From rescripting their day to including an afternoon nap, to learning a new skill, Delhiites are finding ways to make the most of a trying time

Should a 1979 law on migrant workers be retained or must it be subsumed under a proposed labour code?

The trio were among thousands of migrant workers who have set out on foot for their home states from Maharashtra in the last few weeks amid lockdown on account for coronavirus.

Most entering Madhya Pradesh from Maharashtra are headed to Uttar Pradesh.

The police arrested a man absconded from the Government Medical College Hospital, Alappuzha, and was trying to cross into Tamil Nadu through the distr

Globally, as of 9 May 2020, there have been 3,862,676 confirmed cases, including 265,961 deaths, reported to WHO.

Universities in Bengal would hold undergraduate and postgraduate end-semester examinations within a month of the lockdown being lifted, education minister Partha Chatterjee said on Saturday after a discussion with vice-chancellors of state varsities.

Baloda Bazaar-Bhatapara district has come up with a great idea to contribute in the fight against the coronavirus pandemic. The amount of financial penalties recovered from the lockdown violators will be used for procuring safety kits for the doctors and health workers.

A cop performed the final rites of a stranger who died of a cardiac stroke. The family members of Pramod Khare (42), a bachelor, are settled in Delhi, Kolkata, Dubai and South Africa could not make it due to the lockdown. The funeral was live-streamed for them.

However, the company says it does not have the urgency to begin production in the factory, but bring back the rhythm of the manufacturing unit.

While many companies are sharing documents digitally, some have also opened their servers to auditors to access the data they require

On Saturday, Samsung India Electronics, counted among the largest in the space, ushered in over 1,000 workers at its facility in Sector 81, Noida

Another 279 patients in Chennai, taking the tally to 3,330

On April 1, four years back, piqued by the incessant jokes in the village at his expense, Bandu Barve decided he’d had enough. It was time for him to

The makers of Yash's movie 'KGF' have planned to sue a local Telugu channel for broadcasting the movie illegally

To curb the increasing number of corona positive cases and the spread of virus infection, the Gandhinagar Collector on Saturday said there would be a total lockdown in Gandhinagar city and Kalol municipality on the lines of Ahmedabad and Surat.

Amid prevalent chaos and uncertainty over access to the essential services and commodities during the lockdown, we bring you the latest updates from your city.

We may be witnessing a slow erosion of the democratic republic and the emergence of the police State, warns Sunanda K Datta-Ray.

Amid prevalent chaos and uncertainty over access to the essential services and commodities during the lockdown, we bring you the latest updates from your city.

We may be witnessing a slow erosion of the democratic republic and the emergence of the police State, warns Sunanda K Datta-Ray.

Rietveld/MEM analysis applied to synchrotron powder X-ray diffraction data of dehydrated CHA zeolites with catalytically active Cu2+ reveals Cu2+ in both the six- and eight-membered rings in the CHA framework, providing the first complete structural model that accounts for all Cu2+. Density functional theory calculations are used to corroborate the experimental structure and to discuss the Cu2+ coordination in terms of the Al distribution in the framework.

Two earthquakes felt by residents in Lochaber  Press and Journal

Coronavirus shock: Pandemic lockdowns have changed how the planet SOUNDS and vibrates  Express.co.uk

Coronavirus: Is lockdown an opportunity for scientific research?  sciencefocus.com

Lockdown has cut Britain's vibrations, seismologists find  The Guardian

Explained: How coronavirus lockdown reduced Earth’s seismic noise levels  The Indian Express

Why the UK's streets have turned silent during coronavirus lockdown  Express.co.uk

European lockdown a boon to seismologists checking Earth's vibrations  E&T Magazine

This article presents an overview of the development of two basic software libraries for image manipulation and data visualization in cryo-EM: emcore and emvis.

The redetermination of the crystal structure of barium oxidotellurate(IV) monohydrate allowed the localization of the hydrogen atoms that were not determined in the previous study [Nielsen, Hazell & Rasmussen (1971). Acta Chem. Scand. 25, 3037–3042], thus making an unambiguous assignment of the hydrogen-bonding scheme possible. The crystal structure shows a layered arrangement parallel to (001), consisting of edge-sharing [BaO6(H2O)] polyhedra and flanked by isolated [TeO3] trigonal pyramids on the top and bottom. O—H⋯O hydrogen bonds of medium strength link adjacent layers along [001].

The title compound (systematic name: bis­{2-[4-(acet­yloxy)-1H-indol-3-yl]ethan-1-aminium} but-2-enedioate), 2C14H19N2O2+·C4H2O42−, has a single protonated psilacetin cation and one half of a fumarate dianion in the asymmetric unit. There are N—H⋯O hydrogen bonds between the ammonium H atoms and the fumarate O atoms, as well as N—H⋯O hydrogen bonds between the indole H atoms and the fumarate O atoms. The hydrogen bonds hold the ions together in infinite one-dimensional chains along [111].

