would you mind changing a subject line when changing the topic of
conversation? Your question below has a little to do with "pdbtools:
how to set the occupancy for an atom selection?".
By the way, will you please let me know from which step we
have the b-factors in the PDB files? Do the b-factors change
with the progression of phenix refinement?
They may be set to a value or stem from a refinement run.
Here is another attempt at convincing you to some reading about
basics: