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 exp-pdb.types
    ReadClashTable exp-pdb-2191-2symm.clash
    SetClashDefinition exp-pdb-2191-2symm

Time

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

# ReadTargetPDB XXX0000.blank.pdb
ReadTargetSeq XXX0000.a2m START_COL
NameTarget XXX0000
PopConform

# Read real conformation

# Read conformation by specifying a PDB id
clearIDs 
AddID REAL_PDB

# DO READ
ReadConformPDBids
# ReadConformPDB XXX0000_domain.real.pdb

SaveConformAsReal

InfilePrefix decoys/
OutFilePrefix decoys/
include read-pdb.under

Time

quit