Error when following tutorial with reduce

[jeremycheminf]

Hello
I'm trying to run the tutorial2/intro from the doc https://meeko.readthedocs.io/en/release-doc/tutorial2.html#env-setup-like-colab
I can run all the steps until reduce where it fails with
TypeError: manager.get_default_pdb_interpretation_params() missing 1 required positional argument: 'self'

Do I need to use a different version of reduct2?

The full traceback is

Starting /home/jeremy/mambaforge/envs/meeko_tutorial/lib/python3.10/site-packages/mmtbx/command_line/reduce2.py

on Tue Sep 30 13:34:13 2025 by jeremy
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, 3kgd_receptor.pdb

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    approach=add add_flip_movers=True

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "3kgd_receptor.pdb"
    }
    default_model = "3kgd_receptor.pdb"
  }
  approach = add remove


Starting job
===============================================================================
Writing model output to 3kgd_receptorH.pdb

                       ----------Loading Model----------


                     ----------Removing Hydrogens----------

Traceback (most recent call last):
  File "/home/jeremy/mambaforge/envs/meeko_tutorial/lib/python3.10/site-packages/mmtbx/command_line/reduce2.py", line 7, in <module>
    run_program(reduce2.Program)
  File "/home/jeremy/mambaforge/envs/meeko_tutorial/lib/python3.10/site-packages/iotbx/cli_parser.py", line 999, in run_program
    task.run()
  File "/home/jeremy/mambaforge/envs/meeko_tutorial/lib/python3.10/site-packages/mmtbx/programs/reduce2.py", line 1307, in run
    self._ReinterpretModel(False)
  File "/home/jeremy/mambaforge/envs/meeko_tutorial/lib/python3.10/site-packages/mmtbx/programs/reduce2.py", line 1078, in _ReinterpretModel
    p = reduce_hydrogen.get_reduce_pdb_interpretation_params(
  File "/home/jeremy/mambaforge/envs/meeko_tutorial/lib/python3.10/site-packages/mmtbx/hydrogens/reduce_hydrogen.py", line 154, in get_reduce_pdb_interpretation_params
    p = mmtbx.model.manager.get_default_pdb_interpretation_params()
TypeError: manager.get_default_pdb_interpretation_params() missing 1 required positional argument: 'self'

[jeremycheminf]

I found the same issue on mmtbx repo, cctbx/cctbx_project#1087 but solution is to downgrade python.

I tried
mamba install cctbx-base==2024.11
And it seems to work as expected

[diogomart]

Thank you for linking the issue in the upstream repository and for posting a solution