CreatePredAlphaCost pred_alpha2k alpha11 T0235.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0235.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 20  \
	pred_alpha2k 3 \
	pred_alpha04 3 \
	constraints 10 \
	hbond_geom 0.1 \
	hbond_geom_backbone 0.1 \
	hbond_geom_beta 0.4 \
	hbond_geom_beta_pair 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.

include T0235.t2k.dssp-ehl2.constraints
include T0235.t2k.dssp-ebghstl.constraints
include T0235.t2k.stride-ebghtl.constraints
include T0235.t2k.str2.constraints
include T0235.t2k.alpha.constraints
include T0235.t2k.bys.constraints

include T0235.t04.dssp-ehl2.constraints
include T0235.t04.dssp-ebghstl.constraints
include T0235.t04.stride-ebghtl.constraints
include T0235.t04.str2.constraints
include T0235.t04.alpha.constraints
include T0235.t04.bys.constraints