The Instruct i2PC from Instruct Spain is organizing the fifth edition of a seminar series on cryoEM and cryoET methods for image processing. We will be gathering expert developers and users so new and existing methods can gain visibility and users can understand the applications and mechanisms of the presented algorithms.
The webinars will be held online without registration, and they are free. You can join the session and launch questions to the speakers through next link: https://conectaha.csic.es/b/bla-rkh-dqa-rpn
The contents and speakers will be:
3rd October (10:00 CET Madrid) – Szu-Chi Chung, Department of Applied Mathematics, National Sun Yat-sen University, No. 70, Lienhai Rd, Kaohsiung, Taiwan – Cryo-forum: A processing framework for orientation information recovery with uncertainty measure and its application in cryo-EM image analysis.
2nd December (11:00 CET Madrid) – Andreas Engel, Case Western Reserver University, Switzerland – Robotic grid preparation of vitrified biomolecules from nano litre volumes.
16th December (15:00 CET Madrid) – Joey Davis, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA – Learning structural heterogeneity from cryo-electron sub-tomograms with tomoDRGN.
More speakers and talks are still to be determined for this seminar series. Please stay tuned for more information.
Dates: November 5-7th 2024 (3 EU afternoons or 3 east US mornings)
Venue:Hybrid format
Aim: The aim of this meeting is to gather feedback and showcase how facilities are using Scipion, demonstrating its capabilities and benefits for Cryo-EM facilities. The event will feature talks and ample time for discussion, aiming to share experiences with Scipion, discuss operational methodologies, and highlight new developments that can enhance our community’s daily workflow.
Conditions: The workshop will be held at the Spanish National Centre for Biotechnology in Madrid, Spain. For the practical session on November 5, in-person attendance is required, and you must select this option on the registration page to ensure we prepare a machine for you. The main workshop on November 6-7 can be attended either in person or remotely. No programming skills are required. We will use in-house bigbluebutton conference system. Verify your browser works at https://demo.bigbluebutton.org/
Program:
We start at: San Francisco – 05:00 // Minneapolis – 07:00 // New York – 08:00 // São Paulo – 09:00 // Madrid – 14:00 // London – 13:00 Beijing – 20:00 // Tokyo – 21:00 // Sydney – 23:00
PRACTICAL COURSE
Tuesday 5th November – In person
14:00 – 14:30 Course Overview – Pablo Conesa, Biocomputing Unit CNB – Madrid, Spain. 14:30 – 15:30 On-the-fly processing – Daniel Marchan, Biocomputing Unit CNB – Madrid, Spain. 15:30 – 16:00 Coffee break 16:00 – 17:00 Processing workflows and templates – Daniel Marchan, Biocomputing Unit CNB – Madrid, Spain. 17:00 – 17:45 Scipion with queue systems – Daniel Marchan, Biocomputing Unit CNB – Madrid, Spain. 17:45 – 18:30 Build your own workflow – Support from CNB staff
WORKSHOP
Wednesday 6th November – Hybrid
14:00 (CET) Welcome – Jose María Carazo , Biocomputing Unit CNB – Madrid, Spain. 14:15 – 14:45 An Overview of Scipion in Facilities – Pablo Conesa, Biocomputing Unit CNB – Madrid, Spain. 14:45 – 15:15 Automated on-the-fly data processing in EMhub is fantastic, but what’s next? – Jose Miguel de la Rosa Trevin, St Jude Children’s Research Hospital – Memphis, USA. 15:15 – 15:45 Lab Management with CEITEC: LIMS Demo and Key Features – Radek Veverka, Central European Institute of Technology at Masaryk University – Brno, Czech Republic. 15:45 – 16:15 Coffee break 16:15 – 16:45 Smart Data Collection with Smartscope – Jonathan Bouvette, Princeton University – New Jersey, USA. 16:45 – 17:15 Enhancing Smart Acquisition: Integrating SPA Processing Feedback with the Scipion-EM-SmartScope Plugin – Alberto Garcia, Biocomputing Unit CNB – Madrid, Spain. 17:15 – 18:00 Discussion and user input gathering
