Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM): 2021 - 2026

Lead Research Organisation: Science and Technology Facilities Council
Department Name: Scientific Computing Department

Abstract

The behaviour of living systems ultimately comes down to the interactions of biological molecules inside cells, and understanding these is vital to numerous human efforts, including controlling disease and improving food production. While experimental techniques such as macromolecular crystallography have for many years given detailed information on important molecules in the cell, many classes of molecules are not amenable to this technique. Moreover, as our understanding of pathways in the cell grows, there is increasing interest in the context in which these molecules operate. In other words, where in the cell do these molecules do their job, and which other cellular components are necessary for their function. Electron cryo-Microscopy (cryoEM) provides very useful information here, and bridges the gap between individual molecules and the whole cell. In the most favourable cases, detailed images of assemblies of molecules can be obtained, while at lower resolutions electron tomograms can show internal molecular details from within intact parts of cells or tissues.

Advances in instrumentation and data processing led to a significant increase in the quality of cryoEM data, which was characterised in 2014 as the "Resolution Revolution", and recognised by the 2017 Nobel Prize in Chemistry. Consequently there has been a surge in interest in the technique from structural and cellular biologists trying to understand a wide range of biological systems. There has been significant investment in the research infrastructure supporting cryoEM, most notably the establishment of several electron microscope facilities around the country. In the last few years, pharmaceutical companies and biotechnology companies have recognised the importance of cryoEM to their discovery pipelines, and have also begun investing in the area. A key component of this research infrastructure is the computational support to manage the data, process the micrographs, and interpret the data in terms of molecular volumes and/or atomic structures. The Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) was established during the period 2012 - 2016 to provide this part of the research infrastructure.

The proposed project is intended to provide continued support to the cryoEM community. One of the major products of the CCP-EM partnership is a software suite for processing cryoEM data collected at microscope facilities. Individual computer programs in this suite are developed independently, either by members of CCP-EM or collaborators. The role of CCP-EM is to collate these programs into a single suite, develop workflows through the suite, and distribute the suite to practising scientists. When done well, this is a win-win arrangement in which scientists get access to a comprehensive set of software in one place, and methods developers get access to a large user base. It is well known, however, that software rapidly becomes unusable if not actively maintained and it is the responsibility of the core team of CCP-EM to ensure the longevity of software in the suite.

We will also expand the scope of the suite. We will improve the tools for validating the structural information obtained, and facilitate the deposition of data in international archives. We will help to drive FAIR principles - that data from cryoEM experiments are accessible and usable to the wider community. We will increase our support for sub-tomogram averaging, a particular technique for obtaining in situ structural information of molecules. Finally, we will make more use of machine learning i.e. advanced algorithms that can learn from the data.

All these advances will be tightly coupled with our on-going user training programme, and support for individual methods developers. We will also continue our very popular annual Spring Symposium, which now provides a forum for 300 researchers to share experiences and to develop the cryoEM community.

Technical Summary

The CCP-EM partnership exists to further strengthen and expand the cryo-EM community. Activities can be broadly divided into three areas: (1) development of the CCP-EM software suite, (2) training programme and community events, and (3) strategic initiatives and outreach. We request funding for a core team of computational scientists to coordinate and develop these activities. Since software development, training and outreach are closely linked, we expect the team to work together in all areas.

The software suite is designed to integrate individual programs from diverse sources into a convenient package for scientists. It provides a framework for collaborating with other developers and helping to make novel methods available to the community. Collaboration is required, and the suite is not intended to be a container for all available software. The core team is developing a set of Python libraries covering a data model, job control, scheduling and workflow definition, which will merge the RELION pipeliner and the existing CCP-EM project manager. We propose to continue this development, integrate it into the production version of RELION, and expand its use to the rest of CCP-EM, facilitating closer integration between reconstruction, model building and data validation.

The extended framework will be used to integrate subtomogram averaging functionality, and develop the link to tomographic reconstruction. We will also develop on-the-fly processing for eBIC (and other facilities), tools for validation and simplified EMDB deposition, automation of data processing workflows and a new combined GUI for CCP-EM and RELION, as well as allowing third-party plugins to be easily incorporated into the pipeline. Machine-learning methods for data-driven analysis will be embedded at all levels.

We will continue to organise the annual Spring Symposium, expand the training programme, contribute to international meetings, and organise hackathons for developers.

Planned Impact

There is widespread interest in the international research community in using cryoEM to tackle big scientific challenges, such as understanding molecular machines in action and membrane complexes in situ. The technological advances enabling this were recognised in the award of the 2017 Nobel Prize in Chemistry. The field has strong links to atomic structure methods, especially crystallography, while electron tomography has strong connections to cell biology. The spatial dimension is needed to understand biological networks and machines, and complements traditional systems biology approaches. By supporting cryoEM research groups in the UK and encouraging a collaborative effort, CCP-EM advances the usage of cryoEM, and has an impact on many structural biology projects.

CCP-EM has an impact on individual researchers through its training and knowledge exchange aspects. The expansion of cryoEM as an important component in the toolkit for understanding cellular and sub-cellular biology relies on the availability of researchers competent in the computational techniques required to interpret the data. Existing researchers will of course benefit through improved software tools and environment. However, we specifically wish to lower the barriers to entry into the field of cryoEM. This applies not only to students and young postdocs, but also to researchers moving from other fields or wishing to use cryoEM as an additional technique.

The problems being addressed by cryoEM are of major importance in biomedical science, e.g. dynamic systems involving protein folding/refolding/misfolding, important in neurodegeneration and other misfolding diseases, virus-host interactions, and drug binding studies. Although our primary focus in the Partnership is on the fundamental science, advances here ultimately have an impact on translational and medical research. We are focussing on a technique rather than a particular scientific area, so the impact is likely to be very broad, leading eventually to improved medicine and health for the nation.

