CreatePredAlphaCost pred_alpha2k alpha11 T0354.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0354.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0354.t06.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 25 dry6.5 30 dry8 22 dry12 5 \
	phobic_fit 3 \
	sidechain 5 \
	n_ca_c	5 bad_peptide 10 \
	bystroff 5 \
	soft_clashes 20  backbone_clashes 2 \
	break 50  \
	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.


#try15's sheet & helix constraints
SheetConstraint (T0354)I22 (T0354)D26	(T0354)W77 (T0354)D81	hbond (T0354)I23	30
SheetConstraint (T0354)D21 (T0354)L30	(T0354)G42 (T0354)L33	hbond (T0354)E24	30
SheetConstraint (T0354)V39 (T0354)D43	(T0354)G68 (T0354)H72	hbond (T0354)A40	30
SheetConstraint (T0354)L79 (T0354)A82	(T0354)H88 (T0354)V85	hbond (T0354)V80	30

HelixConstraint (T0354)M1	(T0354)K18	10
HelixConstraint (T0354)N45	(T0354)A62	10
HelixConstraint (T0354)V94	(T0354)D99	5
HelixConstraint (T0354)I100	(T0354)G106	5
HelixConstraint (T0354)P118	(T0354)H130	1

#increased the dry weights a bit and phobic_fit increased by 1