CreatePredAlphaCost pred_alpha2k alpha11 T0374.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0374.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0374.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 20 \
	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 T0374.dssp-ehl2.constraints
#include T0374.undertaker-align.sheets
#include rr.constraints

HelixConstraint (T0374)D12	(T0374)F19	1
HelixConstraint (T0374)A17	(T0374)F27	1
HelixConstraint (T0374)Y30	(T0374)W35	1
HelixConstraint (T0374)S38	(T0374)E48	1
HelixConstraint (T0374)G91	(T0374)A104	1
HelixConstraint (T0374)N121	(T0374)G132	1

SheetConstraint (T0374)Q2 (T0374)A8	(T0374)D58 (T0374)S52	hbond (T0374)S4	1
SheetConstraint (T0374)R49 (T0374)V56	(T0374)Q69 (T0374)L62	hbond (T0374)G51	1
SheetConstraint (T0374)A55 (T0374)H57	(T0374)L62 (T0374)Q60	hbond (T0374)H57	1
SheetConstraint (T0374)L62 (T0374)N66	(T0374)A84 (T0374)N80	hbond (T0374)F64	1
SheetConstraint (T0374)R111 (T0374)N119	(T0374)L158 (T0374)A150	hbond (T0374)M113	1
SheetConstraint (T0374)Y133 (T0374)R136	(T0374)K156 (T0374)Q153	hbond (T0374)Q134	1
SheetConstraint (T0374)A137 (T0374)R141	(T0374)Q153 (T0374)V149	hbond (T0374)A137	1
SheetConstraint (T0374)H142 (T0374)D143	(T0374)V149 (T0374)R148	hbond (T0374)H142	1

# We will alter the following constraints to get a model that better matches the
# secondary structure prediction:
# SheetConstraint (T0374)N66 (T0374)Q71	(T0374)G79 (T0374)D74	hbond (T0374)Y68	1
# SheetConstraint (T0374)C76 (T0374)L78	(T0374)M113 (T0374)I115	hbond (T0374)C76	1

SheetConstraint (T0374)F75 (T0374)N80	(T0374)R111 (T0374)S116	hbond (T0374)F75	1
SheetConstraint (T0374)V61 (T0374)Q69	(T0374)V83 (T0374)F75	hbond (T0374)Q69	1