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Session Overview
Session
Poster - 08 General: General interest
Time:
Sunday, 15/Aug/2021:
5:10pm - 6:10pm


 


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Presentations

Poster session abstracts

Radomír Kužel



Ducks in space groups! Students grasping 3D-arrangement of symmetry elements with hands-on models

Nico Graw, Dietmar Stalke

Institut für Anorganische Chemie, Georg-August-Universität Göttingen, 37077 Göttingen, Germany

Symmetry considerations are vital in chemistry and even more so in crystallography [1-2]. Typically, students first come into contact with this during their studies in the context of stereochemistry or spectroscopy where usually the Schönflies notation is used. Learning and teaching about molecular symmetry naturally requires spatial imagination. To develop and refine this, models and model kits are of outmost importance and are readily available for a broad range of purposes [3].

The description of crystalline matter from a crystallographer’s point of view naturally requires translational symmetry to be considered. Therefore, the applied framework to learn and discuss about molecular symmetry needs to be extended, also leading to the introduction of the Herman-Mauguin notation. From our teaching experience this transition and especially the introduction of translational symmetry components is difficult and something students struggle with. These difficulties typically culminate when it comes to the combination of symmetry elements and their assembly to give space groups. The connotation in the International Tables for Crystallography, section A [4] is not particularly intuitive to understand and to apply without the help of models.

We herein present large scale (i. e. typically 50 x 50 x 50 cm), physical 3D models of complete space groups (Figure 1) to promote student’s spatial imagination and to help understanding the construction of space groups by symmetry elements. The models were designed and built to fulfil three basic requirements: (1) to be accurate space group representations containing the symmetry symbols, (2) to visually resemble the conventional 2D space group notation if viewed along the respective crystallographic axis and, (3) to allow students to assemble asymmetric units within the unit cell by themselves.

Grabbing fosters grasping!

[1] Jaffé, H. H. (2013). Symmetry in Chemistry; New York: Dover Publications.
[2] Glasser, L. (1967). J. Chem. Educ. 44, 502.
[3] Flint, E. B. (2011). J. Chem. Educ. 88, 907–909.
[4] Brock, C. P.; Hahn, T.; Wondratschek, H.; Müller, U.; Shmueli, U.; Prince, E.; Authier, A.; Kopský, V.; Litvin, D. B.; Arnold, E.; Himmel, D. M.; Rossmann, M. G.; Hall, S.; McMahon, B.; Aroyo, M. I. (2016). International Tables for Crystallography, Volume A; International Union of Crystallography: Chester, England.

The authors would like to thank the Ministry of Science and Culture of Lower Saxony, Germany for funding. We are very grateful for the help of our workshop in constructing the models and the help of Xiaobai Wang in taking the photographs.

External Resource:
Video Link


Helping researchers to solve their structures: automation and user guidance in CCP4 Cloud

Oleg Kovalevskiy, Andrey Lebedev, Eugene Krissinel

CCP4, Rutherford Appleton Laboratory, UKRI STFC, Didcot, United Kingdom

Structure solution in macromolecular crystallography is not always a straightforward process and it may be rather difficult for structural biologists without advanced training. A trained crystallographer exploits an extended set of approaches and tricks, based on the analysis of several indicators, general assessment of the case, and developed strategies for dealing with a particular class of problems. If such an approach, used by an expert, can be formalised in terms of an algorithm, then it can be implemented as a computer program or automated user advice system to help users solving structures quicker and with a higher success rate. It is not surprising then, that programs for macromolecular crystallography are moving towards full automation, taking off burden from researchers and lowering the entry barriers for novice users.

During the last few years, substantial progress has been made towards automation of the whole macromolecular structure determination process. There are a number of examples of successful automatic solutions for various stages of structure determination, such as molecular replacement, experimental phasing, and refinement [1-5].

In this communication, we report two novel automation features implemented in CCP4 Cloud [6], the new system for solving macromolecular structures online, released with CCP4 Software Suite 7.1 in 2020. Automated user advice framework, named Verdicts, provides simple graphical representation of results quality with detailed analysis of points for improvement as part of every task (e.g., refinement) report. The analysis includes suggestions on what could be done in order to improve the result (i.e., which parameters could be optimised). Then, the task can be re-run with the suggested parameters, which can be further adjusted by the user as appropriate.

