The IUCr Newsletter is the web magazine of the International Union of Crystallography. Since 1993, the IUCr Newsletter has been published quarterly and distributed to over 13,000 crystallographers worldwide. In August 2018, it was transformed into a dynamic digital platform with a fresh new look. Its aim remains to bring together the crystallographic community.
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William L. Duax Patricia Potter Jane Griffin The IUCr Newsletter is distributed electronically to 13,000 crystallographers and other interested individuals in 102 countries. Articles from the Newsletter are also available on this web site by following the links on the left-hand side. Feature articles, meeting announcements and reports, information on research or other items of potential interest to crystallographers may be submitted to the editor at any time. Items will be selected for publication on the basis of suitability, content, style, timeliness and appeal. Please send contributions to: newsletter@iucr.org Matters pertaining to advertisements should also be sent to the above address. Email address changes or corrections and requests to be added to the mailing list should be accomplished through the Subscribe and Unsubscribe hyperlinks above. Reuse permissions • The original article in which the material appeared is cited. • Copyright permission is indicated by the wording "Reproduced with permission of the International Union of Crystallography Newsletter". In electronic form, this acknowledgement must be visible at the same time as the reused materials, and must be hyperlinked to the IUCr Newsletter (http://www.iucr.org/news/newsletter). Please be sure to include the following information: • The title, author(s) and page extent of the article you wish to republish, or, in the case where you do not wish to reproduce the whole article, details of the section(s) to be reproduced. • The volume/issue number and year of publication in which the article appeared, and the page numbers of the article. • Details of the publication in which you wish to reprint the Newsletter material. • If the material is being edited or amended in any way, a copy of the final material as it will appear in your publication. • Contact details for yourself, including a postal address. |
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Annual Reports to the IUCr Executive Committee
The IUCr Newsletter (ISSN 1067-0696; coden IUC-NEB) is published quarterly (4x) by the International Union of Crystallography (IUCr Executive Secretary e-mail execsec@iucr.org). Members receive the IUCr Newsletter by virtue of country membership in the IUCr. Periodical postage rates paid at Buffalo, NY and additional mailing offices. POSTMASTER: Please send changes of address to IUCr Newsletter Editorial Office, c/o Hauptmann-Woodward Medical Research Institute, 700 Ellicott St. Buffalo, NY 14203 USA.
We want to thank and acknowledge all of you who have submitted abstracts to the 26th Congress and General Assembly of the International Union of Crystallography Congress 2023. The enthusiastic response from our global community has met all expectations. We are excited that our goal to create a content-rich programme is coming to fruition.
In light of the multiple requests, we have listened. We have re-opened the Call for Abstracts to allow additional time for those who need it. The submission portal will now remain open until 21 February 2023.
Please note also that Early Bird Registration ends on 31 March 2023. All deadlines and dates can be found on our website.
From the IUCr2023 team in Australia, we wish you, wherever you are in the world, a safe and happy holiday season.
3D searching is now possible online using WebCSD. This allows you to search the Cambridge Structural Database (CSD) with constraints on specific parameters: angle, centroid, plane, vector or point on line (dummy points in ConQuest). This feature is now available to all users with a full CSD licence, including academic licences. You do not need to perform an installation or update, the change will be visible next time you log in.
Learn how to set up a 3D search in this tutorial blog.
We are delighted to report that with your help, the CSD has now hit 1.2 million structures! The November 2022 data update contains over 8000 unique structures. Alongside this data release, we are also making enhancements to our CSD software portfolio to help you get the most out of this wealth of data. Learn more about our data and software releases and how to stay up to date here.
In the 7th Crystal Structure Prediction (CSP) Blind Test that ran from October 2020 to September 2022, seven structures of 2D systems that had been experimentally analysed but not published (‘blind’) were released to participants along with some experimental conditions.
The seven 2D structures included Cu- and Si-containing systems that pushed the boundaries of CSP beyond the pharmaceutical sector to areas such as electronics and photonics. Other structures included one of the most challenging systems in CSP Blind Test history – a large, highly polymorphic, pharmaceutical drug candidate – along with agrochemicals and a food flavouring.
