CreatePredAlphaCost pred_alpha2k alpha11 T0356.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0356.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0356.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 50 \
	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 T0356.dssp-ehl2.constraints
#include T0356.undertaker-align.sheets
include rr.constraints

# From T0356.t06.str2.constraints

HelixConstraint 	A330	Q345	0.752
StrandConstraint	I351	Y355	0.676
StrandConstraint	L365	K371	0.719
HelixConstraint 	H377	F388	0.736
StrandConstraint	F397	C401	0.85
HelixConstraint 	W410	T419	0.705
StrandConstraint	R425	N432	0.900
StrandConstraint	M451	D454	0.746
HelixConstraint 	P475	L488	0.63



#Sheet constrains from :  try1-opt2.sheets

SheetConstraint (T0356)E350 (T0356)L356	(T0356)I370 (T0356)R364	hbond (T0356)E350	20
SheetConstraint (T0356)F397 (T0356)D402	(T0356)R425 (T0356)V430	hbond (T0356)I399	20
SheetConstraint (T0356)V398 (T0356)D403	(T0356)G448 (T0356)L453	hbond (T0356)V400	20
SheetConstraint (T0356)D402 (T0356)D403	(T0356)E431 (T0356)N432	hbond (T0356)D403	10
#new SheetConstraint
SheetConstraint (T0356)R425 (T0356)V430	(T0356)R364 (T0356)T369	hbond (T0356)V367	60



#new changes
#StrandConstraint	R425	N432	0.822