The solid-state structures of the salts of two substituted tryptamines, namely N-isopropyl-N-methyl­tryptaminium (MiPT) fumarate {systematic name: [2-(1H-indol-3-yl)eth­yl](meth­yl)propan-2-yl­aza­nium 3-carb­oxy­prop-2-enoate}, C14H21N2+·C4H3O4−, and 4-hy­droxy-N-isopropyl-N-methyl­tryptaminium (4-HO-MiPT) fumarate monohydrate {systematic name: [2-(4-hy­droxy-1H-indol-3-yl)eth­yl](meth­yl)propan-2-yl­aza­nium 3-carb­oxy­prop-2-enoate monohydrate}, C14H21N2O+·C4H3O4−·H2O, are reported. Both salts possess a proton­ated tryptammonium cation and a 3-carb­oxy­acrylate (hydrogen fumarate) anion in the asymmetric unit; the 4-HO-MiPT structure also contains a water mol­ecule of crystallization. Both cations feature disorder of the side chain over two orientations, in a 0.630 (3):0.370 (3) ratio for MiPT and a 0.775 (5):0.225 (5) ratio for 4-HO-MiPT. In both extended structures, N—H⋯O and O—H⋯O hydrogen bonds generate infinite two-dimensional networks.

The solid-state structures of the naturally occurring psychoactive tryptamine norpsilocin {4-hy­droxy-N-methyl­tryptamine (4-HO-NMT); systematic name: 3-[2-(methyl­amino)­eth­yl]-1H-indol-4-ol}, C11H14N2O, and its fumarate salt (4-hy­droxy-N-methyl­tryptammonium fumarate; systematic name: bis­{[2-(4-hy­droxy-1H-indol-3-yl)eth­yl]methyl­aza­nium} but-2-enedioate), C11H15N2O+·0.5C4H2O42−, are reported. The freebase of 4-HO-NMT has a single mol­ecule in the asymmetric unit joined together by N—H⋯O and O—H⋯O hydrogen bonds in a two-dimensional network parallel to the (100) plane. The ethyl­amine arm of the tryptamine is modeled as a two-component disorder with a 0.895 (3) to 0.105 (3) occupancy ratio. The fumarate salt of 4-HO-NMT crystallizes with a tryptammonium cation and one half of a fumarate dianion in the asymmetric unit. The ions are joined together by N—H⋯O and O—H⋯O hydrogen bonds to form a three-dimensional framework, as well as π–π stacking between the six-membered rings of inversion-related indoles (symmetry operation: 2 − x, 1 − y, 2 – z).

In this article, a method is presented to estimate a new local quality measure for 3D cryoEM maps that adopts the form of a `local resolution' type of information. The algorithm (DeepRes) is based on deep-learning 3D feature detection. DeepRes is fully automatic and parameter-free, and avoids the issues of most current methods, such as their insensitivity to enhancements owing to B-factor sharpening (unless the 3D mask is changed), among others, which is an issue that has been virtually neglected in the cryoEM field until now. In this way, DeepRes can be applied to any map, detecting subtle changes in local quality after applying enhancement processes such as isotropic filters or substantially more complex procedures, such as model-based local sharpening, non-model-based methods or denoising, that may be very difficult to follow using current methods. It performs as a human observer expects. The comparison with traditional local resolution indicators is also addressed.

TatD has been thoroughly investigated as a DNA-repair enzyme and an apoptotic nuclease, and still-unknown TatD-related DNases are considered to play crucial cellular roles. However, studies of TatD from Gram-positive bacteria have been hindered by an absence of atomic detail and the resulting inability to determine function from structure. In this study, an X-ray crystal structure of SAV0491, which is the TatD enzyme from the Gram-positive bacterium Staphylococcus aureus (SaTatD), is reported at a high resolution of 1.85 Å with a detailed atomic description. Although SaTatD has the common TIM-barrel fold shared by most TatD-related homologs, and PDB entry 2gzx shares 100% sequence identity with SAV0491, the crystal structure of SaTatD revealed a unique binding mode of two phosphates interacting with two Ni2+ ions. Through a functional study, it was verified that SaTatD has Mg2+-dependent nuclease activity as a DNase and an RNase. In addition, structural comparison with TatD homologs and the identification of key residues contributing to the binding mode of Ni2+ ions and phosphates allowed mutational studies to be performed that revealed the catalytic mechanism of SaTatD. Among the key residues composing the active site, the acidic residues Glu92 and Glu202 had a critical impact on catalysis by SaTatD. Furthermore, based on the binding mode of the two phosphates and structural insights, a putative DNA-binding mode of SaTatD was proposed using in silico docking. Overall, these findings may serve as a good basis for understanding the relationship between the structure and function of TatD proteins from Gram-positive bacteria and may provide critical insights into the DNA-binding mode of SaTatD.

