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 T0472.a2m 1
 NameTarget T0472
// 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 T0472.try10-opt3.pdb	# < try9-opt3 < MQAX8-opt3 <  SAM-T08-server_TS1
# ReadConformPDB T0472.try9-opt3.pdb	# < MQAX8-opt3 <  SAM-T08-server_TS1
# ReadConformPDB  T0472.MQAX8-opt3.pdb	# < SAM-T08-server_TS1
# ReadConformPDB T0472.try8-opt3.pdb	# < try7-opt3 < chimera-N1-C1-3bid
# ReadConformPDB T0472.try7-opt3.pdb	# < chimera-N1-C1-3bid


# a very different approach for final strand to same domain
ReadConformPDB T0472.try6-opt3.pdb # < MQAX1-opt3 < BAKER-ROBETTA_TS4
# ReadConformPDB T0472.MQAX1-opt3.gromacs0.pdb # < BAKER-ROBETTA_TS4


# failed try at final strand (off by 2?)
ReadConformPDB T0472.MQAX7-opt3.pdb	# < RAPTOR_TS1

# Failed try at final strand (off by 4?)
ReadConformPDB T0472.try5-opt3.pdb	# < try4-opt3 <  chimera-N1-C1-3bid
# ReadConformPDB T0472.try4-opt3.pdb	# < chimera-N1-C1-3bid
# ReadConformPDB T0472.try3-opt3.pdb	# < align(3bidA+1wfbA+1r17A+2bz6L+1hzfA) 


# ReadConformPDB T0472.try2-opt3.pdb	# < try1-opt3.gromacs0 < align(3bidA)
# ReadConformPDB T0472.try1-opt3.gromacs0.pdb # < align(3bidA)


ReadConformPDB T0472.MQAU1-opt3.gromacs0.pdb # < SAM-T08-server_TS1
# ReadConformPDB T0472.MQAC1-opt3.gromacs0.pdb  # < SAM-T08-server_TS1


InFilePrefix M1-R55/decoys/
#  ReadConformPDB T0472.try1-opt3.pdb # < align(3bidA)

InFilePrefix P51-T110/decoys/
#  ReadConformPDB T0472.try1-opt3.pdb # < align(3bidA)

InFilePrefix 
// ReadConformPDB T0472.undertaker-align.pdb model 1
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
// ReadConformPDB T0472.undertaker-align.pdb model 2
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
// ReadConformPDB T0472.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
// ReadConformPDB T0472.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
// ReadConformPDB T0472.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