Materials Basel 2017

This page is provided as a generic orientation of the contents of the practical hands-on sessions. The final material will be updated before the beginning of the course.

Theory will be presented on synthetic data generated on the fly by Dynamo. Then, the shown theory can be applied on real data sets brought by the participants themselves, or the data sets prepared in the instructor file share under: /Users/gast/mountedData/workshop2017

Program

The course will start around 10:30, Wednesday morning. Last lecture will finish around 12:30 on Friday. On Friday, after lunch, the computer room will be open till 18:00 and our instructors will stay to assist the participants that chose to stay to work with their own data.

General Introduction

Wednesday afternoon.

• 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

Thursday morning.

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

Classification

Thursday afternoon session.

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

Additional tools

Friday morning session.

• Some tools for tilt series alignment, reconstruction, CTF correction.
• 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

Data sets

In the directory /Users/gast/mountedData/workshop2017 there are folders with real data sets representing typical situations. There are both tomograms and already extracted data folders.

• D1 to D4 are tomograms described here.
• D5-D6 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.

Exercises

Exercises are scheduled for the last day. Nevertheless, feel free to start them any time during the workshop.