# Doppio SPA tutorial

## Introduction

This tutorial will cover some aspects of the single particle analysis (SPA) processing pipeline with the aim of getting familiarity of using Relion 5.0 in the new CCP-EM Doppio GUI.

```{toctree}
:maxdepth: 1
:caption: Contents:
:numbered:
:glob:

*
!index

```

## Setting up a project

This tutorial is written for [STFC's Ada training platform](https://ada.stfc.ac.uk/). Please begin by referring to [Student’s guide to setting up workspaces](https://docs.google.com/document/d/14CgAIZaOMqYIYMDD25mBmgz_hGHtFGMhl7aFpw-UFms/edit?usp=sharing) to set up your virtual machine.

The running parameters for this tutorial were tested on a virtual machine system with Rocky Linux, 1x RTX4000 GPU, 88GB RAM and a 12 core CPU. If using your own machine these parameters may need to be adjusted based on your system specifications.

Before you begin work, click the pencil logo on the green bar. This allows you to change between different Doppio projects. There are a couple of projects in the drop down list which Doppio already knows about. 
```{image} ../_static/images/SPA/0_add_project_button.png
:align: center
:scale: 100%
```

For this tutorial, we have copied the cryo-EM micrographs which you will be processing to the directory `~/doppio_projects/spa-project`. To start a new Doppio project in this directory, click the "add new Doppio project" button (a green cross on a white background).

Use `~/doppio_projects/spa-project` or `/home/<userid>/doppio_projects/spa-project` as the path for the new project directory and then click `ADD`. Note that the `<userid>` value should refer to your own user id and will be different on each workstation. 

```{image} ../_static/images/SPA/0_add_project.png
:align: center
:scale: 100%
```

When it asks if you want to create a new Doppio project in this directory, click `YES`.

Note that another project called `/home/<userid>/doppio_projects/Tutorial5.0` is also available, which contains pre-calculated results for all the jobs. We might refer to it throughout the tutorial if execution is taking a long time to run, or if you wish to compare your results. However, you should make sure to independently complete all the steps in this tutorial to get the most out of this course.