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 T0370.a2m 1 NameTarget T0370 // Now have a random conformation---use PopConform if you don't want it. PopConform Time OutfilePrefix decoys/ InFilePrefix dimer/decoys/ ReadConformPDB T0370.try18-opt2.unpack.gromacs0.repack-nonPC.pdb chain A # best with rosetta ReadConformPDB T0370.try23-opt2.unpack.gromacs0.repack-nonPC.pdb chain A # dense packing, good rosetta score ReadConformPDB T0370.try12-opt2.unpack.gromacs0.repack-nonPC.pdb chain A # best non-chimeric with rosetta ReadConformPDB T0370.try17-opt2.unpack.pdb chain A # best with unconstrained, try23 ReadConformPDB T0370.try21-opt2.unpack.pdb chain A # best with try22.costfcn (other than try18) InFilePrefix decoys/ # ReadConformPDB T0370.try73-opt2.pdb # monomeric source for try18 above # ReadConformPDB T0370.try64-opt2.pdb # monomeric source for non-chimeric. InFilePrefix decoys/ # ReadConformPDB tr370.pdb # model to refine # our models InFilePrefix decoys/ # ReadConformPDB T0370.try46-opt2.gromacs0.repack-nonPC.pdb.gz # best rosetta, helix-inside, sheet Time // Don't put superimposed models into decoys/ // since that could mess up programs that find all decoy files. OutFilePrefix printAllConformPDB refine-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