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

Computers

Download

'Information to be updated

Starting a Dynamo session

'Information to be updated

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:

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)

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:

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.