About fit libraries
===================

Fit libraries are lists of possible positions of your input structures in the EM map (non-redundant rigid body fits).
The positions are used in the `global optimization <https://assembline.readthedocs.io/en/latest/combinations.html>`_ step of Assembline to generate a large number of combinations of the pre-calculated fits
through a Monte Carlo integrative modelling procedure. Each position (fit) has its associated score and p-value,
which are used as *FitRestraints* during the modelling (see figure below).

.. image:: images/assembline_efitter_graph.png
  :width: 1100
  :alt: Efitter pipeline for fit libraries

.. note:: Read more in the Assembline manual `about fit libriaries <https://assembline.readthedocs.io/en/latest/fit_libraries_intro.html>`_ section.

The fit libraries are typically generated by fitting every input structure into the EM map separately, a procedure handled by the ``Efitter`` pipeline of Assembline.

.. note:: This part of the Assembline pipeline (``efitter``) will generate all requested libraries per input structure in a single run (automated) according to user's predefined parameters.

For this tutorial, the fit libraries are already provided in the ``systematic_fits/`` directory in the folders ``CR_Y_complex/`` & ``NR_Y_complex/`` (for the rest of the modelled subcomplexes and Nup116 k.o. models the *global optimization* from Assembline was not used) from our `git repository <https://git.embl.de/rantos/scnpc_tutorial.git>`_.

The ``systematic_fits/`` directory is organized as the following in terms of input data: ::

    systematic_fits/

        # Electron microscopy maps
        em_maps/
 
        #input structures for modelling
        PDB/

Follow the next steps if you want to generate them yourself using the ``Efitter`` pipeline (which is a wrapper around `UCSF Chimera FitMapTool <https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/fitmap.html>`_).

To skip and jump to setting up the integrative modelling sections, move to :doc:`json_setup`