![[Fig. 1]](https://www.iucr.org/__data/assets/image/0011/155792/csp7.png)
More experimental data was released over the course of the test to simulate real world conditions.
Participants included groups from both industry and academia, and all compounds successfully had their experimentally observed crystal structures predicted by at least one group from landscapes of 1K+ potential structures.
In one challenge, a PXRD pattern for an observed crystal structure was provided alongside the 2D chemical structure. This emulated a common situation where a single crystal structure is unable to be obtained, but a poor-quality powder pattern is. This showcased an application of CSP to industrially relevant molecules.
CSP is an ever-evolving discipline and the 7th Blind Test identified future challenges including disorder prediction that had previously been disregarded owing to its complexity but is now more industrially relevant to solve as bigger molecules with more flexible groups are being seen in drug development; more challenges that reflect industrial reality; and continued broadening beyond pharmaceuticals to solid-state devices.
“Thanks to collaborative initiatives like the CCDC blind test, the complex field of CSP is advancing rapidly, taking advantage of machine learning techniques and the availability of ever-more powerful computing resource,” says Dr Jürgen Harter, CEO, CCDC. “I look forward to future Blind Tests addressing challenges such as structure ranking, overprediction and disorder.”
A scientific paper with full results is being prepared and will be submitted for publication in 2023. Preliminary detailed results, including how many groups correctly predicted each target, the lowest rankings, CPU time used and details of methodologies are available by emailing hello@ccdc.cam.ac.uk.
CCDC is planning more webinars and Virtual Workshops for 2023 so do check our events page for more details on dates and topics. If you would like to suggest topics for our sessions in 2023 you can email us at hello@ccdc.cam.ac.uk. If you can’t wait until 2023 we also have five free online courses where you learn about structural chemistry and the CSD. Find out more here. We will also be sponsoring and presenting at the PCCr3 crystallography meeting in Nairobi, Kenya, in January 2023. If you’re attending please say hello to the CCDC team!
12 December 2022
Iranian scientists have been an integral part of the global scientific communities and continuously contributed to the advancement of science and technology. I graduated from Sharif University of Technology in 1998 with a degree in Physics and moved to the west to continue my education. Today, more than half of my life has been spent far away from Iran and is dedicated to scientific research and education. However, I never felt far from the Iranian academic community, as the scientific community around the world is inherently connected. The past three months have been exceedingly troubling times for the Iranian scientific community and students. Today, I’m writing this letter to ask the IUCr leadership, a community that I’ve been connected to for many years, to voice their support for Iranian academics and researchers in these anxious times.
Iranian women are leading a cultural renaissance with massive support from the university students with the rallying cry "Woman, Life, Freedom". University campuses have been at the center of the waves of protest sweeping through Iran, and the academic community of Iran has suffered enormous damage. Hundreds of students have been arrested on campus and sent to prison, University administrations in Iran have been complicit in the abduction of student protesters on campus and have additionally expelled a large number of students for participation in on-campus protests. As such, the academic career of many scientists, who are amongst the brightest minds of Iran, is in disarray and their lives are in danger. University campuses have a universal standing as places for fostering the free exchange of ideas, including peaceful protests. As scientists, there is a tie that binds us to these students and requires us to protect their right to free speech on campus. While the context of this letter is the ongoing struggle for political and social freedoms in Iran, my request is only about the catastrophic consequences of government crackdown in academia. As do all professional societies, the IUCr has also taken positions where political strife and violence has threatened scientists. My hope is that this effort shows our solidarity with and helps avert further harm to the academic community in Iran. I would like to encourage the IUCr to reiterate the following shared values in an open letter and
Thank you for your consideration,
Respectfully
![[sig]](https://www.iucr.org/__data/assets/image/0003/155775/shanti-sig.png)
Shanti Deemyad
The New York Times: ‘Geniuses’ Versus the Guns (6 October 2022)
Nature: ‘I could not keep silent’ (12 October 2022)
Physics Today: STEM scholars worldwide express solidarity with Iranian protesters (19 October 2022)
Oslo based Iran Human Rights Asks Universities Worldwide to Condemn the Islamic Republic’s Encroachment of University Campuses (30 October 2022)
The Guardian: Dozens arrested as Iranian security forces attack university campuses (4 November 2022)
ISNA (Iranian government news agency, use Google Translate): Disciplinary actions against protesters at Sharif University, including the suspensions of 10 students in one day (19 November 2022)
Universityworldnews: Students barred from campuses as state steps up crackdown (22 November 2022)
Shanti Deemyad is Associate Professor of Physics in the Department of Physics and Astronomy at the University of Utah, Salt Lake City, UT, USA; email: deemyad@physics.utah.edu.
