CreatePredAlphaCost pred_alpha2k alpha11 T0384.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0384.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0384.t06.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 15 dry6.5 20 dry8 15 dry12 5 \
	phobic_fit 2 \
	sidechain 3 \
	n_ca_c	5 bad_peptide 10 \
	bystroff 5 \
	soft_clashes 20  backbone_clashes 2 \
	break 80  \
	pred_alpha2k 2 \
	pred_alpha04 2 \
	pred_alpha06 2 \
	constraints 50 \
	hbond_geom 5 \
	hbond_geom_backbone 10 \
	hbond_geom_beta 50 \
	hbond_geom_beta_pair 100 \
	missing_atoms 1 \
	maybe_metal 0.5 \
	maybe_ssbond 1

// remove maybe_ssbond weight if protein known to be in reducing environment.
// remove maybe_metal weight if protein known to have disulfides or
//	known not to bind metal ions.

// Add the following for extra-cellular proteins:
#	known_ssbond 0.5	# and put ssbond command in constraints file

// 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 T0384.dssp-ehl2.constraints
#include T0384.undertaker-align.sheets
#include rr.constraints

#T0384.t06.dssp-ehl2.constraints

StrandConstraint	K3	I7	0.7524
HelixConstraint 	A11	T22	0.6409
StrandConstraint	Q27	Y32	0.808
HelixConstraint 	L36	R45	0.8417
HelixConstraint 	L55	K60	0.626
StrandConstraint	L65	A69	0.6346
HelixConstraint 	L74	S84	0.6209
StrandConstraint	H88	E92	0.6333
HelixConstraint 	P99	K111	0.8913
StrandConstraint	F115	A119	0.6159
HelixConstraint 	E125	D137	0.6737
StrandConstraint	F145	Y150	0.7281
HelixConstraint 	Y181	L189	0.6211
StrandConstraint	D195	Q202	0.6248
StrandConstraint	N210	F216	0.6312
StrandConstraint	V222	G227	0.6342
StrandConstraint	C236	T240	0.7287
StrandConstraint	T244	L247	0.817
StrandConstraint	S255	D260	0.80
StrandConstraint	Q262	Q267	0.75
HelixConstraint 	M277	Q289	0.6277
HelixConstraint 	L300	A317	0.7272

# new : 
#StrandConstraint	S255	D260	0.80
#StrandConstraint	Q262	Q267	0.80


SheetConstraint (T0384)L2 (T0384)L4	(T0384)Y26 (T0384)L28	hbond (T0384)L2	1
SheetConstraint (T0384)L4 (T0384)G8	(T0384)L65 (T0384)A69	hbond (T0384)G5	1
SheetConstraint (T0384)G5 (T0384)G8	(T0384)A30 (T0384)S33	hbond (T0384)V6	1
SheetConstraint (T0384)I49 (T0384)L51	(T0384)I31 (T0384)S33	hbond (T0384)Q50	1
SheetConstraint (T0384)L65 (T0384)I68	(T0384)H88 (T0384)L91	hbond (T0384)V66	1
SheetConstraint (T0384)H88 (T0384)E92	(T0384)F115 (T0384)A119	hbond (T0384)V89	1
SheetConstraint (T0384)F145 (T0384)S152	(T0384)Y239 (T0384)S232	hbond (T0384)F145	1
SheetConstraint (T0384)D144 (T0384)S152	(T0384)Q221 (T0384)N229	hbond (T0384)N146	1
SheetConstraint (T0384)D195 (T0384)Q202	(T0384)Y217 (T0384)N210	hbond (T0384)A196	1
SheetConstraint (T0384)A196 (T0384)Y198	(T0384)E322 (T0384)R320	hbond (T0384)T197	1
SheetConstraint (T0384)N210 (T0384)Y217	(T0384)K228 (T0384)Q221	hbond (T0384)G211	1
SheetConstraint (T0384)P235 (T0384)T240	(T0384)N248 (T0384)G243	hbond (T0384)C236	1
SheetConstraint (T0384)S255 (T0384)D260	(T0384)L268 (T0384)G263	hbond (T0384)F258	1
SheetConstraint (T0384)D260 (T0384)A256	(T0384)T244 (T0384)N248	hbond (T0384)F258	10