scholarly journals Automatic local resolution-based sharpening of cryo-EM maps

2018 ◽  
Author(s):  
Erney Ramírez-Aportela ◽  
Jose Luis Vilas ◽  
Roberto Melero ◽  
Pablo Conesa ◽  
Marta Martínez ◽  
...  

AbstractRecent technological advances and computational developments, have allowed the reconstruction of cryo-EM maps at near-atomic resolution structures. Cryo-EM maps benefit significantly of a “postprocessing” step, normally referred to as “sharpening”, that tends to increase signal at medium/high resolution. Here, we propose a new method for local sharpening of volumes generated by cryo-EM. The algorithm (LocalDeblur) is based on a local resolution-guided Wiener restoration approach, does not need any prior atomic model and it avoids artificial structure 1 factor corrections. LocalDeblur is fully automatic and parameter free. We show that the new method significantly and quantitatively improving map quality and interpretability, especially in cases of broad local resolution changes (as is often the case of membrane proteins).

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 665
Author(s):  
Jacqueline Cherfils ◽  
Jorge Navaza

Single particle cryogenic electron microscopy (cryo-EM) is transforming structural biology by enabling the analysis of difficult macromolecular specimens, such as membrane proteins or large complexes with flexible elements, at near atomic resolution with an accuracy close to that of X-ray crystallography. As the technique continues to improve, it is important to assess and exploit its full potential to produce the most possible reliable atomic models. Here we propose to use the experimental images as the data for refinement and validation, instead of the reconstructed maps as currently used. This procedure, which is in spirit quite similar to that used in X-ray crystallography where the data include experimental phases, should contribute to improve the quality of the models.


Author(s):  
M. Kelly ◽  
D.M. Bird

It is well known that strain fields can have a strong influence on the details of HREM images. This, for example, can cause problems in the analysis of edge-on interfaces between lattice mismatched materials. An interesting alternative to conventional HREM imaging has recently been advanced by Pennycook and co-workers where the intensity variation in the annular dark field (ADF) detector is monitored as a STEM probe is scanned across the specimen. It is believed that the observed atomic-resolution contrast is correlated with the intensity of the STEM probe at the atomic sites and the way in which this varies as the probe moves from cell to cell. As well as providing a directly interpretable high-resolution image, there are reasons for believing that ADF-STEM images may be less suseptible to strain than conventional HREM. This is because HREM images arise from the interference of several diffracted beams, each of which is governed by all the excited Bloch waves in the crystal.


Author(s):  
Kenneth H. Downing ◽  
Hu Meisheng ◽  
Hans-Rudolf Went ◽  
Michael A. O'Keefe

With current advances in electron microscope design, high resolution electron microscopy has become routine, and point resolutions of better than 2Å have been obtained in images of many inorganic crystals. Although this resolution is sufficient to resolve interatomic spacings, interpretation generally requires comparison of experimental images with calculations. Since the images are two-dimensional representations of projections of the full three-dimensional structure, information is invariably lost in the overlapping images of atoms at various heights. The technique of electron crystallography, in which information from several views of a crystal is combined, has been developed to obtain three-dimensional information on proteins. The resolution in images of proteins is severely limited by effects of radiation damage. In principle, atomic-resolution, 3D reconstructions should be obtainable from specimens that are resistant to damage. The most serious problem would appear to be in obtaining high-resolution images from areas that are thin enough that dynamical scattering effects can be ignored.


Author(s):  
N. D. Browning ◽  
M. M. McGibbon ◽  
M. F. Chisholm ◽  
S. J. Pennycook

The recent development of the Z-contrast imaging technique for the VG HB501 UX dedicated STEM, has added a high-resolution imaging facility to a microscope used mainly for microanalysis. This imaging technique not only provides a high-resolution reference image, but as it can be performed simultaneously with electron energy loss spectroscopy (EELS), can be used to position the electron probe at the atomic scale. The spatial resolution of both the image and the energy loss spectrum can be identical, and in principle limited only by the 2.2 Å probe size of the microscope. There now exists, therefore, the possibility to perform chemical analysis of materials on the scale of single atomic columns or planes.In order to achieve atomic resolution energy loss spectroscopy, the range over which a fast electron can cause a particular excitation event, must be less than the interatomic spacing. This range is described classically by the impact parameter, b, which ranges from ~10 Å for the low loss region of the spectrum to <1Å for the core losses.


Author(s):  
David J. Smith

The initial attractions of the high voltage electron microscope (HVEM) stemmed mainly from the possibility of considerable increases in electron penetration through thick specimens compared with conventional 100KV microscopes, although the potential improvement in resolution associated with the decrease in election wavelength had been fully appreciated for many years (eg. Cosslett, 1946)1, even if not realizable in practice. Subsequent technological advances enabled the performance of lower voltage machines to be brought closer to the theoretical limit, to be followed in turn by more recent projects which have been successful, eventually, in achieving even higher resolution with dedicated higher voltage instruments such as those at Kyoto (500KV)2, Munich (400KV)3, Ibaraki (1250KV)4 and Cambridge (600KV)5. It does not necessarily follow however that the performance of journal high voltage microscopes can be easily upgraded, retrospectively, to the same level, as will be discussed in detail below.


