|The IUCr is an International Scientific Union. Its objectives are to promote international cooperation in crystallography and to contribute to all aspects of crystallography, to promote international publication of crystallographic research, to facilitate standardization of methods, units, nomenclatures and symbols, and to form a focus for the relations of crystallography to other sciences.|
It is with great sadness that we announce the death of Frank Allen on 10 November 2014, aged 70.
Frank joined the Chemical Crystallography Group at the University of Cambridge in 1970 and played a pivotal role in the establishment of the Cambridge Structural Database. He went on to become the Scientific Director and then the Executive Director of the Cambridge Crystallographic Data Centre.
Following his retirement in 2008, Frank remained with the CCDC as an Emeritus Research Fellow, enabling him to continue to indulge his passion for structural chemistry.
Frank’s research involved collaboration with many scientists around the world, resulting in over 200 papers. He was also a wonderful teacher, supervising more than 20 doctoral students and introducing many more to structural chemistry through workshops over many years.
His contributions to other influential organisations, his vigorous editorship of Acta Crystallographica, the numerous conferences he organised and presentations he made meant Frank was known to and respected by crystallographers the world over.
Frank has long been a leading figure in international crystallography, and was a wonderful colleague, becoming a friend to all those who worked with him. He will be sadly missed.
A group of crystallographers came together on Wednesday 19 November at the RSC Chemistry Centre, Burlington House, London, UK to discuss Communicating Crystallography as part of the Chemical Crystallography Group Autumn Meeting 2014. The morning session opened with energetic presentations focusing on outreach from Anna Warren (Diamond Light Source), Peter Hoare (University of Newcastle) and Chick Wilson (University of Bath). The afternoon session, which looked at the publishing process and some of the latest activities from the Royal Society of Chemistry, started with Guy Jones, followed by Serin Dabb and then David Sait. After tea, the final session began with a presentation from Brian McMahon (IUCr) entitled “From structural data to structural knowledge”. A discussion of data, databases and deposition with a panel comprising John Helliwell (University of Manchester), Serin Dabb (RSC) and Ian Bruno (CCDC) brought the event to a close. A link to the individual presentations or information relating to them will be made available shortly.
From crystals of cancer drugs to atomic patterns drawn in the sand, a new photography exhibition at the RoyalAlbert Hall, London, UK perfectly captures the beauty and intricacy inherent in the science of crystallography.Illuminating Atoms, by the photographer Max Alexander, depicts a series of documentary images of crystallography experiments in action alongside portraits of modern-day crystallographers.
The exhibition, which is sponsored by the Science & Technology Facilities Council (STFC), the Wellcome Trust, GSK, AstraZeneca, Pharmorphix and the Diamond Light Source, conveys the untold story of crystallography, demonstrating the range of science taking place and the rich and vibrant community working in this field. The final opportunity to view Illuminating Atoms will be Saturday 29 November from 10am to 4pm; for more information, please visit www.stfc.ac.uk/illuminating_atoms_portraits.
Further activities promoting crystallography take place this week. The article "IYCr2014: Spreading the Word About Crystallography in an International Year" by Brian McMahon and Michele Zema (IUCr) will be discussed online from 24 to 26 November during the 2014 Fall Newsletter virtual conference of the DivCHED CCCE of the American Chemical Society. The full article is available here. To take part in the online discussion you need to set up a free account at http://confchem.ccce.divched.org/2014FallCCCENL.
Finally, if you are attending the MRS Fall Meeting in Boston, USA next week, do take the time to visit the IUCr booth #114 where we’ll be pleased to see you. At our booth you can
We look forward to seeing you there.
Knowledge of the three-dimensional structures of proteins is essential for understanding biological processes.
Structures help to explain molecular and biochemical functions, visualize details of macromolecular interactions, facilitate understanding of underlying biochemical mechanisms and define biological concepts.
