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 T0352.a2m 1
 NameTarget T0352
// Now have a random conformation---use PopConform if you don't want it.
 PopConform


Time

OutfilePrefix decoys/


# put believed-to-be-best decoy first

InFilePrefix decoys/
ReadConformPDB T0352.try11-opt2.pdb
ReadConformPDB T0352.try5-opt2.pdb
ReadConformPDB T0352.try4-opt2.pdb
ReadConformPDB T0352.try2-opt2.gromacs0.repack-nonPC.pdb
ReadConformPDB T0352.try1-opt2.pdb

InFilePrefix 
# ReadConformPDB T0352.undertaker-align.pdb model 1
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
# ReadConformPDB T0352.undertaker-align.pdb model 2
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
# ReadConformPDB T0352.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
# ReadConformPDB T0352.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
# ReadConformPDB T0352.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 
	atom P31.CB atom H32.CB atom Q33.CB \
	atom F34.CB atom N35.CB atom S36.CB

#	atom A16.CB atom L16.CB atom L18.CB atom R19.CB \
# 	atom E20.CB atom H21.CB

#	atom W50.CB atom L51.CB atom W53.CB \
#	atom L55.CB atom I56.CB atom P70.CB

Time

quit