Another automation feature, Workflows, was designed for unfolding structure solution Projects, or their parts, automatically using user-supplied data. Such automatically initiated and unfolded Projects may include a number of tasks, arranged in branching Project Trees as if this were done by the user themselves. In common cases without complications, this may result in structure solved, and if not, then a starting Project is offered to the user for analysis and further manipulations, where simple, first-order structure solution attempts are already performed. Any task or branch of the starting Project may be cloned and re-run with optimized parameters, and new tasks may be added as needed. Workflows combine automation and human expert skills, and, therefore, represent an excellent starting point for users with different level of expertise, ranging from novices to experienced crystallographers. Workflows are particularly useful in a common case of processing large sets of isomorphous crystals, because, once structure is solved in one crystal, the process is well-repeatable in systems with moderate modifications.
[1] Winter, G., Lobley, C. M. & Prince, S. M. (2013). Acta Crystallogr D Biol Crystallogr 69, 1260.
[2] Long, F., Vagin, A. A., Young, P. & Murshudov, G. N. (2008). Acta Crystallogr D Biol Crystallogr 64, 125.
[3] Keegan, R. M., Long, F., Fazio, V. J., Winn, M. D., Murshudov, G. N. & Vagin, A. A. (2011). Acta Crystallogr D Biol Crystallogr 67, 313.
[4] Minor, W., Cymborowski, M., Otwinowski, Z. & Chruszcz, M. (2006). Acta Crystallogr D Biol Crystallogr 62, 859.
[5] Wojdyr, M., Keegan, R., Winter, G., Ashton, A., Lebedev, A. & Krissinel, E. (2014). Acta Crystallographica Section A 70, C1447.
[6] Krissinel, E., Uski, V., Lebedev, A., Winn, M. & Ballard, C. (2018). Acta Crystallographica Section D 74, 143.

External Resource:
Video Link


The Argentinian Crystal Growing Contest and other educational activities in Argentina during the COVID-19 pandemic

Sebastián Klinke1,2, Valeria Cintia Fuertes1,3, Vanina Gisela Franco1,4, Clarisa Ester Alvarez1,5, Diego Germán Lamas1,6

1Argentinian Association of Crystallography (AACr); 2Fundación Instituto Leloir, IIBBA-CONICET, Ciudad Autónoma de Buenos Aires, Argentina; 3INFIQC, UNC-CONICET, Facultad de Ciencias Químicas, Córdoba Capital, Pcia. de Córdoba, Argentina; 4Instituto de Física del Litoral, UNL-CONICET, Santa Fe Capital, Pcia. de Santa Fe, Argentina; 5Centro de Estudios Fotosintéticos y Bioquímicos-CONICET, FBioyF-UNR, Rosario, Pcia. de Santa Fe, Argentina; 6ITECA, UNSAM-CONICET, ECyT, Laboratorio de Cristalografía Aplicada, San Martín, Pcia. de Buenos Aires, Argentina

The celebration of the International Year of Crystallography (IYCr2014) in Argentina was an unforgettable experience, with a lot of academic, educational and dissemination activities all over the country including exhibitions, science fairs, art or photo contests, and outreach talks, among other events. Many members of the Argentinian Association of Crystallography (AACr) participated enthusiastically and, in this way, it was possible to bring Crystallography to all provinces in our country. The most important activity launched by the AACr for the IYCr2014 was the “National Crystal Growing Contest for High Schools”, which also involved the organization of 38 short courses on Crystallography and Crystal Growth for training of primary and secondary school teachers all over the country. The students, organized in teams of a maximum of three or individually, had to perform a crystal growing project, guided by their teachers, and submit a short video or written essay presenting their results and conclusions. The contest was a complete success, receiving about 500 projects of high scientific quality and creativity. Through this exciting, funny and hands-on scientific experience, Crystallography and other related scientific fields were promoted along the Argentinian high school community, being also a way to encourage young students to continue exploring Science and developing their scientific skills.

Considering the great success of the first edition, the AACr decided to continue this activity annually in the frame of the “Legacy of the IYCr2014” initiative. The Contest continued to arouse great enthusiasm, with the participation of hundreds of schools and training more than one thousand teachers every year. It is worth to mention that many of them also participated in the “IUCr Crystal Growing Competition for Schoolchildren, the international contest organized by the IUCr, with great success. As such, Argentina has been the country with the highest number of projects submitted in every edition.

