[MMTK] Adding displacements to Protein Configuration

[Jaroslaw Kalinowski]

Maybe you should check what are the arguments for addToConfiguration 
method. In the version I use (2.5.7) it is defined as:

     def addToConfiguration(self, displacement, block=1):
         """Add |displacement| (a ParticleVector object) to the current
         configuration of the universe.
 	...

so it should be called without universe argument:

   universe.addToConfiguration(direction)

1) Why don't you just write a new PDB file? Consider: 
MMTK.PDB.PDBOutputFile('new.pdb').write(universe)