CreatePredAlphaCost pred_alpha2k alpha11 T0330.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0330.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0330.t06.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 15 near_backbone 5 way_back 5 \
	dry5 30 dry6.5 40 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 100  \
	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.


# from try2-opt2.helices
HelixConstraint (T0330)V17      (T0330)Y33
HelixConstraint (T0330)S38      (T0330)G46
HelixConstraint (T0330)D49      (T0330)V56
HelixConstraint (T0330)F71      (T0330)E84
HelixConstraint (T0330)G96      (T0330)S106
HelixConstraint (T0330)F119     (T0330)L129
HelixConstraint (T0330)A145     (T0330)E150
HelixConstraint (T0330)I154     (T0330)G164
HelixConstraint (T0330)T178     (T0330)D189
HelixConstraint (T0330)T201     (T0330)R207
HelixConstraint (T0330)T220     (T0330)L228

# from try2-opt2.sheets
SheetConstraint (T0330)L5 (T0330)F8     (T0330)I172 (T0330)I175 hbond (T0330)L5 1
SheetConstraint (T0330)T4 (T0330)D9     (T0330)V110 (T0330)L115 hbond (T0330)V6 1
SheetConstraint (T0330)L14 (T0330)K16   (T0330)I10 (T0330)G12   hbond (T0330)L15        1
SheetConstraint (T0330)G113 (T0330)T116 (T0330)F138 (T0330)F141 hbond (T0330)L114       1
SheetConstraint (T0330)F141 (T0330)A142 (T0330)N118 (T0330)F119 hbond (T0330)A142       1
SheetConstraint (T0330)V173 (T0330)D177 (T0330)R191 (T0330)V195 hbond (T0330)I174       1
SheetConstraint (T0330)I193 (T0330)A196 (T0330)T212 (T0330)K215 hbond (T0330)A194       1