The insight that cryoEM provides to disease mechanisms is attracting the attention of a number of pharmaceutical companies. Around a dozen companies have purchased licences to use the CCP-EM software suite, and this number is growing. Company R&D staff also regularly attend our events. As well as helping to elucidate the underlying mechanisms of disease, cryoEM allows scientists to visualise the effect of drug molecules on proteins and complexes, in a near-native environment. As the technique matures, it is likely to become part of the drug development pipeline. Other industries (biotechnology, agribusiness) will also potentially benefit from the extra insight into biological processes provided by cryoEM.

By uniting the UK cryoEM community, the Partnership will have an impact on the strategy for future developments. By acting together, the UK cryoEM community will have a stronger voice. This will be used to influence software developers, instrument manufacturers and data standards development. They will also be able to provide input for national and international policy makers and funders. Finally, CCP-EM will take part in public engagement events to help strengthen the public understanding and appreciation of biomedical research.

Publications

10 25 50
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Collinson LM (2023) Volume EM: a quiet revolution takes shape. in Nature methods

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Joseph AP (2022) Atomic model validation using the CCP-EM software suite. in Acta crystallographica. Section D, Structural biology

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Palmer C (2022) Real space in cryo-EM: the future is local in Acta Crystallographica Section D Structural Biology

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Ploscariu N (2021) Improving sampling of crystallographic disorder in ensemble refinement. in Acta crystallographica. Section D, Structural biology

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Simpkin AJ (2021) Redeployment of automated MrBUMP search-model identification for map fitting in cryo-EM. in Acta crystallographica. Section D, Structural biology

 
Description EMDataResource Ligand Model Challenge 2021
Geographic Reach Multiple continents/international 
Policy Influence Type Contribution to new or improved professional practice
Impact The recommendations of this challenge will lead to more accurate modelling of ligands in macromolecular structure determination. This is basic science and the impacts will be downstream, and hard to link directly, but should lead to e.g. more reliable structure-based drug design.
URL https://challenges.emdataresource.org/?q=2021-model-challenge
 
Description Advancing Imaging Through Collaborative Projects
Amount $425,817 (USD)
Organisation Chan Zuckerberg Initiative 
Sector Private
Country United States
Start 03/2023 
End 03/2025
 
Description Establishing the Accessible Computational Regimes for Biomolecular Simulations at Exascale
Amount £471,209 (GBP)
Funding ID EP/Y008693/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 05/2023 
End 11/2024
 
Description Knowledge Assets Grant Fund: Enhanced UI for CCP-EM Software Suite
Amount £100,000 (GBP)
Organisation Department for Business, Energy & Industrial Strategy 
Sector Public
Country United Kingdom
Start 12/2021 
End 03/2022
 
Description Molecular structure from images under physical constraints
Amount £1,000,000 (GBP)
Organisation Alan Turing Institute 
Sector Academic/University
Country United Kingdom
Start 03/2021 
End 10/2023
 
Description Particle classification and identification in cryoET of crowded cellular environments
Amount £146,006 (GBP)
Funding ID BB/Y514007/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 02/2024 
End 08/2025
 
Description AIMLAC CDT - Aberystwyth, Bangor, Cardiff, Swansea, Bristol 
Organisation Swansea University
Country United Kingdom 
Sector Academic/University 
PI Contribution We provide placements for students on this CDT programme. Specifically for the 2020/2021 cohort, we provided 2 placements. The students worked on projects concerning denoising of electron micrographs for cryoEM, and modelling of neutron reflectometry data. Each student has completed a 2 week initial placement, followed by the main 6 month placement. For the 2021/2022 cohort, we provided a further 2 placements. One will continue to refine the cascade machine learning model for segmentation of molecular volumes from cryoEM. The other will work on the CoVal server for linking SARS-CoV-2 variant data with experimental structures. For the 2022/2023 cohort, we are providing one placement on machine learning in cryoEM.
Collaborator Contribution The CDT administers the programme, and matches us up with specific students. The students themselves contribute to our on-going research programme. Typically, they deliver a small piece of coding which can be included in our larger software packages.
Impact One of the students has contributed code to the Macromolecular Machine Learning Toolbox for 3D cryo-EM data segmentation, which is publically available. The collaboration is multi-disciplinary in the sense that the students come from a background of AI in physical sciences, and contribute to projects in the biosciences when with us.
Start Year 2020
 
Description COG UK 
Organisation University of Cambridge
Department School of Clinical Medicine
Country United Kingdom 
Sector Academic/University 
PI Contribution We have developed the CoVal web service for matching sequence mutations of SARS-Cov-2 to available structural data, making use of tools from CCP-EM. We have made this server available to members of the COVID-19 Genomics UK Consortium (COG-UK). We are attending weekly meetings with COG-UK and discussing how we can input structural data into the understanding of the emergence of SARS-Cov-2 variants.
Collaborator Contribution The members of COG UK are providing advice on variants of interest, which we can focus on for the CoVal server. We expect to get early access to sequence data in the UK.
Impact The collaboration brings together our structural biology expertise with the sequencing/bioinformatics expertise of COG-UK. It is still early days, but we hope to feed into the scientific/policy advice which COG UK gives to the UK government.
Start Year 2020
 
Description Co-development of in situ cryogenic electron tomography 
Organisation University of Pittsburgh
Country United States 
Sector Academic/University 
PI Contribution We have developed computational pipelines for processing cryogenic electron tomograms obtained from cellular samples, extracting target particles and generating sub-tomogram averages. The workflows have made use of CCP-EM's Pipeliner technology, wrapping Relion software and other 3rd party programs. We have run these pipelines on datasets provided by the partner as part of their research. This provides us with challenging case studies, and returns in situ structures for their research.
Collaborator Contribution The partner has made available several tilt series from cryogenic electron tomography of cellular samples. They have provided the metadata necessary for processing, and have provided feedback on the results of our processing.
Impact Outputs are in situ structures of macromolecular complexes of interest, which will be published. This is a collaboration between our computational group and the experimental group of Zachary Freyberg at Pitt.
Start Year 2023
 
