CreatePredAlphaCost pred_alpha2k alpha11 T0318.t2k.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 6 \
	constraints 50 \
	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.


# taken from T0318.t2k.str2.constraints
StrandConstraint        Q3      V6      10
StrandConstraint        L20     V23     10
HelixConstraint         T47     I56     10
StrandConstraint        H73     T76     10
HelixConstraint         N89     L97     10
StrandConstraint        N108    A115    10
HelixConstraint         L121    T130    10
StrandConstraint        V150    K154    10
HelixConstraint         T164    A174    10


SheetConstraint (T0318)L20 (T0318)V23   (T0318)V6   (T0318)Q3   hbond (T0318)L20        10
SheetConstraint (T0318)S19 (T0318)K25   (T0318)A72  (T0318)P78  hbond (T0318)I21        10
SheetConstraint (T0318)H73 (T0318)D79   (T0318)H110 (T0318)E116 hbond (T0318)L74        10
SheetConstraint (T0318)V109 (T0318)F111 (T0318)G140 (T0318)R142 hbond (T0318)F111       10
SheetConstraint (T0318)L113 (T0318)Y117 (T0318)V150 (T0318)K154 hbond (T0318)A115       10