CreatePredAlphaCost pred_alpha2k alpha11 T0355.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0355.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0355.t06.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 15 dry6.5 30 dry8 25 dry12 5 \
	phobic_fit 2 \
	sidechain 5 \
	n_ca_c	5 bad_peptide 10 \
	bystroff 5 \
	soft_clashes 40  backbone_clashes 2 \
	break 100  \
	pred_alpha2k 4 \
	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 T0355.dssp-ehl2.constraints
//include T0355.undertaker-align.sheets
//include rr.constraints

SheetConstraint (T0355)P32 (T0355)R36	(T0355)G245 (T0355)A249	hbond (T0355)A34	10
SheetConstraint (T0355)D71 (T0355)V72	(T0355)V66 (T0355)E67	hbond (T0355)D71	10
SheetConstraint (T0355)F116 (T0355)K120	(T0355)M143 (T0355)A147	hbond (T0355)I118	10
SheetConstraint (T0355)E144 (T0355)R146	(T0355)K163 (T0355)F165	hbond (T0355)G145	10
SheetConstraint (T0355)L190 (T0355)F192	(T0355)P224 (T0355)L226	hbond (T0355)A191	10
SheetConstraint (T0355)L226 (T0355)G228	(T0355)G245 (T0355)I247	hbond (T0355)V227	10

SheetConstraint (T0355)F192 (T0355)L190 (T0355)A166 (T0355)V164	hbond (T0355)F192	50
SheetConstraint (T0355)G63 (T0355)I65 (T0355)P35 (T0355)Y37	hbond (T0355)G63	50
SheetConstraint (T0355)A117 (T0355)A119 (T0355)L64 (T0355)V66	hbond (T0355)A117	50



HelixConstraint (T0355)M1	(T0355)N7	1
HelixConstraint (T0355)N10	(T0355)I15	1
HelixConstraint (T0355)F16	(T0355)C28	1
HelixConstraint (T0355)D47	(T0355)G60	1
HelixConstraint (T0355)G81	(T0355)R94	1
HelixConstraint (T0355)A99	(T0355)A111	1
HelixConstraint (T0355)R128	(T0355)A135	1
HelixConstraint (T0355)I214	(T0355)A220	1
HelixConstraint (T0355)N232	(T0355)T243	1
HelixConstraint (T0355)A249	(T0355)E254	1
HelixConstraint (T0355)L252	(T0355)W259	1
HelixConstraint (T0355)L264	(T0355)R275	1
HelixConstraint (T0355)A273	(T0355)L278	1
HelixConstraint (T0355)E279	(T0355)H285	1