CreatePredAlphaCost pred_alpha2k alpha11 T0344.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0344.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0344.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 \
	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.

HelixConstraint (T0344)K106 (T0344)S113
HelixConstraint (T0344)L116 (T0344)E126
HelixConstraint (T0344)R59 (T0344)R70

//SheetConstraint (T0344)R2 (T0344)A5
//SheetConstraint (T0344)V76 (T0344)L79
//SheetConstraint (T0344)E130 (T0344)A133

SheetConstraint (T0344)L166 (T0344)G169		(T0344)Y173 (T0344)V176		hbond (T0344)G169	1
SheetConstraint (T0344)N177 (T0344)K179		(T0344)I183 (T0344)G185		hbond (T0344)I183	1
SheetConstraint (T0344)S198 (T0344)S202		(T0344)K208 (T0344)Y212		hbond (T0344)S202	1

//include T0344.dssp-ehl2.constraints
//include T0344.undertaker-align.sheets
//include rr.constraints