.. figure:: /docs/images/scipion_logo.gif
   :width: 250
   :alt: scipion logo

.. _user-documentation:

Graphical interface manuals
===========================

The following guides show you how to perform certain actions using the GUI:

.. toctree::
    :maxdepth: 1

    Introduction to Scipion's GUI <scipion-gui>
    Using the default viewer for Scipion objects <showJ>
    Using the default viewer for Coordinates objects <picker>
    How to install plugins <plugin-manager>


Tutorials
=========

These tutorials provides a quick introduction to processing with Scipion.

Single particle tutorials
-------------------------

.. toctree::
    :maxdepth: 1

    Single particles tutorials <single-particle-tutorials>


Tomography tutorials
--------------------

.. warning::

   Tomography functionality is almost ready to be open for betatesting. For now, betatesting is only open upon request. If you
   are willing to help this project, please contact us at scipion@cnb.csic.es

.. toctree::
    :maxdepth: 1

    Tomography tutorials <tomography-tutorials>

Model Building
--------------
.. toctree::
    :maxdepth: 1

    Model Building by Homology <tutorials/modelBuilding/Homology/index>
    Build initial model with Alphafold <tutorials/modelBuilding/Alphafold/index>

Processing How To's
===================

Importing Data
--------------------
`Importing Data <importingData>`__: Importing data is the first step
for any Scipion project. Find out how to import movies, micrographs,
CTFs, and particles and which are the formats currently supported.

Creating subsets
----------------------
`Creating subsets <protUserSubSet>`__: Find out how to create subsets
from micrographs, particles, volumes or from 2D/3D classifications.
This tool is valid for results from any package.

FAQ
---------
`FAQ <faq>`__: Frequently Asked Questions

Relion in Scipion
-----------------------
`Relion in Scipion <relion-in-scipion>`__: Check how to use Relion inside Scipion.
Some of the original Relion FAQ are addressed.