CreatePredAlphaCost pred_alpha2k alpha11 T0361.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0361.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0361.t06.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 25 dry6.5 25 dry8 40 dry12 6 \
	phobic_fit 4 \
	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 5 \
	hbond_geom 5 \
	hbond_geom_backbone 10 \
	hbond_geom_beta 50 \
	hbond_geom_beta_pair 50 \

// 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.


#from try9-opt2 helices:
HelixConstraint (T0361)T5       (T0361)L10
HelixConstraint (T0361)L10      (T0361)A15
HelixConstraint (T0361)N18      (T0361)I29
HelixConstraint (T0361)H27      (T0361)G33
HelixConstraint (T0361)L38      (T0361)N45
HelixConstraint (T0361)D46      (T0361)V54
HelixConstraint (T0361)V54      (T0361)G62
HelixConstraint (T0361)D66      (T0361)L77
HelixConstraint (T0361)A76      (T0361)L84
HelixConstraint (T0361)L84      (T0361)E100
HelixConstraint (T0361)T104     (T0361)T112
HelixConstraint (T0361)V119     (T0361)K133
HelixConstraint (T0361)K136     (T0361)T168