EMBO workshop 2016

Dynamo will be used for the subtomogram averaging part of the EMBO course on Image Processing for CryoEM data.

This page will guide you through

We will be using two different computing resources:

• Local Linux workstations
• Remote GPUs

Teaching materials

Data sets

In the directory /g/teachinglab/data/DYNAMO there are folders with real data sets representing typical situations. There are both tomograms and already extracted data folders.

• T1 to T4 are tomograms described here.
• P1-P2 are folders containing different formatted data folders.

An additional data set of 5ht3 particles is available through this Google drive link. This data sets includes several thousands of particles. If you want to work with the whole data set, it is a good idea to download it directly into your CSCS account.

General Introduction

Tuesday 30 August 2016.

• Basic Dynamo jargon

• tutorial on basic elements: help, data and metadata formats.
• tutorial on the basic concept in Dynamo alignment: the project.

after the coffee break:

• Basic walkthrough: creating a catalogue, picking particles, launching a project.
• Further work:
  • tutorial on the use command line operations for general purposes.
  • tutorial on the use of the command line to manage projects.

Data management and modeling

Wednesday 31 August (first part).

• tutorial on membrane modeling with dmslice
• Filament models with dtmslice
  • tutorial
  • walkthrough
• Reusing model workflows ( walkthrough)
• Further work: catalogue

Classification

Wednesday 31 August (second part).

• PCA Basic concepts.
• Multirefererence Analysis
  Basic concepts.
  walkthrough
• Further work
  • Commandline operations with PCA

Additional tools

Thursday, 1 September.

• Subboxing

  motivation slide: extraction of vertices from icosahedral viruses

  Basic subboxing tutorial

  advanced subboxing tutorial: combining with MRA (tutoriall)

  suggested data set: prd1 Capsides (in the folder of isolated particles)

• Manual alignment.
• Exercises