Here we are approaching the end of 2022. Already. Some of us are getting ready for Christmas (or at least for a short vacation and some family time), others just want to finish this year and move to a new one.
Whereas internet teaching and hybrid meetings will stay with us for good we can now plan for limited travel and for some irreplaceable gatherings in person.
I am just back from the Fifth Meeting of the Latin American Crystallographic Association (LACA), very well organized in a hybrid mode by Andrea Araya in San José in Costa Rica. A lot of progress has been made since the creation of LACA in 2013. Some legal aspects still have to be smoothed out but the energy of the crystallographers there cannot be underestimated. The Fifth LACA School, organized by Andrea Araya and José Reyes-Gasga on the subject of “Polymorphism: Applications in Industry”, was hosted in the Costa Rica National Center for High Technology facilities (hybrid again). It was well attended by students from the LACA region.
In Africa the OpenLab program is slowly coming back after the COVID-induced break. We hope for the active involvement of all the major vendors of crystallographic equipment. Claude Lecomte has organized the first, very successful OpenLab in Mauritania in November 2022; the next one will be coming in May 2023 in Franceville (Gabon). Michele Zema, the IUCr Executive Outreach Officer, has reported that 15 students from Benin, Burkina Faso, Cameroon, Côte d’Ivoire, Ghana, Guinea, Nigeria, Senegal as well as Jamaica and India were selected to participate in the two-week training session on single-crystal diffraction at the X-TechLab in Benin from 21 November to 2 December 2022. Students could bring their own crystals and collect data using the new Bruker AXS D8 Eco diffractometer, which was also used for tutorials and demonstrations. The X-TechLab, funded by the Benin Government and whose implementation was facilitated by IUCr–IUPAP–ICTP LAAAMP within the framework of the IUCr-UNESCO OpenLab, is now operational and open for collaborations with researchers from all over Africa. New instruments, including a Panalytical Empyrean powder diffractometer and a microtomograph, will be installed soon and available starting from early next year.
The world is still not a safe place. A brutal war is raging in Ukraina. The scientific community is trying to help displaced Ukrainian researchers. The Polish Academy of Sciences (PAS) and the U.S. National Academy of Sciences have recently launched a grant program to support Ukrainian research teams. The design of the grant program allows scholars in Ukraine to continue research under the supervision of experienced principal investigators from Ukraine, hosted for up to three years at the PAS. The deadline for grant applications is 16 January 2023.
In Ethiopia we have just had to cancel the IUCr–COSPAR Workshop ”Crystallography for Space Sciences” due to safety concerns. In Iran and other places in the world men and women are fighting for political and social freedom. In Afghanistan women are recently being forbidden to study at the Universities.
As a member of the International Science Council (ISC), the IUCr supports the right to share in and to benefit from advances in science and technology as described in the Universal Declaration of Human Rights and it is very concerned about increasing threats to scientific freedom and other human rights around the world.
At the forthcoming IUCr Congress in Melbourne in August 2023, the General Assembly delegates will vote on formally incorporating our fifth Regional Associate, the African Crystallographic Association (AfCA) – constituted in November 2021. To commemorate this special event, and to mark the 75th anniversary of the first IUCr Congress and the first volume of Acta Crystallographica, IUCr Journals are planning to put together a special collection of articles from African researchers, which will be published online to coincide with the Congress.
