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 monomeric-50pc.rot InFilePrefix /projects/compbio/experiments/undertaker/spots/ # ReadAtomType pdb-name.types # ReadClashTable pdb-1332-2symm.clash # SetClashDefinition pdb-2symm ReadAtomType exp-pdb.types ReadClashTable exp-pdb-1332-2symm.clash SetClashDefinition exp-pdb-2symm CreateBurialCost dry5 monomeric-50pc-dry-5.spot smoothed-monomeric-50pc-dry-5.hist CreateBurialCost wet6.5 monomeric-50pc-wet-6.5.spot smoothed-monomeric-50pc-wet-6.5.hist log CreateBurialCost dry6.5 monomeric-50pc-dry-6.5.spot smoothed-monomeric-50pc-dry-6.5.hist CreateBurialCost gen6.5 monomeric-50pc-generic-6.5.spot smoothed-monomeric-50pc-generic-6.5.hist CreateBurialCost dry8 monomeric-50pc-dry-8.spot smoothed-monomeric-50pc-dry-8.hist CreateBurialCost dry10 monomeric-50pc-dry-10.spot smoothed-monomeric-50pc-dry-10.hist CreateBurialCost dry12 monomeric-50pc-dry-12.spot smoothed-monomeric-50pc-dry-12.hist CreateAlphaCost alpha monomeric-smoothed-alpha.hist CreateAlphaCost alpha_prev monomeric-smoothed-alpha-1.hist -1 Time //Need to read in target before specific fragments or alignments can // be read, also before constraints can be defined. InFilePrefix ReadTargetSeq T0216.a2m NameTarget T0216 # Now have a random conformation---use PopConform if you don't want it. PopConform InFilePrefix /projects/compbio/lib/alphabet/ ReadAlphabet alpha.alphabet InFilePrefix CreatePredAlphaCost pred_alpha_prev alpha11 T0216.t2k.alpha.rdb 1 alpha_prev Time // include best previously found decoys! InFilePrefix decoys/ // include read-pdb.under # put believed-to-be-best decoy first ReadConformPDB decoysT0216.try3-opt2.pdb # PrintConformSheets decoys/try1-opt2.sheets ReadConformPDB old1-218/decoys/T0216.try9-opt2.pdb.gz # PrintConformSheets 1-218/decoys/robetta1.sheets # rintConformHelices decoys/robetta1.helices ReadConformPDB 216-435/decoys/T0216.try6-opt2.pdb.gz # PrintConformSheets decoys/robetta2.sheets # PrintConformHelices decoys/robetta2.helices # ReadConformPDB robetta-model3.pdb # PrintConformSheets decoys/robetta3.sheets # PrintConformHelices decoys/robetta3.helices # # ReadConformPDB robetta-model4.pdb # PrintConformSheets decoys/robetta4.sheets # PrintConformHelices decoys/robetta4.helices # # ReadConformPDB robetta-model5.pdb # PrintConformSheets decoys/robetta5.sheets # PrintConformHelices decoys/robetta5.helices # InFilePrefix # ReadConformPDB T0216.t2k.undertaker-align.pdb model 1 # PrintConformSheets decoys/align1.sheets # ReadConformPDB T0216.t2k.undertaker-align.pdb model 2 # PrintConformSheets decoys/align2.sheets # ReadConformPDB T0216.t2k.undertaker-align.pdb model 3 # PrintConformSheets decoys/align3.sheets # ReadConformPDB T0216.t2k.undertaker-align.pdb model 4 # PrintConformSheets decoys/align4.sheets # ReadConformPDB T0216.t2k.undertaker-align.pdb model 5 # PrintConformSheets decoys/align5.sheets Time # Don't put superimposed models into decoys/ # since that could mess up programs that find all decoy files. OutFilePrefix printAllConformPDB best-super.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