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 T0340.a2m 1 NameTarget T0340 // 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/ ReadConformPDB T0340.try11-opt2.pdb //highest scoring in Undertaker # ReadConformPDB T0340.try9-opt2.pdb //not as polished as try11 # ReadConformPDB T0340.try7-opt2.pdb //not as polished as try9 # ReadConformPDB T0340.try3-opt2.pdb # ReadConformPDB T0340.try2-opt2.pdb # ReadConformPDB T0340.try8-opt2.pdb # ReadConformPDB T0340.try4-opt2.pdb ReadConformPDB T0340.try6-opt2.gromacs0.repack-nonPC.pdb.gz //Rosetta's favorite # ReadConformPDB T0340.try1-opt2.gromacs0.repack-nonPC.pdb.gz //Rosetta's second favorite ReadConformPDB T0340.try1-opt2.pdb // fully automatic InFilePrefix decoys/servers/ # ReadConformPDB ROBETTA_TS3.pdb # ReadConformPDB ROBETTA_TS4.pdb # ReadConformPDB ROBETTA_TS1.pdb InFilePrefix decoys/ ReadConformPDB T0340.try12-opt2.pdb // first run from 1tp5A InFilePrefix ReadConformPDB T0340.undertaker-align.pdb model 1 # from 1g9oA # PrintConformSheets align1.sheets # PrintConformHelices align1.helices # ReadConformPDB T0340.undertaker-align.pdb model 2 # PrintConformSheets align2.sheets # PrintConformHelices align2.helices ReadConformPDB T0340.undertaker-align.pdb model 3 # PrintConformSheets align3.sheets # PrintConformHelices align3.helices ReadConformPDB T0340.undertaker-align.pdb model 4 # PrintConformSheets align4.sheets # PrintConformHelices align4.helices #ReadConformPDB T0340.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