Göttingen Workshop 2024

Workshop

This workshop will take place from April the 10 to April the 12th 2024.

The workshop provides hands-on training in all practical aspects of tomography and sub-tomogram averaging using our software Dynamo, encompassing all stages of the pipeline: alignment and reconstruction of tilt series, tomogram visualization and archiving, particle selection and extraction, and subtomogram alignment, averaging, refinement and classification. No previous experience is required. Computing infrastructure will be provided in place, and we welcome participants to bring their own data sets to work on them during this three-days course.

Computing resources

Laptops

For the first two days, participants will bring their own laptops . However, each participant should also install in their laptop prior to the workshop:

• (R2024a version), a licence free trial version is available.
• Dynamo  : prior to installation make sure you have a compiler. On Linux you probably have one by default. On Mac, Xcode needs to be installed. On Windows, the recommended option is to install it via Matlab:

https://es.mathworks.com/help/matlab/matlab_external/install-mingw-support-package.html

Then,

  >> tar -xvf dynamo_temp_1.1.532.tar

Launch the installed package inside MATLAB.

 >> run <DYNAMO_ROOT>/dynamo_activate.m

Wait while some packages are compiled. Activate it again.

• Chimera

Workshop data

The data that will be used during the workshop can be downloaded using the google drive link: https://drive.google.com/drive/folders/10lZjjKj1tMfVL_RYJioaK12ji3_RdrNT?usp=drive_link

In detail, the data for the respective modules is as follows (for a total of about 8GB):

Module and data source

Module	Data source
Starters Guide: subtomogram averaging	Data generated locally by Dynamo
Models: Filaments	Data generated locally by Dynamo
Models: Vesicles	Data generated locally by Dynamo
Models: Surfaces	Data generated locally by Dynamo
Template Matching	https://drive.google.com/drive/folders/1EXXGPMQZhD0lKurzaQ6Nz0Vypj3WUkJP?usp=drive_link (750MB)
Alignment of tilt series	https://drive.google.com/drive/folders/1VPYk91xJ6cLCSy6Mg4UX_dDLHHIhhbp9?usp=drive_link (600MB)
Virus like particles	https://drive.google.com/drive/folders/1Vr108rtKI7knFOmzL06-nfFm1KCKdq4e?usp=drive_link (4.6GB)
Spherical geometries	https://drive.google.com/drive/folders/1arrd1KcscsvCDEasmNISShujWjWCYjlw?usp=drive_link (64 MB)
Principal Component Analysis	Data generated locally by Dynamo
Complete walkthrough on FHV virus	https://drive.google.com/drive/folders/10j1mGTV-4srVV2Hg98eWkAPhPeAbU5BQ?usp=drive_link (2GB)

Access to computational resources

On the third day, a more advanced tutorial will be completed. For this we will to access a server which will host the data. Access details will be updated here.

Time Schedule

• On the first two days, we will present the basic tools in the Dynamo environment.
• The third day will be devoted to a hands-on guide on two practical cases:
  • Protocols for Subtomogram Averaging of Membrane Proteins in the Dynamo Software Package Navarro PP, Stahlberg H and Castaño-Díez D (2018). Front. Mol. Biosci. 5:82.
  • Step-by-step guide to efficient subtomogram averaging of virus-like particles with Dynamo Scaramuzza S, Castaño-Díez D (2021). PLoS biology. 19(8):e3001318.

• On the third day participants are encouraged to make a flash presentation (3 mins, max. slides) describing their past or planned research in tomography. We will study the particular cases of interest of each participant, and identify tools of possible relevance inside the Dynamo environment, designing with the participants viable processing workflows combining Dynamo and other packages.

Day 1 (Morning) General tools

Module	Time	Subject
0	09:30 - 10:00	Research Talk
1	10:00 - 10:45	General introduction: Hands-on guide to basic tools. Basic Dynamo jargon Basic formats for data and metadata
2	11:00 - 12:30	Starters Guide: subtomogram averaging
3	13:30 - 14:00	General modeling
3a	14:00 - 14:45	Models: Filaments Additional material: Coordinated extraction from several filaments
3b	14:45 - 15:30	Models: Vesicles
3c	15:30 - 16:30	Models: Surfaces

Day 2 General Tools

Module	Time	Subject
4	09:30 - 10:15	Template Matching
5	10:15 - 11:30	Principal Component Analysis
6a	11:30 - 12:00	Alignment of tilt series: Manual
6b	12:00 - 12:30	Alignment of tilt series: GUI
6c	12:30 - 12:45	Alignment of tilt series: command line

Day 2 (Afternoon): Practical cases

Module	Time	Subject	FHV	13:30- 17:00	FHV

Day 3 (Whole day): Practical case: High resolution workflow.

Module	Time	Subject	HIV1	09:30 - 17:00	High Resolution workflow for HIV1: preprocessing High Resolution workflow for HIV1: Dynamo manipulations High Resolution workflow for HIV1: binding with Relion

Additional material:

• Coordinated extraction from several vesicles
• Walkthrough on creation of 3d scenes
• Walkthrough on placement of averages on table positions

Instructors

• Daniel Castano-Diez (CSIC Bilbao, Spain).
• Raffaele Coray (CSIC Bilbao, Spain).
• Alma Vivas-Lago (CSIC Bilbao, Spain).