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

Time


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

InFilePrefix 

 ReadTargetSeq TR389.a2m 1
 NameTarget TR389
// Now have a random conformation---use PopConform if you don't want it.
 PopConform


Time

OutfilePrefix decoys/


# put believed-to-be-best decoy first
InFilePrefix decoys/
// include read-pdb.under
ReadConformPDB TR389.try10-opt3.pdb
ReadConformPDB TR389.try9-opt3.gromacs0.repack-nonPC.pdb
#
ReadConformPDB TR389.try8-opt3.gromacs0.pdb
#
ReadConformPDB TR389.try6-opt3.pdb
ReadConformPDB TR389.try5-opt3.gromacs0.repack-nonPC.pdb
#
# ReadConformPDB TR389.try3-opt3.pdb
# ReadConformPDB TR389.try3-opt3.repack-nonPC.pdb
# ReadConformPDB TR389.try2-opt3.gromacs0.pdb
# ReadConformPDB TR389.init.pdb
# PrintConformSheets init.sheets
# PrintConformHelices init.helices
# ReadConformPDB T0389.try10-opt1-scwrl.pdb


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