Please plan to come to Melbourne; it will be an amazing Congress, with many attractions and a very strong program. The abstract submission deadline has been extended to 21 February 2023 so there is still time to present your best results. In recognition of retired crystallographers’ long-term dedication and outstanding contributions to our community, the Congress Organizers have decided to offer them a reduced registration fee. The retiree rate is only available for the Early Bird period, which ends on 31 March 2023. The IUCr President's Fund application deadline is 18 March 2023.
If you have a free minute during the holiday break, please check your entry in the World Directory of Crystallographers (WDC). There is a chance that it has not been updated for some time. If you are a Commission Chair, please also check to see if your Members and Consultants are included in the WDC. It all adds up to creating and strengthening this community.
I am also encouraging you all to start (or continue) participating in the IUCr Crystal growing competition for schoolchildren. Other international scientific organizations are copying this very successful program and we are very proud of this fact. Elementary and high-school students need to understand at an early age the beauty of science, and there is a lot of satisfaction from the side of students and coaches when amazing crystals are being presented and highly prized on international forums! See a report from Poland in an earlier issue of the IUCr Newsletter here and one from Vietnam in this issue here.
With the end of December approaching fast I want to wish you all a happy and joyful 2023. We intend to make it a successful and important Congress Year. We just hope it will also be healthy and safe.
Our experimental knowledge of structure in atomic detail is derived from the electron density or electrostatic potential map interpreted as an atomic model. Conversely, we calculate the theoretical map from our model and comparison of both sources is used to refine (Urzhumtsev & Lunin, 2019) and improve this knowledge or assess its correctness. In this issue of IUCrJ, Urzhumtsev & Lunin (2022) revisit first principles underlying imperfections in the experimental maps in order to propose a map calculation with variables to account for atomic displacement and local resolution linked to each atom. The new maps reflect the observed inhomogenous resolution with superior accuracy and their expression is nearer to physical reality, along with the useful feature of simplifying the necessary calculation of derivatives with respect to all parameters.
The last decade has seen an expansion of powerful experimental structural techniques, the ‘resolution revolution’ in cryoEM (Kühlbrandt, 2014), micro-electron diffraction (Clabbers et al., 2022) or serial crystallography from tiny crystals (Standfuss & Spence, 2017), that are gaining importance in expanding the basis for macromolecular structural knowledge. These methods provide information down to the atomic level but frequently, resolution varies to a large degree across different areas of the map, leading to the observation of very different local limits as illustrated in Fig. 1. The effect, prominent in maps where the main distortions are caused by harmonic disorder of the structure and limited resolution, may also be relevant in X-ray or neutron crystallography and is presented in a general way. Addressing differences in local resolution is recognized as essential to avoid misleading and over-interpretation of cryoEM reconstructions (Vilas et al., 2020). The work of Urzhumtsev and Lunin illustrates the shortcomings and limitations of accounting for this phenomenon through a combination of atomic displacement parameters and global resolution cut-off. While the atomic positional disorder blurs atomic densities, the resolution cut-off, alongside this, generates Fourier ripples, which significantly contribute to the map far from the atomic centre. Both types of distortion can be described by the same mathematical operation of a convolution but require different functions. Instead, the authors suggest a method to calculate model maps at every point, extending the concept of a local resolution down from a region to the characterization of each individual atom. This value will naturally be adjusted on the fly in the course of refinement.
In the absence of an analytic expression of the convolution between the Gaussian function accounting for displacement and the interference function limiting resolution, the latter has been recast into a shell decomposition allowing the calculation, in a closed analytical form, of the atomic model map distorted by restricted resolution and positional disorder.
The particular implementation and large-scale refinement tests on real data remain to be explored for each envisaged application, and it is anticipated that such development will soon follow. Nevertheless, the present work provides proof of principle of the superior effect of accounting for Fourier ripples with synthetic data calculated for a protein model and establishes the computational advantages.
