CreatePredAlphaCost pred_alpha2k alpha11 T0312.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0312.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0312.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 T0312.dssp-ehl2.constraints
# include T0312.undertaker-align.sheets
include rr.0.1.constraints

SheetConstraint (T0312)G9 (T0312)D17	(T0312)L118 (T0312)V110	hbond (T0312)K10	1
SheetConstraint (T0312)L16 (T0312)G19	(T0312)F111 (T0312)A108	hbond (T0312)D17	1
SheetConstraint (T0312)A38 (T0312)V46	(T0312)P119 (T0312)F111	hbond (T0312)H39	1
# we've exended the constraint below to get residues 72,71 in a better place (try2)
SheetConstraint (T0312)H39 (T0312)V46	(T0312)N78 (T0312)E71	hbond (T0312)I40	1
SheetConstraint (T0312)S48 (T0312)I51	(T0312)E109 (T0312)F106	hbond (T0312)S48	1
SheetConstraint (T0312)V50 (T0312)Y53	(T0312)I72 (T0312)P69	hbond (T0312)I51	1
SheetConstraint (T0312)V50 (T0312)G52	(T0312)F106 (T0312)H104	hbond (T0312)G52	1
SheetConstraint (T0312)L73 (T0312)S80	(T0312)K96 (T0312)H89	hbond (T0312)S74	1
SheetConstraint (T0312)V92 (T0312)K96	(T0312)L105 (T0312)Y101	hbond (T0312)L94	1