Diamond Workshop 2017

This page is provided as a generic orientation of the contents of the practical hands-on sessions in Diamond (November 2017). 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.

Program

Exact schedule will be updated here.

General Introduction

Guided presentation:

• Basic Dynamo jargon

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

Working on your own:

• 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.

Geometric modeling

Short guided presentation:

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

Working on your own:

• For the morning session: complete the advanced starters guide (~2 hours)
• In the afternoon, after the research talks, we will focus on the extraction of particles from densely packed spherical geometry (~1 hour)

FHV tutorial on isolated membrane events (advanced starters guide)

HIV tutorial on densely packed slices

Template matching

Working on your own:

• We will follow this walkthrough for automated identification of proteosomes on a real tomogram through template matching. (~1 hour)

Template matching

Classification

Short guided presentation:

• PCA Basic concepts.
• Multirefererence Analysis
  Basic concepts.
  walkthrough (~10 min)
• Further work
  • Commandline operations with PCA

Creation of 3D scenes

Working on your own:

• Walkthrough on the FHV data set (~1hour)

Scene creation.

Further support material.

• Walkthrough on depiction and manipulation of triangulations (synthetic data).

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 (tutoriall)

  advanced subboxing tutorial: combining with MRA tutorial

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

• Manual alignment.
• Exercises

Data sets

The data sets will be updated here.

Exercises

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