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 T0365.a2m 1
 NameTarget T0365
// 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 T0365.try14-opt2.pdb	# best unconstrained
ReadConformPDB T0365.try1-opt2.gromacs0.repack-nonPC.pdb	# best rosetta
ReadConformPDB T0365.try15-opt2.pdb	# slightly different good model
ReadConformPDB T0365.try16-opt2.pdb	# based on 1xwmA, another 6-helix bndl
ReadConformPDB T0365.try12-opt2.pdb	# different alignment of first helix


# ReadConformPDB T0365.try8-opt2.pdb	# too close to try14
# ReadConformPDB T0365.try10-opt2.pdb	# too close to try14 and try15
# ReadConformPDB T0365.try11-opt2.pdb	# crummy packing of D143-V195
# ReadConformPDB T0365.try3-opt2.pdb	# foam
# ReadConformPDB T0365.try1-opt2.pdb	# use gromacs0.repack-nonPC version

InFilePrefix 
# ReadConformPDB T0365.undertaker-align.pdb model 1
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
# ReadConformPDB T0365.undertaker-align.pdb model 2
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
# ReadConformPDB T0365.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
# ReadConformPDB T0365.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
# ReadConformPDB T0365.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 A212.CB atom A135.CB atom L208.CB atom C128.CB atom V205.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