CreatePredAlphaCost pred_alpha2k alpha11 T0342.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0342.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0342.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 0 \
	sidechain 5 \
	n_ca_c	5 bad_peptide 10 \
	bystroff 5 \
	soft_clashes 50  backbone_clashes 2 \
	break 140  \
	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 T0342.dssp-ehl2.constraints
//include T0342.undertaker-align.sheets
//include rr.constraints

//from K140-L188/decoys/try2-opt2.helices
HelixConstraint (T0342)K140	(T0342)N150
HelixConstraint (T0342)P153	(T0342)E164
HelixConstraint (T0342)A162	(T0342)G170
HelixConstraint (T0342)S173	(T0342)L188


//from K140-L188/rr.constraints

Constraint I142.CB I176.CB -10. 7.0 14.0 0.66403688641
Constraint I143.CB I163.CB -10. 7.0 14.0 0.527894230104
Constraint I143.CB I176.CB -10. 7.0 14.0 0.526326319204
Constraint I143.CB Y168.CB -10. 7.0 14.0 0.457410377483
Constraint I143.CB L160.CB -10. 7.0 14.0 0.416281453771
Constraint I143.CB L152.CB -10. 7.0 14.0 0.414317083942
Constraint I142.CB I163.CB -10. 7.0 14.0 0.383365430016
Constraint I163.CB V172.CB -10. 7.0 14.0 0.360783654795
Constraint I143.CB K159.CB -10. 7.0 14.0 0.351609237113
Constraint I142.CB L160.CB -10. 7.0 14.0 0.347572329163
Constraint I163.CB I176.CB -10. 7.0 14.0 0.33901019818 
Constraint I143.CB V172.CB -10. 7.0 14.0 0.336007490605
Constraint I142.CB L152.CB -10. 7.0 14.0 0.333010666327