CreatePredAlphaCost pred_alpha2k alpha11 T0263.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0263.t04.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 10 near_backbone 5 way_back 5 dry5 10 dry6.5 20 dry8 15 dry12 10 \
	phobic_fit 2 \
	sidechain 1 \
	bystroff 5 \
	soft_clashes 10  backbone_clashes 2 \
	break 20  \
	pred_alpha2k 3 \
	pred_alpha04 3 \
	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.

#from  T0263.t04.dssp-ehl2.constraints
HelixConstraint 	G16	N31	0.6339
HelixConstraint 	E59	N75	0.8062

StrandConstraint	L4	F9	0.6147
StrandConstraint	L37	E43	0.6113
StrandConstraint	A50	F56	0.6195
StrandConstraint	V81	D87	0.7319

# from t04.bys.constraints
StrandConstraint        E90     P91     0.684
StrandConstraint        A98     A101    0.635


# from try2-opt2.sheets
SheetConstraint M1 H8	P91 K84		hbond A2	7
SheetConstraint A2 F11	T57 H48		hbond T3	7
SheetConstraint F9 N12	V82 E79		hbond A10	7
SheetConstraint F36 E43	F56 E49		hbond L37	7

# scaffolding constraints picked by looking at 1lq9A
Constraint Y54.CA L100.CA	17.136	19.136	21.136	1.8
Constraint Y54.CA Q97.CA	13.342	15.342	17.342	1.8
Constraint Y54.CA A98.CA	14.874	16.874	18.874	1.8

Constraint W41.CA L100.CA	20.007	22.007	24.007	1.8
Constraint W41.CA Q97.CA	19.854	21.854	23.854	1.8
Constraint W41.CA A98.CA	20.160	22.160	24.160	1.8

Constraint F36.CA L100.CA	21.717	23.717	25.717	1.8
Constraint F36.CA Q97.CA	16.991	18.991	20.991	1.8
Constraint F36.CA A98.CA	18.682	20.682	22.682	1.8


# 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 M1.CB L76.CB -10. 7.0 14.0 0.596 bonus
Constraint A2.CB L76.CB -10. 7.0 14.0 0.531 bonus
Constraint M1.CB S93.CB -10. 7.0 14.0 0.454 bonus
Constraint I30.CB L73.CB -10. 7.0 14.0 0.424 bonus
Constraint Q6.CB A50.CB -10. 7.0 14.0 0.347 bonus
Constraint T42.CB H69.CB -10. 7.0 14.0 0.329 bonus