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 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.

//include T0356.dssp-ehl2.constraints
//include T0356.undertaker-align.sheets
//include rr.constraints

# from M1-R180/try1-opt2.helices and .sheets:

HelixConstraint (T0356)M1	(T0356)G20	20
HelixConstraint (T0356)E34	(T0356)A45	20
HelixConstraint (T0356)E80	(T0356)L92	20
HelixConstraint (T0356)K110	(T0356)M120	20
HelixConstraint (T0356)L118	(T0356)L125	20
HelixConstraint (T0356)N143	(T0356)W151	20

SheetConstraint (T0356)L22 (T0356)I25	(T0356)P48 (T0356)L51	hbond (T0356)K23	50
SheetConstraint (T0356)L50 (T0356)E53	(T0356)K71 (T0356)A74	hbond (T0356)L51	50
SheetConstraint (T0356)P55 (T0356)G57	(T0356)M75 (T0356)M77	hbond (T0356)K56	50
SheetConstraint (T0356)V73 (T0356)M75	(T0356)E97 (T0356)E99	hbond (T0356)A74	50
SheetConstraint (T0356)C130 (T0356)I134	(T0356)A156 (T0356)T160	hbond (T0356)Q131	50
SheetConstraint (T0356)G127 (T0356)K133	(T0356)K96 (T0356)K102	hbond (T0356)Q132	50


#From T160-F340/try5-opt2.helices and .sheets:

HelixConstraint (T0356)G199	(T0356)H210	20
HelixConstraint (T0356)I228	(T0356)T233	20
HelixConstraint (T0356)T233	(T0356)T238	20
HelixConstraint (T0356)D327	(T0356)F340	20

SheetConstraint (T0356)T160 (T0356)H170	(T0356)L183 (T0356)R173	hbond (T0356)T160	50
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
#SheetConstraint (T0356)A226 (T0356)T227	(T0356)V219 (T0356)A220	hbond (T0356)A226	50
SheetConstraint (T0356)A226 (T0356)I228	(T0356)A245 (T0356)L247	hbond (T0356)T227	50
SheetConstraint (T0356)T251 (T0356)V255	(T0356)D262 (T0356)C258	hbond (T0356)T251	50
SheetConstraint (T0356)V272 (T0356)Y276	(T0356)H308 (T0356)F304	hbond (T0356)L273	50

#From T320-S496/try5-opt2.helices and .sheets

HelixConstraint (T0356)P326	(T0356)V339	20
HelixConstraint (T0356)V339	(T0356)F348	20
HelixConstraint (T0356)Y374	(T0356)Q391	20
HelixConstraint (T0356)R408	(T0356)D422	20
HelixConstraint (T0356)P434	(T0356)S442	20
HelixConstraint (T0356)F440	(T0356)S445	20
HelixConstraint (T0356)D474	(T0356)N493	20

SheetConstraint (T0356)E350 (T0356)L356	(T0356)I370 (T0356)R364	hbond (T0356)E350	50
SheetConstraint (T0356)Y363 (T0356)V368	(T0356)A424 (T0356)L429	hbond (T0356)L365	50
SheetConstraint (T0356)F397 (T0356)D402	(T0356)R425 (T0356)V430	hbond (T0356)I399	50
SheetConstraint (T0356)V398 (T0356)D403	(T0356)G448 (T0356)L453	hbond (T0356)V400	50
SheetConstraint (T0356)D402 (T0356)D403	(T0356)E431 (T0356)N432	hbond (T0356)D403	50