CreatePredAlphaCost pred_alpha2k alpha11 T0273.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0273.t04.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 5 near_backbone 5 way_back 5 dry5 15 dry6.5 20 dry8 15 dry12 5 \
	phobic_fit 2 \
	sidechain 1 \
	bystroff 5 \
	soft_clashes 10  backbone_clashes 2 \
	break 20  \
	pred_alpha2k 1 \
	pred_alpha04 5 \
	constraints 10 \
	hbond_geom 1 \
	hbond_geom_backbone 1 \
	hbond_geom_beta 5 \
	hbond_geom_beta_pair 10

// 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.

# again these don't seem quite as strong as the t04
# include T0273.t2k.dssp-ehl2.constraints
# include T0273.t2k.dssp-ebghstl.constraints
# include T0273.t2k.stride-ebghtl.constraints
# include T0273.t2k.str2.constraints
# include T0273.t2k.alpha.constraints
# include T0273.t2k.bys.constraints

include T0273.t04.dssp-ehl2.constraints
include T0273.t04.dssp-ebghstl.constraints
include T0273.t04.stride-ebghtl.constraints
include T0273.t04.str2.constraints
include T0273.t04.alpha.constraints
include T0273.t04.bys.constraints

# my designed sheets...
SheetConstraint Q27  R30	V38  R35	hbond R30	10.0	# s1^vs2
SheetConstraint D86  V90	A113 V117	10.0	# s4||s5
SheetConstraint A113 V117	L141 V145	10.0	# s5||s6
SheetConstraint L141 V145	F155 A151	10.0	# s6^vs7
# SheetConstraint G66  F69	  F75 ??
# file generated by validate2rr
# based on 280 inputs
# using the /projects/compbio/experiments/protein-predict/casp6/networks/NN280-240n300.net.28 network
# limited to score of .30 or greater.
# The score is an approximation of the probability
Constraint V143.CB V154.CB -10. 7.0 14.0 0.91
# Constraint L127.CB L144.CB -10. 7.0 14.0 0.78
# Constraint G42.CA R118.CB -10. 7.0 14.0 0.605
Constraint L16.CB L36.CB -10. 7.0 14.0 0.596 bonus
Constraint R30.CB R92.CB -10. 7.0 14.0 0.585 bonus
Constraint P40.CB S72.CB -10. 7.0 14.0 0.582 bonus
Constraint L56.CB V90.CB -10. 7.0 14.0 0.579 bonus
Constraint L135.CB P157.CB -10. 7.0 14.0 0.567 bonus