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 40 dry6.5 50 dry8 40 dry12 7 \
	phobic_fit 2 \
	sidechain 4 \
	n_ca_c	5 bad_peptide 10 \
	bystroff 5 \
	soft_clashes 60  backbone_clashes 2 \
	break 250  \
	pred_alpha2k 2 \
	pred_alpha04 2 \
	pred_alpha06 2 \
	constraints 100 \
	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


# I will use T0356.t06.dssp-ehl2.constraints

#HelixConstraint 	V334	K346	0.6924
StrandConstraint	I351	Y355	0.6223
#new
StrandConstraint	S362	K371	0.9
#HelixConstraint 	G376	L389	0.6526
#StrandConstraint	F397	C401	0.8585
StrandConstraint	K396	C401	0.9
#HelixConstraint 	W410	T419	0.7114
StrandConstraint	T427	V430	0.6614
#StrandConstraint	M451	D454	0.7817
StrandConstraint	S449	A455	0.90
#HelixConstraint 	P475	L488	0.6352

#try1-opt2.helices
HelixConstraint (T0356)D327	(T0356)V339 1
HelixConstraint (T0356)V339	(T0356)F348 1
HelixConstraint (T0356)Y374	(T0356)Q391 1
HelixConstraint (T0356)R408	(T0356)D422 1
HelixConstraint (T0356)P434	(T0356)S442 0.0
HelixConstraint (T0356)F440	(T0356)S445 0.0
HelixConstraint (T0356)D474	(T0356)L488 1
HelixConstraint (T0356)D486	(T0356)N493 1


# try1.sheet constraints
SheetConstraint (T0356)E350 (T0356)L356	(T0356)K371 (T0356)L365	hbond (T0356)E350	0.7
SheetConstraint (T0356)F397 (T0356)D402	(T0356)R425 (T0356)V430	hbond (T0356)I399	0.7
SheetConstraint (T0356)V398 (T0356)D403	(T0356)G448 (T0356)L453	hbond (T0356)V400	0.7
SheetConstraint (T0356)D402 (T0356)D403	(T0356)E431 (T0356)N432	hbond (T0356)D403	0.7