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 T0321.a2m 1 NameTarget T0321 // Now have a random conformation---use PopConform if you don't want it. PopConform Time // include best previously found decoys! InFilePrefix decoys/ OutfilePrefix decoys/ // include read-pdb.under # put believed-to-be-best decoy first ReadConformPDB T0321.try3-opt2.pdb ReadConformPDB T0321.try2-opt2.pdb ReadConformPDB T0321.try1-opt2.pdb ReadConformPDB T0321.try4-opt2.pdb InFilePrefix ReadConformPDB T0321.undertaker-align.pdb model 1 ReadConformPDB T0321.undertaker-align.pdb model 2 ReadConformPDB T0321.undertaker-align.pdb model 3 ReadConformPDB T0321.undertaker-align.pdb model 4 ReadConformPDB T0321.undertaker-align.pdb model 5 Time // Don't put superimposed models into decoys/ // since that could mess up programs that find all decoy files. OutFilePrefix printAllConformPDB best-models.pdb superpose # Can specify a set of atoms as optional arguments of printAllConformPDB # to give initial set of atoms to align. # Format: atom A7.CA atom K252.CA ... Time quit