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 T0405.a2m 1
 NameTarget T0405
// 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/
// include read-pdb.under
# ReadConformPDB T0405.MQAC1-opt3.gromacs0.pdb
# ReadConformPDB T0405.MQAU1-opt3.gromacs0.pdb
# ReadConformPDB T0405.try2-opt3.gromacs0.pdb
# ReadConformPDB T0405.try1-opt3.gromacs0.pdb
# ReadConformPDB T0405.try4-opt3.gromacs0.pdb
# ReadConformPDB T0405.try3-opt3.pdb

ReadConformPDB chimera-try10-baker1-zhang2.pdb

# ReadConformPDB servers/Zhang-Server_TS5
# ReadConformPDB servers/Zhang-Server_TS2
#     PrintConformHelices Zhang-Server_TS2.helices
ReadConformPDB servers/Zhang-Server_TS1
#     PrintConformHelices Zhang-Server_TS1.helices
# ReadConformPDB servers/BAKER-ROBETTA_TS3
# ReadConformPDB servers/BAKER-ROBETTA_TS1
#    PrintConformSheets BAKER-ROBETTA_TS1.sheets

Time


// Don't put superimposed models into decoys/
// since that could mess up programs that find all decoy files.
OutFilePrefix
printAllConformPDB 10-baker1-zhang2-zhang1.pdb superpose 	\
	residue A135 residue W136 residue L137 residue L138 \
	residue G139 residue E140 residue V141 residue V142 \
	residue E143 resiude M144 residue N145 resiude E146

#	residue A205 residue L208 residue K253 residue K249

# 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