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Instruct course on flexibility analysis using Scipion. Madrid, April 06 – 10, 2026

Venue

National Center for Biotechnology (CNB), Madrid, Spain
Madrid, April 06 – 10, 2026

Contact Us – I2PC – Instruct Image Processing Center

Overall Aims and Course Outline
Cryo-Electron Microscopy (CryoEM) has become a well-established technique for determining the three-dimensional structures of biological macromolecules. It currently achieves atomic resolution and enables the study of conformationally heterogeneous samples as well as macromolecular complexes. CryoEM complements other structural techniques such as X-ray crystallography and Nuclear Magnetic Resonance and is currently the fastest-growing technique in atomic structure depositions in public databases like the PDB.

The aim of this course is to introduce participants to the analysis of conformational flexibility/heterogeneity, a crucial step in CryoEM image processing to obtain dynamic information in the form of conformational landscapes. The I2PC has extensive experience in organizing courses on this topic, with previous editions being in high demand.

This course is intended for researchers at all levels.

Motivation for the I2PC Course on Conformational and Compositional Heterogeneity
The goal is to introduce researchers to flexibility/heterogeneity analysis, one of the most advanced areas in Single Particle Analysis (SPA). The course will cover the theory behind the most commonly used methods in the field and include hands-on practical sessions within the Scipion Flexibility Hub environment, facilitating the use of multiple tools within a single workflow.

Expected Impact for Young Researchers
Flexibility analysis in CryoEM is an emerging technique that enables the capture of different conformations of studied macromolecules. Gaining expertise in this area provides an added value for researchers with prior experience in CryoEM image processing, enhancing their analytical capabilities and understanding of the structural dynamics of biomolecules.

 

Contacts

Lead contact:
Carlos Oscar Sorzano
email: coss@cnb.csic.es

Administrative Contact:
Blanca Benitez
email: blanca@cnb.csic.es

Tutors

Marcos Gragera(MG) – Single Particle Analysis specialist, BCU/I2PC
David Herreros (DH) – Flexibility Hub head developer, BCU
Carlos Oscar Sorzano (COS) – Group leader, BCU; Technical Director, I2PC.
Eduardo Garcia (EG)-  PhD student, BCU
Maximilian Zoech (MZ) – PhD student, BCU

Registration Fee

  • Academic Registration Fee Instruct countries: Predocs & Postdosc 50€
  • Academic Registration Fee Instruct countries: Others 100€
  • Academic Registration Fee Non Instruct countries: Predocs & Postdosc 100€
  • Academic Registration Fee Non Instruct countries: Others 150€
  • Industrial Registration Fee 300€

ACOMMODATIONS

Additionally, on our campus, there is a student residence that might have rooms available for those dates. Here are the links:

Residencia UAM: https://resa.es/residencias/madrid/erasmo/

Registration Here (Online registration opens February 16.)

Agenda

 Times are expressed in CET time Zone

DAY 1: 

14:00 – 14:45: Introduction to Scipion and flexibility in CryoEM (DH)
14:45 – 15:30: Preparing the project, importing the data, and how to work with Scipion (DH)
15:30 – 16:00: HetSIREN (Theory) (DH)
16:00 – 16:30: Coffee break
16:30 – 17:30: HetSIREN (Practice) (DH)
17:30 – 17:45: End of the day

DAY 2: 

09:30 – 10:00: Review from the previous day
10:00 – 11:00: Landscape exploration: interactive tools (DH)
11:00 – 11:30: Coffee break
11:30 – 12:30: Landscape exploration: interactive tools (DH)
12:30 – 13:00: Zernike3D (Theory)
13:00 – 14:00: Lunch break
14:00 – 15:00: Zernike3D (Practice)
15:00 – 15:30: ZART and flexible refinement (Theory) (DH)
15:30 – 16:00: ZART (Practice) (DH)
16:00 – 16:30: Coffee break
16:30 – 17:00: ZART (Practice)
17:00 – 17:15: End of the day

DAY 3: 

09:30 – 10:00: Review from the previous day
10:00 – 10:30: CryoDRGN (Theory) (MZ)
10:30 – 11:00: CryoDRGN (Practice) (MZ)
11:00 – 11:30: Coffee break
11:30 – 12:00: CryoDRGN (Practice) (MZ)
12:00 – 12:30: OpusDSD (Theory) (EG)
12:30 – 13:00: OpusDSD (Practice) (EG)
13:00 – 14:00: Lunch break
14:00 – 14:30: OpusDSD (Practice) (EG)
14:30 – 15:00: 3DVA (Theory) (G)
15:00 – 16:00: 3DVA (Practice) (MG)
16:00 – 16:30: Coffee break
16:30 – 17:00: How to interpret machine learning results (MZ)
17:00 – 17:15: End of the day

DAY 4: 

09:30 – 10:00: Review from the previous day
10:00 – 10:30: 3DFlex (Theory) (EG)
10:30 – 11:00: 3DFlex (Practice) (MG)
11:00 – 11:30: Coffee break
11:30 – 12:00: 3DFlex (Practice) (MG)
12:00 – 12:30: Dynamight (Theory) (MZ)
12:30 – 13:00: Dynamight (Practice) (MG)
13:00 – 14:00: Lunch break
14:00 – 14:30: Dynamight (Practice) (MG)
14:30 – 15:00: FlexConsensus (Theory) (DH)
15:00 – 16:00: FlexConsensus (Practice) (DH)
16:00 – 16:30: Coffee break
16:30 – 17:00: Open questions, limitations, frontiers in flexibility (DH)
17:00 – 17:15: End of the day

DAY 5:     

09:30 – 10:00: Review from the previous day.
10:00 – 10:30: An overview of Instruct services and Flexibility Hub (MG)
10:30 – 11:00: Hands-on on real data examples/One-to-one meetings between interested participants and course tutors.
11:00 – 11:30: Coffe break
11:30 – 13:00: Hands-on on real data examples/One-to-one meetings between interested participants and course tutors.
13:00 – 14:00: Lunch break
14:00 – 14:30: Hands-on on real data examples/One-to-one meetings. between interested participants and course tutors.
14:30 – 15:00: Closing remarks and end of the course.

Contact

Lead contact:
Carlos Oscar Sorzano
email: coss@cnb.csic.es

Administrative Contact:
Blanca Benitez
email: blanca@cnb.csic.es

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