Enrico, here are the steps (check for typos as I was typing all the below from memory):
1) read in a mmcif file (which I think I can do following the tutorial);
pdb_inp = iotbx.pdb.input(file_name = "4znn.pdb") # can be PDB or mmCIF model = mmtbx.model.manager(model_input = pdb_inp)
2) trim the solvent and hydrogen atoms (probably I can do it following the tutorial);
model_no_H = model.remove_hydrogens() model_no_water = model.remove_solvent() though better: selection = model.selection("not (element H or element D or water)") model_trimmed = model.select(selection)
3) run reduce2 to get hydrogens in the nuclear positions (no clue);
Run mmtbx.reduce OR mmtbx.reduce2 OR mmtbx.hydrogenate to add H. I have no idea about the difference between the three commands (perhaps just the mess that someone has to finally get brave enough to clean!), but all three are supposed to add H. Also, you should be able to access the above calls programmatically, at Python script level, not running in the CL.
4) get the full content of the unit cell (no clue).
Do you mean expand to P1 (if original symmetry is not P1)? If so, then hierarchy = model.get_hierarchy().expand_to_p1() Happy to answer questions! Pavel