CreatePredAlphaCost pred_alpha2k alpha11 T0219.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0219.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 2 \
	pred_alpha04 4 \
	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 T0219.t2k.dssp-ehl2.constraints
include T0219.t2k.dssp-ebghstl.constraints
include T0219.t2k.stride-ebghtl.constraints
include T0219.t2k.str2.constraints
include T0219.t2k.alpha.constraints
include T0219.t2k.bys.constraints

include T0219.t04.dssp-ehl2.constraints
include T0219.t04.dssp-ebghstl.constraints
include T0219.t04.stride-ebghtl.constraints
include T0219.t04.str2.constraints
include T0219.t04.alpha.constraints
include T0219.t04.bys.constraints


# I'm not sure about the initial sheet constraints---I may have to
# tweak them, but let's start with the alignments we get consistently.

# from alignment to 1mzeA
SheetConstraint T5 S7		A205 I207	hbond E6
SheetConstraint E10 S11		V32 A33		hbond S11
SheetConstraint L31 R34		Y217 T214	hbond A33
SheetConstraint N60 V65		E87 L82		hbond N61
SheetConstraint K130 K137	T238 A231	hbond K130
SheetConstraint G140 K143	S228 S225	hbond F142
SheetConstraint A144 F146	S225 W223	hbond H145
SheetConstraint Y149 Q157	G240 T232	hbond T150
SheetConstraint T150 Q155	P219 T214	hbond N151
SheetConstraint I156 G158	A234 T232	hbond Q157
SheetConstraint E159 A165	T211 A205	hbond K160
SheetConstraint E159 K166	D229 L222	hbond T161


# from alignment to 1h2kA
SheetConstraint T5 S7		A205 I207	hbond E6
SheetConstraint E10 S11		V32 A33		hbond S11
SheetConstraint L31 R34		Y217 T214	hbond A33
SheetConstraint N60 V66		E87 F81		hbond N61
SheetConstraint K130 K137	T238 A231	hbond Y134
SheetConstraint G140 K143	S228 S225	hbond F142
SheetConstraint A144 F146	S225 W223	hbond H145
SheetConstraint Y149 Q157	G240 T232	hbond T150
SheetConstraint T150 Q155	P219 T214	hbond N151
SheetConstraint I156 G158	A234 T232	hbond Q157
SheetConstraint E159 A165	T211 A205	hbond K160
SheetConstraint E159 K166	D229 L222	hbond T161

#from try1-opt2
SheetConstraint Y59 V66		A88 F81		hbond V63
SheetConstraint K130 K137	T238 A231	hbond Y134
SheetConstraint G140 F142	S228 T226	hbond F142
SheetConstraint A144 F146	S225 W223	hbond H145
SheetConstraint Y149 Q157	G240 T232	hbond T150
SheetConstraint T150 Q155	P219 T214	hbond N151
SheetConstraint E159 A165	T211 A205	hbond K160
SheetConstraint E159 K166	D229 L222	hbond T161