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 T0500.a2m 1
 NameTarget T0500
// 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 T0500.try6-opt3.gromacs0.pdb	# < chimera-try4-try3

ReadConformPDB T0500.MQAY1-opt3.gromacs0.repack-nonPC.pdb	# < BAKER-ROBETTA_TS4
	# best Rosetta energy

ReadConformPDB T0500.MQAC1-opt3.gromacs0.repack-nonPC.pdb # < SAM-T08-server_TS1
# ReadConformPDB T0500.MQAU1-opt3.gromacs0.repack-nonPC.pdb # < SAM-T08-server_TS1

# ReadConformPDB T0500.try5-opt2.gromacs0.repack-nonPC.pdb	# < try4-opt2 < try3-opt1 < chimera-try2-P433-V575 
# ReadConformPDB T0500.try4-opt3.gromacs0.repack-nonPC.pdb	# < try3-opt1 < chimera-try2-P433-V575 
# ReadConformPDB T0500.try3-opt3.repack-nonPC.pdb # < chimera-try2-P433-V575 + chimera-MQAU1-601-S800 
ReadConformPDB T0500.try2-opt3.repack-nonPC.pdb # < chimera-MQAU1-S401-P600 +MQAC1-opt3.gromacs0.repack-nonPC

ReadConformPDB T0500.try7-opt3.gromacs0.repack-nonPC.pdb # < chimera-MQAY1-try6

# ReadConformPDB T0500.try1-opt3.gromacs0.repack-nonPC.pdb
# ReadConformPDB T0500.try1-init.pdb

InfilePrefix 

# InfilePrefix A1-A200/decoys/
# ReadConformPDB T0500.try1-opt3.pdb
# InfilePrefix M101-A300/decoys/
# ReadConformPDB T0500.try1-opt3.pdb
# InfilePrefix K201-K400/decoys/
# ReadConformPDB T0500.try1-opt3.pdb
# InfilePrefix A301-G500/decoys/
# ReadConformPDB T0500.try1-opt3.pdb
# InfilePrefix S401-P600/decoys/
# ReadConformPDB T0500.try1-opt3.pdb
# InfilePrefix P430-P679/decoys/
# ReadConformPDB T0500.try2-opt3.pdb
# InfilePrefix P501-S700/decoys/
# ReadConformPDB T0500.try1-opt3.pdb
# InfilePrefix T601-S800/decoys/
# ReadConformPDB T0500.try1-opt3.pdb
# InfilePrefix P701-E829/decoys/
# ReadConformPDB T0500.try2-opt3.gromacs0.pdb


InFilePrefix 
// ReadConformPDB T0500.undertaker-align.pdb model 1
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
// ReadConformPDB T0500.undertaker-align.pdb model 2
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
// ReadConformPDB T0500.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
// ReadConformPDB T0500.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
// ReadConformPDB T0500.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