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 T0368.withLigand.a2m 1
 NameTarget T0368
// 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 T0368.try34-opt2.pdb
InFilePrefix decoys/
// include read-pdb.under

ReadConformPDB T0368.try33-opt2.pdb


#these two are the best scoring models, 
#they are polishing runs of try30 and try29 respectively
#ReadConformPDB T0368.try32-opt2.pdb
#ReadConformPDB T0368.try31-opt2.pdb

#these were based on tr368.with.ligand.renum.pdb, try30 is a polishing run 
#ReadConformPDB T0368.try29-opt2.pdb
ReadConformPDB T0368.try30-opt2.pdb

#this the original refinement model, 
#with the ligand attached using Proteinshop
ReadConformPDB tr368.with.ligand.renum.pdb

#InFilePrefix ../decoys/
#ReadConformPDB tr368.pdb

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 \
	atom E74.CB atom A75.CB atom L76.CB \
	atom A79.CB atom D80.CB atom A82.CB atom L83.CB 
	

# 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