The availability of accurate predicted models for protein components of macromolecular complexes (Jumper et al., 2021; Baek et al., 2021) opens new opportunities while demanding advancements in the treatment of errors in experimental determinations. Enhancing the quantitative comparison of calculated and experimental maps will be decisive in extricating unbiased experimental information beyond prior knowledge and the authors – along with the contribution in this paper – raise a number of questions remaining to be addressed. These include the inverse problem of calculating their parameters from the experimental map, the extension of the model to anisotropic displacement parameterization or subatomic resolution scenarios in charge-density studies or the current limitations in the absence of complete data and the need for optimally accounting for atomic scattering where unaccounted environmental effects or dynamic effects occur (Gruza et al., 2020; Samperisi et al., 2022). None of these considerations detracts from the interest of their proposed map calculation and application in refinement but rather adds to the debate.
This development will enable real-space refinement in a more appropriate way and thus be welcomed by the community once implementations tailored to each envisaged application are available in refinement software. In the meantime, this theoretical proposal stirring discussion on how to best connect model and experiment for a critical and accurate assessment is timely, and is a development that will make ripples in the structural sciences.
Professor Kay Diederichs is acknowledged for helpful discussions.
Ministerio de Ciencia e Innovación and European Union Regional Development Fund (MICINN/AEI/FEDER/UE) are acknowledged for grant No. PID2021-128751NB-I00.
Baek, M., DiMaio, F., Anishchenko, I., Dauparas, J., Ovchinnikov, S., Lee, G. R., Wang, J., Cong, Q., Kinch, L. N., Schaeffer, R. D., Millán, C., Park, H., Adams, C., Glassman, C. R., DeGiovanni, A., Pereira, J. H., Rodrigues, A. V., van Dijk, A. A., Ebrecht, A. C., Opperman, D. J., Sagmeister, T., Buhlheller, C., Pavkov-Keller, T., Rathinaswamy, M. K., Dalwadi, U., Yip, C. K., Burke, J. E., Garcia, K. C., Grishin, N. V., Adams, P. D., Read, R. J. & Baker, D. (2021). Science, 373, 871–876.
Clabbers, M. T. B., Shiriaeva, A. & Gonen, T. (2022). IUCrJ, 9, 169–179.
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., Bridgland, A., Meyer, C., Kohl, S. A. A., Ballard, A. J., Cowie, A., Romera-Paredes, B., Nikolov, S., Jain, R., Adler, J., Back, T., Petersen, S., Reiman, D., Clancy, E., Zielinski, M., Steinegger, M., Pacholska, M., Berghammer, T., Bodenstein, S., Silver, D., Vinyals, O., Senior, A. W., Kavukcuoglu, K., Kohli, P. & Hassabis, D. (2021). Nature, 596, 583–589.
Kühlbrandt, W. (2014). Science, 343, 1443–1444.
Samperisi, L., Zou, X. & Huang, Z. (2022). IUCrJ, 9, 480–491.
Standfuss, J. & Spence, J. (2017). IUCrJ, 4, 100–101.
Urzhumtsev, A. G. & Lunin, V. Y. (2019). Crystallogr. Rev. 25, 164– 262.
Urzhumtsev, A. & Lunin, V. Y. (2022). IUCrJ, 9, 728–734.
Vilas, J. L., Heymann, J. B., Tagare, H. D., Ramirez-Aportela, E., Carazo, J. M. & Sorzano, C. (2020). Curr. Opin. Struct. Biol. 64, 74–78.
This article was originally published in IUCrJ (2022). 9, 718–719.
Note: The first follow-up paper on practical applications has recently been published in Acta Cryst. D.
Every quarter, as Editor, I get anxious that we shall not have enough material to publish in the following issue of the IUCr Newsletter. But fear not; somehow, the articles keep coming in, often at the last moment, especially recently. So, in this issue of the IUCr Newsletter, we have much interesting material. I have always encouraged articles on the history of our science, as I believe that it is important for scientists to be aware of how our forefathers struggled to come up with the ideas that today we take for granted.
