CreatePredAlphaCost pred_alpha2k alpha11 T0384.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0384.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0384.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 60 \
	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.

#include T0384.dssp-ehl2.constraints
#include T0384.undertaker-align.sheets
#include rr.constraints

# from try1-opt2.helices
HelixConstraint (T0384)G10      (T0384)A20
HelixConstraint (T0384)K35      (T0384)Y46
HelixConstraint (T0384)L74      (T0384)A85
HelixConstraint (T0384)Q98      (T0384)N113
HelixConstraint (T0384)E125     (T0384)D137
HelixConstraint (T0384)G173     (T0384)L178
HelixConstraint (T0384)G179     (T0384)G191
HelixConstraint (T0384)H275     (T0384)Q290
HelixConstraint (T0384)D302     (T0384)G318

# from try1-opt2.sheets
SheetConstraint (T0384)L2 (T0384)L4     (T0384)Y26 (T0384)L28   hbond (T0384)L2 1
SheetConstraint (T0384)L4 (T0384)G8     (T0384)L65 (T0384)A69   hbond (T0384)G5 1
SheetConstraint (T0384)G5 (T0384)G8     (T0384)A30 (T0384)S33   hbond (T0384)V6 1
SheetConstraint (T0384)I49 (T0384)L51   (T0384)I31 (T0384)S33   hbond (T0384)Q50        1
SheetConstraint (T0384)L65 (T0384)I68   (T0384)H88 (T0384)L91   hbond (T0384)V66        1
SheetConstraint (T0384)H88 (T0384)E92   (T0384)F115 (T0384)A119 hbond (T0384)V89        1
SheetConstraint (T0384)F145 (T0384)S152 (T0384)Y239 (T0384)S232 hbond (T0384)F145       1
SheetConstraint (T0384)D144 (T0384)S152 (T0384)Q221 (T0384)N229 hbond (T0384)N146       1
SheetConstraint (T0384)D195 (T0384)Q202 (T0384)Y217 (T0384)N210 hbond (T0384)A196       1
SheetConstraint (T0384)A196 (T0384)Y198 (T0384)E322 (T0384)R320 hbond (T0384)T197       1
SheetConstraint (T0384)N210 (T0384)Y217 (T0384)K228 (T0384)Q221 hbond (T0384)G211       1
SheetConstraint (T0384)P235 (T0384)T240 (T0384)N248 (T0384)G243 hbond (T0384)C236       1
SheetConstraint (T0384)T246 (T0384)T249 (T0384)T259 (T0384)A256 hbond (T0384)T246       1
# modified this one to the one below SheetConstraint (T0384)S255 (T0384)D260 (T0384)L268 (T0384)G263 hbond (T0384)A256       1
SheetConstraint (T0384)S255 (T0384)D260 (T0384)P269 (T0384)N264 hbond (T0384)A256       10

# for try4	from	to
# constraints	10	60