News

Venue

National Center for Biotechnology (CNB), Madrid, Spain
Madrid, March 27 – 29, 2023
How to find us: https://i2pc.es/contact-us/

Overall aims and course outline

Cryo-Electron Microscopy has established as a mature technique to determine the three-dimensional structure of biological macromolecules. It is currently reaching atomic resolution and it is capable of accessing to the structure of conformationally heterogeneous samples, as well as macromolecular complexes. It is complementary to other structural techniques like X-ray crystallography and Nuclear Magnetic Resonance and at the moment it is the most rapidly growing technique in atomic structure depositions at public databases like PDB.

The aim of the course is to give an overall overview of the image processing in single particle analysis (SPA). The I2PC has a long tradition of organizing courses of image processing and atomic modelling, with Instruct courses that have been heavily oversubscribed and had to be repeated twice in the same year to be able to attend its demand.

With the experience gained in the organization of virtual and in-person courses, we plan to organize this course in an in-person modality. 20 people will be able to physically attend.

The course is aimed at researchers of all levels wanting to adopt electron microscopy as one of the tools at their disposal for elucidating biological structures.

Expected impact for young researchers

CryoEM is the most rapidly growing structural technique. PhD students as well as young post-docs will certainly benefit from approaching this technique. Knowing it will open new doors to new positions worldwide.

Contacts

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

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

Tutors

Carlos Oscar Sorzano Sánchez (COSS), José-María Carazo (JMC), Marcos Gragera (MG), Carlos Perez Mata (CPM)

Program

Day 1: Data processing
9:30 Morning session:
– Movie alignment, Screening micrographs and CTF
– Particle picking and screening
13:00 Lunch Break
14:00 Afternoon session:
– Particle picking and screening
– 2D classification
17:00 End of day

Day 2:
9:30 Morning session
– Initial volume
– 3D classification
13:00 Lunch Break
14:00 Afternoon session
– 3D classification advanced (masking, classification with no alignment…)
– 3D reconstruction
17:00 End of day

Day 3:
9:30 Morning session
– Sharpening, local resolution and validation
13:00 Lunch Break
14:00 Afternoon session
– One-to-one troubleshooting meeting. NEW
17:00 End of day

REGISTRATION

Registration will be free for all attendees.
Fill  your application here.  (Registration is closed)

This course is organized by iNEXT Discovery (UE Proposal:  871037) and I2PC in collaboration with  Instruct – ERIC, an Integrated Structural Biology Infrastructure for Europe and CRIOMECORR Project

Venue

Remote course
June 22th to June 24th (2022) (3 days):
*3 Mornings: Presentations and training.
*2 Afternoons: Personal work.

Aim of the course:

Hands-On Training Course that introduces the  fundamentals and main tools needed to build an atomic model in the context of cryo-EM, starting from a 3D map and the aminoacid sequence of each protein chain. The  tools will be used inside the Scipion framework (de la Rosa-Trevin et al. 2016) and examples will focus on the modeling by homology scenario, including AlphaFold2 prediction models.

Expected impact for young researchers

Atomic models based on high-resolution density maps are the ultimate result of the cryo-EM structure determination process. In this course, we introduce the basic tools needed to perform this task. Ph.D. students, as well as post-docs, will undoubtedly benefit from approaching this technique since atomic models guide our mechanistic interpretation of cryo-EM structures.

Contacts

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

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

Tutors

Marta Martínez (MM), Roberto Marabini (RM)

Schedule and contents:

*June 22th:

• 9:30: Welcome and presentation of the course, dynamics and mentors.
• 10:00: Introduction to model building in the context of cryo-EM and Scipion
• 10:30: Introduction to Scipion (import data)and AWS
• 11:30: Map preprocessing
• 12:00: Break
• 12:15: Introduction to AlphaFold2 (Searching for prediction models)
• 13:00: Searching models by homology
• 13:30: Afternoon task proposal

*June 23th:

• 9:30: Review of contents and follow up of the afternoon task proposal.
• 10:00: Kahoot
• 10:15: Rigid fitting of initial models
• 11:00: Flexible fitting
• 12:00: Break
• 12:15: Flexible fitting (continuation)
•  14:00: Afternoon task proposal

*June 24th:

• 9:30: Review of contents and follow up of the afternoon task proposal.
• 9:45: Presentation of the course questionnaire
• 10:00: Kahoot
• 10:15: Assessment and validation of models
• 11: 00: Building the model of the protein complex
• 11:15: Break
• 11:30: Structure analysis: Chain contacts
• 12:00: Structure analysis: Structure comparison
• 12:30: Submission of structures
• 13:00: Summary
• 13:30: INSTRUCT short message and farewell

REGISTRATIONRegistration Fee: 50€ 
Registration online closed.