![[Fig. 1]](https://www.iucr.org/__data/assets/image/0007/155743/Fig.-1.png)
For example, Jean-Claude Boulliard, Delphine Cabaret and Paola Giura have written an important and detailed account of the life and work of the French cleric René-Just Haüy, sometimes regarded as the father of crystallography. Based on an observation of a broken crystal of Iceland spar (calcite), he inferred that crystalline matter consisted of repeating units (he did not know what they consisted of), which he called “molécules intégrantes.” Although he was not the first to think in such terms – Robert Hooke and Johannes Kepler, for example, also suggested something similar – but it was Haüy who put this on a more scientific basis, for example, through his law of rational indices. We forget, however, just how controversial, and even dangerous, such ideas were in the time and place that he lived (France in the 1790s). Materialism at that point came to be indissociably associated with atheism and atheism with political enemies of the French government. As an example of how Haüy had to be careful, there was an interesting series of lessons published in the archives of the École Normale [1] at the time between someone simply called the “Professeur” and a pupil on the question of heterogeneity or otherwise of solid matter. It is evident that the “Professeur” is Haüy of course!
Readers may recall that some time ago, we published several articles in the Newsletter about the work of Juan Manuel García-Ruiz (“Juanma”) (see an example here) and his study of crystals found associated with the remains of ancient hominids. In this issue, there is an article by Wulf Depmeier celebrating the well-deserved award of the DGK Liebau Prize to Juanma earlier this year. This is followed by an article from Juanma himself, describing some fascinating experiments with chimpanzees where they were introduced to crystals. Most thought-provoking is the way that, given a crystal of quartz, they soon began to take a particular interest in the apparent hexagonal symmetry as seen by looking down the long axis of the crystal. So there seems to be something special about symmetry that causes a response in the chimpanzee’s brain, supporting Juanma’s original suggestion that the discovery of crystals may have played an essential role in the original development of thought processes in humans and an awareness of their surroundings.
Another topical article is a contribution from Istvan Hargittai, this time on the observation of the so-called star polyhedra, a motif that seems to appear in many places. Again, it is the symmetry that attracts attention.
And yet again, the importance of understanding symmetry for crystallographers is raised by Carol Brock, who points out that the IUCr has now made freely available the symmetry diagrams for the 17 plane groups (also known as the wallpaper groups). Carol also reminds us of Escher's wonderful drawings. Escher’s work had been initially spotted by the crystallographer Caroline MacGillavry, who subsequently brought Escher’s work to our attention. I expect that all crystallography teachers have used such drawings to illustrate symmetry principles to students, especially regarding the concept of periodicity in crystals. I would make a point here, though, that the plane groups are two-dimensional symmetry groups, whereas there are no really two-dimensional crystals: atoms are three-dimensional, aren’t they? However, it is perfectly possible to have three-dimensional materials, such as graphene, whose periodicity is only two-dimensional (best described by one of the 80 sub-periodic layer groups). In assessing crystal symmetry, it is important to distinguish between crystal structure on the one hand and the concept of periodicity (usually described by the lattice) on the other.
Again, on the historical theme, Brian Toby has written in memory of Ted Prince, Tony Santoro and Judy Skalick, who are no longer with us. They were three important figures who worked at NIST (National Institute of Standards and Technology, USA) for many years and were well known to many of us. I did not know Judy very much, but I remember several discussions with Ted and Tony. Ted was a formidable mathematician whom I found to be most impressive. Tony had strong opinions, which he expressed freely. My discussions with Tony were always enjoyable and lively: a great character.
Talking about history, 2023 marks the 75th anniversary of the IUCr, founded just after the terrible period of World War II. Jenny Martin has announced that crystallographers around the world will be invited to participate in a refresh of the IUCr’s vision/purpose and values through an online survey in 2023 with the results to be announced during the International Crystallography Congress in Melbourne later that year. By the way, you can find out details of the Congress here.
As usual, we have some obituaries. Sadly, this time all of them were personal friends. Václav Janovec was a colleague working in the scientific area relative to my own research, namely the crystallography of ferroelectrics, and someone with whom I used to discuss symmetry and domain effects in crystals. Ian Munro was the person I first met when I began carrying out early experiments using the NINA synchrotron in Daresbury (UK) and was an enabler for us to carry out experiments, often under challenging conditions. Basia Oleksyn was a friend whom I used to meet during my visits to Kraków, Poland, in the 1980s.
