EMBO workshop 2019

This page describes the contents of the practical hands-on sessions for tomography through Dynamo at the Birkbeck College during the EMBO School for Image processing in Cryo Electron Microscopy (September 2019).

Installing Dynamo on your laptops

Workstations are provided by the organization. These instructions are intended for those students that want to install their own Dynamoversion in their laptops.

Donwload

The Dynamo versions on the three platforms can be obtained in the Downloads page. Please use the indications here to install it in your laptop.

Starting a Dynamo session

You need to run an activation shell (see below for information on how to do it on each platform) that can be used to run alignment projects or to initiate an interactive session using the Dynamo console. For this, you can just type:

dynamo 

on a Dynamo-activated system shell and be patient: the first time a shell initiates a Dynamo process, it can takes several minutes. New invocations to the MCR libraries will be much faster, and commands inside the opened Dynamo session will run immediately.

Linux

On a Linux terminal, type:

 source <DYNAMO_ROOT>/dynamo_activate_linux_with_shippedMRC.sh

Mac

On a Mac termina, type:

 source <DYNAMO_ROOT>/dynamo_activate_mac_with_shippedMRC.sh

Windows

In a DOS terminal write:

C:\ <path to the Dynamo installation>\dynamo_activate_windows.bat 

then open a Dynamo terminal by typing in the DOS

dynamo

If it doesn't work, type:

 set PATH=%PATH%;%MCR_ROOT%\runtime\win64

and then again

C:\ <path to the Dynamo installation>\dynamo_activate_windows.bat

Running a Dynamo project in the standalone

When working with the standalone, it is not convenient to run projects directly pressing [Run] in the dcp GUI. It is a better approach to run the project in a different process.

• Open a new system shell (DOS shell in windows).
• Activate Dynamo in that shell. i.e.,
  • Linux: source <DYNAMO_ROOT>/dynamo_activate_linux_with_shippedMRC.sh
• Do NOT start a Dynamo session, i.e., do not type dynamo in the shell.
• In the terminal, type the name of the execution script.
  • Linux/Mac: ./ptest.exe
  • Windows: ./ptest.bat

Program

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

In the room

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.
• 

  FHV tutorial on isolated membrane events (Practicals Birkbeck 2019)

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

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

HIV tutorial on densely packed slices

• 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.

Instructors

• Daniel Castaño-Díez, University of Basel.
• Giulia Zanetti, Birkbeck College.