SetSeed


// Note: the training atoms are needed for patching up chain breaks
// when reading in conformations.
 InFilePrefix /projects/compbio/experiments/undertaker/atoms-inputs/
 ReadTrainingAtoms monomeric-50pc.atoms
 ReadRotamerLibrary dunbrack-1332.rot


InFilePrefix /projects/compbio/experiments/undertaker/spots/
#    ReadAtomType pdb-name.types
#    ReadClashTable pdb-1332-2symm.clash
#    SetClashDefinition pdb-2symm
    ReadAtomType exp-pdb.types
    ReadClashTable exp-pdb-1332-2symm.clash
    SetClashDefinition exp-pdb-2symm

Time


//Need to read in target before specific fragments or alignments can
// be read, also before constraints can be defined.

InFilePrefix 

 ReadTargetSeq T0242.a2m 
 NameTarget T0242
// Now have a random conformation---use PopConform if you don't want it.
 PopConform

InFilePrefix /projects/compbio/lib/alphabet/
ReadAlphabet alpha.alphabet
InFilePrefix

Time

// include best previously found decoys!
InFilePrefix decoys/
OutfilePrefix decoys/
// include read-pdb.under

# put believed-to-be-best decoy first
ReadConformPDB T0242.try1-opt2.pdb


InFilePrefix decoys/
ReadConformPDB       FUGMOD_SERVER_TS2.pdb
PrintConformSheets   FUGMOD_SERVER_TS2.sheets
PrintConformHelices  FUGMOD_SERVER_TS2.helices

ReadConformPDB       FUGMOD_SERVER_TS3.pdb
PrintConformSheets   FUGMOD_SERVER_TS3.sheets
PrintConformHelices  FUGMOD_SERVER_TS3.helices

ReadConformPDB       FUGMOD_SERVER_TS5.pdb
PrintConformSheets   FUGMOD_SERVER_TS5.sheets
PrintConformHelices  FUGMOD_SERVER_TS5.helices

ReadConformPDB       robetta-model1.pdb
PrintConformSheets   robetta-model1.sheets
PrintConformHelices  robetta-model1.helices

ReadConformPDB       robetta-model2.pdb
PrintConformSheets   robetta-model2.sheets
PrintConformHelices  robetta-model2.helices

ReadConformPDB       robetta-model3.pdb
PrintConformSheets   robetta-model3.sheets
PrintConformHelices  robetta-model3.helices

ReadConformPDB       robetta-model4.pdb
PrintConformSheets   robetta-model4.sheets
PrintConformHelices  robetta-model4.helices

ReadConformPDB       robetta-model5.pdb
PrintConformSheets   robetta-model5.sheets
PrintConformHelices  robetta-model5.helices

ReadConformPDB       robetta-model6.pdb
PrintConformSheets   robetta-model6.sheets
PrintConformHelices  robetta-model6.helices

ReadConformPDB       robetta-model7.pdb
PrintConformSheets   robetta-model7.sheets
PrintConformHelices  robetta-model7.helices

ReadConformPDB       robetta-model8.pdb
PrintConformSheets   robetta-model8.sheets
PrintConformHelices  robetta-model8.helices

ReadConformPDB       robetta-model9.pdb
PrintConformSheets   robetta-model9.sheets
PrintConformHelices  robetta-model9.helices

ReadConformPDB       robetta-model10.pdb
PrintConformSheets   robetta-model10.sheets
PrintConformHelices  robetta-model10.helices

Time



quit