Delft Workshop 2017

From Dynamo
Revision as of 18:42, 15 August 2017 by Daniel Castaño (talk | contribs)
Jump to navigation Jump to search

A guide to use Dynamo during the TU Delft workshop for Cryo-EM. This covers the afternoon session of the 6th of September of 2017.

Preinstalling the software

We suggest students to install and test the software before departing for the workshop.

To work on own laptops

If you want to work with your own laptop, we advice you to preinstall Matlab on it.

Free license for Matlab

You can get a trial version of Matlab and install it on your laptop. The license will be valid for 30 days.

Standalone version

Dynamo can be used as a standalone (i.e., without Matlab ) in Linux and Mac systems.

To work on the servers of TU Delft

Computer access

Access the course account with your password.

Opening a Linux terminal

We need to create a command terminal. Right click on the screen and select Open Terminal in the menu . A Linux command window will popup. Please create a folder for this course.

mkdir tomo
 cd  tomo 

Starting Dynamo

In the Linux terminal, open Matlab through:

matlab & 

it will take some secons. Then, in the Matlab window write:

 run /ISB2017/dynamo/dynamo_activate.m 

This will activate Dynamo in the current Matlab session.


The tomogram for the second tutorial is located in the location /ISB2017/Course_material/July19/crop.rec

Make a local copy by typing in the Matlab window:

!cp /ISB2017/Course_material/July19/crop.rec . 

(the "!" signs just passes the cp order to Linux)


Introduction to tomography and subtomogram averaging

45 minutes of presentation to introduce tomography, subtomogram averaging and Dynamo.

Tutorial 1: Getting started

on screen presentation/hands-on practical. The presentation will loosely the introductory materials in:

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

After the introduction of these general concepts, will follow together the basic hands-on tutorial of Dynamo.

Advanced getting started

After the coffee break at 16:00 participants will follow the advanced introduction on a reduced data set from a real tomogram.


  1. Daniel Castaño-Díez, BioEM Lab, University of Basel
  2. Paula Pérez-Navarro, C-CINA, University of Basel
  3. Cynthia Taveneau, Institut Curie, Paris