Description Coronavirus Structural Task Force 
Organisation University of Hamburg
Country Germany 
Sector Academic/University 
PI Contribution The Coronavirus Structural Task Force aims to provide structural information on proteins from the SARS-Cov-2 virus. As well as structures from the internatinoal repositories PDB and EMDB, the Task Force provides quality assessment, and in some cases improved structural modelling. Joseph Agnel from the CCP-EM team has provided many of the validation tools used by the Task Force, and has improved some of the viral structures and deposited them on their web site.
Collaborator Contribution Our partners provide the dissemination site for our efforts to improve the structural modelling for SARS-Cov-2.
Impact The collaboration is between structural biologists from different international groups.
Start Year 2020
 
Description Global Phasing Ltd collaboration 
Organisation Global Phasing
Country United Kingdom 
Sector Private 
PI Contribution We bring prior work on development of a software framework for single particle analysis by Relion, which the partnership is building on. We also bring our established relationship with the Relion development team, with the eBIC facility, and with the wider community.
Collaborator Contribution Global Phasing Ltd bring expertise on developing automated data processing pipelines in crystallography, as well as specific software such as Buster. Their contribution is in terms of background IP and current staff effort.
Impact The output will be improved software for processing single particle cryoEM datasets, which will be deployed at the eBIC facility and distributed as part of the CCP-EM software suite. The project is supported by internal funds of Global Phasing and CCP-EM, as well as a Proof of Concept award from STFC. Prototype software has been developed, and a first version will be released soon. The work combines structural biology, data management and software engineering.
Start Year 2019
 
Description Leeds EM facility 
Organisation University of Leeds
Department Astbury Biostructure Laboratory
Country United Kingdom 
Sector Academic/University 
PI Contribution Help to scope computational requirements of the new Electron Microscopy facility. Later, we will help with installation, and writing of custom software pipelines. We have contributed to training events held at Leeds in Sept 2016, July 2017 and Dec 2018.
Collaborator Contribution Advice on software required by Electron Microscopy facilities. This advice was included in a grant application submitted in February 2016, as well as informing on-going plans. Neil Ranson was included as a CoI in the 2020 proposal for the renewal of CCP-EM.
Impact Material for inclusion in the CCP-EM renewal grant application, concerning the software infrastructure needs of cryoEM facilities. Election of Neil Ranson (Leeds) as Deputy Chair of CCP-EM. Leeds hosted a Relion workshop in September 2016, an MD/EM workshop in July 2017 and a cryoEM workshop in Dec 2018.
Start Year 2015
 
Description eBIC collaboration 
Organisation Diamond Light Source
Country United Kingdom 
Sector Private 
PI Contribution eBIC (electron Bio-Imaging Centre) at Diamond Light Source provides scientists with state-of-the-art experimental equipment and expertise in the field of cryo-electron microscopy, for single particle analysis and cryo-tomography. As part of CCP-EM, my group are providing computational support to users of eBIC, in the form of installing software and direct assistance. We benchmark certain key codes, and have optimised their usage on Diamond compute clusters. We plan to co-develop software pipelines to enable users to get rapid feedback on their data collection.
Collaborator Contribution eBIC provides a pool of cryoEM users who can provide feedback on the developing CCP-EM software suite, and provide test datasets. Diamond staff will also help to co-develop software pipelines for rapid feedback.
Impact The collaboration involves hardware development (microscope and computational resources), application software development, and structural biology. We maintain a set of EM software on Diamond systems, available to users of eBIC. We have benchmarked version 2.0 of the Relion software on a GPU platform at Diamond. We have helped with the installation of cryoSPARC at Diamond. We have implemented the Relion-IT pipeline for automatic processing of micrographs during a user visit, and are now trialling the CCP-EM pipeliner.
Start Year 2015
 
Title Buccaneer in CCP-EM 
Description The Buccaneer pipeline is available within the CCP-EM graphical user interface. Given a cryoEM map, obtained for example from single particle reconstruction, and the sequence of the expected protein molecules, the pipeline will build and refine an atomic model. This is a crucial step in the interpretation of experimental data from cryoEM. In comparison to other model building tools, Buccaneer can handle relatively low resolution. Buccaneer is an important part of the annual CCP-EM Icknield training school on model building and refinement. It was also used in our team's submission to the 2019 Model Metrics Challenge (organised by the global EM Data Resource https://www.emdataresource.org/). 
Type Of Technology Software 
Year Produced 2017 
Impact The pipeline has been used in CCP-EM workshops, and has helped several researchers with their structural biology projects. The Buccaneer pipeline remains an important component of the CCP-EM software suite, and is updated periodically by the main author. 
 
Title CCP-EM Doppio 
Description Doppio is the new GUI front-end for the CCP-EM software suite. It is written in Javascript with the intention of deploying it both locally (desktop or browser) and remotely (via web). The latter has been used to support training courses with the student display remote from the server performing the computation. Interfaces for each possible task are defined by the CCP-EM Pipeliner framework. Doppio manages input to the task and displays results using a wide toolkit of graphs, images and 3D viewers. Work is managed via projects, and graph-based views illustrate progress through a project. Alpha releases were made in August 2022 and February 2023. The first beta release was made in April 2023. After several rounds of feedback and improvement, the first official release is planned for April 2024. This project will be released under the terms of the CCP-EM academic and commercial software licences. 
Type Of Technology Software 
Year Produced 2022 
Impact As the software is in beta release, and used by a small set of power users, the impacts are minimal so far. It has however been used for training courses since 2023. The impact will grow when it becomes the default GUI for CCP-EM. 
URL https://www.ccpem.ac.uk/docs/doppio/user_guide.html
 
