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 T0319.a2m 1
 NameTarget T0319
// Now have a random conformation---use PopConform if you don't want it.
 PopConform


Time

OutfilePrefix decoys/
// include read-pdb.under

# put believed-to-be-best decoy first
InFilePrefix decoys/
ReadConformPDB T0319.try1-opt2.pdb
ReadConformPDB T0319.try4-opt2.pdb
ReadConformPDB T0319.try6-opt2.pdb
ReadConformPDB T0319.try8-opt2.pdb
ReadConformPDB T0319.try3-opt2.pdb

# ReadConformPDB T0319.try2-opt2.gromacs0.repack-nonPC.pdb
# ReadConformPDB T0319.try7-opt2.gromacs0.repack-nonPC.pdb
# ReadConformPDB T0319.try9-opt2.pdb



InFilePrefix decoys/servers/
# ReadConformPDB SAM_T06_server_TS1.pdb
# ReadConformPDB Pmodeller6_TS3.pdb
# ReadConformPDB ROBETTA_TS4.pdb
# ReadConformPDB Pmodeller6_TS2.pdb
# PrintConformSheets Pmodeller6_TS2.sheets
# ReadConformPDB Pmodeller6_TS4.pdb
# ReadConformPDB Pcons6_TS1.pdb
# PrintConformSheets Pcons6_TS1.sheets
# ReadConformPDB ROBETTA_TS2.pdb
# PrintConformSheets ROBETTA_TS2.sheets

InFilePrefix 
# ReadConformPDB T0319.undertaker-align.pdb model 1
# ReadConformPDB T0319.undertaker-align.pdb model 2
# ReadConformPDB T0319.undertaker-align.pdb model 3
# ReadConformPDB T0319.undertaker-align.pdb model 4
# ReadConformPDB T0319.undertaker-align.pdb model 5

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