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 T0386.a2m 1 NameTarget T0386 // Now have a random conformation---use PopConform if you don't want it. PopConform Time OutfilePrefix decoys/ InFilePrefix decoys/ ReadConformPDB T0386.try4-opt2.gromacs0.repack-nonPC.pdb InFilePrefix L225-T299/decoys/ ReadConformPDB T0386.try1-opt2.pdb Time // Don't put superimposed models into decoys/ // since that could mess up programs that find all decoy files. OutFilePrefix printAllConformPDB for-chimera-4-1.pdb superpose \ atom E228.CA atom F229.CA atom M230.CA \ atom H231.CA atom T232.CA atom M233.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