EMBO workshop 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

Tutorials

Connection

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

https://login.cryst.bbk.ac.uk/guacamole/#/ 

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

pwd

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

 /d/embo2021/u/emboXX

where XX stands for your actual workshop participant number.

Opening Dynamo

First you load the standalone version of Dynamo:

 module load dynamo/v1.1.524

and then it will be available

Dynamo console started.

Dynamic of the course

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

Demostration

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:

/d/embo2021/d/dynamo 

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

Contents

Alignment of tilt series

We will align the same tilt series tilt series with three different approaches.

The data is available at:

/d/embo2021/d/dynamo/

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

Models

Helical models

tutorial

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:

/d/embo2021/d/dynamo/t20s.mrc

Subtomogram averaging

Introduction

Guided presentation:

• 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: creating a catalogue, picking particles, launching a project.

Advanced starters guide

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

/d/embo2021/d/dynamo/crop.rec 

To use chimera path you need in the tutorial is

 TBI 

Seed oversampling

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

/d/embo2021/d/dynamo/v17.rec

High resolution pipelines

VLPs

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.