SetSeed

InfilePrefix 
// Note: the training atoms are needed for patching up chain breaks
// when reading in conformations.
InFilePrefix /projects/compbio/experiments/undertaker/atoms-inputs/
ReadTrainingAtoms dunbrack-40pc-3157.atoms

# The rotamer library need not be from the same set of chains as the TrainingAtoms.
# It encodes the most probable conformations of sidechain and backbone
# for each residue type.
ReadRotamerLibrary dunbrack-40pc-3157.rot

Time


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

InFilePrefix 

# ReadTargetPDB TR476.blank.pdb
ReadTargetSeq TR476.a2m 2
NameTarget TR476
PopConform

InFilePrefix

include costfcn-init.under
# include MQA_init.costfcn
include try3.costfcn

Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/

InFilePrefix 
# ReadTemplateAtoms Template.atoms

// Switch to the following (commenting out the TryAllAlign)
// to polish existing models
InfilePrefix decoys/
# include read-pdb.under
ReadConformPDB TR476.pdb.gz

OutfilePrefix decoys/
SCWRLConform
NameConform TR476-scwrl
PrintConformPDB TR476-scwrl.pdb

CostConform
Time