Topics
Data analysis
International School on Quantum Crystallography
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In Erice
How To Use New Semiconductor Data in the CSD for Research and Design
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In Online
4.00pm (GMT), 11am (EST)
New data and software to assess and design semiconductors' optical and electronic properties are now available. This latest update is from work by the CCDC with the Universities of Strathclyde and Liverpool, to enhance the Cambridge Structural Database (CSD) for semiconductors research. They focus on crucial parameters like charge transfer integral and photoluminescence, linking them to chemical structures to design innovative semiconducting materials.
Tahereh Nematiaram, from the University of Strathclyde, will show a dataset comprising 48,182 organic semiconductors, sourced from the CSD. These semiconductors were selected through a computational funnel procedure and stability in a solid state. The dataset includes relevant electronic properties and wavefunctions for further analysis, offering a low-bias resource for exploring new applications of well-known materials. It serves as a benchmark for testing computational screenings and demonstrates the potential for repurposing established organic molecules across various research fields.
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During this webinar, you'll learn:
- How to effectively this new dataset of organic semiconductors, including electronic properties and wavefunctions, for innovative research applications.Â
- How to apply computational methods for screening and repurposing established organic molecules to facilitate advancements in various research fields.
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Who should attend:
- Solid-state computational chemists
- Data scientists working with chemical data.
- Solid form scientists in academia or industry.
- Cheminformaticians.
- Scientists working on the design of semiconductors.
- Computational Materials Scientist
Rietveld and Pair distribution function (PDF) analysis workshop
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In Stuttgart
In particular, the following topics will be covered:Â
ï‚· Basics of powder diffraction and Rietveld Refinement
ï‚· The profile of a Bragg reflection
ï‚· Determination of the Instrument Resolution Function (IRF) for powder diffractometers
ï‚· Whole Powder Pattern-Fitting techniques (WPPF)
ï‚· The intensity of a Bragg reflection
ï‚· Correction factors for diffraction angles and intensity
ï‚· Methods to develop a starting model for crystal structure determination
ï‚· Penalty-functions, constraints, restraints
ï‚· Rigid Bodies (RB) (flexible polyhedra, molecules, z-matrices)
 Strategies for structure determination, global optimization in direct space, Charge-Flipping (CF)
ï‚· Difference-Fourier-analysis in combination with Rietveld refinement
ï‚· Isotropic and anisotropic microstructural parameters
ï‚· Using the ICDD PDF5+ database for phase identification and str file export
ï‚· Quantitative Phase Analysis (QPA)
ï‚· Different methods for quantifying the amorphous content
ï‚· Alternative ways of describing crystal structures
ï‚· Sequential and parametric Rietveld refinementsÂ
ï‚· Stacking faulted superstructures
ï‚· The making of Rietveld-Plots for publication
ï‚· Basics of total scattering and pair distribution function analysis
ï‚· Obtaining the pair distribution function from total scattering data
ï‚· Determining and accounting for effects of instrumental resolution
ï‚· Small-box crystal structure refinement
ï‚· Modelling nanoparticle structures and particle size distributions
ï‚· Simulated annealing and large-box approachÂ
Main tutors:Â
Sebastian Bette (MPI-FKF), Robert E. Dinnebier (MPI-FKF), Martin Etter (DESY), John Evans (Uni. Durham), Paolo Scardi (Uni. Trento), Maxwell W. Terban (Momentum Transfer)Â Â
International School on Quantum Crystallography 2025 â€" Erice, Italy
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In Erice, Italy
During this school, we will provide an accessible and in-depth education in quantum mechanics and related semi-empirical methods, tailored to provide a solid foundation in understanding materials structure, physicochemical properties, and the response of materials to physical changes and experimental probes. The theoretical foundations of crystallographic experiments will be briefly recalled, and the methodology of data collection and analysis for quantum crystallography methods will be presented and trained in detail. Speakers at this school will go beyond just theoretical calculations, to demonstrate the deep interplay between theory and experiment: for example, by showing how experimental observations could be used to restrain or constrain first-principles calculations or otherwise showing how calculations could improve the interpretation of an experimental result.
In keeping with this overall aim, the synergy between theoretical and experimental areas will be highlighted to provide a holistic view of the different fields in Quantum Crystallography. This area of knowledge is going through an important boost in the last years, thanks to new coupled approaches and new communities getting in touch with each other. This school will bring together students from these two communities, feeding this new area of knowledge and letting interdisciplinary grow among the students.
