[cctbxbb] reduce2 and cell construction from python script

Hi Enrico, CC Oleg I hope Oleg can comment on this. Pavel On 2/13/25 13:55, Enrico Ravera wrote:

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 ha scritto:

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