The human genome and follow-up sequencing projects have revolutionized biology and medicine; structural genomic programmes have developed and applied structure-determination pipelines to a wide range of protein targets, facilitating the visualization of macromolecular interactions and the understanding of their molecular and biochemical functions.
A paper recently published by Mizianty et al. (2014). Acta Cryst. D70, 2781-2793; doi:10.1107/S1399004714019427 seeks to address the fundamental question of whether the three-dimensional structures of all proteins and all functional annotations can be determined using X-ray crystallography.
The researchers set out to perform the first large scale analysis of its kind covering all known complete proteomes (the sets of proteins thought to be expressed by an organism whose genome has been completely sequenced, as defined by the UniProt Consortium in 2012) and all functional and localization annotations available in the Gene Ontology for the corresponding proteins.
The Canadian and US team show that current X-ray crystallographic knowhow combined with homology modeling can provide structures for 25% of modelling families (protein clusters for which structural models can be obtained through homology modelling), with at least one structural model produced for each Gene Ontology functional annotation. The coverage varies between super-kingdoms, with 19% for eukaryotes, 35% for bacteria and 49% for archaea, and with those of viruses following the coverage values of their hosts. It is shown that the crystallization propensities of proteomes from the taxonomic super kingdoms are distinct. The use of knowledge-based target selection is shown to substantially increase the ability to produce X-ray structures.
Talking to the IUCr Mizianty commented “We believe our method has helped to advance our understanding of the coverage by X-ray structures of proteins and complete proteomes on a global scale”.
X-rays have been at the heart of imaging since their discovery at the end of the nineteenth century. Now, Pierre Thibault and colleagues at University College London, UK and the Paul Scherrer Institute in Switzerland, hope that a new twist on an old favorite will extend and give them dose-limited resolution and sensitivity through the development of X-ray ptychography.
X-ray ptychography is a scanning coherent diffractive imaging technique, the team explains. The technique first suggested in the 1970s involves illuminating the sample with a structured, often confined source and measuring the resulting diffraction pattern for different overlapping positions of the sample, the term is from the Greek "fold" and "writing". Ultimately, ptychography promises to solve the diffraction-pattern phase problem in X-ray studies.
Coherent diffractive imaging (CDI) techniques, of which ptychography is just one, are all underpinned by the lack of a lens to focus the image. Instead of focusing, a mathematical algorithm is used to reconstruct the image of the sample from the collected diffraction patterns. Such a lensless system thus bypasses many of the technical constraints of lenses, which for X-rays are often inefficient, may introduce aberrations, and strongly limit resolution. Lensless, however, means phase is lost, which is where the overlapping folds of ptychography are exploited.
"Ptychography may approach imaging speeds familiar from full-field methods while retaining its inherently quantitative nature and metrological versatility," the team explains Thibault et al. (2014). J. Synchrotron Rad. 21,1011-1018; doi:10.1107/S1600577514015343. "Beyond promises of high throughput, spectroscopic applications in three dimensions become feasible, as do measurements of sample dynamics through time-resolved imaging or careful characterization of decoherence effects." The team suggests that additional technological and analytical advances in bright X-ray sources are now needed to help this field mature and to allow it to enter the realm of high-throughput studies and even three-dimensional spectroscopy.
"Ptychography's active development and sustained rate of successes hints at its potential as an important player in contemporary questions on data acquisition strategies, information content and feature extractions," the team reports, hinting that so-called "big data" methods of the kind usually reserved for particle physics and high-speed tomography, will come to the fore.
"In a way there are many next steps," Thibault told the IUCr. "In the paper we mention 'quantitative improvements', namely improve speed and size of field of view, and 'qualitative improvements', or improving resolution and sensitivity. Beyond this, the goal would be moving to four dimensions, that is adding one extra axis, either spectrum (spectro-tomography) or time (tomographic movies).
