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)L22 (T0356)T26	(T0356)A49 (T0356)E53   hbond (T0356)L22	50
#SheetConstraint (T0356)L50 (T0356)N54	(T0356)C64 (T0356)M60	hbond (T0356)L50	50
SheetConstraint (T0356)K123 (T0356)L125	(T0356)I134 (T0356)Q132	hbond (T0356)K123	40
SheetConstraint (T0356)K133 (T0356)V135	(T0356)C150 (T0356)M148 hbond (T0356)K133	40
SheetConstraint (T0356)I147 (T0356)C150	(T0356)T166 (T0356)L163 hbond (T0356)I147	40

SheetConstraint (T0356)P48 (T0356)N54	(T0356)C64 (T0356)Y58	hbond (T0356)L50	50
SheetConstraint (T0356)G162 (T0356)P169	(T0356)Y179 (T0356)E172	hbond (T0356)T164	50
SheetConstraint (T0356)L22 (T0356)I25	(T0356)L50 (T0356)E53   hbond (T0356)K23	50

HelixConstraint (T0356)M1	(T0356)Q19	20
HelixConstraint (T0356)D30	(T0356)T36	20
HelixConstraint (T0356)E34	(T0356)R44	20
HelixConstraint (T0356)F67	(T0356)M77	20
HelixConstraint (T0356)E80	(T0356)K90	20
HelixConstraint (T0356)G89	(T0356)E97	20
HelixConstraint (T0356)F104	(T0356)L111	20
HelixConstraint (T0356)D109	(T0356)N119	20