CreatePredAlphaCost pred_alpha2k alpha11 T0368.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0368.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0368.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 50  \
	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 T0368.dssp-ehl2.constraints
#include T0368.undertaker-align.sheets
#include rr.constraints

#Helix constraints

HelixConstraint	A10	V22	50
HelixConstraint	Y26	I39	50
HelixConstraint	A56	G68	50
HelixConstraint	F72	Y85	50
HelixConstraint	K98	G113	50
HelixConstraint	G117	E129	50
HelixConstraint	K135	V147	50
HelixConstraint	R151	P164	50

#Hbond Constraints
Hbond	E25.N	Q20.O	30
Hbond	R116.N	L111.O	30
Hbond	G115.N	D112.O	30
Hbond	G115.N	L111.O	30
Hbond	M43.N	S40.O	30
Hbond	E47.N	P44.O	30
Hbond	S71.N	G68.O	30
Hbond	R134.N	I131.O	30
Hbond	E137.N	R134.O	30
Hbond	K141.N	T138.O	30
Hbond	A168.N	G165.O	30