The Thibault paper forms part of the special issue in the Journal of Synchrotron Radiation: Diffraction-Limited Storage Rings and New Science Opportunities. Guest Editors: Mikael Eriksson and J. Friso van der Veen.
|Figure 1: 2014 Nobel Prize winners for Physics|
Epitaxial layers of gallium nitride (GaN) – material that exists in the laboratory only – on single-crystal sapphire substrate produce a blue light which can be converted to white light using a phosphor coating. Today these new LEDs are replacing traditional light bulbs and fluorescent tubes worldwide. The white LED lamps are bright, efficient and long lasting. They have improved the quality of life of billions of people around the world: owing to low power requirements these lamps can be powered by cheap, local, solar energy. This discovery directly benefits all of us.
A great deal of information about the Nobel Prize Winners, the blue light emitting diode and its advantages for the whole world can be found in the scientific literature and on the internet. There are interviews, press releases and popular articles.
The reason why we are writing this note is to stress how important to this world-changing discovery is the challenging crystal growth and epitaxial deposition work performed at the beginning of the success path.
To achieve the next step, leading to a high efficiency laser, a new, reliable method of obtaining bulk single crystals of GaN had to be created, implemented and become affordable. This is happening right now as large, high quality GaN crystals are being grown by either high-pressure or amonothermal methods. As this is achieved, many other obstacles, from cutting the bulk crystal in a specific orientation to reducing the number of dislocations, still have to be overcome.
|Figure 2: Gallium nitride crystal. Courtesy of the archives of the IWC Sciences|
|Figure 3: Final of the Spanish schools crystallisation competition|
For many years the IUCr has regularly and generously supported crystal-growth schools and conferences around the world an example can be seen here. These meetings act as forums where new ideas can be formed, discussed and promoted. In the time of scientific budget cuts and limits on basic research in many countries these IUCr activities, as well as those such as the international crystal growth competition for elementary and high-school students, create new interest in the old art of growing crystals. These activities build solid scientific foundations within the future generation of researchers, who – now in their school years – cannot only enjoy the happiness of creating something new and very material: the crystal, but also – and this is extremely important at any age – be applauded and recognized for doing it.Hanna Dabkowska and Andrea Zappettini
The United Nations proclaimed 2014 the International Year of Crystallography. Due to many of the activities and events taking place throughout the year, it is obvious, more so than in previous years, how crystallography strengthens and enriches all natural sciences. Take for example the breathtaking developments at modern large scale facilities, like third generation synchrotrons, X-ray free-electron lasers and neutron spallation sources, and the various remarkable improvements recently made to home facilities. The sealed X-ray tube has been almost totally replaced today by reliable microfocus or rotating anode sources, stronger by many orders of magnitude when compared to W. C. Röntgen's original device. The same is valid for detector technology, where the original film or scintillation detector, even the image plate, is nowadays almost totally substituted by charge-coupled devices (CCDs, CMOSs). Even they will become outdated very soon when we look at the most recent developments of the single-photon counting hybrid pixel area detector.
This new class of detector combines the virtues of speed of an area detector with the advantageous low noise and extremely high dynamic range of a point detector. The first pixel detectors have been designed and optimized for use with synchrotrons (e.g. PILATUS or EIGER from Dectris, or XPAD from imXPAD). Unfortunately, due partly to cost, data collection and software integration issues, these detectors have not yet reached the typical university laboratory. That is until now [Wenger et al. (2014). Acta Cryst. B70, 783-791; doi: 10.1107/S2052520614017338]. For the first time a group of authors present a pixel detector mounted on a commercial goniometer, equipped with a microfocus X-ray source, to generate high-resolution X-ray data.
The researchers have shown in the paper that high quality diffraction data suitable for accurate charge density studies can be collected by following their set-up.
The charge-density community will be eager to see further developments from this team such as a reduction in data acquisition time, addressing blind detector areas and improved data reduction to tackle estimated systematic errors and intensity variances.
This news story is a short excerpt taken from the commentary [Stalke (2014). Acta Cryst. B70, 781-782; doi: 10.1107/S2052520614021349].