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 T0381.a2m 1 NameTarget T0381 // 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 M1-S91/decoys/ ReadConformPDB T0381.try1-opt2.pdb InFilePrefix decoys/ // include read-pdb.under ReadConformPDB T0381.try1-opt2.pdb Time // Don't put superimposed models into decoys/ // since that could mess up programs that find all decoy files. OutFilePrefix printAllConformPDB try1-opt2sub+try1-opt2.pdb superpose \ atom S85.CB atom Y86.CB atom L87.CB \ atom S88.CB atom S89.CB atom L90.CB atom S91.CB \ # 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