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 30 \
	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 try29-opt2.helices
# HelixConstraint (T0344)V4	(T0344)E18 (Removed, doesn't match secondary structure prediction)
HelixConstraint (T0344)T53	(T0344)R59
HelixConstraint (T0344)E61	(T0344)R70
HelixConstraint (T0344)P94	(T0344)L99
HelixConstraint (T0344)G105	(T0344)L112
HelixConstraint (T0344)K110	(T0344)Q117
HelixConstraint (T0344)D115	(T0344)E126
HelixConstraint (T0344)P140	(T0344)A153
HelixConstraint (T0344)A153	(T0344)G164

# From try29-opt2.sheets
SheetConstraint (T0344)G21 (T0344)A24	(T0344)G54 (T0344)D51	hbond (T0344)I23	1
SheetConstraint (T0344)T25 (T0344)A27	(T0344)D49 (T0344)P47	hbond (T0344)V26	1
SheetConstraint (T0344)A27 (T0344)K32	(T0344)Y44 (T0344)E39	hbond (T0344)L29	1
SheetConstraint (T0344)V76 (T0344)T82	(T0344)L91 (T0344)G85	hbond (T0344)H78	1
SheetConstraint (T0344)Y173 (T0344)I178	(T0344)L188 (T0344)I183	hbond (T0344)E175	1
SheetConstraint (T0344)K182 (T0344)S187	(T0344)S202 (T0344)G197	hbond (T0344)I183	1
SheetConstraint (T0344)G197 (T0344)V203	(T0344)Y212 (T0344)G206	hbond (T0344)S198	1
SheetConstraint (T0344)G206 (T0344)P213	(T0344)F223 (T0344)V216	hbond (T0344)K208	1