CreatePredAlphaCost pred_alpha2k alpha11 T0338.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0338.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0338.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 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 T0338.dssp-ehl2.constraints
#include T0338.undertaker-align.sheets
include rr.constraints

#include constraints from try1.opt2 alignment

HelixConstraint (T0338)A1	(T0338)E10
HelixConstraint (T0338)T8	(T0338)E13
HelixConstraint (T0338)E27	(T0338)N46
HelixConstraint (T0338)S48	(T0338)H66
HelixConstraint (T0338)N72	(T0338)E88
HelixConstraint (T0338)K93	(T0338)A101
HelixConstraint (T0338)P107	(T0338)K115
HelixConstraint (T0338)E125	(T0338)G138
HelixConstraint (T0338)H145	(T0338)V151
HelixConstraint (T0338)D149	(T0338)T154
HelixConstraint (T0338)K152	(T0338)R158
HelixConstraint (T0338)S160	(T0338)S174
HelixConstraint (T0338)K185	(T0338)S201
HelixConstraint (T0338)S208	(T0338)W215
HelixConstraint (T0338)T223	(T0338)Q236
HelixConstraint (T0338)N243	(T0338)N250