Title CCP-EM pipeliner 
Description CCP-EM pipeliner is a software library / framework underpinning workflows in cryogenic Electron Microscopy (cryoEM) and Tomography (cryoET). It is based around defined node types which can be used to link together jobs, and to trace provenance of data. It tracks metadata, and collates metadata to accompany deposition of structural data to the PDB / EMDB. It defines interfaces that can be viewed in the CCP-EM Doppio GUI. It was initially developed to support single particle workflows in the Relion software, and will eventually replace the scheduler framework used currently. It is now being expanded to other CCP-EM software, and is being used to develop deposition tools in collaboration with PDBe/EMDB staff at EMBL-EBI. A first hackathon was held in March 2022 to encourage software developers in cryoET to adopt it. The core team is now implementing cryoET functionality in Pipeliner, as part of a collaboration with the University of Pittsburgh. Alpha releases were made in August 2022 and February 2023. The first beta release was made in April 2023. After several rounds of feedback and improvement, the first official release is planned for April 2024. 
Type Of Technology Software 
Year Produced 2022 
Open Source License? Yes  
Impact The hackathon in March 2022 not only encouraged the use of CCP-EM pipeliner, but was also a catalyst to bring together multiple software development groups in cryoET. This led to some coordination of efforts, and should lead to better software provision for end users. A project on sub-tomogram averaging of respiratory complexes is using the CCP-EM Pipeliner to develop workflows. 
URL https://ccpem-pipeliner.readthedocs.io/en/latest/
 
Title CCP-EM version 1 
Description The CCP-EM software suite provides a collection of programs for cryoEM single particle reconstruction and building of atomic models. The suite as a whole has an STFC licence, and is licensed free of charge to non-profit users, and for a charge to for-profit users. Nevertheless, many of the component programs are available separately under Open Source licences. Version 1 was released April 2018, with updates 1.1 in July 2018, 1.2 in December 2018, 1.3 in April 2019, 1.4 in November 2019, 1.5 in October 2020, and 1.6 in April 2022. This first official release of the CCP-EM software suite mainly covered fitting and refinement of atomic models into single particle reconstructions, combining experience gained in CCP4 with high resolution maps with other techniques more appropriate to lower resolution maps. Since that initial release, the suite has expanded to include tools for map analysis and manipulation. Version 1.2 included for the first time pre-compiled binaries for Relion, the most popular software for single particle reconstruction. Besides providing a convenient way of viewing Relion projects on a personal machine, the inclusion of Relion is the basis of on-going efforts to integrate reconstruction with downstream map interpretation. The CCP-EM suite also includes software libraries such as mrcfile, clipper-python and relion-it, which are being used by third-party developers and facility sites for customised workflows. Version 1.6 (April 2022) included the new Servalcat wrapper for atomistic model refinement with Refmac5. There were also a number of new validation tools, including Privateer, 3D-Strudel and PI-score. Stable nightly builds are made available (latest 8/11/22) which contain some useful updates. The version 1 release sequence is now frozen, pending the release of version 2 based on Pipeliner/Doppio (see other entries). 
Type Of Technology Software 
Year Produced 2018 
Impact The suite is used by many academic and industrial cryoEM groups worldwide to solve novel macromolecular structures. These are deposited in the Electron Microscopy Data Bank (EMDB) and the Protein Data Bank (PDB), from where they can be employed in wider biomedical applications. At the moment (early 2023) we have around 30 commercial licences, indicating usage in pharma and biotech. The academic usage is estimated to be several thousand. The two papers describing the suite itself have been cited 290 times to date (as at March 2023), with individual programs from the suite cited many more times. 
URL http://www.ccpem.ac.uk/download.php
 
Title CCP-EM version 2 (beta) 
Description Version 2 of the CCP-EM software suite is a major update. It is built on the Doppio GUI and the Pipeliner framework, which together provide more functionality for workflows, results display and metadata tracking. Compared with version 1, will also contain several major new programs, such as Relion v5, TEMPy v2, Moorhen, Model-Angelo and CheckMySequence. This version is currently in beta release, with the aim to formally launch it by May 2024. It will be released under the terms of the CCP-EM academic and commercial software licences. 
Type Of Technology Software 
Year Produced 2024 
Impact Version 2 is being used in CCP-EM training courses. Besides familiarising students with the new software, it provides a good platform for teaching cryoEM. 
 
Title Macromolecular Machine Learning (MML) Toolbox for 3D cryo-EM data segmentation 
Description We have developed a collaborative software toolbox that includes a number of methods and pre-processing steps common to applying machine learning to 3D macromolecular data. The aim is to improve the accessibility of machine learning techniques to the members of the community and lower the technical entry barrier to applying them. Notable features: * Command line tool and Python API * Set of custom loss functions to handle volume background imbalance * 3 modes of pre- and post-processing including .mrc headers * customisable architecture * loading and saving data * data structure for holding maps and models * 8 different metrics and visualisations for performance tracking The toolbox is being used in several internal and external machine learning projects. It has also been released to collaborators in the CCP-EM consortium, for example at Delft, NL. These application projects are in turn driving the further development of the toolbox. The toolbox is the main destination of code developed under the BBSRC-funded project to develop a cascaded neural network for identifying low resolution features in cryoEM maps. Recent additions include: 1) Set up the cascade architecture in the ML-protein-toolbox 2) Add a data augmentation routine by initial volume rotations and filter by class representation. 3) Add an intermittent HDF5 storage for batches of tiles and a tracking mechanism (tile origin and index) to reduce memory issues with cascade 4) Implement DeepLabV3+ architecture which is one of the best performers in image segmentation tasks (makes use of atrous convolutions) but computationally heavy. The toolbox has been further developed in 2023. It has been restructured to work with PyTorch. We have added a set of loss-functions especially to deal with class-imbalance problems. The toolbox is expected to be production ready in future releases of the CCP-EM software suite. 
Type Of Technology Software 
Year Produced 2020 
Open Source License? Yes  
Impact The toolbox has been used in at least 5 different software development projects, and has an impact indirectly through these. 
 
Description CCP-EM Pipeliner/Doppio Workshop 2024 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact In partnership with eBIC for Industry, CCP-EM hosted a two-day workshop on the applications of Pipeliner/Doppio focused on its use in industry drug-discovery projects and in central facilities. This workshop aimed to help those managing company or public cryoEM faciitilies set up and manage our new pipeliner/Doppio software package and use it to automate workflows and manage the data produced.

The workshop was intended for cryo-EM and computational scientists with experience processing single-particle data and will focus on setting up pipeliner/Doppio in a multi-user environment and using its features to streamline and automate workflows. Participants received hands-on experience with fully automated processing of a ligand-bound enzyme dataset collected at DLS.