Workshops will provide hands-on tutorials on the use and development of software related to the topics, including the development of required input data, and using case studies.
Additionally, the school will benefit from the synergy with the Electron Crystallography School running in parallel, with several lectures shared between the two schools. This will offer a unique opportunity to explore interdisciplinary applications of crystallography in quantum science and structural research.
Diamond-CCP4 Data Collection and Structure Solution Workshop 2024
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In Diamond Light Source
This is the 11th jointly organised Diamond-CCP4 Data Collection and Structure Solution Workshop on practical macromolecular crystallography.
When is it?
The main part of the course will take place across two weeks, ensuring a wide programme is covered and enough breaks and networking opportunities are provided. Students are expected to attend the full workshop including the two preparation days as follows:
Before fishing crystals: Tuesday 29th October 2024 online, via Zoom
Before data collection day: Tuesday 19th November 2024 online, via Zoom
Main Workshop: Monday 25th November - Monday 2nd December 2024 in person at Diamond Light Source, with a free day on Saturday 30th November.
What is the format?
The workshop will consist of presentations and tutorials delivered by experts in the field, plus one day of data collection time at Diamond's excellent MX beamlines. Students will be able to work alongside experts on their own projects, tackling all aspects of structure solution, from data collection through to phasing, refinement and validation. See here the detailed programme for the event. (Please note the programme is subject to some minor change).
Who can apply?
The course is intended for graduate students, postdoctoral researchers and early career scientists in the area of structural biology. Some experience of crystallography and data collection is expected, and applications from students who can bring an interesting project with them (crystals and previously collected datasets) will be favoured.
International School on Electron Crystallography 2025 â€" Erice, Italy
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In Erice, Italy
We are excited to announce the International School on Electron Crystallography, which will be held in the charming town of Erice, Italy, from 30 May - 7 June 2025. This event will bring together leading experts, researchers, and students in the field of electron crystallography to explore the latest developments and techniques.
Dates: 30 May - 7 June 2025
Location: Ettore Majorana Foundation and Centre for Scientific Culture, Erice, Italy
About the School:
The International School on Electron Crystallography offers a comprehensive learning experience for participants at all levels, from beginners to advanced researchers. Through lectures, hands-on tutorials, and interactive sessions, attendees will gain valuable insights into the principles and applications of electron crystallography, including electron diffraction, 3D electron diffraction (3D ED), structure determination, and the latest innovations in the field.
Key Topics:
- Fundamentals of electron crystallography and diffraction
- 3D electron diffraction techniques
- Structure determination of molecular and inorganic materials
- Applications in nanomaterials, pharmaceuticals, and structural biology
- Recent advances in instrumentation and data analysis
Who Should Attend:
The school is designed for students, postdocs, and professionals working in electron microscopy, crystallography, materials science, chemistry, physics, and related disciplines. Whether you are new to electron crystallography or looking to deepen your expertise, this school provides a unique opportunity to expand your knowledge and network with experts in the field.
Travel and Grants:
Various travel grants from different organizations will be advertised on the school's webpage to support student participation.
How to Apply:
Details on registration, abstract submission, and travel grant applications will be made available on the official website: https://crystalerice.org/2025/
Join us in Erice for an inspiring week of learning, networking, and exploring the beautiful surroundings of Sicily!
For further information, please visit our website or contact the course directors: Alexander Eggeman (University of Manchester, UK), Mauro Gemmi (Istituto Italiano di Tecnologia, Pisa, IT), Tatiana Gorelik (Forschungszentrum Juelich, DE).
26th Heart of Europe Biocrystallography Meeting
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In Kraków
CCDC Virtual Workshop: Introduction to Pharmacophore Searching Using CSD-CrossMiner
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In Online
If you are working in the field of drug discovery and want to learn how to perform pharmacophore searches to uncover new ligands, then this free, 90-minute, hands-on workshop is for you!
Pharmacophore searching is a key component in many drug discovery efforts and represents an effective mechanism of virtual screening, for example. In this approach, a pharmacophore query is created to describe features that are essential for the molecule to carry out its function. The query is then used to identify new possible lead compounds by searching a three-dimensional structural database.
In this free 90-minute hands-on CCDC Virtual Workshop, designed for complete beginners to CSD-CrossMiner, you will learn hands-on the basics of how to perform a pharmacophore search using the CCDC's software CSD-CrossMiner.
