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 T0316.a2m 1
 NameTarget T0316
// 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/
ReadConformPDB T0316.try21-opt2.pdb 
ReadConformPDB T0316.try8-opt2.pdb 
ReadConformPDB T0316.try14-opt2.pdb 
ReadConformPDB T0316.try9-opt2.repack-nonPC.pdb	# from ROBETTA_TS4
ReadConformPDB T0316.try11-opt2.pdb
# ReadConformPDB T0316.try15-opt2.pdb


#ReadConformPDB T0316.try4-opt2.repack-nonPC.pdb
#ReadConformPDB T0316.try1-opt2.pdb
# ReadConformPDB T0316.try12-opt2.pdb 
# ReadConformPDB T0316.try10-opt2.pdb
# ReadConformPDB T0316.try6-opt2.pdb

InFilePrefix 
#ReadConformPDB T0316.undertaker-align.pdb model 1
#ReadConformPDB T0316.undertaker-align.pdb model 2
#ReadConformPDB T0316.undertaker-align.pdb model 3
#ReadConformPDB T0316.undertaker-align.pdb model 4
#ReadConformPDB T0316.undertaker-align.pdb model 5

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