CreatePredAlphaCost pred_alpha2k alpha11 T0296.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0296.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0296.t06.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 5 near_backbone 5 way_back 5 dry5 5 dry6.5 10 dry8 5 dry12 1 \
	phobic_fit 2 \
	sidechain 5 \
	n_ca_c	5 bad_peptide 10 \
	bystroff 5 \
	soft_clashes 20  backbone_clashes 2 \
	break 50  \
	pred_alpha2k .1 \
	pred_alpha04 .1 \
	pred_alpha06 .1 \
	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 T0296.dssp-ehl2.constraints
include rr.0.1.constraints

include decoys/try7-opt2.helices
include decoys/try7-opt2.constraints

# the sheets from try7 which has the sheets < 230 correct.
# I can keep those and work on the
SheetConstraint (T0296)I48 (T0296)T49	(T0296)N72 (T0296)K73	hbond (T0296)T49	5
SheetConstraint (T0296)V71 (T0296)S76	(T0296)G112 (T0296)L117	hbond (T0296)K73	5
SheetConstraint (T0296)G113 (T0296)S115	(T0296)S146 (T0296)N148	hbond (T0296)F114	5
SheetConstraint (T0296)C144 (T0296)G150	(T0296)V179 (T0296)F185	hbond (T0296)S145	5
SheetConstraint (T0296)I209 (T0296)N210	(T0296)V184 (T0296)F185	hbond (T0296)N210	5
# These MAY be forming the other sheet (in the "2nd" domain).
# This next one is dubious - we're not using it
# SheetConstraint (T0296)G265 (T0296)L269	(T0296)T415 (T0296)M419	hbond (T0296)D268	10
SheetConstraint (T0296)S344 (T0296)L345	(T0296)A326 (T0296)F327	hbond (T0296)L345	10
SheetConstraint (T0296)I364 (T0296)I366	(T0296)A394 (T0296)R396	hbond (T0296)A365	10
# the missing constraint??
SheetConstraint (T0296)T22 (T0296)G26	(T0296)A394 (T0296)I398	hbond (T0296)T22	50
# I still need to connect 36x to 34x (I think)