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-2191.rot


InFilePrefix /projects/compbio/experiments/undertaker/spots/
    ReadAtomType exp-pdb.types
    ReadClashTable exp-pdb-2191-2symm.clash
    SetClashDefinition exp-pdb-2191-2symm

Time


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

InFilePrefix 

 ReadTargetSeq T0333.a2m 1
 NameTarget T0333
// Now have a random conformation---use PopConform if you don't want it.
 PopConform


Time

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

# put believed-to-be-best decoy first
ReadConformPDB T0333.try6-opt2.pdb
ReadConformPDB T0333.try5-opt2.pdb

# very similar to try6:
# ReadConformPDB T0333.try4-opt2.pdb
# ReadConformPDB T0333.try3-opt2.repack-nonPC.pdb

ReadConformPDB T0333.try1-opt2.pdb

# very similar to try5:
# ReadConformPDB T0333.try2-opt2.repack-nonPC.pdb

InFilePrefix 
ReadConformPDB T0333.undertaker-align.pdb model 1 # from 2c1xA
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
ReadConformPDB T0333.undertaker-align.pdb model 2 # from 2acvA
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
#ReadConformPDB T0333.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
#ReadConformPDB T0333.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
#ReadConformPDB T0333.undertaker-align.pdb model 5
# PrintConformSheets align5.sheets
# PrintConformHelices align5.helices

Time


// Don't put superimposed models into decoys/
// since that could mess up programs that find all decoy files.
OutFilePrefix
printAllConformPDB best-models.pdb superpose 

# Can specify a set of atoms as optional arguments of printAllConformPDB
# to give initial set of atoms to align.
# Format: 	atom A7.CA	atom K252.CA	...

Time

quit