CreatePredAlphaCost pred_alpha2k alpha11 T0354.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0354.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0354.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 100  \
	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 T0354.dssp-ehl2.constraints
#include T0354.undertaker-align.sheets
#include rr.constraints

#include T0354.t06.str2.constraints
HelixConstraint 	I3	I17	1.0
StrandConstraint	I22	D26	0.85
StrandConstraint	R36	A40	0.856
HelixConstraint 	N45	E61	1.0
#too small to keep
#StrandConstraint	S69	E70	0.2
StrandConstraint	W77	D81	0.85
StrandConstraint	V85	V89	0.85
HelixConstraint 	V94	R95	0.611
HelixConstraint 	Y98	A102	0.633
HelixConstraint 	S120	V122	0.626

#include sheet constrains from try5-opt2.sheets

#SheetConstraint (T0354)L9 (T0354)E15	(T0354)R36 (T0354)G42	hbond (T0354)I11	1
#SheetConstraint (T0354)A10 (T0354)E15	(T0354)G83 (T0354)H88	hbond (T0354)E12	1
SheetConstraint (T0354)R36 (T0354)G42	(T0354)I66 (T0354)H72	hbond (T0354)I38	1
#SheetConstraint (T0354)V85 (T0354)V89	(T0354)Q107 (T0354)F111	hbond (T0354)V87	1

#include try-opt2.sheets and new one
SheetConstraint (T0354)S28 (T0354)S32	(T0354)A40 (T0354)R36	hbond (T0354)L30	1
#new (goal: to line up all three strands)
SheetConstraint (T0354)V80 (T0354)E76	(T0354)V89  (T0354)V85	hbond (T0354)V86	1
SheetConstraint (T0354)V85 (T0354)V89	(T0354)S110 (T0354)G114	hbond (T0354)V86	1