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 T0339.a2m 1 NameTarget T0339 // 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 ReadConformPDB T0339.monomer-from-try9-opt2-dimer.pdb # < try10 < try6 < 1p3wA ReadConformPDB T0339.monomer-from-try6-opt2-dimer.pdb # < try2 < try1 < 1t3iA ReadConformPDB T0339.try17-opt2.gromacs0.repack-nonPC.pdb ReadConformPDB T0339.monomer-from-try8-opt2-dimer.pdb # < try11 < try8 ReadConformPDB T0339.try9-opt2.pdb # < try7 < try5 < 1eg5A # ReadConformPDB T0339.try6-opt2.pdb # mainly 1p3wA #ReadConformPDB T0339.try6-opt2.gromacs0.repack-nonPC.pdb #ReadConformPDB T0339.try5-opt2.pdb # mainly 1eg5A InFilePrefix # ReadConformPDB T0339.undertaker-align.pdb model 1 # 1t3iA # PrintConformSheets align1.sheets # PrintConformHelices align1.helices #ReadConformPDB T0339.undertaker-align.pdb model 2 # 1v2dA # PrintConformSheets align2.sheets # PrintConformHelices align2.helices # ReadConformPDB T0339.undertaker-align.pdb model 3 # 1wyuB # PrintConformSheets align3.sheets # PrintConformHelices align3.helices #ReadConformPDB T0339.undertaker-align.pdb model 4 # 1yjsA # PrintConformSheets align4.sheets # PrintConformHelices align4.helices #ReadConformPDB T0339.undertaker-align.pdb model 5 # 1kl1A # 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