after loading the structure from the pdb file does this line do the trick for
you?:

my_structure = my_structure.expand_to_p1(sites_mod_positive=True)

It should give you a completly filled unit cell with all symmetry operations
applied and all atom coordinates in the interval [0,1[.

Two questions:

1) isn't this a method of the X-ray structure object, not one of the PDB objects?

2) won't it split up molecules to keep the sites all inside the unit cell?

I'm getting annoyed that it's not easier to do this kind of lattice generation for proteins, so I may just try coding it myself later today or tomorrow. (I'd like to figure out something analogous to the 'symexp' function in PyMOL, but I think that's a little more work.)

-Nat