CreatePredAlphaCost pred_alpha2k alpha11 T0379.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0379.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0379.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 T0379.dssp-ehl2.constraints
//include T0379.undertaker-align.sheets
//include rr.constraints


//helix constraints determined from best-models 
HelixConstraint (T0379)N17	(T0379)A31	3
HelixConstraint (T0379)M36	(T0379)E57	3
HelixConstraint (T0379)R60	(T0379)L71	3
HelixConstraint (T0379)Q74	(T0379)L84	3

//helix constriants from try1-opt2
HelixConstraint (T0379)S88	(T0379)L98	1 
HelixConstraint (T0379)V114	(T0379)M119	1
HelixConstraint (T0379)G127	(T0379)F133	1
HelixConstraint (T0379)A139	(T0379)G144	1
HelixConstraint (T0379)E150	(T0379)G161	1
HelixConstraint (T0379)G173	(T0379)R182	1
HelixConstraint (T0379)N195	(T0379)K208	1

//sheet constraints from try1-opt2
SheetConstraint (T0379)R3 (T0379)D8	(T0379)E166 (T0379)D171	hbond (T0379)N4	10
SheetConstraint (T0379)N4 (T0379)D8	(T0379)R103 (T0379)L107	hbond (T0379)I5	10
SheetConstraint (T0379)L13 (T0379)H15	(T0379)L9 (T0379)G11	hbond (T0379)I14	10
SheetConstraint (T0379)L13 (T0379)R18	(T0379)S88 (T0379)F83	hbond (T0379)H15	10
SheetConstraint (T0379)F105 (T0379)N109	(T0379)K136 (T0379)S140	hbond (T0379)L106	10
SheetConstraint (T0379)L168 (T0379)D171	(T0379)H186 (T0379)C189	hbond (T0379)F169	10