CreatePredAlphaCost pred_alpha2k alpha11 T0325.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0325.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0325.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 T0325.dssp-ehl2.constraints
#use try16.helices
HelixConstraint (T0325)V19	(T0325)G30	1
HelixConstraint (T0325)F44	(T0325)S54	1
HelixConstraint (T0325)V80	(T0325)G88	1
HelixConstraint (T0325)F90	(T0325)E97	1
#made this one long helix, instead of two
HelixConstraint (T0325)N101	(T0325)K118	5
HelixConstraint (T0325)L140	(T0325)Y150	1
HelixConstraint (T0325)L167	(T0325)R174	1
HelixConstraint (T0325)S189	(T0325)S203	1
HelixConstraint (T0325)M229	(T0325)E236	1
HelixConstraint (T0325)V243	(T0325)R250	1
HelixConstraint (T0325)N256	(T0325)M262	1

#include T0325.undertaker-align.sheets
#use try16.sheets
SheetConstraint (T0325)K4 (T0325)I7	(T0325)I252 (T0325)A255	hbond (T0325)L6	1
SheetConstraint (T0325)L6 (T0325)A10	(T0325)V207 (T0325)N211	hbond (T0325)I7	1
SheetConstraint (T0325)I8 (T0325)D11	(T0325)S34 (T0325)A37	hbond (T0325)A10	1
SheetConstraint (T0325)S34 (T0325)P39	(T0325)L58 (T0325)H63	hbond (T0325)T36	1
SheetConstraint (T0325)G61 (T0325)H63	(T0325)H125 (T0325)D127	hbond (T0325)V62	1
SheetConstraint (T0325)D124 (T0325)D127	(T0325)L154 (T0325)A157	hbond (T0325)I126	1

#include rr.constraints

#add in these constraints, to try to keep 102-117 in the same place
#as the alignments, even though there is an insertion afterwards

Constraint V105.CB L139.CB -10. 7.0 14.0 1 
Constraint L102.CA A147.CA -10. 8.0 10.0 5 
Constraint V105.CA A147.CA -10. 8.0 10.0 5 
Constraint N69.CA L139.CA -10. 6.0 8.0 3