Venue
Madrid´s Institute for Material Sciences (ICMM-CSIC), Madrid, Spain
Madrid, June 22nd – 26th, 2026
How to find us: Contact | ICMM
Overall Aims and Course Outline
Cryo-Electron Microscopy (Cryo-EM) allows the determination of three-dimensional structures of biological macromolecules at atomic resolution. This course provides an overview of image processing in Single Particle Analysis (SPA) using Scipion. In the first part of the course, participants will learn the fundamentals of reconstructing biological structures from single particle images obtained through cryo-EM, employing state-of-the-art software in the field.
The second part of the course will focus on interpreting reconstructed maps through atomic modeling. We will use the Scipion platform, integrating tools such as Coot, Chimera, Refmac, and AlphaFold. This course is open to researchers of all levels.
The course will be held in-person and is designed for researchers at any stage of their career who are interested in incorporating Cryo-EM into their research.
Expected Impact for Young Researchers
This course will equip young researchers with the knowledge and skills necessary to apply Cryo-EM in the study of biological macromolecules. Through training in image processing and the interpretation of reconstructed maps, participants will be able to address the structural characterization of biomolecules. These approaches will enhance the understanding of molecular mechanisms and facilitate the use of Cryo-EM as a tool in biomedical and biotechnological research.
Tutors
Marcos Gragera(MG) – Single Particle Analysis specialist, BCU/I2PC
Marta Martinez (MM) – Modelling specialist, BCU/I2PC
Roberto Marabini (RM) – Professor, UAM, Collaborator BCU/I2PC
Deborah Cezar Mendonca – Biologie structurale intégrative, BCU/I2PC
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
- Hotel Chamartín The One (****): Calle Agustín de Foxá, s/n 28036 Chamartín, Madrid. Reservas: reservas@hotelchamartintheone.com
- Hotel Exe Plaza (****): Paseo de la Castellana 191, Madrid, 28045, España. Reservas: reservas@hotelexeplaza.com
- Hotel Crisol Via Castellana (****): Paseo de la Castellana, 220, Madrid, 28046, España. Reservas: reservas@hotelviacastellana.com
- VP Jardín de Tres Cantos (***): Avenida de los Encuartes, 17, Tres Cantos, 28760, España. tc@vphoteles.com
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/
Online registration will close on 31 May 2026 at 12:00 PM
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Day 1 |
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10:30 – 11:00 |
Badge Pick-up & Welcome |
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11:00 – 13:00 |
Movie alignment, screening Movie alignment, CTF estimation and micrograph curation |
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13:00 – 14:00 |
Lunch Break |
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14:00 – 16:00 |
Strategies for particle picking |
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16:00 – 16:30 |
Coffee break |
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16:30 – 17:30 |
2D classification |
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17:30 |
End of day |
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Day 2 |
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09:30 – 11:00 |
Initial volume & 3D classification |
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11:00 – 11:30 |
Coffee break |
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11:30 – 13:00 |
3D Refinement |
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13:00 – 14:00 |
Lunch Break |
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14:00 – 16:00 |
Advaced methods for 3D classification & Refinement (I) |
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16:00 – 16:30 |
Coffee break |
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16:30 – 17:30 |
Advaced methods for 3D classification & Refinement (II) |
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17:30 |
End of day |
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Day 3 |
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09:30 – 11:00 |
Postprocessing: Sharpening, local resolution, anisotropy assessment and validation metrics (I) |
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11:00 – 11:30 |
Coffee break |
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11:30 – 13:00 |
Postprocessing: Sharpening, local resolution, anisotropy assessment and validation metrics (II) |
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13:00 – 14:00 |
Lunch Break |
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14:00 – 16:00 |
Asymmetric features and symmetry expansion. |
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16:00 – 16:30 |
Coffee break |
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16:30 – 17:30 |
Asymmetric features and localized reconstruction. |
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Day 4 |
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09:30 – 10:15 |
Introduction to model building in cryo-EM |
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10:15 – 11:00 |
Getting the initial model (homology, AlphaFold and ModelAngelo) |
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11:00 – 11:30 |
Coffee break |
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11:30 – 12:00 |
Structure analysis: Structure comparison |
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12:00 – 13:00 |
Rigid fitting; Introduction to flexible fitting (Coot) |
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13:00 – 14:00 |
Lunch Break |
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14:00 – 16:00 |
Flexible fitting (Phenix & Refmac) and Validation & Review Kahoot |
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16:00 – 16:30 |
Coffee break |
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16:30 – 17:30 |
Model building of an alternative structure |
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Day 5 |
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09:30 – 09:45 |
Presentation of course questionnaire |
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09:45 – 11:00 |
Building the model of the whole protein |
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11:00 – 11:30 |
Coffee break |
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11:30 – 12:00 |
Submission of maps and structures to EMDB |
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12:00 – 12:30 |
Structure analysis: chain contacts |
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12:30 – 13:00 |
Structural search |
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13:00 |
Lunch Break and end of the day |
