// Note: the training atoms are needed for patching up chain breaks // when reading in conformations. InFilePrefix /projects/kestrel/users/karplus/burial/undertaker/atoms-inputs/ ReadTrainingAtoms monomeric-50pc.atoms ReadRotamerLibrary monomeric-50pc.rot InFilePrefix /projects/kestrel/users/karplus/burial/undertaker/spots/ ReadAtomType pdb-name.types ReadClashTable pdb-atom-name.clash SetClashDefinition pdb-atom-name CreateBurialCost wet6.5 monomeric-50pc-wet-6.5.spot smoothed-monomeric-50pc-wet-6.5.hist log CreateBurialCost dry6.5 monomeric-50pc-dry-6.5.spot smoothed-monomeric-50pc-dry-6.5.hist CreateBurialCost gen6.5 monomeric-50pc-generic-6.5.spot smoothed-monomeric-50pc-generic-6.5.hist CreateBurialCost dry8 monomeric-50pc-dry-8.spot smoothed-monomeric-50pc-dry-8.hist CreateBurialCost dry10 monomeric-50pc-dry-10.spot smoothed-monomeric-50pc-dry-10.hist CreateBurialCost dry12 monomeric-50pc-dry-12.spot smoothed-monomeric-50pc-dry-12.hist CreateAlphaCost alpha monomeric-smoothed-alpha.hist CreateAlphaCost alpha_prev monomeric-smoothed-alpha-1.hist -1 Time //Need to read in target before specific fragments or alignments can // be read, also before constraints can be defined. InFilePrefix ReadTargetPDB T0151.blank.pdb NameTarget T0151 PopConform // get rid of uneeded all-zero conformation InFilePrefix /projects/compbio/lib/alphabet/ ReadAlphabet alpha.alphabet InFilePrefix CreatePredAlphaCost pred_alpha2 alpha11 T0151.t2k.alpha.rdb 2 alpha alpha_prev SetCost gen6.5 0.2 wet6.5 0.2 dry6.5 1.0 dry8 1.0 dry12 1 \ radius_norm 0 radius_fit 0.2 \ sidechain 0.2 \ clashes 1 sidechain_clashes -0.2 backbone_clashes 0.5 \ break 5 \ constraints 0.01 \ pred_alpha2 1 \ contact_order 1 // known_ssbond 0.5