Instruct course on flexibility analysis and integrative modelling using Scipion. Madrid, June 19 – 23, 2023


National Center for Biotechnology (CNB), Madrid, Spain
Madrid, June 19 – 23, 2023
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Overall aims and course outline

Cryo-Electron Microscopy has established itself as a mature technique to determine the three-dimensional structure of biological macromolecules. It is currently reaching atomic resolution and is capable of accessing 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 the PDB.
The aim of the course is to introduce attendees to two techniques that are normally needed at the end of the Cryo-Electron Microscopy image processing pipeline: 1) understanding the possible continuous heterogeneity/flexibility of the sample, helping to obtain dynamical information in the form of conformational landscapes, and 2) interpreting the reconstructed map by means of an atomic model. 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.
We will use our software platform Scipion to present these two topics. Scipion is an integrative platform that allows interoperability among different software packages. In the domain of flexibility analysis, we include our own developments in Xmipp as well as tools coming from CryoDrgn, ProDy and HEMNMA. For the atomic modelling part, we include software like Coot, Chimera, Refmac, Phenix, and AlphaFold. In addition to simplifying the access to all these software packages in an integrated manner, Scipion adds a traceability and reproducibility layer so that any other researcher can understand the modelling workflow followed to reach a particular model.
This course is addressed to investigators at all levels.

Expected impact for young researchers

Atomic modelling of the CryoEM map is currently at the moment the natural next step once the map is reconstructed. Flexibility analysis is currently not so common, but the advantage of CryoEM is that it can capture the different conformations of the macromolecules under study. Both techniques are valuable assets in young researchers already with a background on image processing in CryoEM.


Lead contact:
Carlos Oscar Sorzano

Administrative Contact:
Blanca Benitez


I2PC staff: David Herreros (DH), James Krieger (JK), Marcos Gragera (MG), Marta Martínez (MM), Roberto Marabini (RM), Daniel del Hoyo (DDH)
CNRS IMPMC-CNRS UMR 7590. Sorbonne Université: Remi Vuillemot (RV)

You can fill your registration here (Online registration closed)

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€
Day 1: June 19, 2023

09:30: Introduction to Scipion and AWS
10:15: Introduction to macromolecular flexibility and Flexibility Hub
10:30: Flexibility approaches (theory): 
– Deformation field-based approach
– Density-based approach
11:00: Coffee break
11:30: Presentation of the dataset to be used during the practical session
11:45: Estimation of conformational landscapes
12:45: Flexibility consensus (theory)
13:30: Lunch
14:30: Flexibility consensus (practice)
15:15: Dimensionality reduction of estimated landscapes
16:00: Coffee break
16:30: Conformational landscape analysis tools
– Interactive landscape clustering and real-time inspection of conformations
– Best number of clusters analysis
18:00 – 18:30: End of the day
Day 2 June 20, 2023

09:30: Review from the previous day
09:45: Conformational landscape analysis tools (continuation)
– Interactive landscape annotation and real-time inspection of conformations (2D-based tools)
11:00: Coffee break
11:30: Conformational landscape analysis tools (continuation)
– Interactive landscape annotation and real-time inspection of conformations (3D-based and hybrid tools)
13:30: Lunch
14:30: Extracting conformational states from landscape selections:
Application of deformation fields to maps and structural models + strain/rotation analysis + motion statistics
15:00: Interactive local analysis of motions
15:30: Heterogeneity correction with ZART (theory)
16:00: Coffee break
16:30: Heterogeneity correction with ZART (practice)
17:15: Heterogeneity correction of different landscapes states with ZART
18:00 – 18:30: End of the day
Day 3 June 21, 2023

09:00: Review from the previous day
9:45: Introduction to atomic structure ensemble analysis, normal mode analysis, and ProDy
10:15: Ensemble analysis with ProDy ensemble construction, PCA and landscape projection, and motion analysis with NMWiz
11:00: Coffee break
11:30: Conformational landscapes from normal modes and molecular dynamics using ContinuousFlex (theory and practice)
13:30: Lunch
14:30: Introduction to model building in cryo-EM
  – How to get a first estimation of the model (homology, alphafold, modelangelo)
15:15: Presentation of the data used in the practical session
– Kahoot
15:45 min: Map preprocessing – I
  16:00: coffee break
16:30: Map preprocessing – II
17:00 : Getting a first estimate of the model
18:00-30: End of the day
Day 4 June 22, 2023

09:30 Structure analysis: Structure comparison
10:15: Rigid fitting of initial models
11:00: Coffee Break
11:30: Flexible fitting (coot) and validation (phenix)
13:30: lunch
14:30: Flexible fitting (coot) and validation (phenix) (cont)
15:30: kahoot
16:00: coffee break
16:30: Model building of the Beta sub-unit
18:00-30: end of the day
Day 5 June 23, 2023

09:30: Presentation of the course questionnaire
09:45: Building the model of the protein complex
10:30: kahoot.
11:00: Coffee Break
11:30: Submission of structures to EMDB. Understanding the validation report.
12:00: Structure analysis: Chain contacts
13:00: INSTRUCT short message and farewell
13:30: lunch and end of the day

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