Difference between revisions of "Pasteur workshop 2017"

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Contents to be updated before the 19th of July.
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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 ==
 
== Computer access ==
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Access the course account with your password.
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=== Opening a Linux terminal ===
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We need to create a command terminal.  Right click on the screen and select  <tt>Open Terminal in the menu</tt> . A Linux command window will popup. Please create a folder for this course.
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<nowiki>mkdir tomo
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cd  tomo </nowiki>
  
 
=== Starting ''Dynamo''===
 
=== Starting ''Dynamo''===
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In the Linux terminal, open Matlab through:
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<tt>matlab & </tt>
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it will take some secons. Then, in the Matlab window write:
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<tt> run /ISB2017/dynamo/dynamo_activate.m </tt>
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This will activate ''Dynamo'' in the current Matlab session.
  
 
===  Data ===
 
===  Data ===
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The tomogram for the second tutorial is located in the location  <tt>/ISB2017/Course_material/July19/crop.rec</tt>
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Make a local copy by typing in the Matlab window:
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<tt>!cp /ISB2017/Course_material/July19/crop.rec . </tt>
  
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(the "!" signs just passes the cp order to Linux)
  
  
 
== Program==
 
== Program==
  
; Introduction to tomography and subtomogram averaging
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===Introduction to tomography and subtomogram averaging===
:presentation
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45 minutes of presentation to introduce tomography, subtomogram averaging and ''Dynamo''.
; Getting started .
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: on screen presentation and hands-on tutorial
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=== Tutorial 1: Getting started===
; Advanced getting started.
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: hands-on tutorial
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on screen presentation/hands-on practical. The presentation will loosely the introductory materials in:
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* [http://{{SERVERNAME}}/w/doc/misc/introductionTablesAndData.pdf tutorial on] basic elements: help, data and metadata formats.
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* [http://{{SERVERNAME}}/w/doc/misc/introductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''.
  
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After the introduction of these general concepts,  will follow together the [[starters guide | basic hands-on tutorial]] of ''Dynamo''.
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=== Advanced getting started===
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After the coffee break at 16:00 participants will follow the [[advanced starters guide| advanced introduction]] on a reduced data set from a real tomogram.
  
 
== Instructors ==
 
== Instructors ==

Latest revision as of 10:09, 19 July 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.

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