Topics:
- Running cryoEM workflows with pipeliner and Doppio GUI
- Automating workflows by scripting with the pipeliner API
- Tools for data management and LIMS/electronic notebook integration
- Setup and configuration of pipeliner/Doppio
Year(s) Of Engagement Activity 2024
 
Description CCP-EM Spring Symposia (hybrid) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The annual CCP-EM Spring Symposium is the flagship meeting of the consortium. The conference aims to provide a forum to highlight state of the art developments in computational cryoEM and related themes as well as showcasing outstanding recent biological applications. We aim to promote an inclusive, friendly atmosphere welcoming both old and new to the community. Topics include instrument technology, sample preparation, image processing, single particle reconstruction, tomography and model building. The event also includes the Diamond Light Source biological cryo-imaging user meeting which presents developments at the Electron Bio-Imaging Centre (eBIC) & B24 (beamline for 3D Correlative Cryo-Imaging for the Life Sciences).

After the first 5 meetings, the 6th and 7th editions moved online due to the covid19 pandemic. In 2022, we were able to move to a hybrid format with 150 attending an in-person meeting at the East Midlands Conference Centre, Nottingham. The meeting was also broadcast to an online audience ( 914 registered, 1140 unique views, 340 concurrent views). The scientific organisers Doryen Bubeck (Imperial) and Paula da Fonseca (Glasgow) oversaw an exciting two days of talks, while the STFC core team took care of conference organisation. As in previous years, talks from the symposium are published in Acta Crystallographica D.

The hybrid meeting was held again in April 2023, with over 270 delegates at the East Midlands Conference Centre (Nottingham University) and over 750 unique attendees joining via Zoom from 40 different countries. The in-person attendance was a significant increase on the previous year, showing the vibrant state of the cryoEM community. An exciting programme was arranged by our scientific organisers Dr. Vicki Gold (University of Exeter) and Dr Stephen Muench (University of Leeds). There were 19 speakers from high profile institutes (including STFC, DLS, Franklin, MRC-LMB, Chan Zuckerberg Imaging Institute, Max Planck, and Universities of Birkbeck, Cambridge, Harvard, Leeds). This year we were also proud to announce the public beta release of our new CCP-EM Doppio software - an end-to-end package for processing single particle cryoEM data and atomic model building.
Year(s) Of Engagement Activity 2022,2023
URL https://www.ccpem.ac.uk/training/spring_symposium_2023/spring_symposium_2023.php
 
Description CCP-EM Spring Symposia (virtual) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The 2020 and 2021 CCP-EM Spring Symposia were held online in a virtual format due to the COVID-19 situation. The conference was hosted on Zoom and was free of charge, but with registration required.

The conference aims to provide a forum to highlight state of the art developments in computational cryoEM and related themes as well as showcasing outstanding recent applications. We aim to promote an inclusive, friendly atmosphere welcoming both old and new to the community. Also included is the Diamond Light Source Biological Cryo-imaging User Meeting (eBIC & B24). Topics include instrument technology, sample preparation, image processing, single particle reconstruction, tomography and model building.

The Scientific organisers for 2020 were Helen Saibil (Birkbeck) and Christos Savva (University of Leicester), and for 2021 Giulia Zanetti (Birkbeck) and Christopher Aylett (Imperial). All other organisation was by STFC.

Because of the online format, we reached a much larger audience than normal. In 2020, we had about 3000 registered, with around 1000 logged in to the sessions at any one time. The numbers were slightly less in 2021, but still much larger than the original in-person meetings. We believe that by the second year of the pandemic, there was some fatigue with the number of on-line conferences. Based on these experiences, we plan to make future Spring Symposia hybrid events, combining the advantages of in-person meetings with the reach and accessibility of on-line meetings.

Speakers slides are made available on our website, and recordings of talks are on YouTube (on the STFC channel, also linked from our website). These are recognised as important resources for our community.
Year(s) Of Engagement Activity 2020,2021
URL https://www.ccpem.ac.uk/symposium.php
 
Description CCP-EM developers model building workshop Jan 2023 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact CCP-EM core team hosted a workshop at the Coseners House, Abingdon in January 2023. The workshop was aimed at the interrnational community of methods developers, with around 30 attending in person. The general aim was to encourage communication amongst this group, around the topic of atomic model building for cryoEM. A specific aim was to encourage uptake of the CCP-EM Pipeliner toolkit which is the basis of version 2 of the CCP-EM software suite. Writing wrappers for software using the Pipeliner toolkit enables pipeline construction and helps to track metadata through a project. While CCP-EM core staff can write these wrappers, it is preferable if the primary developers adopt this way of working. We successfully helped several developers migrate to the toolkit.
Year(s) Of Engagement Activity 2023
 
Description CCP-EM lunchtime bytes 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Tom Burnley, on behalf of CCP-EM, presented a Lunchtime Byte on the 2nd day of the CCP4 Study Weekend, held in Nottingham in January 2023. This is a chance to showcase CCP-EM software for cryoEM to the attendees of the Study Weekend. Although the conference is for crystallographers, most structural biologists will use both techniques, and hence there was a lot of interest in Tom's talk.
The session was repeated for the January 2024 Study Weekend, also held at Nottingham.
Year(s) Of Engagement Activity 2023,2024
URL https://ccp4sw.org/programme/
 
Description CCP-EM website 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The CCP-EM website is used for dissemination of the aims of CCP-EM, advertising our meetings and workshops, as well as 3rd party meetings of interest to our community.

The CCP-EM software suite is available via the website as downloadable packages. There is a dedicated tutorials page https://www.ccpem.ac.uk/tutorials.php for users to learn how to use the software.

