CreatePredAlphaCost pred_alpha2k alpha11 T0216.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0216.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 T0216.t2k.dssp-ehl2.constraints
# include T0216.t2k.dssp-ebghstl.constraints
# include T0216.t2k.stride-ebghtl.constraints
# include T0216.t2k.str2.constraints
# include T0216.t2k.alpha.constraints
# include T0216.t2k.bys.constraints

# for try2, I'm going with the t2k constraints
# switching back to t04 for hairpins in try7
# EXCEPT for some 'bogus' helices (or are they bogus??)
HelixConstraint 	F3	K16	2.613
# should these next two be combined?
StrandConstraint	E20	L26	0.6364	# s1
StrandConstraint	F31	A36	0.603	# s2
# StrandConstraint	E20	R34 3.0
# should these next two be combined?
StrandConstraint	D39 	A46 	3.0	# s3a
StrandConstraint	N50	K57	3.6225	# s3b
StrandConstraint	K60	R65	0.6023	# s4
StrandConstraint	Y101	Y107	0.8	# s5 ??
HelixConstraint 	E73	S81	2.6412
HelixConstraint 	K117	A130	0.6182
StrandConstraint	V137	K145	0.8	# s6a-b
# HelixConstraint 	K145	T154	0.6474
# HelixConstraint 	F171	A176	0.6017
HelixConstraint 	P198	L212	0.6601
StrandConstraint	V148	N155	0.8	# s6c
StrandConstraint	D166	A176	0.8	# s7b
# StrandConstraint V21 A36	10.0
# StrandConstraint D39 K54	10.0

# include T0216.t04.dssp-ehl2.constraints
include T0216.t04.dssp-ebghstl.constraints
include T0216.t04.stride-ebghtl.constraints
include T0216.t04.str2.constraints
include T0216.t04.alpha.constraints
include T0216.t04.bys.constraints

# let's try an make a couple of hairpins - again!
Constraint L35.CB L40.CB	0 5 9	5.0
Constraint K57.CB T61.CB	0 5 9	5.0

# for try3, we add some sheets (hope we have directions right)
# for try4, I changed the next one's hbond
# for try5, we 'break' the sheets but bind the ends
SheetConstraint	V51 V55 	F64 K60 	5.0 # hbond K54	# s3b,s4
SheetConstraint A36 S32 	D39 Y43 	hbond A36	5.0	# s2,s3a
# for try4, I'm adding this next one.
# SheetConstraint E27 I23 	F31 L35 	10.0 # hbond E27	10.0	# s1,s2

# for try6 we examine 21-35 ^v 
# for try6 we'll add this connection
# SheetConstraint V21 A36 	K54 D39 	hbond A36	10.0	# s1-2, 

# for try2, I'm including the first 2 rr constraints
# and some with bonuses
Constraint S24.CB K151.CB -10. 7.0 12.0 2.633
Constraint S24.CB N50.CB -10. 7.0 12.0 2.608
Constraint S24.CB K54.CB -10. 7.0 12.0 0.522	bonus
Constraint S24.CB T61.CB -10. 7.0 12.0 0.514	bonus
Constraint Q22.CB K54.CB -10. 7.0 12.0 0.489	bonus
Constraint S24.CB S163.CB -10. 7.0 12.0 0.486	bonus
Constraint S24.CB T63.CB -10. 7.0 12.0 0.466	bonus
Constraint Q22.CB E52.CB -10. 7.0 12.0 0.445	bonus