Appion

h1. Align Tilt-Series (Appion-Protomo)

Appion-Protomo is a semi-automated implementation of Protomo 2.4.1, with the option of fully automated batch tilt-series processing.

For a technical overview of Protomo and for diagnosing Protomo-specific issues, refer to the Protomo User's Guide: http://www.electrontomography.org/?page_id=317

Here is a list of all YouTube links to Appion-Protomo workshops:

* Dec 7, 2016: https://www.youtube.com/watch?v=rDBz-l4lgyQ

This wiki page will soon be populated with a series of video tutorials covering:

# Intro video of what will be covered and where you can download everything

# The "This is how simple it can be!" video

# How Protomo aligns, Protomo output, how to tell if a tilt-series is well aligned

# Coarse Alignment and Summary webpages

# Refinement and Summary webpages

# Reconstruction

# Batch processing, fully automated mode, CTF correction, dose compensation

# Screening and Tilt-Series Collection tips

# How to use Appion-Protomo to align tilt-series that are not in the database

# Examples

# Troubleshooting