Materials Basel 2017

This page is provided as a generic orientation of the contents of the practical hands-on sessions. Computer access is described here

Program

The course will start at 10 o'clock, Wednesday morning. Last lecture will finish around 12:30 on Friday. On Friday, after lunch, the computer room will be open till 18:00 and our instructors will stay to assist the participants that chose to stay to work with their own data.

General Introduction

Wednesday afternoon.

Guided presentation:

• Basic Dynamo jargon

• tutorial on basic elements: help, data and metadata formats.
• tutorial on the basic concept in Dynamo alignment: the project.

after the coffee break:

Working on your own:

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

Thursday morning / afternoon.

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:

• For the morning session: complete the advanced starters guide (~2 hours)
  the data can be found in
  ~/data/data/crop.rec
  a central file is available in
  ~/clab-share/data/crop.rec
• In the afternoon, after the research talks, we will focus on the extraction of particles from densely packed spherical geometry (~1 hour)
  To get the data, please write in the linux terminal
  wget https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/hivv/v17.rec

wget https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/hiv/v17.rec

Before going for lunch, please write in a linux terminal:

 /clab-share/bringDataLocal.sh

Template matching

Thursday morning.

Working on your own:

• We will follow this walkthrough for automated identification of proteosomes on a real tomogram through template matching. (~1 hour)
  To get the data, please write in the linux terminal
  wget https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/t20s/t20s.mrc

Classification

Friday morning

Short guided presentation:

• PCA Basic concepts.
• Multirefererence Analysis
  Basic concepts.
  walkthrough (~10 min)
• Further work
  • Commandline operations with PCA

Creation of 3D scenes

Friday morning

Working on your own:

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

Further support material.

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

Additional tools

Friday morning session.

• Some tools for tilt series alignment, reconstruction, CTF correction.
• 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

In the directory /Users/gast/mountedData/workshop2017 there are folders with real data sets representing typical situations. There are both tomograms and already extracted data folders.

• D1 to D4 are tomograms described here.
• D5-D6 are folders containing different formatted data folders.

An additional data set of 5ht3 particles is available through this Google drive link. This data sets includes several thousands of particles. If you want to work with the whole data set, it is a good idea to download it directly into your CSCS account.

Exercises

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