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 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 T0356.dssp-ehl2.constraints
#include T0356.undertaker-align.sheets
#include rr.constraints

#  New constraints from Secondary Structure Predictions:

HelixConstraint (T0356)D8	(T0356)Q18	10
HelixConstraint (T0356)L33	(T0356)R44	10
HelixConstraint (T0356)P70	(T0356)G76	10
HelixConstraint (T0356)V82	(T0356)L95	10
HelixConstraint (T0356)K102	(T0356)K110	10
HelixConstraint (T0356)P112	(T0356)L118	10

# From sep alphabets:

Hbond	(T0356)L22.N	(T0356)L16.O	3
Hbond	(T0356)E21.N	(T0356)L16.O	5
Hbond	(T0356)G47.N	(T0356)T42.O	5
Hbond	(T0356)Q79.N	(T0356)A74.O	5
Hbond	(T0356)N175.N	(T0356)T166.O	5
Hbond	(T0356)G168.N	(T0356)R173.O	5
Hbond	(T0356)T166.N	(T0356)N175.O	5
Hbond	(T0356)M75.O	(T0356)G78.N	5
Hbond	(T0356)D141.O	(T0356)R144.N	5
Hbond	(T0356)W151.O	(T0356)D154.N	5

SheetConstraint (T0356)L163 (T0356)R167 (T0356)I178 (T0356)Q174	hbond (T0356)N175	50
SheetConstraint (T0356)L50 (T0356)N54	(T0356)C64 (T0356)M60	hbond (T0356)L51	50
SheetConstraint (T0356)K123 (T0356)L125	(T0356)I134 (T0356)Q132	hbond (T0356)K123	50
SheetConstraint (T0356)K133 (T0356)V135	(T0356)C150 (T0356)M148 hbond (T0356)K133	50
SheetConstraint (T0356)I147 (T0356)C150	(T0356)T166 (T0356)L163 hbond (T0356)I147	50

SheetConstraint (T0356)K23 (T0356)L27	(T0356)L50 (T0356)N54	hbond (T0356)K23	50