Difference between revisions of "EMBO workshop 2021"

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  <tt>https://login.cryst.bbk.ac.uk/guacamole/#/ </tt>
in your browser <br />
in your browser. '''At this stage you should maximise your browser'''
'''At this stage you should maximise your browser'''
* Enter your Guacamole credentials.
* Enter your Guacamole credentials.
=== Connecting to your machine ===
=== Connecting to your machine ===

Revision as of 11:07, 16 July 2021

These tutorials takes place virtually on the 11th and 13th of September of 2021 (14-18:30), as a part of the EMBO workshop for Image processing in cryoEM



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

  • A set of credentials to enter Guacamole (the platform for connecting via browser)
  • A set of course credentials to enter the actual machines where the course will be done.

Connecting to guacamole

  • Go to the direction

in your browser. At this stage you should maximise your browser

  • Enter your Guacamole credentials.

Connecting to your machine

Dynamic of the course

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

all students are connected to the main room; goals of the module will be explained by an instructor.
Individual work
students go the breakout rooms they have been assigned and perform the tasks of the walkthrough in the tutorial.
an instructor will be assigned to each breakout room.
Common discussion
on the last 5 minutes of the module, we come back to the general breakout room for discussion of problems found.

Data location

Each module has one or several walkthroughs. The data of the walkthroughs is sometimes synthetic and created on the fly, and sometimes a data set is necessary. In such cases, the text of walkthrough will point to an on-line location where the data can be downloaded.
During this course, the data will be also available in the filesystem, you will not need to download it.

The general repository for the data is:


Time schedule

This time schedule is tentative

Mock run

Time Subject
11:00 Introduction
11:30 Starters guide

Day 1: Tomography

Time Subject
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 Subject
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 three different approaches.

The data is available at:


Manual alignment of tilt series

We will click manually on the gold beads of our test tilt series Walkthrough on manual marker clicking

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:


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:


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.