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-2191.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 

ReadTargetPDB dimer/decoys/dimer-from-try2-opt2-template-1s5uA.pdb
NameTarget T0362

MakeGenericFragmentLibrary
Time


InFilePrefix 

Time

# If multimer is not already in pdb, but needs crystal symmetries to generate,
# then fetch the "biological unit" from pdb and use the following commands:
ReadTemplatePDB 1s5u.pdb1 model 1 name 1s5uA
ReadTemplatePDB 1s5u.pdb1 model 2 name 1s5uB

OutFilePrefix 4mer/decoys/

InFilePrefix 1s5uA/
ReadFragmentAlignment NOFILTER 1s5uA.4mer-a2m
InFilePrefix
PrintMultimerPDB 4 4mer-from-try2-opt2-template-1s5uA.pdb
Time