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 T0338.a2m 1 NameTarget T0338 // 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 # from 1kxu (in order by try15.costfcn) # from monomer try3 # ReadConformPDB T0338.try15-opt2.pdb # try15.costfcn favorite ReadConformPDB T0338.try15-opt2.unpack.gromacs0.repack-nonPC.pdb # rosetta favorite # ReadConformPDB T0338.try10-opt2.pdb # monomer try3 # ReadConformPDB T0338.try14-opt2.pdb # monomer try3 # ReadConformPDB T0338.try5-opt2.pdb # monomer try3 ReadConformPDB dimer-1kxu-try3-opt2.pdb # monomer try3 # from monomer try4 ReadConformPDB T0338.try4-opt2.pdb # monomer try4 # ReadConformPDB dimer-1kxu-try4-opt2.pdb # monomer try4 # ReadConformPDB dimer-1kxu-try1-opt2.pdb # ReadConformPDB dimer-1kxu-try5-opt2.pdb # ReadConformPDB dimer-1kxu-try6-opt2.pdb # from 1zp2 # ReadConformPDB T0338.try13-opt2.pdb # moved # ReadConformPDB T0338.try12-opt2.pdb # moved #ReadConformPDB T0338.try8-opt2.pdb ReadConformPDB T0338.try16-opt2.pdb #based off try8 with constraints #ReadConformPDB T0338.try17-opt2.pdb #based off proteinshopped dimer-try3 # ReadConformPDB dimer-1zp2-try3-opt2.pdb # from 1jkw (like 1kxu, but tighter) ReadConformPDB dimer-1jkw-try4-opt2.pdb # monomer try4 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 \ residue I38 residue A55 residue A80 residue L83 residue A84 \ atom K86.CB residue L126 atom E130.CB residue L137 atom F139.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