Delft Workshop 2017

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 download, install and test the software before departing for the workshop. Data should also be downloaded beforehand.

Downloading Dynamo

Download the package in these google links for linux or Mac respectively. After download (~4Gb), proceed to install and test

Testing your standalone installation

Activate your installation by typing in a Linux shell the activation script:

 source <path to installation>/dynamo_activate_linux_shippedMCR.sh

or correspondingly for Mac:

 source <path to installation>/dynamo_activate_mac_shippedMCR.sh

and then, to test the activated installation:

dynamo

Free license for Matlab

If the standalone installation works, you don't need to install further elements. However, we advice you to preinstall Matlab on your laptop. This makes the work with Dynamo much easier

You can get a trial version of Matlab and install it on your laptop. The license will be valid for 30 days. After installing Matlab, you can download the Dynamo version for your platform.

Testing your Matlab installation

Inside the Matlab shell type:

 run <path to installation>/dynamo_activate.m

Virtual machines

If your system does not recognize the libraries provided in your package, you always have the option of installing a Virtual Machine in your system that emulates the Ubuntu distribution of linux. In this environment, Dynamo will run without errors, although the performance of the graphics system will be severely decreased. We recommend to use this device as a last resource.

Download an Ubuntu distribution

The version 16.04.3 of Ubuntu can be download as an iso file here

Download the virtual machine

A virtual machine can be downloaded here. A detailed walkthrough on the diverse steps can be found here

Data

Data should be downloaded beforehand:

wget  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/hiv/v17.rec
wget  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/t20s/t20s.mrc
wget  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/fhv/crop.rec 

Computer access

Will be announced during the course.

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.

Program

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.

Instructors

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