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 20 \
	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
#keep rr constraints, but not the bonus ones
Constraint I76.CB M133.CB -10. 7.0 14.0 0.601545537313
Constraint H60.CB S77.CB -10. 7.0 14.0 0.574932381932
Constraint M59.CB L83.CB -10. 7.0 14.0 0.552654894108
Constraint L83.CB M133.CB -10. 7.0 14.0 0.550353958212
Constraint A55.CB S77.CB -10. 7.0 14.0 0.542377608627
Constraint E130.CB F139.CB -10. 7.0 14.0 0.531776376545
Constraint A80.CB M133.CB -10. 7.0 14.0 0.516473237024
#change this bonus to real constraint so keep helix closer to core
Constraint I38.CB V97.CB -10. 7.0 14.0 1.5


#from try1-opt2.helices
HelixConstraint (T0338)A1	(T0338)E10	1
HelixConstraint (T0338)T8	(T0338)E13	1	
HelixConstraint (T0338)E27	(T0338)N46	1
HelixConstraint (T0338)S48	(T0338)H66	1
HelixConstraint (T0338)N72	(T0338)E88	1
#HelixConstraint (T0338)K93	(T0338)A101	1
#want to make this helix longer
HelixConstraint (T0338)L94	(T0338)L105	3
#HelixConstraint (T0338)P107	(T0338)K115	1
#do not want previous helix
#HelixConstraint (T0338)E125	(T0338)G138	1
#want to make this helix longer
HelixConstraint (T0338)C116	(T0338)L137	3
HelixConstraint (T0338)H145	(T0338)V151	1
HelixConstraint (T0338)D149	(T0338)T154	1
HelixConstraint (T0338)K152	(T0338)R158	1
HelixConstraint (T0338)S160	(T0338)S174	1
HelixConstraint (T0338)K185	(T0338)S201	1
HelixConstraint (T0338)S208	(T0338)W215	1
HelixConstraint (T0338)T223	(T0338)Q236	1
HelixConstraint (T0338)N243	(T0338)N250	1