Dear Pavel, many thanks. It ran until the reduce2 part, where it gives the
following error:
File
"/home/ravera/miniconda3/envs/cctbx/lib/python3.13/site-packages/mmtbx/monomer_library/pdb_interpretation.py",
line 1572, in resolve_unexpected
mod_mod_id = mod_dict["NH1NOTPRO"]
the file i am parsing is https://files.rcsb.org/view/2GIM.cif
Any clues?
Cheers,
E.
Il giorno gio 13 feb 2025 alle ore 20:42 Pavel Afonine
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