Prato Workshop 2019

This page describes the contents of the practical hands-on sessions in Prato (28th-29th April 2019).

Computers

Entering the terminal

The login and password are written in the front board.

Create a Linux term by pressing CTRL+ALT+T.

Starting a Dynamo session

Dynamo is already preinstalled in the file system of Prato. You can activate it through

 source ~/ws/opt/dynamo/dynamo_linux_activate_shippedMCR.sh 

After Dynamo and Chimera have been loaded, you can start a session with:

 dynamo 

Opening the Dynamo console inside a linux shell with the command dynamo

Bringing the data to the local machine

The tutorials will ask you to download some datasets. The data should be available in the folder ~/data/dynamo/. Check that you find three files with:

 ls ~/data/dynamo/*

You should see the files crop.rec,t20s.mrc and v17.rec. Let us know if it is not the case.

Program

Before the hands-on session, we will go to this presentation for a general introduction of the Dynamosoftware.

General Introduction

Clicking particles in the Starters guide

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.
• Advanced starters guide on a real tomogram. (~2 hours)
• 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

Geometric modeling for surfaces and filaments

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:

FHV tutorial on isolated membrane events (advanced starters guide)

HIV tutorial on densely packed slices

• In the afternoon, after the research talks, we will focus on the extraction of particles from densely packed spherical geometry on HIV viral capsides (~1 hour)

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

Adaptive bandpass filtering

Working on your own:

• We will follow this walkthrough to create a small synthetic data set that illustrates the principles of adaptive bandpass filtering, a way of conducting a golden standard alignment procedure . (~40 mins)

Classification

Short guided presentation:

• PCA Basic concepts.
  advanced subboxing tutorial: combining with PCA and MRA tutorial
• 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

Wednesday afternoon session.

• 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.

Organizers

• Tom Burnley, STFC.
• Daniel Castaño-Díez, BioEM Lab, University of Basel.
• Colin Palmer, STFC.

Instructors

• Daniel Castaño-Díez, University of Basel.
• Colin Palmer, STFC.
• Paula Navarro, University of Basel.
• Stefano Scaramuzza, University of Basel.