What we will cover
In this workshop we will focus on performing a pharmacophore search using CSD-CrossMiner. The session will include presentations and demonstrations by CCDC expert tutors and a hands-on part for you to try the software, with the tutors available to help you and answer your questions.
You will learn:
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What CSD-CrossMiner is and how it can be used in your research.
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How to navigate the CSD-CrossMiner interface.
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How to set up an interactive pharmacophore query.
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How to perform pharmacophore searches across biologically relevant subsets of the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB).
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How to analyse and interact with your results, and save them.
The workshop will be recorded and all registered participants will have access to the recording.
Software requirements
As this is an interactive workshop, you’ll need access to CSD-CrossMiner with a CSD-Discovery or CSD-Enterprise licence. Full academic licences include the software we use in this workshop. If you are unsure whether your institution already has a license, please get in touch with us using the form on the Contact Us webpage.
If you do not have access to the CSD, we can provide you with a temporary licence. When you register, please check "No" to the question:Â "Do you or your institution have a current full CSD licence?" and we'll get you set up.
If you have already got the CSD installed you will need to check you have the most up to date version of the software. Click here for more information.
Entry Requirements
This workshop is open to everyone who wants to learn hands-on how to use CSD-CrossMiner to perform pharmacophore searches in the CSD and PDB. This is an entry-level session, so anyone can join and no prior experience is required.
Who should attend?
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Discovery scientists.
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Research scientists investigating pharmacophore searching and drug discovery.
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PhD and post-doc level scientists in academia interested in pharmacophore searching and drug discoveryÂ
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 Industrial / commercial scientists working in pharmacophore searching and drug discovery.
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Scientists using computational methods in drug discovery.
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Educators in the biochemistry and biomedical area looking to incorporate the CSD into their teaching.
CCDC Virtual Workshop: ConQuest to Mercury â€" From Searching to Data Analysis
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In Online
If you are looking to search for crystal structures in the Cambridge Structural Database (CSD) to gain insights into your own structures and trends in the database, and you wish to improve your searching skills and enhance them with deeper structural analysis tools, then this free, 90-minute, hands-on workshop is for you!
The Cambridge Structural Database (CSD) now contains data for over 1.25M organic and metal-organic crystal structures. The database is fully discoverable and accessible and CoreTrustSeal certified data repository; it is used by researchers across the pharmaceutical, agrochemical, and fine chemicals industries to predict and guide future discoveries.
In this free 90-minute hands-on CCDC Virtual Workshop, you will learn hands-on the how to search the CSD using ConQuestand how to gain more insights into the results using the Data Analysis module in Mercury.
What we will cover
In this workshop you will explore a workflow to have an in-depth look at trends and behaviours of defined 3D parameters, such as inter- and intra- molecular distances, angles and torsions, and crystallographic parameters for relevant groups of structures in the CSD. The session will include presentations and demonstrations by CCDC expert tutors and a hands-on part for you to try the software, with the tutors available to help you and answer your questions.
You will learn:
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How to set up a search of the CSD using ConQuest.
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Tips and trick on searching in ConQuest and how to define 3D parameters for further analysis.
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How to export ConQuest results to Mercury and analyse them with the Data Analysis module.Â
The workshop will be recorded and all registered participants will have access to the recording.
Software requirements
As this is an interactive workshop, you’ll need access to ConQuest and Mercury.
All academic licenses give you access to the full range of features covered in this workshop. If you are unsure whether your institution already has a license, please get in touch with us using the form on the Contact Us webpage.
If you do not have access to the CSD, we can provide you with a temporary licence. When you register, please check "No" to the question:Â "Do you or your institution have a current full CSD licence?" and we'll get you set up.
If you have already got the CSD installed you will need to check you have the most up to date version of the software. Click here for more information.
Entry requirements
This workshop is open to everyone who wants to learn hands-on how to search, visualize and analyse structures in the CSD, from beginners to experienced users.
Familiarity with the basics of Mercury would be ideal. If you have not used Mercury before, we would recommend the following module from our on-demand CSDU courses:
 Who should attend?
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Crystallographers and structural scientists.
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Academic and industrial chemists interested in exploring molecules in the solid form.
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PhD and post-doc researchers in the field of crystallography and materials science.
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Researchers and scientists who work with the CSD or their own structural databases.
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Industrial scientists using structural informatics to design new materials.
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Educators looking to incorporate the CSD into their teaching.
