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 T0386.a2m 1
 NameTarget T0386
// 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 M1-L75/decoys/
# ReadConformPDB T0386.try1-opt2.pdb

# InFilePrefix A50-E250/decoys/
# ReadConformPDB T0386.try3-opt2.pdb

InFilePrefix 
ReadConformPDB chimera-model2-stage1.pdb

InFilePrefix L225-T299/decoys/
ReadConformPDB T0386.try1-opt2.pdb


// include read-pdb.under


Time


// Don't put superimposed models into decoys/
// since that could mess up programs that find all decoy files.
OutFilePrefix

# printAllConformPDB chimera-model2-stage1.pdb superpose atom T65 atom A66 atom Y67 

printAllConformPDB chimera-model2-stage2.pdb superpose atom L225 atom L226 atom K227 


# 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