Difference between revisions of "Prato Workshop 2018"

From Dynamo
Jump to navigation Jump to search
Line 8: Line 8:
To activate ''Dynamo''
To activate ''Dynamo''
<tt> export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libstdc++.so.6</tt>
  <tt> activate_dynamo </tt>
  <tt> activate_dynamo </tt>
Line 27: Line 26:
You only need to do  this if you want to use the  GPU projects:
You only need to do  this if you want to use the  GPU projects:
<tt> export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libstdc++.so.6</tt>
  <tt>export LD_LIBRARY_PATH=/usr/local/cuda-9.1/lib64:$LD_LIBRARY_PATH</tt>
  <tt>export LD_LIBRARY_PATH=/usr/local/cuda-9.1/lib64:$LD_LIBRARY_PATH</tt>
  <tt>cd ~/ws/opt</tt>
  <tt>cd ~/ws/opt</tt>

Revision as of 08:33, 12 April 2018

This page describes the contents of the practical hands-on sessions in Diamond (11th-12th November 2018).


Activating Dynamo

To activate Dynamo


Start a Dynamo console

Type in the shell:


Run Dynamo projects in a different shell

It is inconvenient to run projects in the Dynamo console. Instead, do the following:

  • Open a new Linux terminal
  • Activate Dynamo
  • go to the folder containing the project. Type the name of the project executable (extension .exe). For a project called myProject:

Compiling Dynamo for the GPU

You only need to do this if you want to use the GPU projects:

 export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libstdc++.so.6
export LD_LIBRARY_PATH=/usr/local/cuda-9.1/lib64:$LD_LIBRARY_PATH
cd ~/ws/opt
sudo make clean 
sudo make all


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

General Introduction

Clicking particles in the Starters guide

Guided presentation:

We will take one hour to go over the basic technical aspects of Dynamo. This material is covered by the guides below:

  • 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: on synthetic data. Covers creating a catalogue, picking particles, launching a project. (~1.5 hours)
  • Related materials (not covered in this course):
    • tutorial on the use command line operations for general purposes.
    • tutorial on the use of the command line to manage projects.

Particle picking

Geometric modeling for surfaces and filaments

Short guided presentation (~1 hour):

Case studies

Working on your own:

Further work

Due to time constraints, we will not cover all functionalities of Dynamo in this course. With the basis acquired in these two days, participants can complete on their own the rest of the program.

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)


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.


Exercises are scheduled for the last day. Nevertheless, feel free to start them any time during the workshop.


  • Alex de Marco, Monash University.


  • Daniel Castaño-Díez, University of Basel.
  • Misha Kudryashev, MPI Frankfurt