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 T0330.a2m 1
 NameTarget T0330
// Now have a random conformation---use PopConform if you don't want it.
 PopConform


Time

// include best previously found decoys!
InFilePrefix decoys/
OutfilePrefix decoys/



# model 1: the best model so far
ReadConformPDB T0330.try11-opt2.pdb

# model 2: next best---very similar.
ReadConformPDB T0330.try12-opt1.pdb
# ReadConformPDB T0330.try7-opt2.pdb

# model 3: try5-opt2 the model try7 is based on
#	replaced by try10-opt2, optimized from try5-opt2.gromacs0
ReadConformPDB T0330.try10-opt2.pdb
#ReadConformPDB T0330.try5-opt2.pdb

# model 4: the best alternative model
# ReadConformPDB T0330.try9-opt2.pdb
# Rosetta favourite (out of all models!):
ReadConformPDB T0330.try9-opt2.gromacs0.repack-nonPC.pdb.gz

#: the only alignment model that doesn't look pants (similar to try5,7)
InFilePrefix 
 ReadConformPDB T0330.undertaker-align.pdb model 1


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 \
	residue M1 residue F8 residue D9 residue D11 residue L14 \
	residue T116 \
	residue N149 residue I175 residue D177 residue D181

# 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