CreatePredAlphaCost pred_alpha2k alpha11 T0254.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0254.t04.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 3 near_backbone 3 way_back 3 dry5 5 dry6.5 6 dry8 5 dry12 2 \
	phobic_fit 2 \
	sidechain 6 \
	bystroff 5 \
	soft_clashes 20  backbone_clashes 2 \
	break 40  \
	pred_alpha2k 3 \
	pred_alpha04 3 \
	constraints 10 \
	hbond_geom 1 \
	hbond_geom_backbone 1 \
	hbond_geom_beta 10 \
	hbond_geom_beta_pair 20

// Add the following for extra-cellular proteins:
#	known_ssbond 0.5	# and put ssbond command in constraints file
#	maybe_ssbond 0.5

// 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.

# from include T0254.t2k.dssp-ehl2.constraints
StrandConstraint	L4	R7	0.6351	# s1
StrandConstraint	F36	L40	0.7217	# s2
#StrandConstraint	T43	A47	0.607	# bogus?
StrandConstraint	Y52	W59	0.6201	# s3
StrandConstraint	L88	P94	0.7758	# s4
# 
HelixConstraint 	A11	L29	0.6734	
HelixConstraint 	Q64	L81	0.7706

# include T0254.t2k.dssp-ehl2.constraints
# include T0254.t2k.dssp-ebghstl.constraints
# include T0254.t2k.stride-ebghtl.constraints
# include T0254.t2k.str2.constraints
# include T0254.t2k.alpha.constraints
# include T0254.t2k.bys.constraints
# 
# include T0254.t04.dssp-ehl2.constraints
# include T0254.t04.dssp-ebghstl.constraints
# include T0254.t04.stride-ebghtl.constraints
# include T0254.t04.str2.constraints
# include T0254.t04.alpha.constraints
# include T0254.t04.bys.constraints

# from try1-opt2 (slightly extended)
# SheetConstraint P2   F6  	F38  N42 	hbond L4  	8	# s1 || s2
# SheetConstraint P2   F6  	V57  P53 	hbond R5  	8	# s1 ^v s3
# SheetConstraint P53  F60 	L88  L95 	hbond V55 	10	# s3 || s4
# #SheetConstraint Y100 L102	F107 Q105	hbond L102		# bogus?  
# # 
# HelixConstraint V9	S16	5
# HelixConstraint L17	S30	5
# HelixConstraint E63	L82	10

# from try2-opt2
SheetConstraint P2   F6  	F38  N42	hbond L4        8       # s1 || s2
SheetConstraint M1   L4  	L58  V55	hbond M1        8       # s1 ^v s3
SheetConstraint P53  F60 	L88  L95	hbond V55       10      # s3 || s4
SheetConstraint Y100 L102	F107 Q105	hbond L102              # bogus?  
#
HelixConstraint V9	S16	5
HelixConstraint L17	S30	5
HelixConstraint T66	L82	10