The COVID-19 pandemic has represented a global challenge since March 2020 and many congresses, courses and outreach activities could not take place or had to be postponed. However, as 2020 progressed, some of these difficulties were overcome. Many virtual courses were organized and some of them, thanks to the online modality, reached new regions or countries. Therefore, the AACr decided to continue with the Contest, this time proposing students to work from home with simple and inexpensive materials, without any danger. In addition, bibliographic research works related to Crystallography were also accepted in the 2020 edition, allowing the participation of students that could not grow crystals at home or school but that were interested in joining our activity. Many students accepted the challenge and 90 works were received. Many of them involved the growth of single or polycrystals, but others were interesting research projects related to the history of Crystallography and some of the great milestones of our science field. The short courses on Crystallography and Crystal Growth, taught in a new virtual format, were very successful too, receiving a large number of new participants not only from Argentinian cities not visited by AACr members in the previous years, but also from all over Latin America. In this way, 15 online short courses were organized, with the participation of over 4,000 teachers. The year finished with a virtual awards ceremony, opened to the general public, in which the finalists selected by the jury had the opportunity to share their experience.

In conclusion, even though 2020 has been a very difficult year, the AACr has continued with the dissemination of Crystallography, and similar activities are nowadays in progress in the frame of the 2021 edition of the National Crystal Growing Contest.

Acknowledgements: We are grateful to the following institutions for supporting in the National Crystal Growing Contest: IUCr, Argentinian Research Council (CONICET) through its VocAr Initiative (Programa de Promoción de Vocaciones Científicas), Balseiro Foundation, and Argentinian Ministry of Science, Technology and Innovation. Special thanks to the AACr members, regional representatives and local Education Ministries that help us organize this federal activity.

External Resource:
Video Link


Alarm sounded for lack of bringing and building crystallography in Ethiopia

Alebel Nibret Belay

Bahir Dar University, Bahir Dar, Ethiopia

Alarm sounded for lack of bringing and building crystallography in Ethiopia

Alebel N.Belay1
1
Department of Chemistry, Bahir Dar University, P.O.Box 79, Bahir Dar, Ethiopia.
Email: crossispower@gmail.com or alebel.nibret@bdu.edu.et

As you know the current population of Africa is 1,374,451,375 as of Monday, July 26, 2021, based on the latest United Nations estimates. Africa population is equivalent to 16.72% of the total world population. Africa ranks number two among regions of the world (roughly equivalent to "continents"), ordered by population. With over 110 million inhabitants, Ethiopia is one of the most populous landlocked countries in the world, as well as the second-most populous nation on the African continent after Nigeria.

Bahir Dar University is now among the largest universities in the Federal Democratic Republic of Ethiopia, with more than 52,830 students in its 219 academic programs; 69 undergraduate, 118 masters, and 32 PhD programs. The vision of Bahir Dar University is to become one of the ten premier research universities in Africa by 2025. For instance, basic and in-depth skill and knowledge in introduction to Crystallography, Crystal Chemistry, Chemical crystallography, etc., and most favoured technique for structure determination of proteins and biological macromolecules for undergraduate and postgraduate students will be compulsory in future. Currently, BDU students’ and the rest part of Ethiopia still have had many challenges to start the extensive practical classes in crystallography using equipment like Single-crystal X-ray diffraction. Because of problems associated with potential future Ethiopian Crystallographic Association (EthCA) and working it for most advanced technology and many other emerging applications are evident [1, 2]. Indeed, a senior scientist helping young scientists to achieve their potential is important but it is often difficult to establish exactly when a scientific multidiscipline began. This is also true when trying to identify the moment when a particular field of research got a foothold in a new geographical region like Ethiopia.

Therefore, the main goal of this presentation is too aware and build knowledge, scientific research work and acquire experience to promote science through crystallography as a vehicle further in Ethiopia (my home country, Bahir Dar University, Ethiopia), Africa and beyond. Due to this we are trying to continue the thrust to establish a Steering Committee for a potential future establishment of an Ethiopian Crystallographic Association (EthCA). Moreover, experiences I got from different conference start with IUCr2014 in Bloemfontein, South Africa, the PCCr1 meeting in Dschang, Cameroon, in 2016, IUCr meeting in Hyderabad, India, in 2017 and so on were helped us to achieve our objective [2-5]. But the African Crystallographic Association’s (AfCA) 2017 report shown to pursue a follow-up meeting of all potential members of the AfCA Steering Committee, or representatives, to determine further actions for the immediate future, but still nothing to did it and see any on-going progress practically regarding to establishing crystallography in Ethiopian. This might be effect of COVID-19 in financial crises.

