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 TR429.a2m 22
 NameTarget TR429
// 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 TR429.pdb
#  PrintConformSheets init.sheets
#  PrintConformHelices init.helices

InFilePrefix  decoys/

ReadConformPDB TR429.try5-opt3.pdb	# < chimera-try4-C4

ReadConformPDB	TR429.try8-opt3.gromacs0.repack-nonPC.pdb	# < try7-opt3.gromacs0 < chimera-N4-try5
	# best Rosetta energy
# ReadConformPDB TR429.try7-opt3.gromacs0.repack-nonPC.pdb	# < chimera-N4-try5

ReadConformPDB TR429.try4-opt3.gromacs0.pdb	# < chimera-N3-try3

ReadConformPDB TR429.try6-opt3.gromacs0.pdb	# < chimera-N2-C2	

ReadConformPDB TR429.try9-opt3.pdb	# < try2-opt3.gromacs0 < TR429
# ReadConformPDB TR429.try2-opt3.pdb	# < TR429


# ReadConformPDB TR429.try3-opt3.gromacs0.pdb	# < chimera-try1-C1


InFilePrefix  decoys/
# ReadConformPDB TR429.try1-opt3.pdb

InFilePrefix  E22-A101/decoys/
# ReadConformPDB TR429.try5-opt3.pdb name N-try5 # < try4-opt2 < try3-opt3 < chimera-try1-init
# ReadConformPDB TR429.try4-opt3.pdb name N-try4 # < try3-opt3 < chimera-try1-init
# ReadConformPDB TR429.try3-opt3.pdb name N-try3 # < chimera-try1-init
# ReadConformPDB TR429.try2-opt3.pdb name N-try2	# < TR429
# ReadConformPDB TR429.try1-opt3.pdb name N-try1

InFilePrefix  R100-P176/decoys/
# ReadConformPDB TR429.try4-opt3.gromacs0.pdb name C-try4	# < R100-P176/try1-opt3
# ReadConformPDB TR429.try3-opt3.gromacs0.pdb name C-try3 # < try3-opt3 < chimera-try2-C1
# ReadConformPDB TR429.try1-opt3.gromacs0.pdb name C-try1 # < align(2f5kA)
# ReadConformPDB TR429.try2-opt3.pdb name C-try2	# < TR429 



InFilePrefix 
// ReadConformPDB TR429.undertaker-align.pdb model 1
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
// ReadConformPDB TR429.undertaker-align.pdb model 2 # < align(2bkdN)
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
// ReadConformPDB TR429.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
// ReadConformPDB TR429.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
// ReadConformPDB TR429.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 N-best-models.pdb superpose \
 	residue Y33 residue A36 residue D38 residue A43 residue Q48 \
	residue I76 residue Y77 residue K80 residue V89 residue N93 

printAllConformPDB C-best-models.pdb superpose \
	residue Y149 residue A150 residue V153 residue C162 residue F166 \
	residue D133 residue E135 residue S137 residue N151 residue G155 

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