.. 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>

Image processing resources
==========================

`Very complete Youtube list about cryoem image processing videos <https://www.youtube.com/playlist?list=PLQjWIcrmtc4JjyC-_BM99_XW-VsDa4_i3>`__

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
--------------------

.. 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>
    Build initial model with ModelAngelo <tutorials/modelBuilding/ModelAngelo/index>

Flexibility hub
---------------
.. toctree::
    :maxdepth: 1

    Flexibility Hub tutorial main page <tutorials/flexibilityHub/main_page>

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

Importing data
--------------
:ref:`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
----------------
:ref:`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.

Threads, mpis and GPUs
----------------------
Understanding these common execution parameters it is always important
but at the same time confusing. We try to explain them :ref:`here <threadsmpigpus>`

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

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