Thursday 7th November – Hybrid
14.00 (CET) Enhancing Efficiency: Best Practices and Automations for On-the-Fly Processing in SPA Workflows – Daniel Marchan, Biocomputing Unit CNB – Madrid, Spain. 14:30 – 15:00 NextPyP: A scalable platform for single-particle cryo-EM/ET image analysis – Alberto Bartesaghi Duke University – Durham , USA. 15:00 – 15:30 Using Scipion to enable diverse cryo-ET workflows to explore Neurodegeneration at UCSF – Eric Tse, Institute for Neurodegenerative Diseases UCSF – San Francisco, USA. 15:30 – 16:00 Coffee break 16:00 – 16:30 Scipion use Case: Stream processing at CNB Facility – Javier Chichon, CryoEM Facility CNB – Madrid, Spain. 16:30 – 17:00 Expanding access to cryo-EM through specimen preparation robotics and platform-independent remote imaging – Mario Borgnia, National Institute of Environmental Health Sciences – Durham, USA 17:00 – 18:00 Discussion and conclusions
Further details, such as class locations, meeting links, title updates, and instructions for reaching the centre, will be provided in the months leading up to the workshop.
Madrid’s Institute for Material Sciences (ICMM-CSIC), Madrid, Spain Madrid, June 17 – 21, 2024 How to find us: Contact | ICMM (csic.es)
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.
Motivation for the I2PC course on conformational and compositional heterogeneity: We want this course to help researchers to get introduced in the area of flexibility/heterogeneity analysis, one of the most advanced topics in SPA. For some of the most used methods in the field (some developed by us, some by others) we will present the theory behind the method and perform a short practical. We will do so within the integrative Scipion Flexibility Hub environment, to help in the use of these multiple methods.
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.
Contacts
Lead contact: Carlos Oscar Sorzano email. coss@cnb.csic.es
09:00-09:15 Welcome 09:15 – 10:15: Introduction to the compute environment to be used in this course (aws/scipion) 10:15 – 11:00:General introduction to model building in cryo-EM 11:00 – 11:30: Coffee break 11:30 – 13:00: Introduction to the data used in the practical session in homology modeling (details here) and de novo modeling 13:00-13:30: Map preprocessing I 13:30-14:30: Lunch break 14:30-16:00: Getting a first estimate of the model “de novo” (AlphaFold & ModelAngelo) and by sequence homology. 16:00-16:30: Coffee break 16:30-17:00: Continuation of first estimation 17:00-17:30: Structure analysis: Structure comparison 17:30-18:00: Rigid Fitting of Initial Models 18:00: End of the day
DAY 2: Modelling
09:00-09:30: Review yesterday’s work 09:30-11:00: Flexible fitting (Coot) and Validation 11:00-11:30: Coffee break 11:30-13:30: Flexible fitting and Validation 13:30-14:30: Lunch break 14:30-15:00: Review Kahoot students, teacher 15:00-16:00: Coffee break 16:30-17:00 Building the model of the whole protein Chain merge & symmetrization 17:00-17:30: Submission of structures to EMDB. Understanding the validation report. Haemoglobin PDB full validation report Comparison validation scores PDB structure 17:30: Structure analysis: chain contacts Structural search 18:30:End of the day
DAY 3: Flexibility
