CreatePredAlphaCost pred_alpha2k alpha11 T0316.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0316.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0316.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 T0316.dssp-ehl2.constraints
#include T0316.undertaker-align.sheets
#include rr.constraints

#From T0316.dssp-ehl2.constraints:
StrandConstraint	R8	M13	0.732
HelixConstraint 	D18	E28	0.7937
StrandConstraint	V33	K39	0.6431
HelixConstraint 	Y56	Q65	0.8878
StrandConstraint	Y70	V73	0.7347
HelixConstraint 	E76	R92	0.7186
HelixConstraint 	F109	T118	0.833
StrandConstraint	Y123	T126	0.6904
HelixConstraint 	P177	L182	0.6971

#From T0316.undertaker-align.sheets:
SheetConstraint (T0316)T7 (T0316)M13	(T0316)Y31 (T0316)F37	hbond (T0316)V9		1
SheetConstraint (T0316)V10 (T0316)V11	(T0316)V124 (T0316)A125	hbond (T0316)V10	1
SheetConstraint (T0316)I34 (T0316)K39	(T0316)P69 (T0316)N74	hbond (T0316)G35	1
SheetConstraint (T0316)Y123 (T0316)T126	(T0316)K166 (T0316)F169	hbond (T0316)V124	1

#New constraints:
Hbond	Y31.N	L26.O	5
Hbond	I68.N	A63.O	5
Hbond	A121.N	A116.O	5