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 InFilePrefix /projects/compbio/experiments/protein-predict/casp7/T0375/ ReadTargetSeq T0375.a2m 1 InFilePrefix /projects/compbio/experiments/protein-predict/casp7/T0375/ Include /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0375/manyalignments-good-all.under ExtractAlignmentsContacts 8 all.constraints OptimizeConstraints all.constraints align.constraints rejected.constraints noncontact.constraints probabilities.dat PrintContacts align.constraints align.constraints_v3 PrintContacts align.constraints.bonus align_bonus.constraints_v3 PrintContacts rejected.constraints rejected.constraints_v3 PrintContacts rejected.constraints.bonus rejected_bonus.constraints_v3 PrintContacts noncontact.constraints non_contacts.constraints_v3 PrintContacts noncontact.constraints.bonus non_contacts_bonus.constraints_v3 PrintContacts all.constraints all.constraints_v3 quit