9:30 – 10:00: Introduction to macromolecular flexibility and Flexibility Hub 10:00 – 10:15: Presentation of the dataset and workflows of the day (Zernike3D – HetSIREN) 10:15 – 11:00: Zernike3Deep (Theory) 11:00 – 11:30: Coffee break 11:30 – 12:30: Zernike3Deep (Practice) 12:30 – 13:00: HetSIREN (Theory) 13:00 – 14:00: Lunch break 14:00 – 15:00: HetSIREN (Practice) 15:00 – 15:30: Dimensionality reduction of estimated landscapes 15:30 – 16:00: Landscape exploration: interactive tools 16:00 – 16:30: Coffee break 16:00 – 17:00: Landscape exploration: interactive tools 17:00 – 17:30: End of the day
DAY 4: Flexibility
9:30 – 10:00: Review from the previous day 10:00 – 10:15: Presentation of the workflows of the day (FlexConsensus – ZART – CryoDRGN) 10:15 – 11:00: Should we trust our conformational landscapes? FlexConsensus (Theory) 11:00 – 11:30: Should we trust our conformational landscapes? FlexConsensus (Practice) 11:30 – 12:00: Coffee break 12:00 – 12:30: Should we trust our conformational landscapes? FlexConsensus (Practice) 12:30 – 13:00: Beyond motion blurr: ZART and flexible refinement (Theory) 13:00 – 14:00: Lunch break 14:00 – 15:00: Beyond motion blurr: ZART and flexible refinement (Practice) 15:00 – 15:30: CryoDRGN (Theory) 15:30 – 16:00: CryoDRGN (Practice) 16:00 – 16:30: Coffee break 16:30 – 17:00: CryoDRGN (Practice) 17:00 – 17:30: Landscape exploration: interactive tools 17:30 – 18:00: End of the day
DAY 5: Flexibility
9:30 – 9:45: Review from the previous day 9:45 – 10:00: Presentation of the workflows of the day (ContinuousFlex – 3DVA – 3DFlex – Prody) 10:00 – 11:00: ContinuousFlex 11:00 – 11:30: Coffee break 11:30 – 12:00: 3DVA (Theory) 12:00 – 13:00: 3DVA (Practice) 13:00 – 14:00: Lunch break 14:00 – 14:30: 3DFlex (Theory) 14:30 – 15:30: 3DFlex (Practice) 15:30 – 16:00: Prody 16:00 – 16:30: Coffee break 16:00 – 17:00: Prody 17:00 – 17:30: End of the day (closing remarks)
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.
Tutors:
I2PC: Carlos Oscar Sorzano Sánchez, Jose-María Carazo, Marcos Gragera, Carlos Perez Mata CryoEM CNB-CSIC: Francisco Javier Chichón.
Hybrid course. December 10 – 13, 2024 from 16:00 to 21:30 CET. You do not need to install any special software to connect. A modern browser should be enough.
Overall aims and course outline
By using image processing algorithms, it becomes possible to pinpoint the macromolecules of interest within the electron tomograms. Subsequently, researchers can extract small subtomograms from these locations and identify similar particles, facilitating their averaging and the recognition of diverse conformations. This process, referred to as subtomogram averaging, has played a pivotal role in elucidating an increasing number of macromolecular structures, achieving resolutions ranging from 20 to 3 A.
The course is designed to offer a comprehensive overview of the whole image processing workflow in Electron Tomography (ET). This includes tasks such as aligning the tilt series, reconstructing 3D tomograms, identifying particles, performing subtomogram averaging or even to perform a tomogram segmentation, all inside Scipion integration framework.
With the experience gained in the organisation of virtual and in-person courses, we intend to organise this course in a hybrid format. We will be able to accommodate up to 20 individuals for in-person attendance. However, other 20 participants will attend remotely. In total, we can host 40 attendees.
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
CryoET is one of the most promising structural techniques, and it bridges the gap between structural and molecular biology and cell biology. Ph.D. students, as well as post-docs, will undoubtedly benefit from approaching this technique. Knowing it will open new doors to new positions worldwide.
Prerequisites
You will need to bring a laptop with a modern browser
We will provide machines with the required software through Amazon Web Services.
