CreatePredAlphaCost pred_alpha2k alpha11 T0360.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0360.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0360.t06.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 25 dry6.5 30 dry8 20 dry12 5 \
	phobic_fit 3 \
	sidechain 5 \
	n_ca_c	10 bad_peptide 15\
	bystroff 5 \
	soft_clashes 60  backbone_clashes 2 \
	break 120  \
	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 0

// 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 T0360.dssp-ehl2.constraints
//include T0360.undertaker-align.sheets
//include rr.constraints

//from try1-opt2.helices
HelixConstraint (T0360)M1	(T0360)M18	1
HelixConstraint (T0360)Q23	(T0360)I31	1
HelixConstraint (T0360)I48	(T0360)L56	1
HelixConstraint (T0360)D60	(T0360)R66	1
HelixConstraint (T0360)V67	(T0360)R73	1
HelixConstraint (T0360)R74	(T0360)L81	1

//from try2-opt2.helices
HelixConstraint (T0360)T99	(T0360)H109	1
HelixConstraint (T0360)Q107	(T0360)Q114	1
HelixConstraint (T0360)V112	(T0360)E141	1

SheetConstraint (T0360)Y35 (T0360)V37	(T0360)K42 (T0360)R40	hbond (T0360)V37	1
SheetConstraint (T0360)R87 (T0360)D89	(T0360)P43 (T0360)A45	hbond (T0360)F88	2

Constraint I27.CB I64.CB -10. 7.0 14.0 2
Constraint I27.CB F41.CB -10. 7.0 14.0 2
Constraint Y77.CB L81.CB -10. 7.0 14.0 2
Constraint Y77.CB V98.CB -10. 7.0 14.0 2