From 2D images to 3D structures: A practical course on Electron Microscopy Single Particle Analysis. Madrid, May 17 - 20, 2016


National Center for Biotechnology (CNB), Madrid, Spain


Electron Microscopy is experiencing a resolution revolution (Khulbrant, W., 2014, Elife 13:3), dramatically increasing its capacity to solve the structure of macromolecular complexes close to atomic resolution. It is in this context that we propose a joint computational course between the Instruct Image Processing Center (I2PC) and the Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM, a member of CCISB). The course will run for five days, from Monday lunch to Friday lunch, at the CNB-CSIC in Madrid. Tutors from Spain and the UK will address the complete image processing workflow typical for macromolecular structural determination, from processing the raw images taken on the electron microscope to the interpretation of the derived 3D volumetric structure in terms of atomistic models.

The course will make extensive use of the I2PC software integration framework Scipion, accessing the most widely used software suites in the field, such as EMAN, Relion, Frealign and XMIPP, as well as the CCP-EM/CCP4 program suite for the fitting of atomic structures.

The course is open to investigators at all levels. We will work with examples data, but participants can bring their own data to look at if they wish.


Lead Contact:
Jose Maria Carazo (
Deputy Contact:
Martyn Winn (
Administrative Contact:
Ms. Blanca Benitez (


Download the programme (PDF)

We recommend that you read these papers before Tuesday:

(You can click in any session title to download its corresponding slideshow)

Tuesday, May 17

08:30 - 09:00
09:00 - 09:15
Jose Maria Carazo: Introduction to the course
09:15 - 10:00
Jose Maria Carazo: "Introduction to 3D EM"
10:00 - 11:00
Carlos Oscar Sorzano: "Basic Background: Fourier transform, central section theorem, sampling"
11:30 - 12:00
Practical work. Jose Miguel de la Rosa: "Introduction to Single Particle workflow in Scipion".
12:00 - 13:00
Josue Gomez: "DDD, Screening micrographs and CTF"
14:00 - 15:00
Practical work. Josue Gomez: "particle picking and screening"
15:00 - 16:00
Practical work. Jose Miguel de la Rosa: "2D classification"
16:30 - 17:30
Practical work. Javier Vargas: "Initial volume"
17:30 - 18:30
Practical work. Roberto Melero: "Alignment, classification, and reconstruction - I"

Wednesday, May 18

09:00 - 10:30
Practical work. Roberto Melero: "Alignment, classification, and reconstruction - II"
11:00 - 12:00
Practical work. Carlos Oscar Sorzano: "Validation and analysis"
12:00 - 13:00
Presentation. Pablo Conesa: "Scipion Web Tools"
14:00 - 15:00
Lecture: Ardan Patwardhan: "EMDB and PDB"
15:00 - 16:00
Martyn Winn: "Overview of techniques for fitting and refining atomic models"
16:30 - 18:30
Agnel Praveen Joseph: "Scoring and assessment of model fitting"
18:30 - 19:30
Practical work. Agnel Praveen Joseph: "Rigid body fitting and scoring of multi-component assemblies"
Data files: [ rigid_fitting_data.tar.gz ]

Thursday, May 19

09:00 - 10:00
Tom Burnley: "Introduction to CCP-EM software"
Martyn Winn: Atomic structures refinement in cryoEM maps
10:00 - 11:00
Practical work. Tom Burnley: "Model building and refinement with Coot and Refmac"
11:30 - 13:00
Practical work. Agnel Praveen Joseph: "Flexible fitting with FlexEM"
14:00 - 14:30
Tom Burnley: "High resolution: model building in Coot"
14:30 - 16:00
Practical work. Martyn/Tom: “Model building in Coot”
Data file: [ coot_tutorial_files.gz ]
16:30 - 18:00
Practical work. Tom Burnley: "Model building and refinement with Coot and Refmac"
Session files: [ Refmac tutorial(pdf) ] refmac_tutorial_data.tar ]
18:00 - 18:30
Joan Segura: "Incorporating Bioinformatics Annotations: 3DBionotes"

Friday, May 20

9:00 - 10:00
Ardan Patwardhan: "Volume matching with SMaSB / PDBeShape"
10:00 - 11:00
Practical work. Agnel Praveen Joseph: "Volume matching with PDBeShape"
11:30 – 13:00
Practical work. Students revise model fitting, building and refinement for their structures.


Registration was closed on April 1st, 2016.

 Registration Fee
Instruct countriesNon Instruct countries
Students160 €200 €
Senior Research220 €250 €
Industry400 €500 €

Additionally, there are 10 accommodation grants for attendees from Instruct countries

If you want to apply for a travel grant, please send an e-mail to including:

Payment information

Bank transfer to:
Centro Nacional de Biotecnología - CNB
Bank Name:
Santander Central Hispano
Julio Palacios, 23. 28029, Madrid. Spain
0049 5926 41 2816155571
ES91 0049 5926 4128 1615 5571

Please include your name in the wire concept

This course is funded by Instruct, an Integrated Structural Biology Infrastructure for Europe.