CCDC Virtual Workshop: First Steps in Protein-Ligand Docking With GOLD
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In Online
If you are working in the field of drug discovery and want to learn step-by-step how to perform protein-ligand docking, then this free, 90-minute, hands-on workshop is for you!
In drug discovery, it is important to understand how a small molecule (ligand) and a protein will bind. Protein-ligand docking is a computational method to predict the configuration of such interactions and an important step during drug design.
In this free 90-minute hands-on CCDC Virtual Workshop, designed for complete beginners to GOLD, you will learn hands-on the basics of how to perform protein-ligand docking using the CCDC's docking software GOLD.
What we will cover
In this workshop we will focus on performing a docking simulation using GOLD. The session will include presentations and demonstrations by CCDC expert tutors and a hands-on part for you to try the software, with the tutors available to help you and answer your questions.
You will learn:
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The basics of the Hermes interface, the CCDC’s 3D visualiser for proteins.
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Step-by-step basics of docking using GOLD.
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Where to get started with your docking simulation and how to run a standard protein-ligand dock with GOLD.
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How to identify the correct binding modes reliably and with confidence.
The workshop will be recorded and all registered participants will have access to the recording.
Software requirements
As this is an interactive workshop, you’ll need access to GOLD, which can be found in CSD-Discovery or CSD-Enterprise licence. Full academic licences include the software we use in this workshop. If you are unsure whether your institution already has a license, please get in touch with us using the form on the Contact Us webpage.
If you do not have access to the CSD, we can provide you with a temporary licence. When you register, please check "No" to the question:Â "Do you or your institution have a current full CSD licence?" and we'll get you set up.
If you have already got the CSD installed you will need to check you have the most up to date version of the software. Click here for more information.
Entry Requirements
This workshop is open to everyone who wants to learn hands-on how to use GOLD to perform protein-ligand docking simulations. This is an entry-level session, so anyone can join and no prior experience is required.
Who should attend?
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Discovery scientists.
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Research scientists investigating protein-ligand docking.
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PhD and post-doc level scientists in academia interested in protein-ligand docking.
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Industrial / commercial scientists working on protein-ligand docking.
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Scientists using computational methods in drug discovery.
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Educators in the biochemistry and biomedical area looking to incorporate the CSD into their teaching.
CCP-EM/Diamond Icknield Workshop
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In Harwell
This 5-day course is largely aimed at structural biologists with EM maps suitable for modelling building and refinement. This course will host some of the leading software developers and provide ample contact time to allow delegates to discuss their data in detail alongside traditional lectures and tutorials. This is a comprehensive course for EM model building covering advanced use of LocScale, ModelAngelo, Buccaneer, findMySequence-checkMySequence, EM_placement, Coot/Moorhen, TEMPy-REFF, ISOLDE, Refmac-Servalcat, Privateer, new validation tools and AlphaFold-DB & EMDB/PDBe updates. It will cover all aspects of modelling building including: map optimisation, automated model building, model fitting, medium resolution refinement, high resolution refinement, interactive refinement, validation and deposition.
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* Confirmed tutors / topics: Tom Burnley (CCP-EM) : CCP-EM Doppio Arjen Jakobi (TU Delft) : LocScale Sjors Scheres (MRC-LMB) : Relion5 and ModelAngelo Randy Read (University of Cambridge) : EM-placement Grzegorz Chojnowski (EMBL) : FindMySequence/CheckMySequence Maya Topf, Joseph Beton and Aaron Sweeney (CSSB Hamburg) : TEMPy-REFF, Chem-EM Judit Debreczeni (Astrazeneca), Lucrezia Catapano (MRC-LMB) and Paul Bond (University of York): Coot / Moorhen Soon Wen Hoh and Paul Bond (University of York) : Buccaneer/ModelCraft Rob Nicholls (CCP4) and Rangana Warshamanage (CCP-EM) : Refmac/Servalcat Tristan Croll (AltosLabs) : ISOLDE TBC (University of York) : Privateer PDBe (EBI) : AlphaFold-DB and 3D-Beacons Agnel Joseph (CCP-EM) : Model validation Kyle Morris (EBI) : EMDB deposition and validation
Registration of interest will close either when all places are taken or by Friday 12th July 2024
Stanford-SLAC Cryo-EM Center (S2C2) Single-Particle Cryo-Electron Microscopy Image Processing Workshop
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In Stanford and virtual
This workshop will be in a hybrid format (virtual and in-person) and at no cost to attend. It's designed for researchers who have prior experience in Cryo-EM structural determination.
