Materials Basel 2019

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

Before downloading any workshop data, please check the directory ~/data since most of the needed material is already available there.

Dynamo version

The current dynamo version is in this file

Matlab crash course

From 9 to 11 a crash course in Matlab will be imparted by Mathworks instructors. The documentation can be opened with:

libreoffice --writer /clab-share/matlabCourse/CrashCourseMATLAB.docx &

Program

The course will start at 11'30 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.

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.

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.

Template matching

Tuesday afternoon.

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

Geometric modeling

Working on your own:

• For the Wednesday morning session: complete the advanced starters guide (~2 hours)
  the data can be found in
  ~/data/crop.rec
  a central file which you can copy 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/hiv/v17.rec

Short guided presentation:

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

Alignment and reconstruction

These new features in Dynamo are at the testing stage.

• Walkthrough on manual marker clicking

• Walkthrough on GUI based tilt series alignment

• Walkthrough on command line based tilt series alignment

Creation of 3D scenes

Thursday afternoon.

Working on your own:

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

Further support material.

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

Classification

Friday afternoon.

Short guided presentation:

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

Additional tools and exercises

• Getting a Structure from Multiple Tomograms:

  - In this exercise on VLPs you will be given 6 tomograms of HIV Capsids and the goal is to reach a structure in which alpha helices start to be visible.

• Usage of GPUs
• 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
• Collection of Small Exercises