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 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 T0316.dssp-ehl2.constraints
#include T0316.undertaker-align.sheets
#include rr.constraints

# From M1-A183/try2.costfcn:
#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


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

#From A130-I373/try3.costfcn:

# From T0316.dssp-ehl2.constraints:
#HelixConstraint 	P177	E185	0.8526
#StrandConstraint	D229	E232	0.6788
#StrandConstraint	L236	Y239	0.6474
#StrandConstraint	L236	Y239	0.6474
#StrandConstraint	L305	Y313	0.6061
#StrandConstraint	V320	V324	0.8455
#StrandConstraint	T329	F333	0.7496
#StrandConstraint	A345	Y349	0.8561

# New structure constraints:
#HelixConstraint		D281	F295	3
#StrandConstraint	R131	R134	15
#StrandConstraint	V140	V146	15
#StrandConstraint	T153	L156	15
#HelixConstraint		S160	M168	5
#HelixConstraint		K176	G187	5

#HelixConstraint		N206	Y214	5



# New sheet constraints:
#SheetConstraint (T0316)C307 (T0316)F311	(T0316)H323 (T0316)K319	hbond (T0316)C307	15
#SheetConstraint (T0316)K319 (T0316)H323 (T0316)I332 (T0316)K328 hbond (T0316)V320	15
#SheetConstraint	(T0316)T329 (T0316)F333 (T0316)Y349 (T0316)A345 hbond (T0316)I332	15


#SheetConstraint (T0316)R131 (T0316)R134	(T0316)R144 (T0316)H141 hbond (T0316)R131	15
#SheetConstraint	(T0316)H141 (T0316)R144	(T0316)L156 (T0316)T153 hbond (T0316)M142	15
#SheetConstraint (T0316)T153 (T0316)L156 (T0316)I202 (T0316)I199 hbond (T0316)Y154	15

# Hbond constraints from o_notor2/n_notor2
#Hbond		E184.O	G187.N		3
#Hbond		Q218.O	R221.N		3
#Hbond		E335.O	R338.N		3
#Hbond		L188.N	A183.O		3

#Sheet constraints for the parallel sheet:
#SheetConstraint (T0316)Y70 (T0316)N74 (T0316)G35 (T0316)K39 hbond (T0316)Y70	15
#SheetConstraint (T0316)V33 (T0316)F37 (T0316)V9  (T0316)M13 hbond (T0316)I34	15
#SheetConstraint (T0316)V9  (T0316)G12 (T0316)Y123 (T0316)T126 hbond (T0316)V10	15
#SheetConstraint (T0316)V124 (T0316)A125 (T0316)T190 (T0316)A191 hbond (T0316)V124	15