User Documentation
Table of Contents:
Introduction to Scipion: 
This tutorial provides a quick introduction to processing with Scipion. It is designed to take a short time while illustrating the main concepts. The tutorial uses 3 micrographs from the Grigorieff BPV dataset. A final virus 3D map is obtained.
Guide: scipion_tutorial_intro.pdf
Initial model estimation 
This tutorial uses different methods to obtain an initial 3D map. Methods covered are RCT, Ransac, Eman and Reconstruct Significant.
Guide: scipion_tutorial_initialvolume.pdf
Mix-and-match in Scipion: 
This tutorial presents a more complete workflow of Cryo-EM single particles inside Scipion. It is focused on demonstrate the combination of different EM-packages. This tutorial follows the processing pipeline described for Relion 1.3 tutorial with Beta-galactosidase data.
Guide: scipion_tutorial_betagal.pdf
You may download a fully solved project of this tutorial from here.
Model Building 
The recent development of single-particle electron cryo-microscopy (cryo-EM) allows structures to be solved at almost atomic resolutions. Providing a basic introduction to model building, this tutorial shows a workflow aimed at obtaining high-quality atomic models from cryo-EM data by using \scipion software framework..
Guide: scipion_tutorial_SAXS.pdf
Initial volume validation by SAXS This tutorial provides a guide to the validation of the initial volume estimations using SAXS curves in Scipion.
Guide: scipion_tutorial_SAXS.pdf
Full processing video tutorial: 4 video tutorials in a list to go from movies to a 3D volume using betagalactosidase data.
- Scipion GUI: Get familiar with the Scipion GUI.
- ShowJ: The default viewer for Scipion objects. It can display data in gallery and table modes and navigate through different blocks of data. Single images are opened using Image Window.
- Particle Picker: The Xmipp Particle Picker allows the user to iterate over the micrographs to pick particles either manually or automatically, or visualize them. It is the default viewer for Scipion coordinates.
- Importing Data: 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: Find out how to create subsets from micrographs, particles, volumes or from 2D/3D classifications. This tool is valid for results from any package.
- How to create 2D masks: Guide to creating 2D masks, either interactively or through protocols.
- FAQ: Frequently Asked Questions
- Troubleshooting
- Relion in Scipion: Check how to use Relion inside Scipion. Some of the original Relion FAQ are addressed.
- 2015 - 05: Presentation at IGBMC, Strasbourg.
- 2015 - 04: Scipion_20150428_Cambridge.pdf Scipion presentation at MRC-LMB, Cambridge.
- 2014 - 09: Scipion_20140915_Scripps.pdf Scipion overview presented at Scripps.