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 T0307.a2m 1
 NameTarget T0307
// 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/

#Firas' 2 best models:
#try24 scores best with its costfcn and unconstrained
ReadConformPDB T0307.try24-opt2.pdb

# Martin's best model so far:
# - beta bridge where I think it ought to be
# - 4 helices that flank the bridge are roughly in the right place
ReadConformPDB T0307.try26-opt2.pdb

# an early six-helix bundle
ReadConformPDB T0307.try3-opt2.pdb

# a mess built on top of an EFhand motif (in the wrong place)
ReadConformPDB T0307.try1-opt2.pdb

#try25 is based on ROBETTA's model 4
ReadConformPDB T0307.try25-opt2.pdb
#InFilePrefix decoys/servers/
#ReadConformPDB ROBETTA_TS4.pdb

InFilePrefix 

# has the EF-hand motif but in the wrong place
#ReadConformPDB T0307.undertaker-align.pdb model 3

# looks like a protein, ish
#ReadConformPDB T0307.undertaker-align.pdb model 1


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