CreatePredAlphaCost pred_alpha2k alpha11 T0262.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0262.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 3 \
	pred_alpha04 3 \
	constraints 25 \
	hbond_geom 1 \
	hbond_geom_backbone 1 \
	hbond_geom_beta 10 \
	hbond_geom_beta_pair 15

// 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.

# get the conserved histidines together
Constraint H85.NE2  H147.NE2	3.0  4.0  5.0	1.8
Constraint H85.NE2  H166.NE2	3.0  4.0  5.0	1.8
Constraint H85.NE2  H190.NE2	3.0  4.0  5.0	1.8
Constraint H147.NE2 H166.NE2	3.0  4.0  5.0	1.8
Constraint H147.NE2 H190.NE2	3.0  4.0  5.0	1.8
Constraint H166.NE2 H190.NE2	3.0  4.0  5.0	1.8

# from T0262.t04.dssp-ehl2.constraints
StrandConstraint	V92	L94	0.6171
# StrandConstraint	A100	R101	0.6026	# too short for a StrandConstraint
StrandConstraint	Y134	L136	0.789
StrandConstraint	E140	Y145	0.6321
StrandConstraint	I163	H166	0.6447
StrandConstraint	K188	L191	0.6228
StrandConstraint	A210	V214	0.8106
StrandConstraint	K225	R228	0.6782
StrandConstraint	V233	V236	0.7153

HelixConstraint 	R74	R84	0.6164
HelixConstraint 	V102	K111	0.8744
HelixConstraint 	E119	G124	0.6004	# conflicts with s3 StrandConstraint
HelixConstraint 	E170	E178	0.8562
HelixConstraint 	L195	V199	0.6408
HelixConstraint 	V216	R221	0.8944
HelixConstraint 	P241	E246	0.7081

# hand generated from t04.str2 predictions
StrandConstraint	V92 	L94 	2.0	# s1      
StrandConstraint	W99 	R101	2.0	# s2      
# StrandConstraint	I122	L127	2.0	# s3      # conflicts with HelixConstraint
StrandConstraint	R133	R137	2.0	# s4      
StrandConstraint	E140	Y145	2.0	# s5      
StrandConstraint	I149	P155	2.0	# s6      
StrandConstraint	L164	H166	2.0	# s7      
StrandConstraint	L187	L191	2.0	# s8      
StrandConstraint	A210	V214	2.0	# s9      
StrandConstraint	K225	R228	2.0	# s10     
StrandConstraint	V233	V236	2.0	# s11     

# from try1-opt2.sheets   (s2  ^v s4 ??)
SheetConstraint 	G98 R101	N138 E135	hbond A100	2.0 # conflict with s3 ^v s4

# anti parallel sheet constraints
SheetConstraint 	V92  L94 	R101 W99 	hbond L94	2.0 # s1  ^v s2

# SheetConstraint 	I122 A126	R137 R133	hbond V125	2.0 # s3  ^v s4  # conflict with s2 ^v s4
SheetConstraint 	R133 R137	R144 E140	hbond R137	2.0 # s4  ^v s5
SheetConstraint 	E140 Y145	E154 I149	hbond Y145	2.2 # s5  ^v s6

SheetConstraint 	K225 R228	V236 V233	hbond R228	2.0 # s10 ^v s11