15:00 – Welcome – (José Maria Carazo & Carlos Oscar Sorzano) 15:15 – Introduction to Electron Tomography – (José Luis Vilas) 15:35 – Course Introduction (Machines & Scipion) – (Pablo Conesa) 16:00 – Import Tilt Series, Automatic alignment – (José Luis Vilas) 17:00 – 15 minutes break 17:15 – CTF estimation and correction – (José Luis Vilas) 18:30 – Tomogram reconstruction – (José Luis Vilas) 20:00 – eTomo – (José Luis Vilas) 20:30 – End of session
DAY 2:
From tomograms to subtomograms: Picking
15:00 – ThermoFisher – Cryo-FIB microscopes for cryo-electron tomography and volume electron microscopy 16:00- Non-directional picking with cryolo and SPA leap – (Pablo Conesa) 17:00- 15 minutes break 17:15 – Dynamo – (Pablo Conesa) 20:30 – End of session
The course will take place in person at CNB-CSIC December 12 – 15, 2023 from 09:00 to 18:00 CET You do not need to install any special software to connect. A modern browser should be enough.
Overall aims and course outline
Cryo-electron Tomography is a rapidly growing technique that can visualize cell organelles and biological macromolecules in their cellular context. Image processing algorithms allow the identification of the macromolecules of interest in the electron tomograms. Then, by extracting small subtomograms around those locations and identifying those similar particles, we may average them and recognize their different conformations. This latter process is called subtomogram averaging and has allowed solving a growing number of macromolecules with a resolution between 20-5A.
The course aims at providing a comprehensive overview of the whole image processing pipeline in Electron Tomography (ET) from the movie alignment of the tilt series, 3D reconstruction of the tomogram, particle identification, and subtomogram averaging, all inside Scipion integration framework.
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
CryoET is one of the most promising structural techniques, and it bridges the gap between structural and molecular biology and cell biology. Ph.D. students, as well as post-docs, will undoubtedly benefit from approaching this technique. Knowing it will open new doors to new positions worldwide.
Prerequisites
You will need to bring a laptop with a modern browser
We will provide machines with the required software through Amazon Web Services.
I2PC: Carlos Oscar Sorzano Sánchez, Jose-María Carazo, Pablo Conesa, Federico de Isidro, David Herreros, Jorge Jiménez, Patricia Losana, Jose Luis Vilas, Borja Rodriguez, CryoEM CNB-CSIC: Francisco Javier Chichón, Jose Javier Conesa. Ramón y Cajal Researcher – Department of Information and Communication Engineering – University of Murcia: Antonio Martínez
9:30 – Welcome – (Jose Maria Carazo & Carlos Oscar Sorzano) 9:45 – Course introduction – (Jose Luis Vilas) 10:00 – Tomography in Scipion – (Jose Luis Vilas) 10:30 – Import Tilt Series, automatic alignment – (Federico de Isidro) 11:30 – 10 minutes break 11:40 – CTF estimation and correction – (Federico de Isidro) 13:00 – Lunch break 14:00 – Tomogram reconstruction – (Federico de Isidro) 15:30 – 10 minutes break 15:40 – eTomo – (Grigory Sharov) 17:00 – AreTomo, ctfFind4 and novaCTF(Grigory Sharov) 17:30 – End of session
DAY 2:
From tomograms to subtomograms- Picking and segmentation
9:30 – Non-directional picking with cryolo and SPA leap – (Borja Rodriguez) 11:10 – 10 minutes break 11:20 – Non-directional picking with cryolo and SPA leap – (Borja Rodriguez) 12:45 – Lunch break 13:45 – Tomogram denoising and membrane segmentation – (Antonio Martinez) 14:15 – Membrane picking with PySeg – (Jorge Jiménez) 15:00 – Dynamo – (Pablo Conesa) 16:00 – 10 minutes break 16:10 – Practice: Dynamo – (Pablo Conesa) 17:30 – End of session
DAY 3:
Processing subtomograms
9:30 – Subtomogram averaging with RELION4 – (Patricia Losana) 11:30 – 10 minutes break 11:40 – Subtomogram Averaging with RELION4 – (Patricia Losana) 13:00 – Lunch Break 14:00 – Subtomogram Averaging with EMAN – (Jorge Jiménez) 15:00 – 10 minutes break 15:10 – Subtomogram Averaging with EMAN – (Jorge Jiménez) 17:30 – End of session
DAY 4: morning session
Tomogram Interpretation
9:30 – Tomogram segmentation. Basic use of SuRVoS for cellular tomogram segmentation and basic analysis. 3D rendering using ChimeraUSFC with masked data – (Francisco Javier Chichón) 12:00/12:30 – End of coruse. Wrap Up.