2020 ◽  
Author(s):  
Di Liu ◽  
Yaming Shao ◽  
Joseph A. Piccirilli ◽  
Yossi Weizmann

<p>Though advances in nanotechnology have enabled the construction of synthetic nucleic acid based nanoarchitectures with ever-increasing complexity for various applications, high-resolution structures are lacking due to the difficulty of obtaining good diffracting crystals. Here we report the design of RNA nanostructures based on homooligomerizable tiles from an RNA single-strand for X-ray determination. Three structures are solved to near-atomic resolution: a 2D parallelogram, an unexpectedly formed 3D nanobracelet, and a 3D nanocage. Structural details of their constituent motifs—such as kissing loops, branched kissing-loops and T-junctions—that resemble natural RNA motifs and resisted X-ray determination are revealed. This work unveils the largely unexplored potential of crystallography in gaining high-resolution feedback for nanostructure design and suggests a novel route to investigate RNA motif structures by configuring them into nanoarchitectures.</p>


Author(s):  
А.С. Алексеев ◽  
А.А. Никифоров ◽  
А.А. Михайлова ◽  
М.Р. Вагизов

В связи со старением информационных материалов о состоянии лесов существует потребность в разработке новых методов таксации древостоев, основанных на применении последних научно-технических достижений в области теории структуры и продуктивности древостоев, дистанционных методов изучения лесов, информационных и ГИС технологий. В статье приведены результаты разработки и проверки нового метода определения таксационных характеристик сомкнутых насаждений на основе правила 3/2 и подобных ему правил Хильми и Рейнеке, с одной стороны, и определения числа деревьев на единице площади по снимку сверх высокого разрешения, полученного с помощью БПЛА, с другой. С теоретической точки зрения эта зависимости величин запаса, средней высоты и среднего диаметра от числа стволов на единице площади относятся к классу аллометрических связей, очень часто встречающихся при количественном описании соотношений частей биологических систем разных уровней иерархии, от организмов до экосистем. Параметры аллометрических зависимостей запаса, средних высоты и диаметра от числа стволов на единице площади были определены для основных лесообразующих пород по данным таблиц хода роста нормальных (полных) древостоев с теоретическим показателем степени и затем использованы для расчетов. Число деревьев на единице площади определялось по снимку с разрешением 7,13 см/пиксель, полученному с помощью 4-роторной платформы. Обработка материалов аэрофотосъемки была выполнена в специализированной фотограмметрической системе Agisoft Photoscan. В результате были получены ортофотоплан и цифровая модель поверхности крон деревьев на изучаемую территорию с определением их высот. Для автоматизированной обработки полученных изображений с целью получения значений числа деревьев на единицу площади был создан специализированный скрипт на языке Java. Погрешности определения таксационных характеристик древостоев предлагаемым методом не выше установленных действующими нормативными материалами. Every time there is a demand for new innovative methods of forest resources estimation based on last achievements in theoretical science, remote sensing methods, information and GIS-technologies. In the paper are presented a new method and the results of its application to forest stands growing stock, mean height and diameter determination. The method is based on rule 3/2 and similar Reineke and Hilmy rules, on one hand and high resolution image made by unmanned aerial vehicle, which used for determination of number of trees per area unit, on other. The above rules are well known in quantitative biology as an allometric and widely used for description of different kind of relations in biological systems of various scale: from organisms to ecosystems. Parameters of above allometric relationships between growing stock, mean height and diameter and stems density per area unit was determine on the base of full stock growth and yield tables for main tree species and after used for experimental calculations. The number of trees per area unit was determined after special treatment of high resolution image made by unmanned flying machine. The growing stock, mean height and diameter determined by suggested method was compared with the data of regular forest inventory. Comparison gives positive result and method may be recommended for further development.


Author(s):  
Dominik Wehrli ◽  
Matthieu Génévriez ◽  
Frédéric Merkt

We present a new method to study doubly charged molecules relying on high-resolution spectroscopy of the singly charged parent cation, and report on the first spectroscopic characterization of a thermodynamically stable diatomic dication, MgAr2+.


FEBS Letters ◽  
2010 ◽  
Vol 584 (12) ◽  
pp. 2539-2547 ◽  
Author(s):  
Yo Sonoda ◽  
Alex Cameron ◽  
Simon Newstead ◽  
Hiroshi Omote ◽  
Yoshinori Moriyama ◽  
...  

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