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 T0320.a2m 210
 NameTarget T0320
// 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 T0320.try8-opt2.pdb
ReadConformPDB T0320.try2-opt2.pdb
ReadConformPDB T0320.try5-opt2.pdb
#ReadConformPDB T0320.try7-opt2.pdb
#ReadConformPDB T0320.try3-opt2.pdb
#ReadConformPDB T0320.try4-opt2.pdb
#ReadConformPDB T0320.try6-opt2.pdb
# 
# InFilePrefix 
# ReadConformPDB T0320.undertaker-align.pdb model 1
# # PrintConformSheets align1.sheets
# #PrintConformHelices align1.helices
# ReadConformPDB T0320.undertaker-align.pdb model 2
# # PrintConformSheets align2.sheets
# #PrintConformHelices align2.helices
# ReadConformPDB T0320.undertaker-align.pdb model 3
# # PrintConformSheets align3.sheets
# #PrintConformHelices align3.helices
# ReadConformPDB T0320.undertaker-align.pdb model 4
# # PrintConformSheets align4.sheets
# #PrintConformHelices align4.helices
# ReadConformPDB T0320.undertaker-align.pdb model 5
# PrintConformSheets align5.sheets
#PrintConformHelices align5.helices

InFilePrefix decoys/servers/
#ReadConformPDB ROBETTA_1.pdb.gz
#ReadConformPDB ROBETTA_2.pdb.gz
#ReadConformPDB ROBETTA_3.pdb.gz
#ReadConformPDB ROBETTA_4.pdb.gz
#ReadConformPDB ROBETTA_5.pdb.gz
#ReadConformPDB ROBETTA_6.pdb.gz
#ReadConformPDB ROBETTA_7.pdb.gz
#ReadConformPDB ROBETTA_8.pdb.gz
#ReadConformPDB ROBETTA_9.pdb.gz
#ReadConformPDB ROBETTA_10.pdb.gz
Time

InFilePrefix decoys/
#ReadConformPDB decoys/T0320.try1-opt2.Robettalign.gz
#this is try1-opt2 but only from 237-306 to align with Rosetta

// 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