Dear Stefano.
From the PDB file, I see that there is an A+B (protein) and C chain (ZN).
The A and B chain is two molecules I guess.
This helped me solve it in the relax prompt:
help(pipe.create)
pipe.create('new','relax_disp')
help(structure.read_pdb)
# The smallest possible info
structure.read_pdb(file='BpUreE_apo_model_full.pdb')
# Defining molecule 1
structure.read_pdb(file='BpUreE_apo_model_full.pdb', dir=None, read_mol=1, set_mol_name='SpUreE_SC', read_model=None, set_model_num=None, alt_loc=None, merge=False)
# Defining names for the two molecules
structure.read_pdb(file='BpUreE_apo_model_full.pdb', dir=None, set_mol_name=['SpUreE_SC_1','SpUreE_SC_2'])
structure.read_pdb(file='BpUreE_apo_model_full.pdb', dir=None, read_mol=None, set_mol_name=['SpUreE_SC_1','SpUreE_SC_2'], read_model=None, set_model_num=None, alt_loc=None, merge=False)
I hope it helps :-)
Best
Troels