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 T0289.a2m 1 NameTarget T0289 // Now have a random conformation---use PopConform if you don't want it. PopConform Time // include best previously found decoys! InFilePrefix decoys/ OutfilePrefix decoys/ // include read-pdb.under # put believed-to-be-best decoy first # replace with polished version ReadConformPDB T0289.try24-opt2.pdb # InfilePrefix decoys/servers/ # ReadConformPDB ROBETTA_TS5.pdb InFilePrefix decoys/ ReadConformPDB T0289.try23-opt2.pdb InFilePrefix decoys/ ReadConformPDB T0289.try22-opt2.pdb # ReadConformPDB SAM_T06_server_TS1.pdb # ReadConformPDB RAPTORESS_TS2.pdb InFilePrefix ReadConformPDB T0289.undertaker-align.pdb model 1 #PrintConformSheets align1.sheets #PrintConformHelices align1.helices # ReadConformPDB T0289.undertaker-align.pdb model 2 #PrintConformSheets align2.sheets #PrintConformHelices align2.helices # ReadConformPDB T0289.undertaker-align.pdb model 3 #PrintConformSheets align3.sheets #PrintConformHelices align3.helices ReadConformPDB T0289.undertaker-align.pdb model 4 #PrintConformSheets align4.sheets #PrintConformHelices align4.helices # ReadConformPDB T0289.undertaker-align.pdb model 5 #PrintConformSheets align5.sheets #PrintConformHelices align5.helices 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 # 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