CreatePredAlphaCost pred_alpha2k alpha11 T0356.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0356.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0356.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 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.

#sheets taken from try5.sheets

SheetConstraint (T0356)T160 (T0356)H170 (T0356)L183 (T0356)R173 hbond (T0356)T160       40
SheetConstraint (T0356)R180 (T0356)I184 (T0356)M191 (T0356)N187 hbond (T0356)Q182       50
SheetConstraint (T0356)L189 (T0356)R192 (T0356)V217 (T0356)A220 hbond (T0356)I190       50
#warning says it's too close, and it's not predicted, so leave a low weight
SheetConstraint (T0356)A226 (T0356)T227 (T0356)V219 (T0356)A220 hbond (T0356)A226       1
#turn off, doesn't look right:
#SheetConstraint (T0356)A226 (T0356)I228 (T0356)A245 (T0356)L247 hbond (T0356)T227       1
#predicted helix:
# SheetConstraint (T0356)T251 (T0356)V255 (T0356)D262 (T0356)C258 hbond (T0356)T251       1
SheetConstraint (T0356)V272 (T0356)Y276 (T0356)H308 (T0356)F304 hbond (T0356)L273       100

#changed last sheet constraint to insert what is currently a helix at 303-310
#to be an anti-parallel strand to try to make a 6 strand anti-parellel sheet

SheetConstraint (T0356)I271 (T0356)Y276	(T0356)I309 (T0356)F304	hbond (T0356)L273	50
#making this strong first and then on the next run I will try to other side of the 271-276 strand
SheetConstraint (T0356)I309 (T0356)F304 (T0356)H318 (T0356)G323	hbond (T0356)V306	90

#from try5.helices
HelixConstraint (T0356)G199     (T0356)H210	40
HelixConstraint (T0356)I228     (T0356)T233	40
#not predicted as helix:
#HelixConstraint (T0356)T233     (T0356)T238	
#helix looks weird, will change to str2 prediction
#HelixConstraint (T0356)D327     (T0356)F340
HelixConstraint (T0356)P329     (T0356)F340	40

#adding in helices that haven't formed yet:
HelixConstraint (T0356)P225     (T0356)L229	50
HelixConstraint (T0356)E241     (T0356)L247	50