The website also hosts specialist information, such as a description of the MRC file format.
Year(s) Of Engagement Activity 2012,2013,2014,2015,2016,2017,2018,2019,2020,2021,2022
URL http://www.ccpem.ac.uk
 
Description CCP-EM workshop satellite to ECM33 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact We held a joint CCP4/CCP-EM workshop with a focus on theory and practice in computational approaches in bio-crystallography and Cryo-EM single particle analysis This was an in-person event taking place at Synchrotron SOLEIL - CNRS - Cea Paris-Saclay, with one day devoted to CCP4 and one day devoted to CCP-EM. Around 20 students were introduced to the CCP-EM software suite, and some of the methods behind it.
We received positive feedback on the course, and maintained links with some of the students afterwards. Discussion continued on a dedicated Slack channel.
Year(s) Of Engagement Activity 2022
URL https://www.ecm33.fr/ccp4andccpemworkshops
 
Description CCP4/CCP-EM course Spring8 Nov 2023 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This was a joint CCP-EM/CCP4 workshop at the Spring8 synchrotron in Japan, held in November 2023. It lasted a week, and for the CCP-EM component, students were taken through structure solution by single particle analysis followed by model building and refinement. Tutorials used the CCP-EM software suite including Relion v4, accessed through the new Doppio interface. Computations were run remotely on the STFC Cloud, located at Harwell UK (which provides a pre-configured platform for tutorials).
Year(s) Of Engagement Activity 2023
 
Description CCP4/CCPEM workshop at IUCr 2023 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This workshop took place in Melbourne on Monday 21 August (8am - 6pm) and Tuesday 22 August (8am - 4pm) 2023

The CCP4 group is a long standing provider of software for the structural biology community. CCP4 along with it's sister group in Cryo-EM propose to undertake a 2-day workshop on the use of the CCP4 and CCP-EM suites for structural solution, in a similar manner to the workshop before the ECM 2022. The workshop will demonstrate the use of the CCP4Cloud platform and the new CCP-EM Doppio interface. This is of direct relevance to the IUCr community of crystallographers and Cryo-EMers. The typical CCP4 demo/tutorial covers all steps of the MX structure solution process including data processing, phasing (modification of AlphaFold2 models), refinement and model building. The CCP-EM day at the ECM covered single particle cryo-EM, although on the timescale of the IUCr it would be expected that this would be extended to include some tomography. At the workshop it would be expected that students could bring their own laptops and, therefore, be able to follow the tutorials.

The workshop introduced students (attending the 26th Congress and General Assemby of the International Union of Crystallography) to CCP-EM and CCP4 software for solving their macromolecular structures. This is part of the wider training plan for the community, increasing the computational skills of experimental structural biologists.
Year(s) Of Engagement Activity 2023
URL https://iucr2023.org/workshops/
 
Description CCPEM contribution to EMBO courses on Image Processing for cryo EM 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The EMBO course on Image processing for cryo-electron microscopy is held every other year at Birkbeck, and is very popular. Over 10 days, it teaches all aspects of cryoEM including sample preparation, microscope operation, data processing and structure modelling.
The core team of CCP-EM contributed to the 2017 course in several ways. We gave an invited lecture on CCP-EM, and we supported several hands-on computer tutorials. We also directly sponsored the event, allowing more students to be supported.
We contributed again to the 2019 course. This time we ran two practicals: "Fitting of structures, flexible fitting (Flex-EM), model validation (TEMPy)" and "Local sharpening (LocScale), de novo structure building (CCP-EM, REFMAC)". CoIs from the current CCP-EM grant delivered 7 of the lectures. CCP-EM again sponsored the event.
In 2021, CCP-EM collaborators gave several talks, and CCP-EM core staff ran several computer practicals. We again provided sponsorship to help support students. The event was virtual this year, and STFC provided AV support (mainly via Zoom) which we arranged.
The CCP-EM core team contributed again in September 2023, running a practical on model building and improvement using CCP-EM software. We also co-hosted a roundtable on "Integrated, open software for science: advantages and challenges". CCP-EM was also able to sponsor the course, in order to support the number and diversity of students.
The course trains around 50 students and postdocs in cryoEM each time, and is a major contributor to skills development for cryoEM. It is run by Birkbeck College, London, who are an important partner in CCP-EM. In terms of teaching, it is a community effort. In addition to the specific activities mentioned above, CCP-EM plays an indirect role in supporting this community and coordinating efforts.
Year(s) Of Engagement Activity 2017,2019,2021,2023
URL https://meetings.embo.org/event/23-cryo-em-image-processing
 
Description Contribution to SWSBC meeting on structural biology 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact The annual meeting of the South West Structural Biology Consortium is a forum for research groups in the South West of England to come together to present their research and build networks amongst each other. Founded in 2001, this annual consortium rotates around the Universities of Bath, Bristol, Cardiff, Exeter, Reading, Portsmouth, Southampton, Sussex and UCL. It is particularly aimed to PhD students, Postdocs and ECRs.

The meeting was originally for macromolecular crystallography, but there is an increasing component of cryogenic electron microscopy and tomography, as well as electron diffraction and serial crystallography. In 2021, Colin Palmer from the CCP-EM core team presented a talk on "The CCP-EM software suite for cryoEM" introducing the students to what is available in CCP-EM. The CCP-EM core team were invited again to the July 2023 meeting in Southampton. This time, Tom Burnley gave a live demonstration of the latest CCP-EM software.
Year(s) Of Engagement Activity 2021,2023
URL https://swsbc2023.soton.ac.uk/
 
Description Dutch CryoEM School (June 2022) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The Dutch Cryo-EM School took place from 27 June to 02 July 2022 in Leiden and Delft. The aim of this school is to teach the basic principles and practical aspects of image processing to structural and molecular biologists wishing to determine macromolecular structures by cryoEM. The course will cover all aspects of cryoEM structure determination, ranging from sample preparation over data collection to processing and interpretation of high-resolution image data, for both single particle images and tomograms, and will be aimed at advanced PhD students and postdocs using cryoEM for structural analysis.

