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/T0326/
ReadTargetSeq T0326.a2m 1

InFilePrefix /projects/compbio/experiments/protein-predict/casp7/T0326/

# include the alignments
Include /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0326/manyalignments-good-all.under

#include the constraints to score the models
Include /projects/compbio/experiments/protein-predict/casp7/T0326/align.constraints_v3.costfcn

#include the models
InFilePrefix /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0326/
Include servers-clean.under

ExtractAlignmentsContacts 8 all3.constraints metaserver both
OptimizeConstraints all3.constraints align3.constraints rejected3.constraints noncontact3.constraints probabilities.dat

PrintContacts align3.constraints align.constraints_meta03
PrintContacts align3.constraints.bonus align_bonus.constraints_meta03
PrintContacts rejected3.constraints rejected.constraints_meta03
PrintContacts rejected3.constraints.bonus rejected_bonus.constraints_meta03
PrintContacts noncontact3.constraints non_contacts.constraints_meta03
PrintContacts noncontact3.constraints.bonus non_contacts_bonus.constraints_meta03
PrintContacts all3.constraints all.constraints_meta03

quit