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 T0308.a2m 1 NameTarget T0308 // Now have a random conformation---use PopConform if you don't want it. PopConform Time OutfilePrefix decoys/ // include read-pdb.under # put believed-to-be-best decoy first InFilePrefix decoys/ # refined from tr308: ReadConformPDB T0308.try9-opt2.pdb ReadConformPDB T0308.try6-opt2.gromacs0.repack-nonPC.pdb ReadConformPDB T0308.try10-opt2.pdb ReadConformPDB T0308.try12-opt2.gromacs0.repack-nonPC.pdb ReadConformPDB T0308.try7-opt2.pdb # ReadConformPDB T0308.try6-opt2.pdb # ReadConformPDB T0308.try8-opt2.pdb # ReadConformPDB tr308-scwrl.pdb #nReadConformPDB tr308.pdb # not from refinement, but from own backbone prediction: # ReadConformPDB T0308.try4-opt2.gromacs0.repack-nonPC.pdb # ReadConformPDB T0308.try5-opt2.pdb 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