.. _program_tomo_make_reference:

relion_tomo_make_reference
==========================

This program runs ``relion_postprocess`` on the pair of reference half maps set in the input |optimisation_set| or generated by :ref:`program_tomo_reconstruct_particle` so they can be used by the different refinement programs more easily.

This program creates an output |optimisation_set| file and a ``Postprocess`` folder within the output directory.

Optimisation set arguments:
---------------------------

- ``--i`` and/or ``--p``, ``--t``, ``--mot`` and ``--man``: input optimisation-set and/or its components (see |optimisation_set|).
- ``--opt_mask``: Mask to be used for subsequent optimisation procedures. This argument updates the output |optimisation_set| file.

General program arguments:
--------------------------

- ``--rec``: Reconstruction path of a :ref:`program_tomo_reconstruct_particle` job (The ``--o`` argument). If this argument is set, half maps in input |optimisation_set| file are ignored.
- ``--mask``: Mask to be used for FSC computation. This argument *does not* updates the output |optimisation_set| file.
- ``--o``: name of the output directory (that will be created).

.. |optimisation_set| replace:: :ref:`optimisation set <sec_sta_optimisation_set>`