This course is organized by I2PC in collaboration with Instruct – ERIC, an Integrated Structural Biology Infrastructure for Europe and CRIOMECORR Project

Venue

Remote course
December 14-18, 2020 from 09.30-18.00 CET

Overall aims and course outline

Cryo-Electron Microscopy has established as a mature technique to determine the three-dimensional structure of biological macromolecules. It is currently reaching atomic resolution and it is capable of accessing to the structure of conformationally heterogeneous samples, as well as macromolecular complexes. It is complementary to other structural techniques like X-ray crystallography and Nuclear Magnetic Resonance and at the moment it is the most rapidly growing technique in atomic structure depositions at public databases like PDB.

The aim of the course is to give an overall overview of the whole process of single particle analysis (SPA) starting from sample preparation, image acquisition at the microscope, image processing and atomic modelling. The I2PC has a long tradition of organizing courses of image processing and atomic modelling, with Instruct courses that have been heavily oversubscribed and had to be repeated twice in the same year to be able to attend its demand. In this edition of the course we have included the sample preparation and image acquisition part, which will be done in the recently established high-end CryoEM facility at the CNB, which incorporates a Thermofisher Talos Arctica (200kV) and JEOL CryoARM 300 (300 kV). The CNB CryoEM facility is in the process of being incorporated into the offer of the Instruct catalogue. For this reason, we have extended our traditional 3 days course into a 5 days course that includes sample preparation and image acquisition.

For logistic reasons and travelling restrictions, the whole course will be given online. An additional benefit of this circumstance is that the course can be recorded and stay as a permanent course in Instruct. Although the course is online we will try to keep the interactions with attendees. For this reason, we will limit the maximum number of attendees to 20.

The course is aimed at researchers of all levels wanting to adopt electron microscopy as one of the tools at their disposal for elucidating biological structures.

Expected impact for young researchers

CryoEM is the most rapidly growing structural technique. PhD students as well as young post-docs will certainly benefit from approaching this technique. Knowing it will open new doors to new positions worldwide.

Contacts

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

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

Tutors
Marta Martínez (MM), Carlos Oscar Sorzano Sánchez (COSS), Roberto Marabini (RM), Roberto Melero (RME), Jose-María Carazo (JMC), José-María Valpuesta (JMV), Javier Chichón (JC)

Program

Day 1: Data acquisition 9:30       Introduction to the course (JMC, JMV, COSS) 9:35       Introduction to CryoEM (JMV) 10:20     Break 10:30    Introduction to camera detectors (JC) 11:20    Break 11:30    Sample preparation NEGATIVE STAIN (JMV) 12:30    Lunch Break 13:30    Sample preparation VITRIFICATION (JC) 14:20    End of day	Day 2: Data acquisition 9:30       Data Acquisition Lecture 10:20    Break 10:30    Grid Clipping and Microscope loading (JC) 11:20    Break 11:30    Screening 12:30    Lunch Break 13:30    General discussion 14:20    End of day
Day 3: Data processing 9:30    Movie alignment, Screening micrographs and CTF (COSS) 10:20  Break 10:30  Particle picking and screening (COSS) 11:20  Break 11:30  2D classification (COSS) 12:30  Lunch Break 13:30  Personal practice 16:30  General discussion 17:00  End of day	Day 4: Data processing 09:30    Initial volume (COSS) 10:20    Break 10:30    Alignment, classification, and reconstruction (COSS) 11:20    Break 11:30    Validation and analysis  (COSS) 12:20    Lunch Break 13:30    Personal practice 16:30    General discussion 17:00    End of day
Day 5: Data modelling 09:30    Homology modelling (MM, RM) 10:20     Break 10:30     Model alignment and refinement (MM, RM) 11:20    Break 11:30    Model validation (MM, RM) 12:20    Lunch Break 13:30    Model validation (MM, RM) 14:30    General discussion; Dissemination: Infrastructure access through Instruct and iNext-Discovery (RME, JMC, COSS) 14:30    End of day work*	* Virtual machines and I2PC staff will be available until 17:30 for those who want to access.

Key dates:

October 26 – November 20, 2020: Submission of the course application
23– 30 November, 2020: Communication of awarded applications  

REGISTRATION

Registration will be free for all attendees.
Fill  your application here.  (Registration is now closed)

This course is funded by Instruct – ERIC, an Integrated Structural Biology Infrastructure for Europe and CRIOMECORR Project