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/


InFilePrefix decoys/
# ReadConformPDB T0487.try7-opt3.pdb	# < try6-opt3.gromacs0 < chimera-try5-try13
ReadConformPDB chimera-try7-try3.pdb
ReadConformPDB T0487.MQAU1-opt3.gromacs0.repack-nonPC.pdb	# < GS-KudlatyPred_TS2 

Time


// Don't put superimposed models into decoys/
// since that could mess up programs that find all decoy files.
OutFilePrefix
printAllConformPDB for-chimera-try7-try3-MQAU1.pdb superpose \
	residue R114 residue L117 residue R120 residue R137 \
	residue H139 residue A140

# 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