CreatePredAlphaCost pred_alpha2k alpha11 T0344.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0344.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0344.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 50 \
	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 T0344.dssp-ehl2.constraints
// include T0344.undertaker-align.sheets
// include rr.constraints


# From try8-opt2 helices:
# Remove this helix.  Conflicts with sheet we're trying to make.
# HelixConstraint (T0344)P19	(T0344)E31	1

# A poorly predicted Helix
# HelixConstraint (T0344)R35	(T0344)Y44	5
HelixConstraint (T0344)D49	(T0344)K73	5
HelixConstraint (T0344)P94	(T0344)L99	5
HelixConstraint (T0344)G105	(T0344)Q117	5
HelixConstraint (T0344)D115	(T0344)E126	5
HelixConstraint (T0344)P140	(T0344)A153	5
HelixConstraint (T0344)A153	(T0344)G164	5


# From try8-opt.sheets:
SheetConstraint (T0344)V4 (T0344)A6	(T0344)V12 (T0344)G10	hbond (T0344)V4	5
SheetConstraint (T0344)L79 (T0344)T82	(T0344)L88 (T0344)G85	hbond (T0344)D80	5
SheetConstraint (T0344)Y173 (T0344)I178	(T0344)L188 (T0344)I183	hbond (T0344)E175	5
SheetConstraint (T0344)K182 (T0344)S187	(T0344)S202 (T0344)G197	hbond (T0344)I183	5
SheetConstraint (T0344)G197 (T0344)V203	(T0344)Y212 (T0344)G206	hbond (T0344)S198	5
SheetConstraint (T0344)G206 (T0344)P213	(T0344)F223 (T0344)V216	hbond (T0344)K208	5


# New sheet we're trying to make:
SheetConstraint (T0344)L13 (T0344)I3	(T0344)I20 (T0344)V30	hbond (T0344)I3	20