SetSeed


// Note: the training atoms are needed for patching up chain breaks
// when reading in conformations.
 InFilePrefix /projects/compbio/experiments/undertaker/atoms-inputs/
ReadTrainingAtoms monomeric-50pc.atoms
ReadRotamerLibrary dunbrack-2191.rot

InFilePrefix /projects/compbio/experiments/undertaker/spots/
    ReadAtomType exp-pdb.types
    ReadClashTable exp-pdb-2191-2symm.clash
    SetClashDefinition exp-pdb-2191-2symm

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 near_backbone near-backbone-center.spot smoothed-near-backbone-2spot.hist near-backbone-count.spot
CreateBurialCost way_back way-back-center.spot smoothed-way-back-2spot.hist way-back-count.spot

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 dunbrack-2191-alpha.hist
CreateAlphaCost alpha_prev  dunbrack-2191-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 T0296.blank.pdb
ReadTargetSeq T0296.a2m 1
NameTarget T0296
PopConform

InFilePrefix /projects/compbio/lib/alphabet/
ReadAlphabet alpha.alphabet
Time

InFilePrefix
include unconstrained.costfcn
Time

// include all previously found decoys!
InFilePrefix decoys/
ReadConformPDB servers/CaspIta-FOX_TS1.pdb.gz
NameConform CaspIta-FOX_TS1
SCWRLConform
NameConform CaspIta-FOX_TS1-scwrl
ReadConformPDB servers/CaspIta-FOX_TS2.pdb.gz
NameConform CaspIta-FOX_TS2
SCWRLConform
NameConform CaspIta-FOX_TS2-scwrl
ReadConformPDB servers/CaspIta-FOX_TS3.pdb.gz
NameConform CaspIta-FOX_TS3
SCWRLConform
NameConform CaspIta-FOX_TS3-scwrl
ReadConformPDB servers/CaspIta-FOX_TS4.pdb.gz
NameConform CaspIta-FOX_TS4
SCWRLConform
NameConform CaspIta-FOX_TS4-scwrl
ReadConformPDB servers/CaspIta-FOX_TS5.pdb.gz
NameConform CaspIta-FOX_TS5
SCWRLConform
NameConform CaspIta-FOX_TS5-scwrl

# include read-pdb+servers.under
Time

OutFilePrefix decoys/
ReportCost score-all+servers.unconstrained.rdb
CostConform
Time

PrintConformBreaks all.breaks
ClashConform all.clashes
Time

# print out the constraints, to verify that the requested ones were
# 	actually the ones desired.
# PrintConstraints

quit