SetSeed // Note: the training atoms are needed for patching up chain breaks // when reading in conformations. InFilePrefix /projects/compbio/experiments/undertaker/atoms-inputs/ ReadTrainingAtoms dunbrack-2191.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 T0339.a2m START_COL # ReadTargetPDB T0339.blank.pdb NameTarget T0339 // Now have a random conformation---use PopConform if you don't want it. PopConform // get rid of random conformation Time MakeGenericFragmentLibrary Time // The following alignments are believed to be good: InfilePrefix 1eg5A/ ReadFragmentAlignment NOFILTER SCWRL T0339-1eg5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m InfilePrefix 1p3wA/ ReadFragmentAlignment NOFILTER SCWRL T0339-1p3wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m PrintAlignmentsSheets T0339.1eg5A-1p3wA.sheets // May want to add extra arguments to the following, to // specify highly conserved residues or atoms to focus on when superposing. quit