CreatePredAlphaCost pred_alpha2k alpha11 T0338.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0338.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0338.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 40  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 T0338.dssp-ehl2.constraints
include T0338.undertaker-align.sheets
include rr.constraints

#including T0338.dssp-ehl2.constraints

HelixConstraint 	T8	E13	0.632
HelixConstraint 	A24	R44	0.8305
HelixConstraint 	Q49	M64	0.7131
HelixConstraint 	K73	E88	0.6162
HelixConstraint 	L94	C104	0.6655
HelixConstraint 	Q122	T136	0.6807
StrandConstraint	I141	T142	0.6532
HelixConstraint 	T148	V157	0.6469
HelixConstraint 	K161	S174	0.6742
HelixConstraint 	P186	W200	0.809
HelixConstraint 	L224	E239	0.7605

# Extra helix contrains
HelixConstraint 	A101	L108	0.632