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 T0342.a2m 1 NameTarget T0342 // 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/ // include read-pdb.under ReadConformPDB T0342.try22-opt2.gromacs0.repack-nonPC.pdb InFilePrefix decoys/ProteinShop/ ReadConformPDB try23-shifted.pdb # InFilePrefix K140-L188/decoys/ # ReadConformPDB T0342.try2-opt2.gromacs0.repack-nonPC.pdb Time // Don't put superimposed models into decoys/ // since that could mess up programs that find all decoy files. OutFilePrefix printAllConformPDB try22+shifted.pdb superpose Time quit