// Note: the training atoms are needed for patching up chain breaks
// when reading in conformations.
InFilePrefix /projects/kestrel/users/karplus/burial/undertaker/atoms-inputs/
ReadTrainingAtoms monomeric-50pc.atoms
ReadRotamerLibrary monomeric-50pc.rot

InFilePrefix /projects/kestrel/users/karplus/burial/undertaker/spots/
    ReadAtomType pdb-name.types
    ReadClashTable pdb-atom-name.clash
    SetClashDefinition pdb-atom-name

CreateBurialCost dry5 monomeric-50pc-dry-5.spot smoothed-monomeric-50pc-dry-5.hist

CreateBurialCost wet6.5 monomeric-50pc-wet-6.5.spot smoothed-monomeric-50pc-wet-6.5.hist log
CreateBurialCost dry6.5 monomeric-50pc-dry-6.5.spot smoothed-monomeric-50pc-dry-6.5.hist
CreateBurialCost gen6.5 monomeric-50pc-generic-6.5.spot smoothed-monomeric-50pc-generic-6.5.hist

CreateBurialCost dry8 monomeric-50pc-dry-8.spot smoothed-monomeric-50pc-dry-8.hist
CreateBurialCost dry10 monomeric-50pc-dry-10.spot smoothed-monomeric-50pc-dry-10.hist
CreateBurialCost dry12 monomeric-50pc-dry-12.spot smoothed-monomeric-50pc-dry-12.hist

CreateAlphaCost alpha monomeric-smoothed-alpha.hist
CreateAlphaCost alpha_prev  monomeric-smoothed-alpha-1.hist -1

Time


//Need to read in target before specific fragments or alignments can
// be read, also before constraints can be defined.

InFilePrefix 

ReadTargetPDB T0132.blank.pdb
NameTarget T0132
PopConform	// get rid of uneeded all-zero conformation



InFilePrefix /projects/compbio/lib/alphabet/
ReadAlphabet alpha.alphabet
InFilePrefix
CreatePredAlphaCost pred_alpha2 alpha11 T0132.t2k.alpha.rdb 2 alpha alpha_prev

// add constraints to tack on first short strand
Constraint 75	119	2.0 2.7 3.2 	// N R11 O V16
Constraint 84	114	2.0 2.7 3.2 	// O R11 N V16


// add constraints to hold first strand onto sheet
// I THINK THIS IS MISALIGNED:
// Constraint 131	629	2 5.12 7	// CB L18 	CB L86
// Constraint 139	623	2 5.12 7	// CB L19 	CB C85
// Constraint 147	614	2 5.12 7	// CB R20 	CB Q84

// add constraints for hbonds in the first strand
Constraint	121	610	2.0 2.7 3.2 	// L17 N G83 O
Constraint	127	608	2.0 2.7 3.2 	// L17 O G83 N
Constraint	137	594	2.0 2.7 3.2 	// L19 N C81 O
Constraint	143	590	2.0 2.7 3.2 	// L19 O C81 N

// add constraints for strand ending at F122
Constraint	678	919	2.0 2.7 3.2 	// I93 N F122 O
Constraint	684	910	2.0 2.7 3.2 	// I93 O F122 N
Constraint	695	901	2.0 2.7 3.2 	// I95 N F120 O
Constraint	701	892	2.0 2.7 3.2 	// I95 O F120 N
Constraint	712	883	2.0 2.7 3.2 	// V97 N A118 O
Constraint	717	880	2.0 2.7 3.2 	// V97 O A118 N
Constraint	728	870	2.0 2.7 3.2 	// V99 N T116 O
Constraint	733	865	2.0 2.7 3.2 	// V99 O T116 N
Constraint	749	856	2.0 2.7 3.2	// V101 N C114 O 
Constraint	754	852	2.0 2.7 3.2	// V101 O C114 N 
Constraint	765	838	2.0 2.7 3.2	// K103 N R112 O

// add constraints to keep edge strand close
Constraint	459	909	2.0 2.7 3.2 	// A63 N T121 O
Constraint	462	903	2.0 2.7 3.2 	// A63 O T121 N
// remove constraints near the bulge
// Constraint	480	890	2.0 2.7 3.2 	// N S66   O V119
// Constraint	484	885	2.0 2.7 3.2 	// O S66   N V119
// The next two constraints are buggy:
  // Constraint	494	870	2.0 2.7 3.2 	// N68 N T116 O
  // Constraint	500	865	2.0 2.7 3.2 	// N68 O T116 N

Constraint	494	878	2.0 2.7 3.2 	// N68 N D117 O
Constraint	500	872	2.0 2.7 3.2 	// N68 O D117 N
Constraint	513	863	2.0 2.7 3.2	// N I70 O V115
Constraint	519	858	2.0 2.7 3.2	// O I70 N V115

// add constraint to keep helix straight
Constraint 273	385	20 22.5  27	// CA W38 	CA E53


// After jiggling got things tight (try23), I removed the helix
// packing constraints since they may have been driving things in
// the wrong direction.

// add constraints to pack helices:
    // I'm having trouble deciding between the next two for I149
    // Constraint 1129 335	0 3.1 5	// CD1 I149  CA M45
    // Constraint 1129 355	0 3.1 5	// CD1 I149  CA I49
    
//     Constraint 1077	376	0 3.1 5	// CD2 L142  CA K52
//    Constraint 1108 351     0 4 8   // CD2 L146 CB A48

    // I'm no longer happy with this one
    // Constraint 1146	336	0 4 8	// C E151 CG M45




// I'm no longer convinced this is right.
// add constraints to make N-terminus be on "right" side of sheet
// Constraint 10	309	-20 6.0 15.0	// CA S2 CA Q42

SetCost gen6.5 0.2 wet6.5 0.2 dry5 1.0 dry6.5 1.0 dry8 1.0 dry12 1 \
	radius_norm 0 radius_fit 0.2 \
	sidechain 0.2 \
	clashes 2 sidechain_clashes -0.2 backbone_clashes 0.5 \
	break 7  \
	constraints 0.05 \
	pred_alpha2  1 \
	contact_order 1

//	known_ssbond 0.5
//	alpha 1 alpha_prev 1 \