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 T0495.a2m 1
 NameTarget T0495
// Now have a random conformation---use PopConform if you don't want it.
 PopConform


Time

OutfilePrefix decoys/

InFilePrefix decoys/
ReadConformPDB T0495.try12-opt3.pdb	# <try10-opt1 <try8-opt3.gromacs0 <  align(2okfA)
# try13 has worse breaks than try12 but has attempted (and failed) to move the C-terminal helix
# ReadConformPDB T0495.try13-opt3.pdb	# <try10-opt1 <try8-opt3.gromacs0 <  align(2okfA)
# ReadConformPDB T0495.try10-opt3.pdb	# <try8-opt3.gromacs0 <  align(2okfA)
# ReadConformPDB T0495.try8-opt3.pdb	# <  align(2okfA)
# ReadConformPDB T0495.try16-opt3.gromacs0.pdb # < align(2okfA)
# ReadConformPDB T0495.try9-opt3.pdb	# <  align(2oaiA)
# one sheet: 	1 ^v 2 ^v 3 || 4 || 5 ^v 6


InFilePrefix decoys/
ReadConformPDB T0495.try15-opt3.pdb	# < MQAX9-opt3 < BAKER-ROBETTA_TS5
# ReadConformPDB T0495.MQAX9-opt3.pdb	# < BAKER-ROBETTA_TS5
# two sheets: (	1 ^v 2 ^v 3 || 4 ) (5 ^v 6 ^v 7)

InFilePrefix decoys/
# ReadConformPDB T0495.MQAY1-opt3.gromacs0.repack-nonPC.pdb # < GS-KudlatyPred_TS3
# two sheets: (	1 ^v 2 ^v 3 || 4 ) (5 ^v 6 ^v 7)

InFilePrefix decoys/
# ReadConformPDB T0495.MQAX8-opt3.pdb	# < BAKER-ROBETTA_TS4
# two sheets: (	1 ^v 2 ^v 3 || 4 ) (5 ^v 6 ^v 7)


InFilePrefix decoys/
ReadConformPDB T0495.MQAY4-opt3.gromacs0.repack-nonPC.pdb # < RBO-Proteus_TS4
# best rosetta score
# one sheet (1 ^v 2 ^v 3 )

InFilePrefix dimer/decoys/
ReadConformPDB T0495.try7-opt3.unpack.pdb chain A  # < try6-opt3 < try5-opt3 < chimera-try3-MQAY4
# PrintConformSheets try7-opt3.sheets
# PrintConformHelices try7-opt3.helices
# one sheet 	1 ^v 2 ^v 3 || 4 ^v 5 ^v 6

InFilePrefix decoys/
# ReadConformPDB T0495.try6-opt3.pdb # < try5-opt3 < chimera-try3-MQAY4
# ReadConformPDB T0495.try5-opt3.pdb # < chimera-try3-MQAY4
# ReadConformPDB T0495.try3-opt3.gromacs0.pdb # < align(1hh1A+...+2hjsA)

ReadConformPDB T0495.try2-opt3.gromacs0.pdb # < try1-opt3 < align(1hh1A)
# ReadConformPDB T0495.try1-opt3.gromacs0.pdb # < align(1hh1A)
# ReadConformPDB T0495.try4-opt3.gromacs0.pdb # < align(1hh1A+...+2oaiA)
# one sheet: 	1 ^v 2 ^v 3 || 4 ^v 5 (^v 6 ?)



InFilePrefix decoys/servers/
// ReadConformPDB Zhang-Server_TS2
# PrintConformSheets zhang2.sheets
# PrintConformHelices zhang2.helices
// ReadConformPDB Zhang-Server_TS3
#  PrintConformSheets zhang3.sheets
#  PrintConformHelices zhang3.helices
// ReadConformPDB circle_TS1
#  PrintConformSheets circle1.sheets
#  PrintConformHelices circle1.helices
#  PrintConformHbonds circle1.hbonds


InFilePrefix 
# ReadConformPDB T0495.undertaker-align.pdb model 8
#  PrintConformSheets align8.sheets
# PrintConformHelices align8.helices


// ReadConformPDB T0495.undertaker-align.pdb model 1
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
// ReadConformPDB T0495.undertaker-align.pdb model 2
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
// ReadConformPDB T0495.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
// ReadConformPDB T0495.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
// ReadConformPDB T0495.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 M43 residue G44 residue L45 residue G46 \
	residue W52 resiude V53 residue O54 reside E55

# 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