SetSeed

InfilePrefix 
// Note: the training atoms are needed for patching up chain breaks
// when reading in conformations.
InFilePrefix /projects/compbio/experiments/undertaker/atoms-inputs/
# use a small training set, to speed things up (contents not very important here)
	ReadTrainingAtoms cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz

# 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

InFilePrefix /projects/compbio/experiments/undertaker/spots/
    ReadAtomType exp-pdb.types
    ReadClashTable exp-pdb-2191-2symm.clash
    SetClashDefinition exp-pdb-2191-2symm

Time

MakeGenericFragmentLibrary
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

ReadTemplatePDB decoys/TR476.try22-opt3.pdb name try22
ReadTemplatePDB decoys/TR476.try23-opt3.pdb name try23
ReadTemplatePDB decoys/TR476.try24-opt3.pdb name try24
ReadTemplatePDB decoys/TR476.try25-opt3.pdb name try25
ReadTemplatePDB decoys/TR476.try26-opt3.pdb name try26
ReadTemplatePDB decoys/TR476.try27-opt3.pdb name try27

OutFilePrefix 

ReadFragmentAlignment SCWRL force_alignment NOFILTER shift-helix.a2m e_value 1.0

ExtractAlignmentsContacts 8 all_contacts rank
TIME
OptimizeConstraints all_contacts align rejected noncontact TR476.t06.CB8-sep9.rdb 
TIME
PrintContacts align move_helix.constraints 
PrintContacts rejected rejected_move_helix.constraints