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 TR432.a2m 1 NameTarget TR432 // 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 TR432.try5-opt3.pdb # < try3-opt3 < try2-opt3.gromacs0.repack-nonPC < chimera-init-try1 # best undertaker ReadConformPDB TR432.try4-opt3.repack-nonPC.pdb # < TR432 # optimized directly from provided model InFilePrefix ../T0432/decoys/servers/ # ReadConformPDB LEE-SERVER_TS1 # ReadConformPDB Phyre_de_novo_TS1 # ReadConformPDB FEIG_TS1 ReadConformPDB MULTICOM-REFINE_TS2 InFilePrefix // ReadConformPDB TR432.undertaker-align.pdb model 1 # PrintConformSheets align1.sheets # PrintConformHelices align1.helices // ReadConformPDB TR432.undertaker-align.pdb model 2 # PrintConformSheets align2.sheets # PrintConformHelices align2.helices // ReadConformPDB TR432.undertaker-align.pdb model 3 # PrintConformSheets align3.sheets # PrintConformHelices align3.helices // ReadConformPDB TR432.undertaker-align.pdb model 4 # PrintConformSheets align4.sheets # PrintConformHelices align4.helices // ReadConformPDB TR432.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 for-try4-MULTICOM.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