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/T0360/ ReadTargetSeq T0360.a2m 1 InFilePrefix /projects/compbio/experiments/protein-predict/casp7/T0360/ #Include /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0360/manyalignments-good-all.under Include /projects/compbio/experiments/protein-predict/casp7/T0360/align.constraints_v3.costfcn InFilePrefix /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0360/ Include servers-clean.under ExtractAlignmentsContacts 8 all2.constraints metaserver metaserver OptimizeConstraints all2.constraints align2.constraints rejected2.constraints noncontact2.constraints probabilities.dat PrintContacts align2.constraints align.constraints_meta02 PrintContacts align2.constraints.bonus align_bonus.constraints_meta02 PrintContacts rejected2.constraints rejected.constraints_meta02 PrintContacts rejected2.constraints.bonus rejected_bonus.constraints_meta02 PrintContacts noncontact2.constraints non_contacts.constraints_meta02 PrintContacts noncontact2.constraints.bonus non_contacts_bonus.constraints_meta02 PrintContacts all2.constraints all.constraints_meta02 quit