CreatePredAlphaCost pred_alpha2k alpha11 T0342.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0342.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0342.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 0 \
	n_ca_c	5 bad_peptide 10 \
	bystroff 5 \
	soft_clashes 60  backbone_clashes 2 \
	break 170  \
	pred_alpha2k 2 \
	pred_alpha04 2 \
	pred_alpha06 2 \
	constraints 15 \
	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 T0342.dssp-ehl2.constraints
//include T0342.undertaker-align.sheets
//include rr.constraints

//from try42-opt2.helices
HelixConstraint (T0342)S1	(T0342)G11	1
HelixConstraint (T0342)L27	(T0342)N35	1
HelixConstraint (T0342)N87	(T0342)Q97	1

//from try42-opt2.sheets
SheetConstraint (T0342)S16 (T0342)A21	(T0342)N87 (T0342)V82	hbond (T0342)F17	1
SheetConstraint (T0342)F41 (T0342)D48	(T0342)W84 (T0342)D77	hbond (T0342)C42	1
SheetConstraint (T0342)V43 (T0342)L46	(T0342)Q115 (T0342)V112	hbond (T0342)R45	1
SheetConstraint (T0342)F49 (T0342)F53	(T0342)Q73 (T0342)A69	hbond (T0342)K50	1
SheetConstraint (T0342)Y105 (T0342)T114	(T0342)M127 (T0342)K118	hbond (T0342)I108	1
SheetConstraint (T0342)C122 (T0342)S124	(T0342)L18 (T0342)F20	hbond (T0342)R123	1

//from rr.constraints in the K140-L188 subdomain directory
Constraint I142.CB I176.CB -10. 7.0 14.0 0.86403688641
Constraint I143.CB I163.CB -10. 7.0 14.0 0.727894230104
Constraint I143.CB I176.CB -10. 7.0 14.0 0.726326319204
Constraint I143.CB Y168.CB -10. 7.0 14.0 0.657410377483 bonus
Constraint I143.CB L160.CB -10. 7.0 14.0 0.616281453771 bonus
Constraint I143.CB L152.CB -10. 7.0 14.0 0.614317083942 bonus
Constraint I142.CB I163.CB -10. 7.0 14.0 0.583365430016 bonus
Constraint I163.CB V172.CB -10. 7.0 14.0 0.560783654795 bonus
Constraint I143.CB K159.CB -10. 7.0 14.0 0.551609237113 bonus
Constraint I142.CB L160.CB -10. 7.0 14.0 0.547572329163 bonus
Constraint I163.CB I176.CB -10. 7.0 14.0 0.53901019818 bonus
Constraint I143.CB V172.CB -10. 7.0 14.0 0.536007490605 bonus
Constraint I142.CB L152.CB -10. 7.0 14.0 0.533010666327 bonus

//from K140-L188/try1-opt2.helices
HelixConstraint (T0342)K140	(T0342)N150	2
HelixConstraint (T0342)P153	(T0342)E164	2
HelixConstraint (T0342)A162	(T0342)G170	2
HelixConstraint (T0342)S173	(T0342)L188	2

//from RasMol pick distance

constraint((T0342)I43A.CA, (T0342)I180A.CA) [> 4 = 9.7 < 11] w=10	# (weighted) cost=  1.014 dist=       9.737
constraint((T0342)G81A.CA, (T0342)I180A.CA) [> 6 = 12.4 < 14] w=10	# (weighted) cost=  1.014 dist=       12.362
constraint((T0342)L27A.CA, (T0342)I180A.CA) [> 1 = 6.8 < 8.5] w=10
constraint((T0342)I176A.CA, (T0342)S24A.CA) [> 4 = 9.6 < 11] w=10
constraint((T0342)E155A.CA, (T0342)F41A.CA) [> 8 = 12.5 < 13.5] w=10



//from RasMol pick distance, to close the breaks:

constraint((T0342)Y105.CA, (T0342)V106A.N) [> 0 = 0.5 < 1] w=8
constraint((T0342)V106.CA, (T0342)V107A.N) [> 0 = 0.5 < 1] w=8