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 dimer/decoys/ ReadTargetPDB T0327.try6-opt2.unpack.pdb chain A NameTarget T0327 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 1tbx.pdb1 model 1 name 1tbxA # ReadTemplatePDB 1tbx.pdb1 model 2 name 1tbxB OutFilePrefix dimer/decoys/ InFilePrefix 1tbxA/ ReadFragmentAlignment NOFILTER force_alignment T0327-1tbxA.dimer1-a2m PrintMultimerPDB 2 dimer1-1tbxA-dimer6.pdb ReadFragmentAlignment NOFILTER force_alignment T0327-1tbxA.dimer2-a2m PrintMultimerPDB 2 dimer2-1tbxA-dimer6.pdb ReadFragmentAlignment NOFILTER force_alignment T0327-1tbxA.dimer3-a2m PrintMultimerPDB 2 dimer3-1tbxA-dimer6.pdb Time