CreatePredAlphaCost pred_alpha2k alpha11 T0384.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0384.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0384.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 T0384.dssp-ehl2.constraints
#include T0384.undertaker-align.sheets
#include rr.constraints

# from try3-opt2.sheets
SheetConstraint (T0384)L2 (T0384)L4	(T0384)Y26 (T0384)L28	hbond (T0384)L2	1
SheetConstraint (T0384)L4 (T0384)G8	(T0384)L65 (T0384)A69	hbond (T0384)G5	1
SheetConstraint (T0384)G5 (T0384)G8	(T0384)A30 (T0384)S33	hbond (T0384)V6	1
SheetConstraint (T0384)L65 (T0384)I68	(T0384)H88 (T0384)L91	hbond (T0384)V66	1
SheetConstraint (T0384)H88 (T0384)E92	(T0384)F115 (T0384)A119	hbond (T0384)V89	1
SheetConstraint (T0384)F145 (T0384)S152	(T0384)Y239 (T0384)S232	hbond (T0384)F145	1
SheetConstraint (T0384)D144 (T0384)S152	(T0384)Q221 (T0384)N229	hbond (T0384)N146	25
SheetConstraint (T0384)D195 (T0384)D204	(T0384)Y217 (T0384)D208	hbond (T0384)A196	1
SheetConstraint (T0384)A196 (T0384)Y198	(T0384)E322 (T0384)R320	hbond (T0384)T197	1
SheetConstraint (T0384)N210 (T0384)Y217	(T0384)K228 (T0384)Q221	hbond (T0384)G211	25
SheetConstraint (T0384)L234 (T0384)T240	(T0384)T249 (T0384)G243	hbond (T0384)C236	1
SheetConstraint (T0384)L247 (T0384)T249	(T0384)F258 (T0384)A256	hbond (T0384)N248	1
SheetConstraint (T0384)I257 (T0384)D260	(T0384)Q267 (T0384)N264	hbond (T0384)F258	1

# the one below for edge strand from try6-opt2.sheets
SheetConstraint (T0384)S255 (T0384)D260	(T0384)P269 (T0384)N264	hbond (T0384)A256	25

# from try6-opt2.helices
HelixConstraint (T0384)G10	(T0384)A20	1
HelixConstraint (T0384)K35	(T0384)Y46	1
HelixConstraint (T0384)Q54	(T0384)S61	1
HelixConstraint (T0384)L74	(T0384)A85	1
HelixConstraint (T0384)Q98	(T0384)N113	1
HelixConstraint (T0384)E125	(T0384)D137	1
HelixConstraint (T0384)G173	(T0384)L178	1
HelixConstraint (T0384)G179	(T0384)G191	1
HelixConstraint (T0384)H275	(T0384)Q290	1
HelixConstraint (T0384)Q297	(T0384)A303	1
HelixConstraint (T0384)Y301	(T0384)G318	1