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 the PSI resources. In addition, each participant should installed in their laptop prior to the workshop:

• Matlab (R2023a version), a licence free trial version is available.
• Dynamo
• Chimera

We will publish here the links to

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:
• On the third day participants are encouraged to make a flash presentation

Day 1: Morning

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
3b	14:30 - 14:45	Models: Vesicles
3c	14:45 - 15:00	Models: Surfaces

Day 1: Afternoon

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:	Alignment of tilt series: GUI
6c	Example	Alignment of tilt series: command line

Day 2: Practical cases

Module	Time	Subject
7	09:00 - 11:00	Complete walkthroug }