Prato Workshop 2018

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

Computers

Activating Dynamo

To activate Dynamo

 activate_dynamo 

Start a Dynamo console

Type in the shell:

dynamo

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
• If you are going to use a GPU, you need to make the CUDA libraries visible:

export LD_LIBRARY_PATH=/usr/local/cuda-9.1/lib64:$LD_LIBRARY_PATH

• go to the folder containing the project. Type the name of the project executable (extension .exe). For a project called myProject:

./myProject.exe

Compiling Dynamo for the GPU

You only need to do this if you want to 'compile 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

Materials

If you are not able to follow the tutorials from your laptop, a local offline copy of the materials is available in

~/ws/data/dynamo

To open a pdf file, type:

 evince Dynamo_01_jargon.pdf &

Material list

Files in bold are walkthroughs. Students will complete them on their own.

• Dynamo_01_jargon.pdf

A single slide with the basic concepts in Dynamo.

• Dynamo_02_basic.pdf

Notes covering first on-screen presentation. General commands for visualization.

• Dynamo_03_projects.pdf

General operation of the GUI that creates alignment projects.

• Dynamo_04_starters.pdf

Walkthrough with synthetic data

• Dynamo_05_advanced.pdf

A single slide with the basic concepts in Dynamo.

• Dynamo_06_membranes.pdf

Creation of surfaces modeling membranes in the tomogram browser.

• Dynamo_07_filaments.pdf

Creation of filaments in the tomogram browser.

• Dynamo_08_lattices.pdf

Walkthrough on extraction of particles in densely populated vesicles.

Program

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:

• Basic Dynamo jargon

• 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 (Starters guide): 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):

• tutorial on membrane modeling with dmslice
• Filament models with dtmslice
  • tutorial
  • walkthrough
• Reusing model workflows ( walkthrough)
• Further work: catalogue

Case studies

• Advanced starters guide on a real tomogram. (~3 hours)

Working on your own:

FHV tutorial on isolated membrane events (advanced starters guide)

HIV tutorial on densely packed slices

• Extraction of particles from densely packed spherical geometry on HIV viral capsides (~1 hour)

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)

Template matching

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:

• PCA Basic concepts.
  advanced subboxing tutorial: combining with PCA and MRA tutorial
• Multirefererence Analysis
  Basic concepts.
  walkthrough (~10 min)
• Further work
  • Commandline operations with PCA

Creation of 3D scenes

Working on your own:

• Walkthrough on the FHV data set (~1hour)

Scene creation.

Further support material.

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

Additional tools

Wednesday afternoon session.

• Subboxing

  motivation slide: extraction of vertices from icosahedral viruses

  Basic subboxing (tutoriall)

  advanced subboxing tutorial: combining with MRA tutorial

  suggested data set: prd1 Capsides (in the folder of isolated particles)

• Manual alignment.
• Exercises

Data sets

The data sets will be updated here.

Exercises

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

Organizers

• Alex de Marco, Monash University.

Instructors

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