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

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.

Template matching

Wednesday 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

Thursday morning and afternoon.

Working on your own:

• For the Thursday 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, 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.

Manual alignment of gold beads

Walkthrough on manual marker clicking

GUI based alignment of tilt series

Walkthrough on GUI based tilt series alignment

Command line based alignment of tilt series

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