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 T0487.a2m 1
 NameTarget T0487
// 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 T0487.try10-opt3.gromacs0.repack-nonPC.pdb	# < # try8-op3.gromacs0 < chimera-try7-try3-MQAU1
# ReadConformPDB T0487.try8-opt3.pdb	# < chimera-try7-try3-MQAU1

ReadConformPDB T0487.try9-opt3.pdb	# < try7-opt3.gromacs0
# ReadConformPDB T0487.try7-opt3.pdb	# < try6-opt3.gromacs0 < chimera-try5-try13
# ReadConformPDB T0487.try6-opt3.pdb	# < chimera-try5-try13

ReadConformPDB T0487.try5-opt3.gromacs0.pdb	# < try4-opt3.gromacs0.repack-nonPC <  chimera-N2-MQAU1-C2
# ReadConformPDB T0487.try4-opt3.gromacs0.repack-nonPC.pdb # < chimera-N2-MQAU1-C2

InFilePrefix I173-P263/decoys/
# ReadConformPDB T0487.try13-opt3.pdb	# < try11-opt3.gromacs0 < from-try3


InFilePrefix decoys/
ReadConformPDB T0487.MQAU1-opt3.gromacs0.repack-nonPC.pdb	# < GS-KudlatyPred_TS2 
#  PrintConformSheets MQAU1-opt3.sheets
#  PrintConformHelices MQAU1-opt3.helices
# ReadConformPDB T0487.MQAC1-opt3.gromacs0.repack-nonPC.pdb	# < GS-KudlatyPred_TS2 


ReadConformPDB T0487.try3-opt3.gromacs0.pdb # < try2-opt3.gromacs0 < try1-opt3.gromacs0.repack-nonPC < align(1u04A+1si2A+1zxxA)
# ReadConformPDB T0487.try2-opt3.gromacs0.pdb # < try1-opt3.gromacs0.repack-nonPC < align(1u04A+1si2A+1zxxA)
# ReadConformPDB T0487.try1-opt3.gromacs0.repack-nonPC.pdb # < align(1u04A+1si2A+1zxxA)

InFilePrefix N12-P306/decoys/
# ReadConformPDB T0487.try2-opt3.pdb	# < try1-opt3 < align(1u04A)
# ReadConformPDB T0487.try1-opt3.pdb	# < align(1u04A)

InFilePrefix G302-V685/decoys/
# ReadConformPDB T0487.try2-opt3.pdb	# <t ry1-opt3 < align(1w9hA)
# ReadConformPDB T0487.try1-opt3.pdb	# < align(1w9hA)

InFilePrefix 
// ReadConformPDB T0487.undertaker-align.pdb model 1 # align(1u04A)
#  PrintConformSheets align1.sheets
#  PrintConformHelices align1.helices
// ReadConformPDB T0487.undertaker-align.pdb model 2 # align(1w9hA)
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
// ReadConformPDB T0487.undertaker-align.pdb model 3 # align(1si2A)
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
// ReadConformPDB T0487.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
// ReadConformPDB T0487.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