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-1332.rot


InFilePrefix /projects/compbio/experiments/undertaker/spots/
#    ReadAtomType pdb-name.types
#    ReadClashTable pdb-1332-2symm.clash
#    SetClashDefinition pdb-2symm
    ReadAtomType exp-pdb.types
    ReadClashTable exp-pdb-1332-2symm.clash
    SetClashDefinition exp-pdb-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 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 

 ReadTargetSeq T0235.a2m 
 NameTarget T0235
// Now have a random conformation---use PopConform if you don't want it.
 PopConform

InFilePrefix /projects/compbio/lib/alphabet/
ReadAlphabet alpha.alphabet
InFilePrefix
CreatePredAlphaCost pred_alpha_prev alpha11 T0235.t2k.alpha.rdb 1 alpha_prev

Time

// include best previously found decoys!
InFilePrefix decoys/
OutfilePrefix decoys/

# put believed-to-be-best decoy first
ReadConformPDB T0235.try5-opt2.pdb
ReadConformPDB T0235.try3-opt2.pdb
ReadConformPDB T0235.try1-opt2.pdb

InFilePrefix 
ReadConformPDB T0235.t2k.undertaker-align.pdb model 1
// PrintConformSheets align1.sheets
// PrintConformHelices align1.helices
ReadConformPDB T0235.t2k.undertaker-align.pdb model 2
// PrintConformSheets align2.sheets
// PrintConformHelices align2.helices
// ReadConformPDB T0235.t2k.undertaker-align.pdb model 3
// PrintConformSheets align3.sheets
// PrintConformHelices align3.helices
// ReadConformPDB T0235.t2k.undertaker-align.pdb model 4
// PrintConformSheets align4.sheets
// PrintConformHelices align4.helices
// ReadConformPDB T0235.t2k.undertaker-align.pdb model 5
// PrintConformSheets align5.sheets
// PrintConformHelices align5.helices

Time


// Don't put superimposed models into decoys/
// since that could mess up programs that find all decoy files.
OutFilePrefix
printAllConformPDB best-models.pdb superpose 

# Can specify a set of atoms as optional arguments of printAllConformPDB
# to give initial set of atoms to align.
# Format: 	atom A7.CA	atom K252.CA	...

Time

quit