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 T0289.a2m 1 NameTarget T0289 // Now have a random conformation---use PopConform if you don't want it. PopConform Time // include best previously found decoys! InFilePrefix decoys/ OutfilePrefix decoys/ // include read-pdb.under # put believed-to-be-best decoy first ReadConformPDB T0289.try11-opt2.pdb # InfilePrefix S1-F214/decoys/ # ReadConformPDB T0289.try1-opt2.pdb # InFilePrefix # ReadConformPDB try11-opt2-chopped-to-C217.pdb #InfilePrefix P215-H312/decoys/ #ReadConformPDB T0289.try7-opt2.pdb InfilePrefix A201-H312/decoys/ ReadConformPDB T0289.try2-opt2.pdb #InFilePrefix #ReadConformPDB T0289.undertaker-align.pdb model 1 #PrintConformSheets align1.sheets #PrintConformHelices align1.helices #ReadConformPDB T0289.undertaker-align.pdb model 2 #PrintConformSheets align2.sheets #PrintConformHelices align2.helices #ReadConformPDB T0289.undertaker-align.pdb model 3 #PrintConformSheets align3.sheets #PrintConformHelices align3.helices #ReadConformPDB T0289.undertaker-align.pdb model 4 #PrintConformSheets align4.sheets #PrintConformHelices align4.helices #ReadConformPDB T0289.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 make-chimera2.pdb atom F214 atom P215 atom P216 superpose # PrintAllConformPDB make-chimera3.pdb atom D220 atom V221 atom Y222 atom K223 superpose PrintAllConformPDB make-chimera4.pdb atom Q247 atom D248 atom Q249 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