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 T0361.a2m 1
 NameTarget T0361
// 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/
// include read-pdb.under
ReadConformPDB T0361.try8-opt2.pdb.gz
ReadConformPDB T0361.try1-opt2.gromacs0.repack-nonPC.pdb
ReadConformPDB T0361.try5-opt2.pdb.gz
# ReadConformPDB T0361.try2-opt2.pdb.gz	# too similar to try5
#try14 was based off try9
ReadConformPDB T0361.try18-opt2.pdb.gz
ReadConformPDB T0361.try14-opt2.pdb.gz


#ReadConformPDB ROBETTA_deNovo5.repack.pdb

InFilePrefix decoys/servers/
#ReadConformPDB SAM_T06_server_TS1.pdb


InFilePrefix 
#ReadConformPDB T0361.undertaker-align.pdb model 1
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
#ReadConformPDB T0361.undertaker-align.pdb model 2
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
#ReadConformPDB T0361.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
#ReadConformPDB T0361.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
#ReadConformPDB T0361.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 N118.CB atom V119.CB atom N120.CB atom S121.CB \
	atom I122.CB atom T123.CB

#	atom M80.CB atom D81.CB atom K82.CB atom W83.CB \
# 	atom L84.CB atom Y85.CB atom A86.CB atom D87.CB

# 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