User Documentation

ajimoreno edited this page Jan 22, 2018 · 27 revisions




Table of Contents:

Tutorials


Introduction to Scipion: 12.VolumeChimera.png 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 00.ReconstructedVolume.pngThis 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: 00.ReconstructedVolume.png 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.


Initial volume validation by SAXS 12.VolumeChimera.pngThis 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.


Graphical interface manuals

  • 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.

Processing How To's

  • 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.

Presentations

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