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 T0373.a2m 1 NameTarget T0373 // 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/ ReadConformPDB T0373.try9-opt2.pdb ReadConformPDB T0373.try6-opt2.pdb ReadConformPDB T0373.try1-opt2.pdb ReadConformPDB T0373.try7-opt2.pdb ReadConformPDB T0373.try8-opt2.pdb ReadConformPDB T0373.try5-opt2.unpack.gromacs0.repack-nonPC.pdb ReadConformPDB T0373.try4-opt2.unpack.gromacs0.repack-nonPC.pdb # ReadConformPDB T0373.try4-opt2.pdb # ReadConformPDB T0373.try3-opt2.pdb # ReadConformPDB T0373.try2-opt2.pdb 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 \ atom L56.CB atom L71.CB atom L74.CB atom I80.CB \ atom D88.CB atom R90.CB atom G100.CA # 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