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 T0381.a2m 1 NameTarget T0381 // 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 dimer/decoys/ ReadConformPDB T0381.try10-opt2.unpack.pdb chain A # ReadConformPDB T0381.try9-opt2.unpack.pdb chain A ReadConformPDB T0381.try7-opt2.unpack.pdb chain A ReadConformPDB from-4mer-try3-al4.pdb chain A # duplicate position, so incomplete # ReadConformPDB T0381.try6-opt2.unpack.pdb chain A # ReadConformPDB T0381.try5-opt2.unpack.pdb chain A # ReadConformPDB T0381.try4-opt2.unpack.pdb chain A # ReadConformPDB T0381.try1-opt2.unpack.pdb chain A InFilePrefix decoys/ // include read-pdb.under ReadConformPDB T0381.try18-opt2.pdb # ReadConformPDB T0381.try16-opt2.pdb # ReadConformPDB T0381.try23-opt2.pdb # ReadConformPDB T0381.try10-opt2.pdb # ReadConformPDB T0381.try11-opt2.pdb InFilePrefix # ReadConformPDB T0381.undertaker-align.pdb model 1 # 1mkm t06 # PrintConformSheets align1.sheets # PrintConformHelices align1.helices ReadConformPDB T0381.undertaker-align.pdb model 2 #2g7uA t06 # PrintConformSheets align2.sheets # PrintConformHelices align2.helices #ReadConformPDB T0381.undertaker-align.pdb model 3 # PrintConformSheets align3.sheets # PrintConformHelices align3.helices #ReadConformPDB T0381.undertaker-align.pdb model 4 # PrintConformSheets align4.sheets # PrintConformHelices align4.helices #ReadConformPDB T0381.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 \ atom L103.CB atom G140.CA atom S149.CB \ atom G151.CA atom A213.CB atom P215.CB # 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