// 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 T0139.blank.pdb
NameTarget T0139
PopConform	// get rid of uneeded all-zero conformation


InFilePrefix /projects/compbio/lib/alphabet/
ReadAlphabet alpha.alphabet
InFilePrefix
CreatePredAlphaCost pred_alpha2 alpha11 T0139.t2k.alpha.rdb 2 alpha alpha_prev

// include jmb.constraints
// include jmb2.constraints
// include jmb3.constraints

 include helix-only.constraints

// constraint to move R307 out of core region
constraint 636	582	12 14 20	// R307.CA T300.CA

// create constraints to hold strongly-predicted helices straight
// (LONGER than in NMR solution structure, which has frayed ends)
// Constraint 54	138	17 18 22	// CAs S232-A244
// Constraint 443	589	26 27 32	// CAs E283-Q301

// create constraints to draw together some hydrophobics that look like
// they might be able to get close
// Constraint 75	538	1  3.5  12	// V235.CB	L295.CB
// Constraint 144	460	1  3.5  12	// L245.CB	V285.CB	

// alternative set of hydrophobic constraints:
// Constraint 	126	524	2  4    8	// L242.CD1	L293.CA

SetCost gen6.5 0.1 wet6.5 0.4  dry5 1 dry6.5 9 dry8 5 dry12 1 \
	phobic_fit 0.7 \
	sidechain 0.5 \
	clashes 2 sidechain_clashes -0.2 backbone_clashes 1 \
	break 15 \
	pred_alpha2 1.6  \
	constraints 0.03


//	contact_order 0.07 \
//	contact_order 1 \
//	known_ssbond 0.5 \
// 	alpha 1 alpha_prev 1 \
//	radius_norm 0 radius_fit 0.2 \