Difference between revisions of "Pasteur workshop 2017"
| (22 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
| − | + | 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 == | ||
| + | |||
| + | 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 <tt>Open Terminal in the menu</tt> . A Linux command window will popup. Please create a folder for this course. | ||
| + | <nowiki>mkdir tomo | ||
| + | cd tomo </nowiki> | ||
=== Starting ''Dynamo''=== | === Starting ''Dynamo''=== | ||
| + | |||
| + | In the Linux terminal, open Matlab through: | ||
| + | |||
| + | <tt>matlab & </tt> | ||
| + | |||
| + | it will take some secons. Then, in the Matlab window write: | ||
| + | |||
| + | <tt> run /ISB2017/dynamo/dynamo_activate.m </tt> | ||
| + | |||
| + | This will activate ''Dynamo'' in the current Matlab session. | ||
=== Data === | === Data === | ||
| + | The tomogram for the second tutorial is located in the location <tt>/ISB2017/Course_material/July19/crop.rec</tt> | ||
| + | |||
| + | Make a local copy by typing in the Matlab window: | ||
| + | |||
| + | <tt>!cp /ISB2017/Course_material/July19/crop.rec . </tt> | ||
| + | |||
| + | (the "!" signs just passes the cp order to Linux) | ||
== Program== | == 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: | |
| + | |||
| + | * [http://{{SERVERNAME}}/w/doc/misc/introductionTablesAndData.pdf tutorial on] basic elements: help, data and metadata formats. | ||
| + | * [http://{{SERVERNAME}}/w/doc/misc/introductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''. | ||
| + | |||
| + | After the introduction of these general concepts, will follow together the [[starters guide | basic hands-on tutorial]] of ''Dynamo''. | ||
| + | |||
| + | === Advanced getting started=== | ||
| + | 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 == | ||
| + | # Daniel Castaño-Díez, BioEM Lab, University of Basel | ||
| + | # Paula Pérez-Navarro, C-CINA, University of Basel | ||
| + | # Cynthia Taveneau, Institut Curie, Paris | ||
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.
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
