Pasteur workshop 2017

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A guide to use Dynamo during the practical session of the Pasteur course INTEGRATIVE STRUCTURAL BIOLOGY​ - Mechanisms of Living Organisms, in the afternoon session of the 19th of July of 2017.

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.

Data

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)


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