to be in reducing environment.
// remove maybe_metal weight if protein known to have disulfides or
//	known not to bind metal ions.

// Add the following for extra-cellular proteins:
#	known_ssbond 0.5	# and put ssbond command in constraints file

// 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.

#include T0354.dssp-ehl2.constraints
#include T0354.undertaker-align.sheets
#include rr.constraints

#include T0354.t06.str2.constraints
HelixConstraint 	I3	I17	1.0
StrandConstraint	I22	D26	0.85
StrandConstraint	R36	A40	0.856
HelixConstraint 	N45	E61	1.0
StrandConstraint	S69	E70	0.2
StrandConstraint	W77	D81	0.85
StrandConstraint	V85	V89	0.85
HelixConstraint 	V94	R95	0.611
HelixConstraint 	Y98	A102	0.633
HelixConstraint 	S120	V122	0.626