PSI Workshop 2023

Workshop

The PSI Dynamo workshop will take place from August the 16th to August the 18th in the Paul Scherrer Institute.

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 four-day course.

Computing resources

Laptops

Participants will bring their own laptops to access a PSI server which will host the data. However, each participant should also instal in their laptop prior to the workshop:

• (R2023a 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_1.1.530.tar

Launch the installation,

./dynamo/dynamo_activate.m

Wait while some packages are compiled. Activate it again.

• Chimera

Access to PSI resources

We will publish here a brief guide describing the steps to follow to access the computing resources.

Time Schedule

• On the first day we will present the basic tools in the Dynamo environment.
• The second 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	09:00 - 10:00	Research Talk
1	10:00 - 10:45	General introduction: Hands on
2	11:00 - 12:30	Starters Guide: subtomogram averaging
3	13:30 - 14:00	General modelling
3a	14:00 - 14:30	Models: Filaments Additional material: Coordinated extraction from several filaments
3b	14:30 - 14:45	Models: Vesicles Additional material: Coordinated extraction from several vesicles
3c	14:45 - 15:00	Models: Surfaces

Day 1 (Afternoon) General Tools

Module	Time	Subject
4	15:15 - 15:45	Template Matching
5	15:45 - 16:15	Principal Component Analysis
6a	16:15 - 16:45	Alignment of tilt series: Manual
6b	16:45 - 17:15	Alignment of tilt series: GUI
6c	17:15 - 17:45	Alignment of tilt series: command line

Day 2 (Morning): Practical cases

Module	Time	Subject
FHV	09:00 - 11:00	Complete walkthrough on FHV virus
HIV1	11:15 - 13:00	High Resolution workflow for HIV1: preprocessing

Day 2 (Afternoon): Practical cases

Module	Time	Subject
HIV1	14:00 - 15:30	High Resolution workflow for HIV1: Dynamo manipulations
HIV1	15:45 - 17:00	High Resolution workflow for HIV1: binding with Relion