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Our workshop instructors include Ali Punjani and Team (CryoSPARC), Ellen Zhong and her team (Princeton University), Muyuan Chen (SLAC National Accelerator Laboratory, Stanford University) and Wah Chiu (Stanford University). The workshop will feature the image processing fundamentals, and the latest development in structural heterogeneity, continuous conformational dynamics, map refinement and structure validations. Through case studies and real-world examples, participants will gain practical insights into navigating these complexities and solution opportunities. The instructors will provide their unique perspectives and solutions to address current challenges in high resolution Cryo-EM data analysis.
In-person attendance is limited, so we encourage you to apply at your earliest convenience. Early acceptance for in-person participation will be sent out by August 1st or earlier.
Virtual Webinar: Teaching Enzymology with the PDB
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In Online
• Faculty members who teach biochemistry courses that involve structure-function relationships at all levels.
• Graduate students and post-doctoral fellows who are interested in teaching and science communication.
Key takeaways
• Navigate the RCSB PDB website to visualize each 3D structure and explore various annotations mapped to it.
• Compare the shapes, interactions and functions of groups of PDB structures with similar sequences and/or similar structures.
• Use RCSB PDB data, tools and resources to enhance classroom instructions and build lessons for teaching about enzymes.
Crash Course: Python Scripting for Molecular Docking
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In Online
At the completion of this workshop, users will be able to:
Perform advanced searches of the RCSB Protein Data Bank with the rcsbsearchapi package
Modify chemical structures with the rdkit library
Dock ligands with enzymes, yielding visual and quantitative energy results
This virtual event will take place Thursday, July 18, 2024 from 1-5pm Eastern, 10am-2pm Pacific.
Participation is free, but registration is required. Please register for this event to receive confirmation and the Zoom meeting information by email.
The workshop is intended for:
Undergraduate students in any STEM discipline
Graduate students and postdoctoral researchers in life sciences and data collection
Faculty members who want to incorporate Python scripting into their teaching or research
Professionals involved in collecting and analyzing data, particularly big data
A virtual office hour may be held on Monday July 15 (3pm-5pm Eastern) to help users with Python/Jupyter notebooks before the Crash Course. Please indicate on the registration form if interested.
Questions? Please contact [email protected].
Virtual Webinar: Understanding PDB Validation
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In Online
Who Should Attend?
Professionals and graduate students interested in learning about strategies to take full advantage of PDB data in the fields of:
* Structural biology
* Cheminformatics and computational chemistry
* Bioinformatics and computational biology
Journal article reviewers and editors will also benefit from this webinar.
After the seminar, users will
Learn the primary PDB structure quality metrics
Understand PDB structure quality varies across the archive
Know how to identify good structure(s) for research from RCSB.org.
Participation is free, but registration is required at https://go.rutgers.edu/ikmomgei.
Virtual Webinar: A Deep Dive into Computed Structure Model Exploration at RCSB.org
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In Online
This event will equip you with the knowledge of how to use RCSB.org features to navigate 3D predicted protein structures in the context of experimentally-determined PDB structures.
Registration is required for the Zoom meeting information, but attendance is at no charge.
Please sign up at https://go.rutgers.edu/1ztidbcw.
Contact [email protected] with any questions.
ElCryS24 : Electron Crystallography School 2024
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In Padova, Italy
Drug Design Inspiration from Torsional Data Mining
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In Online
In this webinar Gilles Ouvry of NRG Therapeutics will share how the Cambridge Structural Database (CSD) can be a source of inspiration for drug design.
The majority of the focus will be around mining torsional information from the CSD on common functional groups and highlighting how it has been used in a range of drug discovery projects, creating cheat sheets for medicinal chemists using Conquest and Mercury. Other minable CSD data points will be explored, including using IsoStar to mine intermolecular interactions.
Early career diffraction methods seminar 2024: Collecting Data and Solving Structures; the Good, the Bragg, and the Analysis!
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In Berlin
5th Annual Data Processing Workshop
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In Michigan
This year's workshop will focus on cryo-electron tomography data processing, which will include, in addition to tomography basics, tilt-series alignment, reconstruction, subtomogram averaging, classification, heterogeneity analysis and segmentation through the use of software such as IMOD, Warp/M, Relion, STOPGAP and tomoDRGN (segmentation software to be finalized).
