Pasteur workshop 2017
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.
Contents
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
- Daniel Castaño-Díez, BioEM Lab, University of Basel
- Paula Pérez-Navarro, C-CINA, University of Basel
- Cynthia Taveneau, Institut Curie, Paris