CCP-EM were represented by Tom Burnley, Colin Palmer and Agnel Joseph from the core team at STFC.
Year(s) Of Engagement Activity 2022
URL https://nemi.microscopie.nl/past-events/course-dutch-cryo-em-school-27-june-2-july-2022/
 
Description EM at CCP4 Northern Structural Biology meeting 2023 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact The CCP4 Northern Structural Biology meeting is a regional event for structural biologists in Scotland and northern England. It covers X-ray crystallography, cryoEM, NMR, MS and complementary biophysical techniques, and provides an opportunity for early career scientists to present, network and expand their knowledge.

Tom Burnley and Matt Iadanza from the CCP-EM core team attended and presented on cryoEM and the CCP-EM software suite. In addition to providing skills to ECRs, this helps to embed the consortium in the wider UK structural biology community.
Year(s) Of Engagement Activity 2023
URL https://www.eventbrite.co.uk/e/ccp4-northern-structural-biology-meeting-tickets-664501250127
 
Description EMBO course on Practical integrative structural biology, Hamburg 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Application of integrative structural biology requires an in-depth understanding of both different experimental approaches and computational modeling. To provide advanced training in such a highly interdisciplinary skill set, this EMBO Practical Course will teach how to interpret data from major structural biology techniques and how to integrate this data using computational methods. The course location at the Hamburg Unit of the European Molecular Biology Laboratory and the Center for Structural Systems Biology on the DESY campus will provide on-site synchrotron SAXS and MX beamlines for training. Hands-on practicals will use a well-studied model system, for which data from all main structural biology techniques are available.
This course was held in November 2019. It included 3 members of the CCP-EM core team and a further 4 members of the cryoEM consortium. We provided lectures and hands-on computer tutorials for cryoEM.
The course was held again in November 2022. This time, there was 1 member of the CCP-EM core team and a further 5 members of the cryoEM consortium.
Year(s) Of Engagement Activity 2019,2022
URL https://meetings.embo.org/event/22-structural-bio
 
Description IUCr Satellite workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This remote training event was held as part of a joint workshop on structural biology methods and computational analysis of crystallographic and Cryo-EM data in connection with the XXV Congress and General Assembly of IUCr in Prague, August 2021.

Our computational session on CCP-EM, which followed a similar session for CCP4, covered a general introduction to CCP-EM, single particle reconstruction, model building, refinement and validation. The course was delivered mostly through computer practicals.
Year(s) Of Engagement Activity 2021
URL https://www.ibt.cas.cz/en/core-facilities/centre-of-molecular-structure/courses/2021-iucr-cms-satell...
 
Description Icknield workshops on model building (annual) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The first Icknield Workshop on Model Building and Refinement for High Resolution EM Maps was held at the RAL / Diamond campus, Harwell, UK on 2nd - 4th March 2016. The first course was aimed at structural biologists with high resolution EM maps ready for / in the process of modelling, building and refinement. This three day course hosted some of the leading software developers and provided ample contact time to allow delegates to discuss their data in detail alongside traditional lectures and tutorials.

This is now an annual event, with further instances being held in April 2017, May 2018 and April 2019. After a break due to the pandemic, the workshop returned as a four day course run in Sept 2022 and again in Oct 2023. There are typically 20-22 students, carefully selected in order to give a good coverage of cryoEM labs. This is now a comprehensive course for EM model building covering advanced use of Coot, FindMySequence/CheckMySequence, EM-placement, EMDA, FlexEM/TEMPy-REFF, ISOLDE, LocScale, ModelAngelo, ModelCraft, MolProbity, Privateer, RefmacServalcat and new validation tools (most of which are available in the CCP-EM software suite). It covers all aspects of modelling building including: map optimisation, automated model building, medium resolution refinement, high resolution refinement, interactive refinement, validation and deposition.

Participants are encouraged to bring their own data so that the tutors can help directly. Nevertheless, we are keen to have industry representation as well, and example data is provided in cases where participants own data cannot be shared.

Following positive feedback from the 2023 course, we intend to extend the course to 5 days in 2024.
Year(s) Of Engagement Activity 2016,2017,2018,2019,2022,2023
URL https://www.ccpem.ac.uk/courses.php
 
Description Joint CCPEM CCPBioSim workshop (Apr 2022) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact We helped to organise (and participated in) a two day joint workshop between CCP-EM and CCPBioSim, aiming to build links between the cryoEM (CCP-EM) and biomolecular simulation (CCPBioSim) communities. The workshop was hosted by Leeds, and around 40 people attended in-person or online.
Sessions were held on building links between EM and MD, software tools, simulating EM datasets from MD trajectories, and finding, sharing and validating MD trajectories. With cryoEM increasingly resolving conformational changes, it is timely to forge a closer link to MD techniques which simulate those conformational changes. MD can help with the interpretation of cryoEM datasets, while the latter can be used to validate the sampling achieved by MD.
STFC was represented by Tom Burnley (CCP-EM) and James Gebbie (CCPBioSim). The discussions helped to inform current projects on simulating cryoEM datasets (Parakeet with the Rosalind Franklin Institute) and developing databases of MD trajectories (the DRI-funded Physical Sciences Data Infrastructure).
Year(s) Of Engagement Activity 2022
 
Description Leeds cryoEM training Nov 2023 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact This course is a part of a cryo-EM Wellcome/MRC training program tailored for PhD students and postdocs who wish to use single particle cryo-EM for their research but have very little or no prior experience in single particle cryo-EM. The aim of the course is to give a theoretical knowledge and practical experience in the entire cryo-EM single particle analysis workflow including negative stain TEM, cryo-EM sample preparation, cryo-EM screening and data collection using Titan Krios microscopes, and an introductory overview of the data processing.

Matt Iadanza from the CCP-EM core team taught the image analysis section of the course.
Year(s) Of Engagement Activity 2023
URL https://astbury.leeds.ac.uk/facilities/wellcome-mrc-training-in-cryoem/single-particle-cryoem-be-an-...
 
