CreatePredAlphaCost pred_alpha2k alpha11 T0321.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0321.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0321.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.

# Constraints from try2-opt2, which had the nice hairpin at the end, and was, in
# general a pretty nice model.

SheetConstraint (T0321)F16 (T0321)L17   (T0321)N71 (T0321)Y72   hbond (T0321)L17        1
SheetConstraint (T0321)V18 (T0321)V22   (T0321)E74 (T0321)G78   hbond (T0321)D19        1
SheetConstraint (T0321)V18 (T0321)G24   (T0321)G33 (T0321)H27   hbond (T0321)E20        1
SheetConstraint (T0321)T26 (T0321)R31   (T0321)M48 (T0321)P43   hbond (T0321)S28        1
SheetConstraint (T0321)R31 (T0321)N34   (T0321)R42 (T0321)G39   hbond (T0321)S32        1
SheetConstraint (T0321)E74 (T0321)G78   (T0321)E106 (T0321)N110 hbond (T0321)A75        1
SheetConstraint (T0321)K124 (T0321)H130 (T0321)D143 (T0321)W149 hbond (T0321)V125       1
SheetConstraint (T0321)K124 (T0321)G129 (T0321)D169 (T0321)T174 hbond (T0321)G126       1
SheetConstraint (T0321)Y170 (T0321)C175 (T0321)R195 (T0321)G200 hbond (T0321)V171       1
SheetConstraint (T0321)R194 (T0321)I196 (T0321)L214 (T0321)E216 hbond (T0321)I196       1
SheetConstraint (T0321)L198 (T0321)P201 (T0321)G219 (T0321)V222 hbond (T0321)L198       1
SheetConstraint (T0321)K237 (T0321)Y241 (T0321)K250 (T0321)K246 hbond (T0321)K239       1

HelixConstraint (T0321)M1       (T0321)N10	1
HelixConstraint (T0321)T52      (T0321)G57	1
HelixConstraint (T0321)P59      (T0321)K68	1
HelixConstraint (T0321)G78      (T0321)Y86	1
HelixConstraint (T0321)Q90      (T0321)G96	1
HelixConstraint (T0321)E94      (T0321)R104	1
HelixConstraint (T0321)D111     (T0321)Q117	1
HelixConstraint (T0321)L134     (T0321)E139	1
HelixConstraint (T0321)Y156     (T0321)L165	1
HelixConstraint (T0321)K181     (T0321)L189	1
HelixConstraint (T0321)N225     (T0321)E236	1