Difference between revisions of "EMBO workshop 2021"

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=Contents =
= Modules =
== Alignment of tilt series==  
== Alignment of tilt series==  

Revision as of 12:08, 5 August 2021

The tutorials listed here take place virtually on the 11th and 13th of September of 2021 (14:00-18:30) as part of the EMBO workshop for Image processing in cryoEM.



Please refer to your course material to access your two sets of credentials:

  1. A set of credentials to enter Guacamole (the platform for connecting via browser). These are common to all participants.
  2. A set of course credentials to enter the actual machines where the course will be done: the EMBO21 UserID. These are unique to each participant.

Connecting to guacamole

  • Go to:

in your browser. At this stage you should maximise your browser, otherwise you will have visualisation problems when opening Dynamo.

  • Enter your Guacamole credentials.
Entering guacamole server.

Connecting to your machine

Now you need to select a machine. Please then click on +em and then +Servers - Public and select server Zeus-0-14.

Select a machine.

When you select the machine, you will prompted to use your EMBO21 UserID

Entering your personal course credentials.

This should access your virtual Linux XFCe desktop, which should look like this in your browser

Linux XFCe desktop

If you open a terminal (with the terminal icon) you can test by typing


that you are in the correct path, which should be:


where XX stands for your actual workshop participant number.

Load and run Dynamo

First you load the standalone version of Dynamo:

 module load dynamo/v1.1.524

and then it can be run by simply typing:

Dynamo console started.

Dynamo specific commands are then typed into this so called Dynamo console. For example, try to type the Dynamo command


to see the current version that you are using. Note: Copy paste of commands from your local desktop into the dynamo standalone console on the remote Linux XFCe desktop might not always work. We suggest to additionally open the tutorials that you will be working on in a browser inside the remote Linux XFCe desktop itself, in case you need to copy paste long commands.

Dynamic of the course

The course is divided into different modules, described in the time schedule below. Each module is structured in three stages:

  1. Demostration: All students are connected to the main room. The goals of the module will be explained by an instructor.
  2. Individual work: Students go the assigned breakout rooms to work on the tutorials independently. An instructor will be assigned to each breakout room to help with questions.
  3. Common discussion: In the last 5 minutes of the module, we come back to the general breakout room to wrap up the module.

Data location

Each module has one or several tutorials. The data of the tutorials is sometimes synthetic and created on the fly, and sometimes a data set is necessary. The data will be available in the filesystem. The general repository for the data is:


Time schedule

This time schedule is tentative

Day 1: Tomography

Time Module
14:00 Introduction
14:30 Tilt series alignment: manually
15:00 Tilt series alignment: GUI
15:30 Tilt series alignment: command line
16:00 Break
16:30 Models: catalogue system
17:00 Models: helical symmetry
17:30 Models: vesicles and surfaces
18:00 Template matching

Day 2: Subtomogram averaging

Time Module
14:00 Introduction
14:30 Getting started: synthetic thermosomes
15:30 Advanced tutorial: FHV
16:00 Break
16:30 FHV: continuation
17:00 Seed oversampling
18:00 High resolution pipelines
18:20 Closing remarks


Alignment of tilt series

We will align the same tilt series tilt series with two different approaches. We prepared the first tilt series from the EMPIAR entry 10164, depicting a set of virus like particles (VLP). Move to the directory that contains this data using the command:

 cd prac-5

Double-check by typing


to see all files in the directory. One file should be the following tilt series:


This is a binned version (for quicker processing) with the pixel size is 2.7 Angstrom (original deposition is 1.35).

Automated alignment of tilt series through the GUI

Walkthrough on GUI based tilt series alignment

Automated alignment of tilt series through the command line

Walkthrough on command line based tilt series alignment



Helical models


Vesicle and surface models

tutorial on membrane modeling with dmslice

Reusing models

Reusing model workflows ( walkthrough)

Template matching

walkthrough for automated identification of proteosomes on a real tomogram through template matching. (~1 hour)
The data is available at:


An example of template and its mask are provided as 'average32.em' and 'maskTight32.em'.

Subtomogram averaging


Guided presentation:

Working on your own:

Basic walkthrough: creating a catalogue, picking particles, launching a project.

Advanced starters guide

Complete the advanced starters guide (~2 hours) The data can be found in


To use chimera path you need in the tutorial is


Seed oversampling

Tutorial from densely packed spherical geometry (~1 hour). The data is available at:


Since the final alignment project is run on the standalone version of Dynamo, the 'destination' parameter should be 'standalone' instead of 'matlab_parfor'

High resolution pipelines


Exercise to train a realistic case including all processing steps from catalogue creation to final structure using a reduced dataset. Start with the exercise and refer to the complete walkthrough for guidance or the solution.

Interconnectivity tools

Alister: Not a tutorial per se: this is a presentation on a set of tools to interconnect Dynamo, M and other software.

A set of tools have been developed which provide a means to use the geometrical tools and alignment projects from Dynamo with data preprocessed in Warp. These tools mean that particle picking and alignment can be performed in Dynamo prior to multi-particle refinement in M.