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 5 \
	n_ca_c	5 bad_peptide 10 \
	bystroff 5 \
	soft_clashes 60  backbone_clashes 2 \
	break 100  \
	pred_alpha2k 2 \
	pred_alpha04 2 \
	pred_alpha06 2 \
	constraints 40 \
	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

# from try6-opt2.helices
HelixConstraint (T0384)G10	(T0384)A20	1
HelixConstraint (T0384)K35	(T0384)Y46	1
HelixConstraint (T0384)Q54	(T0384)S61	1
HelixConstraint (T0384)L74	(T0384)A85	1
HelixConstraint (T0384)Q98	(T0384)N113	1
HelixConstraint (T0384)E125	(T0384)D137	1
HelixConstraint (T0384)G173	(T0384)L178	1
HelixConstraint (T0384)G179	(T0384)G191	1
HelixConstraint (T0384)H275	(T0384)Q290	1
HelixConstraint (T0384)Q297	(T0384)A303	1
HelixConstraint (T0384)Y301	(T0384)G318	1


# adding constraints to fix out of phase strand Q262-P269
# used o-sep
Hbond		N264.O		D260.N		20
Hbond		V266.O		F258.N		20

#try5-opt2.sheets
SheetConstraint (T0384)L2 (T0384)L4	(T0384)Y26 (T0384)L28	hbond (T0384)L2	5
SheetConstraint (T0384)L4 (T0384)G8	(T0384)L65 (T0384)A69	hbond (T0384)G5	5
SheetConstraint (T0384)G5 (T0384)G8	(T0384)A30 (T0384)S33	hbond (T0384)V6	5
SheetConstraint (T0384)Q50 (T0384)L51	(T0384)Y32 (T0384)S33	hbond (T0384)Q50	5
SheetConstraint (T0384)L65 (T0384)I68	(T0384)H88 (T0384)L91	hbond (T0384)V66	5
SheetConstraint (T0384)H88 (T0384)E92	(T0384)F115 (T0384)A119	hbond (T0384)V89	5
SheetConstraint (T0384)F145 (T0384)S152	(T0384)Y239 (T0384)S232	hbond (T0384)F145	5
#SheetConstraint (T0384)D144 (T0384)S152	(T0384)Q221 (T0384)N229	hbond (T0384)N146	5
#SheetConstraint (T0384)D195 (T0384)D204	(T0384)Y217 (T0384)D208	hbond (T0384)A196	5
SheetConstraint (T0384)A196 (T0384)Y198	(T0384)E322 (T0384)R320	hbond (T0384)T197	5
#SheetConstraint (T0384)N210 (T0384)Y217	(T0384)K228 (T0384)Q221	hbond (T0384)G211	5
SheetConstraint (T0384)L234 (T0384)T240	(T0384)T249 (T0384)G243	hbond (T0384)C236	5
#SheetConstraint (T0384)244 (T0384)T249	(T0384)T259 (T0384)254	hbond (T0384)N248	5
SheetConstraint (T0384)I257 (T0384)D260	(T0384)Q267 (T0384)N264	hbond (T0384)F258	5
#new
SheetConstraint (T0384)D144 (T0384)S152	(T0384)Y220 (T0384)K228	hbond (T0384)N146	20
SheetConstraint (T0384)N194 (T0384)L203	(T0384)Y217 (T0384)D208	hbond (T0384)D195	20
SheetConstraint (T0384)N210 (T0384)F216	(T0384)G227 (T0384)Q221	hbond (T0384)G211	20
SheetConstraint (T0384)T244 (T0384)T249	(T0384)T259 (T0384)R254	hbond (T0384)N248	20
#from try3.costfcn
SheetConstraint (T0384)D260 (T0384)A256 (T0384)T244 (T0384)N248 hbond (T0384)F258 20