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 T0356.a2m 1 NameTarget T0356 // 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 chimera-domain-1-and-2.pdb // include read-pdb.under #try5 is a polish run of RAPTORESS_TS4 & RAPTORESS_TS5, mostly used TS4 #ReadConformPDB T0356.try5-opt2.gromacs0.repack-nonPC.pdb #try1 is Undertaker's automatic model #ReadConformPDB T0356.try1-opt2.repack-nonPC.pdb #try4 is a polish of SAM_T06_server_TS1, our best scoring server model #ReadConformPDB T0356.try4-opt2.repack-nonPC.pdb #try3 is an Undertaker run using dssp-ehl2 constraints, but no rr constraints #ReadConformPDB T0356.try3-opt2.repack-nonPC.pdb #try2 is an Undertaker run using dssp-ehl2 constraints, but no rr constraints #ReadConformPDB T0356.try2-opt2.repack-nonPC.pdb #InFilePrefix M1-R180/decoys/ #ReadConformPDB T0356.try6-opt2.pdb #InFilePrefix T160-F340/decoys/ #ReadConformPDB T0356.try8-opt2.pdb InFilePrefix T320-S496/decoys/ ReadConformPDB T0356.try3-opt2.pdb InFilePrefix #ReadConformPDB T0356.undertaker-align.pdb model 1 # PrintConformSheets align1.sheets # PrintConformHelices align1.helices #ReadConformPDB T0356.undertaker-align.pdb model 2 # PrintConformSheets align2.sheets # PrintConformHelices align2.helices #ReadConformPDB T0356.undertaker-align.pdb model 3 # PrintConformSheets align3.sheets # PrintConformHelices align3.helices #ReadConformPDB T0356.undertaker-align.pdb model 4 # PrintConformSheets align4.sheets # PrintConformHelices align4.helices #ReadConformPDB T0356.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 chimera-domain-1-and-2-and-3.pdb superpose \ residue P329 residue A330 residue V331 # 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