Finally, on a more cheerful note, I am pleased to be able to congratulate Richard Welberry for his award of the Bragg Medal for his work on diffuse scattering, received during the recent meeting of the Society of Crystallographers in Australia and New Zealand (SCANZ) held in Bendigo.
[1] I am grateful to Caroline Warman of Jesus College Oxford for drawing my attention to this document.
Happy Birthday to the IUCr, which marks its 75th year in 2023! To celebrate this momentous occasion, crystallographers around the world are invited to participate in a refresh of the IUCr’s vision/purpose and values.
The world has changed dramatically over the last 75 years and continues to change at a rapidly increasing pace. We need to be ready to change with it.
Now is the time to acknowledge our past, celebrate our achievements and plan for our future. We want your input on what the IUCr should aspire to be, and where the IUCr should focus its attention.
Watch your inbox for news of the survey, and if you are joining us for the Melbourne Congress, don’t forget to express your interest in the workshop on Tuesday 22 August (1pm – 4pm). We look forward to gathering your thoughts and opinions on the IUCr.
Professor Jenny Martin AC FAA is a Member of the IUCr Executive Committee.
Note from the IUCrAn invitation to complete the survey will be sent to everyone in the World Directory of Crystallographers (WDC). If you are not registered in the WDC or believe your details to be out of date, please register here or update your entry here. Some of the WDC web pages have recently been updated to have a more modern look and feel. Additional functionality has also been added, such as the ability for registrants to edit individual sections of their personal details (see example below).
![[CEO WDC]](https://www.iucr.org/__data/assets/image/0006/155760/CEO-WDC.png) |
The availability of aberration correctors for transmission electron microscopes leads to a significant improvement of the achievable resolution (Batson et al., 2002); for beam-stable materials, sub-ångstrom resolved images can routinely be obtained using modern TEMs. Lens aberrations are inherent properties of electromagnetic elements (Haider et al., 1998). Consequently, their effect is also present in electron diffraction patterns, which are formed at the back focal plane of the objective lens. In addition to the properties of the objective lens, electron diffraction patterns are affected by the characteristics of the diffraction/projector lens system and by the deviation of the electron beam from the optical axis of the microscope, whether intended (precession electron diffraction) or unintended (owing to misalignment).
Electron crystallography based on the analysis of 3D electron diffraction data is a rapidly developing field, demonstrating remarkable achievements in structure analysis of nano- and microcrystals of diverse nature – from minerals to proteins (Gemmi et al., 2019; Gruene & Mugnaioli, 2021). Different instrumental approaches including dedicated electron diffractometers (Heidler et al., 2019) are available. The data reduction is performed using either dedicated programs for electron diffraction (Kolb et al., 2011; Gemmi & Oleynikov, 2013; Palatinus et al., 2019; Wan et al., 2013) or X-ray software [e.g. XDS (Kabsch, 2010), DIALS (Winter et al., 2022), MOSFLM (Battye et al., 2011)]. The structure solution is typically performed with X-ray programs [SHELXT (Sheldrick, 2015), SIR (Burla et al., 2015), Superflip (Palatinus & Chapuis, 2007), Phaser (McCoy et al., 2007)]. The success of dynamical refinement, reliably delivering hydrogen-atom positions (Palatinus et al., 2017) and the absolute configuration (Brázda et al., 2019), clearly demonstrated the potential and necessity of dedicated approaches for the quantitative treatment of effects specific to electron scattering.
Aberrations of electron optical systems bring a distortion field in 2D electron diffraction patterns. These distortions unavoidably propagate into the 3D ED data and deform the complete reciprocal space. The presence of the distortions usually does not hamper the indexing, but may introduce inaccuracy of the lattice parameters, and can lead to improper integration of intensities due to displacement of reflection predictions when mapped back onto 2D frames.
