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 T0348.a2m 1
 NameTarget T0348
// 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 T0348.try20-opt2.pdb
ReadConformPDB T0348.try11-opt2.gromacs0.repack-nonPC.pdb //very similar to try20, but rosetta favorite
//  ReadConformPDB T0348.try18-opt2.pdb	 // almost identical to try20-opt2
// ReadConformPDB T0348.try9-opt2.gromacs0.repack-nonPC.pdb // too similar to try20

ReadConformPDB T0348.try19-opt1.pdb
//ReadConformPDB T0348.try6-opt2.pdb //very similar to try19

# from chimera-M1-K60-2-8
ReadConformPDB T0348.try21-opt2.pdb
# ReadConformPDB T0348.try8-opt2.pdb // too similar to try21


# ReadConformPDB T0348.try12-opt2.gromacs0.repack-nonPC.pdb //ugly after M44

ReadConformPDB T0348.try3-opt2.pdb	

# ReadConformPDB T0348.try1-opt2.pdb	// very similar to try21



InfilePrefix M1-K60/decoys/
# ReadConformPDB T0348.try2-opt2.pdb


InFilePrefix 
# ReadConformPDB T0348.undertaker-align.pdb model 1
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
# ReadConformPDB T0348.undertaker-align.pdb model 2
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
# ReadConformPDB T0348.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
# ReadConformPDB T0348.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
# ReadConformPDB T0348.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