CreatePredAlphaCost pred_alpha2k alpha11 T0351.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0351.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0351.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 15 \
	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 T0351.t06.str2.constraints
HelixConstraint 	L3	K10	0.7
StrandConstraint	F20	N24	0.684
StrandConstraint	Y30	K33	0.643
# I used t06.o_notor2 to adjust this next line a bit
HelixConstraint 	T42	W50	0.818
HelixConstraint 	D63	L72	0.659
# opening up this gap a bit
HelixConstraint 	Q74	E84	0.627
HelixConstraint 	N91	L103	0.606
# this next is more likey than before (watching that H-tag!)
HelixConstraint 	D106	E108	0.607

# sheet designed by: echo "20 25 33 38" | build_sheet.py -t T0351 -o down
SheetConstraint F20  N24  K33  N27  hbond F20 5.0

# almost all of these constraints are for the sheet,
# but I've taken care of the sheet above.
# The constraint from I7 to L22 is of interest...
# Constraint L22.CB L36.CB -10. 7.0 14.0 0.685366627808
Constraint I7.CB L22.CB -10. 7.0 14.0 0.0516539254325
# Constraint I7.CB L36.CB -10. 7.0 14.0 0.470815766559 bonus
# Constraint F20.CB N35.CB -10. 7.0 14.0 0.442361299438 bonus
# Constraint L22.CB I31.CB -10. 7.0 14.0 0.425463872127 bonus
# Constraint F20.CB I31.CB -10. 7.0 14.0 0.376435339257 bonus
# Constraint F20.CB L36.CB -10. 7.0 14.0 0.371157976518 bonus
# Constraint F20.CB E32.CB -10. 7.0 14.0 0.367273373096 bonus
# Although I am not using these next constraints, I notice that
# they strongly suggest that I7 is near L3, implying a helix
# Constraint I7.CB I31.CB -10. 7.0 14.0 0.363489614286 bonus
# Constraint L3.CB Y30.CB -10. 7.0 14.0 0.360993079452 bonus
# Constraint Y4.CB L22.CB -10. 7.0 14.0 0.326550097872 bonus
# I adjusted the next two down by inserting a 1 after the decimal
Constraint L82.CB L98.CB -10. 7.0 21.0 0.1322116290579
Constraint L82.CB I96.CB -10. 7.0 21.0 0.1313963021864
# Constraint I7.CB L53.CB -10. 7.0 14.0 0.310095620118 bonus

# some rr constraints that were not a part of rr.constraints
# boosted by inserting a 1 after decimal
Constraint L36.CB L82.CB  -10. 7.0 21.0 .125
Constraint I31.CB I96.CB  -10. 7.0 21.0 .124