Dynamo Workshop at the International School of Crystallography 2019

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This page describes the contents of the practical hands-on sessions for tomography through Dynamo in at the 54th International School of Crystallography in Erice. A core presentation will be held on site

Installing Dynamo

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.

General Introduction

Clicking particles in the Starters guide

Guided presentation:

  • 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:

Working on your own:

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

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:

Creation of 3D scenes

Working on your own:

Scene creation.

Further support material.

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

Additional tools

Wednesday afternoon session.

Data sets

The data sets will be updated here.



Instructors

  • Daniel Castaño-Díez, University of Basel.
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