In this issue of IUCrJ, Brázda et al. (2022) present a comprehensive analysis of different types of distortions present in electron diffraction patterns, their propagation into the reconstructed reciprocal space, and elaborated methods for their detection and correction. These methods are already implemented in the new version of PETS2 – widely used dedicated software for 3D ED data reduction (Palatinus et al., 2019).
In a general form, the positional shift of a point due to a distortion can be separated into its radial Δr and tangential Δt components [Brázda et al., 2022; equations (6) and (7)]. The axial symmetry of the optical system sets selection rules on the orders of the circular harmonic and polynomial terms, so that n + m should be odd (Smith, 2007; Linck, 2022). For different distortion types, the formulae for radial and tangential distortion components can then be deduced (Table 1), containing different power dependence on r. Magnification, rotation and elliptical distortions [Fig. 1(b)] contain linear dependence on r, parabolic [Fig. 1(c)] is quadratic with r, and barrel [Fig. 1(d)], pincushion [Fig. 1(e)] and spiral [Fig. 1(f)] have cubic dependence on r. The angular part of the distortions, which depends on the azimuth π, is zero-order for magnification, rotation, spiral and barrel–pincushion distortions (they do not depend on φ), first-order for parabolic distortion (the period is 2π), and second-order for elliptical distortion (the period is π).
![[Table 1]](https://www.iucr.org/__data/assets/image/0011/155774/Table-1.png)
![[Fig. 1]](https://www.iucr.org/__data/assets/image/0009/155736/me6200fig1.png)
Figure 1. Different types of distortion in electron diffraction patterns: (a) original undistorted image, (b) elliptical distortion with the distortion axis inclined 30 away from the vertical axis, (c) parabolic (coma) distortion, (d) barrel with a negative ρ03 parameter, (e) pincushion with a positive ρ03, (f) spiral distortion.
An important point of the study of Brázda et al. (2022) is the elaboration of the relationship between different types of distortions and the possibility to correct for them for a given dataset without any additional information. The magnification distortion is equivalent to the scaling factor and is fully correlated with the lengths of the unit-cell vectors. This makes it impossible to decouple from the lengths of the unit-cell vectors, and correct for, without any additional knowledge. The rotation distortion correlates completely with the tilt axis position in the frames, which also makes it difficult to separate, yet it does not affect the values of the unit-cell vectors, solely resulting in the rotation of the orientation matrix.
The elliptical distortion represents a complex case: the component along the tilt axis (and orthogonal to it) is equivalent to stretching or contracting of the complete reciprocal space along the tilt axis, and therefore distorts the lattice perfectly linearly, resulting in the change of the unit-cell parameters (i.e. it is fully correlated with the unit-cell metric). The component away from the tilt axis does lead to the distortion (twisting) of the lattice, which can be corrected for. For a full correction of elliptical distortion, additional knowledge on the crystal class or an additional dataset from a differently oriented crystal is necessary (under the assumption that the elliptical distortion is the same for the two datasets). Distortions with quadratic and cubic dependence on r described by Brázda et al. (2022) lead to specific deformations of the reciprocal lattice, and can be refined simultaneously with the unit-cell parameters.
Accounting for the specified distortions in electron diffraction data has a number of implications. Apart from the obviously more accurate unit-cell parameters, enabling the crystal system determination, and improving the integration of intensities, the final structure models provide a more accurate bond geometry, and finally, better accuracy of the unit-cell parameters improving the findability of the structures within the databases.
In the first publication of the series, Brázda et al. (2022) consider the effect of distortion within 2D frames. The next step is the correction for misalignment of individual frames. It has been demonstrated that the in-frame distortion correction combined with the frame orientation allowed for better visibility of hydrogens in cobalt aluminophosphate (Brázda & Palatinus, 2022) compared with uncorrected data extraction reported in 2017 (Palatinus et al., 2017), and significantly improved (Krysiak, 2022) data reduction and structure analysis of hydrous layer silicate RUB-6 (Krysiak et al., 2020). We therefore look forward to seeing a significant step forward in the accuracy of electron diffraction structure analysis in general, driven by the implementation of more accurate models of electron diffraction data geometry.
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This article was originally published in IUCrJ (2022). 9, 715–717.
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