Description Pipeliner tomography workshops 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact One of the specific objectives of the current CCP-EM grant (2021-2026) is to integrate workflows for sub-tomogram averaging (STA). Cryogenic electron tomography allows the study of isolated but pleiomorphic particles (e.g. enveloped viruses) or of in situ particles (e.g. membrane proteins in the cellular context). Methods for extracting and averaging particles (i.e. STA) are improving, allowing the resolution of sub-nanometre structural details.
The CCP-EM Pipeliner toolkit is being developed to support the next generation CCP-EM software suite, in the first instance covering single particle reconstruction and atomistic model building. In order to explore the application of Pipeliner to tomography workflows, we convened a workshop in March 2022 with leading developers from MRC-LMB, Birkbeck, Crick, eBIC and RFI. There are many workflows being used in different institutes, and we had a good discussion over the pros and cons. It was clear that CCP-EM needs a flexible solution to accommodate diifferent workflows depending on the progress of individual tools and the nature of each particular dataset. We believe Pipeliner can deliver that flexibility, and a few prototype pipelines were coded.
A follow-up workshop was held in March 2023, to take into account the increasing maturity of the CCP-EM Pipeliner toolkit. Developers from MRC-LMB and RFI attended, and we began work on converting their codes to using the Pipeliner toolkit. This work will allow the integration of these workflows into a future version of the CCP-EM software suite. Pipeliner also allows tracking of metadata, so that we can link tomography workflows to deposition to the EMDB/EMPIAR archives.
Year(s) Of Engagement Activity 2022,2023
 
Description Regensburg cryoEM course, Sept 2022 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The CCP-EM team contributed to a course on Single Particle cryoEM of macromolecular complexes, held at the University of Regensburg 26th-30th Sept 2022.
Tom Burnley delivered a lecture on CCP-EM. Members of the wider CCP-EM collaboration also gave tutorials on Relion, Locscale. model building, and Coot.
The course helped to develop skills in using cryoEM for structural biologists, and the feedback was good.
Year(s) Of Engagement Activity 2022
 
Description SEA-COAST workshop Thailand 2024 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact I presented two lectures on "Basics of Cryo Electron Microscopy" and "Structure solution with Cryo EM" to participants of the South-East Asian Crystallographic Overview And Systematic Training (SEA COAST) January 29 - February 7, 2024 King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, Thailand. Although the workshop was primarily aimed at macromolecular structure determination via crystallography, there was substantial interest in cryoEM as an alternative experimental technique. The first cryoEM facility in Thailand is currently being commissioned, and there is interest in building up projects in local universities. I was able to help two participants directly, who had collected cryoEM data at foreign facilities.
Year(s) Of Engagement Activity 2024
URL https://seacoast.kmutt.ac.th/2024/
 
Description Structural Biology DTP course (Aug 2022) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact This course will provide fundamental lectures and practical demonstrations in cryo-EM, from sample preparation and the electron microscope, through to image formation and processing, reconstruction in SPA and cryo-ET, and model building.

This is a hybrid event targeted primarily at Oxford Wellcome Trust Doctoral Training Program (WT DTP) students, but lectures will be made open to the wider community via Zoom and a limited number of in-person places for the lectures are also available. Practical sessions covering sample preparation, cryo-EM screening, SPA data collection and cryo-ET are in-person and limited to first year Oxford Wellcome Trust Doctoral Training Program (WT DTP) students.

CCP-EM contributed the following talks:
Lecture 5: Image processing - Colin Palmer (CCP-EM)
Fitting and building of atomic models - Agnel-Praveen Joseph (CCP-EM)

This contribution is part of CCP-EM's commitment to training the next generation of cryoEM practitioners. It is also part of our close collaboration with the national facility at Diamond/eBIC.
Year(s) Of Engagement Activity 2022
URL https://www.diamond.ac.uk/Home/Events/2022/Cryo-Electron-Microscopy-in-Structural-Biology---DTP-Work...
 
Description Talk on cryoEM to Sri Lanka community 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Rangana Warshamanage (a member of the CCP-EM core team) was invited to give a presentation on cryogenic electron microscopy to a joint meeting of the Sri Lanka Association for the Advancement of Science and the Buckyball Society of the Open University of Sri Lanka. His talk was on "Unveiling the Invisible: A Journey into Seeing Atoms and Molecules" and was on 22nd Feb 2024. CryoEM for high resolution structure determination of macromolecular complexes is not yet established in Sri Lanka, but there is significant interest and the possibility to use facilities in India. His talk helps our mission to engage with structural biology communities worldwide.
Year(s) Of Engagement Activity 2024
 
Description Training on structure validation for biomolecular simulation 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact As part of the annual CCPBioSim training week, I taught a 3 hour workshop on structure validation. Many biomolecular simulations start with a structure from the Protein Data Bank, which may have been determined by crystallography or by cryoEM. The workshop was about how to validate the structures obtained and advice to help pick a good starting point for simulations. The main presentation has been made available on the CCPBioSim website. Computer practicals were also provided via Jupyter notebooks.

The workshop is part of a wider initiative to improve links between the structural biology and biomolecular simulation communities. Both communities need to understand the capabilities and limitations of the other.
Year(s) Of Engagement Activity 2021
URL https://www.ccpbiosim.ac.uk/events/workshop-course-material/eventdetail/135/-/ccpbiosim-training-wee...
 
Description eBIC/CCPEM DTP course 2023 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact The CCP-EM core team contributed lectures and computer practicals to the 'Cryogenic Electron Microscopy in Structural Biology' Course, organised by Diamond Light Source in partnership with CCPEM in August 2023.
This course aimed to provide fundamental lectures and practical demonstrations in cryo-EM, from sample preparation and the electron microscope, through to image formation and processing, reconstruction in SPA and cryo-ET, and model building. It was a hybrid event targeted at researchers new to the field, with lectures broadcast to the wider community via Zoom and a limited number of in-person places available for Oxford Wellcome Trust DTP students and Harwell Campus students & staff (RFI, STFC, RCaH, Diamond). Practical sessions covering sample preparation, cryo-EM screening, SPA data collection and cryo-ET were in-person and limited to first year Oxford Wellcome Trust DTP students.
The course is part of wider efforts to train students and ECRs in cryoEM, and increase the skills base for this technique in the UK.
Year(s) Of Engagement Activity 2023