Keywords: Challenges; crystallography; Establishing, Young scientist, Ethiopia

My thanks and appreciation go to the following institution for supporting me: Crystallographic team of the University of the Free State for the PhD training and fund supported by South Africa’s National research Foundation (NRF) and the World Academy of Science (TWAS) (UIDs 99782). And also UFS, BDU, UNESCO and IUCr for travel grants of various international conferences (real and virtual) since 2014 to present.



AsCA 2022 - 17th Conference of the Asian Crystallographic Association in Korea

Kyeong Kyu Kim, Sangho Lee, Changsuk Oh

Sungkyunkwan University, Suwon, Korea, Republic of (South Korea)

The 17th conference of the Asian Crystallographic Association (AsCA) will be held in Jeju island, Republic of Korea, from October 30th to November 4. The conference venue is the Lotte Hotel, located on the beautiful seaside hill. The conference is planned to be held offline only at this moment. However, depending on the situation of Covid-19, mix of on- and offline meeting will be considered. The local organizing committee welcomes not only Asian crystallographer but also scholars from all over the world to the AsCA conference.

External Resource:
Video Link


University remote teaching in crystal chemistry during the COVID-19 pandemic: positive and negative aspects

Olga V. Grineva

Chemistry Department of Moscow M. V. Lomonosov State University, Moscow, Russia

At the Chemistry Department of the Moscow M. V. Lomonosov State University, the compulsory course “Crystal Chemistry” and numerous elective courses for undergraduate and postgraduate students (devoted to the in-depth study of several crystallographic and crystallochemical topics) do not include extensive practical classes that can be performed only in specially equipped rooms. Therefore, in principle, they can be done remotely without significant changes in content. In fact, remote learning at the Department in the last three semesters differs significantly from the option of education that was called distance learning before the COVID-19 pandemic. Classical distance learning assumes that the student can become acquainted with the teaching materials and perform test tasks conveniently within a specified period. The current procedure of remote learning at the Department may be called classroom-like: there is a schedule of lectures and seminars, while teachers are obliged to conduct live seminars, and live lectures are highly desirable.

Although before the pandemic, in most of the lectures and seminars on the general course “Crystal Chemistry”, the teachers demonstrated space models (polyhedra, individual molecules, Bravais lattices, models demonstrating the effect of symmetry elements, unit cells of inorganic and organic substances), and for some students, this facilitated the perception of the material, but strictly speaking, such demonstrations are not mandatory for a successful understanding of the course. Since 2009, the course includes acquaintance with structure visualization programs, and students have access to cif files for the structures on the must-have list. Before the pandemic, work with such programs was mainly done in the classroom, but students were recommended to download demo versions of the Diamond and Mercury programs for deeper insight, so the teachers already had some experience, which is difficult for students. During the “pandemic” semesters, the work with these programs was done completely at home, and most of the students coped with it successfully. Unfortunately, independent searches according to different criteria in the CSD, which were previously done by students of one of the specialized groups, were not implemented (due to licensing restrictions and a very large database). Demonstration of searches from the teacher’s computer were not quite complete in Zoom when using the usual option of screen sharing since inner windows in ConQuest were not visible, and the setting in Zoom allowing to see everything was undesirable when working with students. Therefore, it was necessary to make additional slides for the presentations. Nevertheless, because the use of computer programs became part of the “Crystal Chemistry” course long before the pandemic, difficulties in the transformations to remote learning were mainly due to the suddenness of the jump and technical problems among some students and teachers (the lack of devices allowing to set up necessary programs and to work with them, as well as with remote resources, poor Internet connection).

The advantages of the remote format for students include watching videos (teachers were required to record both lectures and seminars) as many times as they need to understand. In addition to the videos, many teachers shared other materials. Unfortunately, this format fostered complacancy for some students, but overall, the students’ responses after completing the courses were not worse than in the face-to-face studies.

For teachers, the distance format makes it generally easier to carry out current control of knowledge using computer tests (Moodle is the main program at the Department for these purposes), although, of course, preparing good tests takes a lot of time. Unfortunately, computer tests cannot adequately assess students’ knowledge for all sections of the “Crystal chemistry” course, and in those cases, when students placed the answers to the tasks in the form of pictures, their verification took significantly longer than checking traditional paper forms.

For me, the most inconvenient and time-consuming part of fully remote learning compared to the face-to-face format was exams using Zoom and MS Teams. This is partly due to imperfect programs (for example, in MS Teams, it is inconvenient to draw, much more often than in Zoom, there was the poor quality of communication), but more importantly, it is impossible to determine with absolute certainty whether the student really has a bad connection or is deliberately wasting time and creating interference to somehow find the answer to the question asked.

External Resource:
Video Link


 
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