Aim: The aim of this meeting is to get feedback and showcase how facilities are using Scipion and show what Scipion offers to a Cryo-em facility. There will be talks but also plenty of time for discussion.
Target Audience: Cryo-em facility staff wanting to do or already doing on-the-fly processing.
Conditions: The workshop will be remote. No programming skills are required. We will use in-house bigbluebutton conference system. Verify your browser works at https://demo.bigbluebutton.org/
Program:
San Francisco – 05:00 // Minneapolis – 07:00 // New York – 08:00 // São Paulo – 09:00 // Madrid – 14:00 // London – 13:00 Beijing – 20:00 // Tokyo – 21:00 // Sydney – 23:00
Tuesday 17th October – New developments/Solutions
14.00 (CEST) Welcome – Jose María 14.15-14:40 Introduction to Scipion – Pablo Conesa (CNB) 14:40-15:20 Optimizing Cryo-EM facilities with SmartScope – Jonathan Bouvette (Princeton) 15:20-16:00 Scipion and Smart scope – Alberto García (CNB) 16:00-16:40 EMhub: a web platform for CryoEM centers management and on-the-fly data processing (Jose Miguel de la Rosa (St. Jude Children’s Research Hospital Memphis, TN, USA) 17:20-18:00 Streaming and Unattended Workflows for SPA Processing – Daniel Marchan (CNB)
Wednesday 18th October – Facilities real cases
14.00 (CEST) Data flow in cryo-EM facilities: LMB example – Grigory Sharov (LMB) 14.15-14:40 CM01 and processing pipeline at ESRF – Isai and Olof (ESRF) 14:40-15:20 Setup at CNB – Javier Chichón (CNB) 15:20-16:00 Facilities + Tomography + Scipion – Pablo Conesa (CNB) 16:00-17:45 Discussion and conclusions – Data storage and transfer – IT support – Reporting – Automation: Grid screening, acquisition image processing – Others? 17:45-18.00 “Group picture” + End
Following the tradition, I2PC (Instruct Image
Processing Center) is organizing the forth edition of a seminar series on
cryoEM and cryoET methods for image processing. The aim of the seminar series
is to gather expert developers and users in a same framework where the
algorithms can gain visibility and users can understand the applications and
mechanisms of the presented algorithms.
7th September (Time: 9:00 AM New York, 15:00PM Madrid, 14:00PM London). Bernard Heymann – The implications and resolution of the Ewald sphere issue in cryoEM. National Cryo-EM Program, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc
21th September (Time: 9:00AM Los Angeles, 18:00PM Madrid, 17:00PM London). Petar Petrov – The laser phase plate in cryo-EM: new approaches to image acquisition and analysis. Holger Müller group at UC Berkeley.
5th October (Time: 9:00AM New York, 15:00PM Madrid, 14:00PM London). Christopher JF Cameron – Reliable protein identification in cryo-EM images by machine-learning consensus. Hemant Tagare and Mark Gerstein groups at Yale University.
19th October (Time: 9:00AM New York, 15:00PM Madrid, 14:00PM London). Eduard Baquero – Structural study of a broadly neutralizing anti-HIV-1 antibody from a post-treatment controller. NanoImaging Facility Core Institut Pasteur
National Center for Biotechnology (CNB), Madrid, Spain Madrid, June 19 – 23, 2023 How to find us: https://i2pc.es/contact-us/
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.
Contacts
Lead contact: Carlos Oscar Sorzano email. coss@cnb.csic.es
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)
Youcan fill your registration here (Online registration closed)
Academic Registration Fee Non Instruct countries: Predocs & Postdosc 100€
Academic Registration Fee Non Instruct countries: Others 150€
Industrial Registration Fee 300€
Program
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
Fill your registration here (Online registration closed)
This course is funded by Instruct – ERIC, an Integrated Structural Biology Infrastructure for Europe.
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.
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 applicationhere. (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
