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 TR476.a2m 2
 NameTarget TR476
// 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/

ReadConformPDB TR476.try22-opt3.pdb	# <try21-opt3 < try20-opt3.gromacs0.repack-nonPC < try15-opt3 < try14-opt2 < try13-opt3 < try12-opt3 < try11-opt3 < chimera-MQAX10-try9
# ReadConformPDB TR476.try21-opt3.pdb	# < try20-opt3.gromacs0.repack-nonPC < try15-opt3 < try14-opt2 < try13-opt3 < try12-opt3 < try11-opt3 < chimera-MQAX10-try9
# ReadConformPDB TR476.try20-opt3.pdb	# < try15-opt3 < try14-opt2 < try13-opt3 < try12-opt3 < try11-opt3 < chimera-MQAX10-try9
# ReadConformPDB TR476.try20-opt3.gromacs0.repack-nonPC.pdb	# < try15-opt3 < try14-opt2 < try13-opt3 < try12-opt3 < try11-opt3 < chimera-MQAX10-try9
	# 2nd best Rosetta energy
# ReadConformPDB TR476.try15-opt3.pdb	# < try14-opt2 < try13-opt3 < try12-opt3 < try11-opt3 < chimera-MQAX10-try9
# ReadConformPDB TR476.try13-opt3.pdb	# < try12-opt3 < try11-opt3 < chimera-MQAX10-try9
# ReadConformPDB TR476.try12-opt3.pdb	# < try11-opt3 < chimera-MQAX10-try9
# ReadConformPDB TR476.try11-opt3.pdb	# < chimera-MQAX10-try9

ReadConformPDB TR476.try26-opt3.pdb.gz	# < try24-opt3 < TR476-scwrl
# ReadConformPDB TR476.try24-opt3.pdb.gz	# < TR476-scwrl

ReadConformPDB TR476.try29-opt3.gromacs0.repack-nonPC.pdb.gz	# < try28-opt3 < shifted helix
# ReadConformPDB TR476.try28-opt3.pdb.gz	# < shifted helix


ReadConformPDB TR476.try19-opt3.pdb	# < try9-opt3
# ReadConformPDB TR476.try9-opt3.pdb	# < try5-opt3 < try4-opt2 < try3-opt3
# ReadConformPDB TR476.try5-opt3.pdb	# < try4-opt3 < try3-opt3 < TR476-scwrl
# ReadConformPDB TR476.try4-opt3.pdb	# < try3-opt3 < TR476-scwrl
# ReadConformPDB TR476.try3-opt3.pdb	# < TR476-scwrl

ReadConformPDB TR476.try27-opt3.pdb.gz	# < try25-opt3 < TR476-scwrl
# ReadConformPDB TR476.try25-opt3.pdb.gz	# < TR476-scwrl
# ReadConformPDB TR476.try23-opt3.pdb.gz	# < TR476-scwrl

# ReadConformPDB TR476.try9-opt2.pdb	# < try7-opt3 < try6-opt3 < try5-opt2 < try4-opt2 < try3-opt3 < TR476-scwrl
# ReadConformPDB TR476.try7-opt3.pdb	# < try6-opt3 < try5-opt2 < try4-opt2 < try3-opt3 < TR476-scwrl
# ReadConformPDB TR476.try6-opt3.pdb	# < try5-opt2 < try4-opt2 < try3-opt3 < TR476-scwrl

# ReadConformPDB TR476.try14-opt3.pdb	# < try14-opt2 < try13-opt3 < try12-opt3 < try11-opt3 < chimera-MQAX10-try9

# ReadConformPDB TR476-scwrl.pdb
# ReadConformPDB TR476.pdb
#  PrintConformSheets init.sheets
#  PrintConformHelices init.helices



# ReadConformPDB from-try10.pdb

# ReadConformPDB TR476.MQAX10-opt3.pdb	# < HHpred5_TS1

# ReadConformPDB TR476.try10-opt3.pdb	# < try8-opt3 < alignment
# ReadConformPDB TR476.try8-opt3.pdb	# < alignment



# ReadConformPDB TR476.try2-opt3.pdb	# < try1-opt2
# ReadConformPDB TR476.try1-opt3.pdb
# ReadConformPDB TR476.try1-init.pdb

InFilePrefix 
// ReadConformPDB TR476.undertaker-align.pdb model 1
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
// ReadConformPDB TR476.undertaker-align.pdb model 2
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
// ReadConformPDB TR476.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
// ReadConformPDB TR476.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
// ReadConformPDB TR476.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 \
	residue C4 residue C7 residue C47 residue C50
	

# 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