Current software tools for the automated building of models for macro­molecular X-ray crystal structures are capable of assembling high-quality models for ordered macromolecule and small-molecule scattering components with minimal or no user supervision. Many of these tools also incorporate robust functionality for modelling the ordered water molecules that are found in nearly all macromolecular crystal structures. However, no current tools focus on differentiating these ubiquitous water molecules from other frequently occurring multi-atom solvent species, such as sulfate, or the automated building of models for such species. PeakProbe has been developed specifically to address the need for such a tool. PeakProbe predicts likely solvent models for a given point (termed a `peak') in a structure based on analysis (`probing') of its local electron density and chemical environment. PeakProbe maps a total of 19 resolution-dependent features associated with electron density and two associated with the local chemical environment to a two-dimensional score space that is independent of resolution. Peaks are classified based on the relative frequencies with which four different classes of solvent (including water) are observed within a given region of this score space as determined by large-scale sampling of solvent models in the Protein Data Bank. Designed to classify peaks generated from difference density maxima, PeakProbe also incorporates functionality for identifying peaks associated with model errors or clusters of peaks likely to correspond to multi-atom solvent, and for the validation of existing solvent models using solvent-omit electron-density maps. When tasked with classifying peaks into one of four distinct solvent classes, PeakProbe achieves greater than 99% accuracy for both peaks derived directly from the atomic coordinates of existing solvent models and those based on difference density maxima. While the program is still under development, a fully functional version is publicly available. PeakProbe makes extensive use of cctbx libraries, and requires a PHENIX licence and an up-to-date phenix.python environment for execution.

The performance of automated protein model building usually decreases with resolution, mainly owing to the lower information content of the experimental data. This calls for a more elaborate use of the available structural information about macromolecules. Here, a new method is presented that uses structural homologues to improve the quality of protein models automatically constructed using ARP/wARP. The method uses local structural similarity between deposited models and the model being built, and results in longer main-chain fragments that in turn can be more reliably docked to the protein sequence. The application of the homology-based model extension method to the example of a CFA synthase at 2.7 Å resolution resulted in a more complete model with almost all of the residues correctly built and docked to the sequence. The method was also evaluated on 1493 molecular-replacement solutions at a resolution of 4.0 Å and better that were submitted to the ARP/wARP web service for model building. A significant improvement in the completeness and sequence coverage of the built models has been observed.

Model quality assessment programs estimate the quality of protein models and can be used to estimate local error in protein models. ProQ3D is the most recent and most accurate version of our software. Here, it is demonstrated that it is possible to use local error estimates to substantially increase the quality of the models for molecular replacement (MR). Adjusting the B factors using ProQ3D improved the log-likelihood gain (LLG) score by over 50% on average, resulting in significantly more successful models in MR compared with not using error estimates. On a data set of 431 homology models to address difficult MR targets, models with error estimates from ProQ3D received an LLG of >50 for almost half of the models 209/431 (48.5%), compared with 175/431 (40.6%) for the previous version, ProQ2, and only 74/431 (17.2%) for models with no error estimates, clearly demonstrating the added value of using error estimates to enable MR for more targets. ProQ3D is available from http://proq3.bioinfo.se/ both as a server and as a standalone download.

Image-processing software has always been an integral part of structure determination by cryogenic electron microscopy (cryo-EM). Recent advances in hardware and software are recognized as one of the key factors in the so-called cryo-EM resolution revolution. Increasing computational power has opened many possibilities to consider more demanding algorithms, which in turn allow more complex biological problems to be tackled. Moreover, data processing has become more accessible to many experimental groups, with computations that used to last for many days at supercomputing facilities now being performed in hours on personal workstations. All of these advances, together with the rapid expansion of the community, continue to pose challenges and new demands on the software-development side. In this article, the development of emcore and emvis, two basic software libraries for image manipulation and data visualization in cryo-EM, is presented. The main goal is to provide basic functionality organized in modular components that other developers can reuse to implement new algorithms or build graphical applications. An additional aim is to showcase the importance of following established practices in software engineering, with the hope that this could be a first step towards a more standardized way of developing and distributing software in the field.

A scanning soft X-ray spectromicroscope was recently developed based mainly on the photon-in/photon-out measurement scheme for the investigation of local electronic structures on the surfaces and interfaces of advanced materials under conditions ranging from low vacuum to helium atmosphere. The apparatus was installed at the soft X-ray beamline (BL17SU) at SPring-8. The characteristic features of the apparatus are described in detail. The feasibility of this spectromicroscope was demonstrated using soft X-ray undulator radiation. Here, based on these results, element-specific two-dimensional mapping and micro-XAFS (X-ray absorption fine structure) measurements are reported, as well as the observation of magnetic domain structures from using a reference sample of permalloy micro-dot patterns fabricated on a silicon substrate, with modest spatial resolution (e.g. ∼500 nm). Then, the X-ray radiation dose for Nafion® near the fluorine K-edge is discussed as a typical example of material that is not radiation hardened against a focused X-ray beam, for near future experiments.