==========
User guide
==========

.. toctree::
   :hidden:
   :maxdepth: 2
   :caption: Menu

   guide/overview
   guide/filters
   guide/picking
   guide/neural_network
   guide/chimerax_artiax

The following sections describe the main components and functionality of ``nextPYP``.

.. panels::
   :container: container-fluid pb-1
   :body: bg-primary text-centered text-white font-weight-bold
   :header: text-center
   
   :fa:`globe fa-4x text-white`

   +++

   .. link-button:: guide/overview
      :type: ref
      :text: Overview of GUI
      :classes: btn-outline-primary btn-block stretched-link

   ---

   :fa:`filter fa-4x text-white`

   +++

   .. link-button:: guide/filters
      :type: ref
      :text: Filter micrographs/tilt-series
      :classes: btn-outline-primary btn-block stretched-link

   ---

   :fa:`dot-circle fa-4x text-white`

   +++

   .. link-button:: guide/picking
      :type: ref
      :text: Particle picking
      :classes: btn-outline-primary btn-block stretched-link

   ---

   :fa:`brain fa-4x text-white`

   +++

   .. link-button:: guide/neural_network
      :type: ref
      :text: Neural-network picking
      :classes: btn-outline-primary btn-block stretched-link

   ---

   :fa:`eye fa-4x text-white`

   +++

   .. link-button:: guide/chimerax_artiax
      :type: ref
      :text: Visualization in ChimeraX/ArtiaX
      :classes: btn-outline-primary btn-block stretched-link

.. seealso::

   * :doc:`Installation<install>`
   * :doc:`Tutorials<tutorials>`
   * :doc:`Reference<reference>`