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 30 dry6.5 20 dry8 15 dry12 5 \
	phobic_fit 2 \
	sidechain 5 \
	n_ca_c	5 bad_peptide 10 \
	bystroff 5 \
	soft_clashes 40  backbone_clashes 2 \
	break 100  \
	pred_alpha2k 2 \
	pred_alpha04 2 \
	pred_alpha06 2 \
	constraints 10 \
	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

# try5 polishes try4-opt2
#		from	to
# dry5		15	30
# breaks	50	100
# soft_clashes	20	40

#
#New constraints
#try5-opt2.helices
HelixConstraint (T0384)G10	(T0384)A20
HelixConstraint (T0384)K35	(T0384)Y46
HelixConstraint (T0384)Q54	(T0384)S61
HelixConstraint (T0384)L74	(T0384)A85
HelixConstraint (T0384)Q98	(T0384)N113
HelixConstraint (T0384)E125	(T0384)D137
HelixConstraint (T0384)G173	(T0384)L178
HelixConstraint (T0384)G179	(T0384)G191
HelixConstraint (T0384)H275	(T0384)Q290
HelixConstraint (T0384)Q297	(T0384)A303
HelixConstraint (T0384)Y301	(T0384)G318


#I am going to take try3 strand constraints for 
# StrandConstraint	S255	D260	5
# StrandConstraint	Q262	Q267	5


#try5-opt2.sheets
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)Q50 (T0384)L51	(T0384)Y32 (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)D204	(T0384)Y217 (T0384)D208	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)L234 (T0384)T240	(T0384)T249 (T0384)G243	hbond (T0384)C236	1
#SheetConstraint (T0384)244 (T0384)T249	(T0384)T259 (T0384)254	hbond (T0384)N248	1
SheetConstraint (T0384)I257 (T0384)D260	(T0384)Q267 (T0384)N264	hbond (T0384)F258	1
#new
SheetConstraint (T0384)D144 (T0384)S152	(T0384)Y220 (T0384)K228	hbond (T0384)N146	10
SheetConstraint (T0384)N194 (T0384)L203	(T0384)Y217 (T0384)D208	hbond (T0384)D195	10
SheetConstraint (T0384)N210 (T0384)F216	(T0384)G227 (T0384)Q221	hbond (T0384)G211	10
SheetConstraint (T0384)T244 (T0384)T249	(T0384)T259 (T0384)R254	hbond (T0384)N248	10
#from try3.costfcn
SheetConstraint (T0384)D260 (T0384)A256 (T0384)T244 (T0384)N248 hbond (T0384)F258 10