Difference between revisions of "Dynamo Workshop at the International School of Crystallography 2019"

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(Created page with "This page describes the contents of the practical hands-on sessions in Diamond (28th-29th November 2017). == Computers == === Entering the terminal === The login and passw...")
 
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This page describes the contents of the practical hands-on sessions in Diamond (28th-29th November 2017).  
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This page describes the contents of the practical hands-on sessions for tomography through ''Dynamo''  in at the 54th International School of Crystallography in Erice.
  
 
== Computers ==
 
== Computers ==
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=== Starting a ''Dynamo'' session ===
 
=== Starting a ''Dynamo'' session ===
  
''Dynamo'' is already preinstalled in the file system of Diamond.  You can activate it through
 
  
<tt> module load EM/dynamo </tt>
 
  
As some visualizations are performed with Chimera you need to activate it as well
 
 
<tt> module load chimera </tt>
 
 
After ''Dynamo'' and Chimera have been loaded, you can start a session with:
 
 
<tt> dynamo </tt>
 
 
[[File:dynamo_console.png|thumb|center|800px| Opening the ''Dynamo'' console inside a linux shell with the command <tt>dynamo</tt>]]
 
 
=== Bringing the data to the local machine ===
 
 
Some tutorials during the workshop require downloading big files from the ''Dynamo'' wiki using <tt>wget</tt>. You don't need to do that, as they have been already downloaded into the location  <tt>/dls/tmp/DynamoWorkshop/data</tt>, which is visible by all the computers in the workshop.
 
 
To speed the access to these data sets, it is convenient to make a local copy of them into your own machines. To do so, defore going to lunch, please launch the order:
 
 
<tt>/dls/tmp/DynamoWorkshop/data/fetchDataToLocalMachine.sh</tt>
 
 
from a linux shell. This will copy the data into the directory <tt>~/dynamo/data</tt> in your machine.
 
  
 
== Program ==
 
== Program ==

Revision as of 10:14, 13 February 2019

This page describes the contents of the practical hands-on sessions for tomography through Dynamo in at the 54th International School of Crystallography in Erice.

Computers

Entering the terminal

The login and password are written in the front board.

Starting a Dynamo session

Program

Before the hands-on session, we will go to this presentation for a general introduction of the Dynamosoftware.

General Introduction

Clicking particles in the Starters guide

Guided presentation:

  • tutorial on basic elements: help, data and metadata formats.
  • tutorial on the basic concept in Dynamo alignment: the project.

Working on your own:

  • Basic walkthrough: creating a catalogue, picking particles, launching a project.
  • Advanced starters guide on a real tomogram. (~2 hours)
  • Further work:
    • tutorial on the use command line operations for general purposes.
    • tutorial on the use of the command line to manage projects.

Geometric modeling

Geometric modeling for surfaces and filaments

Short guided presentation:

Working on your own:

Template matching

Working on your own:

  • We will follow this walkthrough for automated identification of proteosomes on a real tomogram through template matching. (~1 hour)

Adaptive bandpass filtering

Working on your own:

  • We will follow this walkthrough to create a small synthetic data set that illustrates the principles of adaptive bandpass filtering, a way of conducting a golden standard alignment procedure . (~40 mins)

Classification

Short guided presentation:

Creation of 3D scenes

Working on your own:

Further support material.

  • Walkthrough on depiction and manipulation of triangulations (synthetic data).

Additional tools

Wednesday afternoon session.

Data sets

The data sets will be updated here.



Instructors

  • Daniel Castaño-Díez, University of Basel.