Diamond Workshop 2017

This page describes the contents of the practical hands-on sessions in Diamond (28th-29th November 2017).

Computers

Entering the terminal

The login and password are written in the front board.

Starting a Dynamo session

Dynamo is already preinstalled in the file system of Diamond. You can activate it through

 module load EM/dynamo 

As some visualizations are performed with Chimera you need to activate it as well

 module load chimera 

After Dynamo and Chimera have been loaded, you can start a session with:

 dynamo 

Opening the Dynamo console inside a linux shell with the command dynamo

Bringing the data to the local machine

Some tutorials during the workshop require downloading big files from the Dynamo wiki using wget. You don't need to do that, as they have been already downloaded into the location /dls/tmp/DynamoWorkshop/data, which is visible by all the computers in the workshop.

To speed the access to these data sets, it is convenient to make a local copy of them into your own machines. To do so, defore going to lunch, please launch the order:

/dls/tmp/DynamoWorkshop/data/fetchDataToLocalMachine.sh 

from a linux shell. This will copy the data into the directory ~/dynamo/data in your machine.

Program

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

General Introduction

Clicking particles in the Starters guide

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 on a real tomogram. (~2 hours)
• Further work:
  • tutorial on the use command line operations for general purposes.
  • tutorial on the use of the command line to manage projects.

Geometric modeling

Geometric modeling for surfaces and filaments

Short guided presentation:

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

Working on your own:

FHV tutorial on isolated membrane events (advanced starters guide)

HIV tutorial on densely packed slices

• In the afternoon, after the research talks, we will focus on the extraction of particles from densely packed spherical geometry on HIV viral capsides (~1 hour)

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

• Tom Burnley, STFC.
• Daniel Castaño-Díez, BioEM Lab, University of Basel.
• Colin Palmer, STFC.

Instructors

• Daniel Castaño-Díez, University of Basel.
• Colin Palmer, STFC.
• Paula Navarro, University of Basel.
• Stefano Scaramuzza, University of Basel.