CreatePredAlphaCost pred_alpha2k alpha11 T0289.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0289.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0289.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 20  backbone_clashes 2 \
	break 50  \
	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 \
	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 T0289.dssp-ehl2.constraints
# include T0289.undertaker-align.sheets
# include rr.constraints

# New constraints
StrandConstraint	A218	V228    0.6000
StrandConstraint	A293	N303    0.6000
StrandConstraint	P259	S263    0.6000
StrandConstraint	K267	L271    0.6000
StrandConstraint	C275	P279    0.6000
HelixConstraint 	E285	K290	0.6002

# New constraints:
SheetConstraint (T0289)P259 (T0289)S261	(T0289)L271 (T0289)K267	hbond (T0289)V260	20
SheetConstraint (T0289)K267 (T0289)L271	(T0289)P279 (T0289)C275	hbond (T0289)L271	20
SheetConstraint (T0289)A218 (T0289)V228	(T0289)A293 (T0289)N303	hbond (T0289)A218	20

# try some rr constraints:
Constraint A240.CB P279.CB -10. 7.0 14.0 0.5
Constraint A261.CB P278.CB -10. 7.0 14.0 0.5
Constraint A260.CB P277.CB -10. 7.0 14.0 0.5
Constraint A239.CB P261.CB -10. 7.0 14.0 0.5