Phaser.MRage: automated molecular replacement.

Phaser.MRage is a molecular-replacement automation framework that implements a full model-generation workflow and provides several layers of model exploration to the user. It is designed to handle a large number of models and can distribute calculations efficiently onto parallel hardware. In addition, phaser.MRage can identify correct solutions and use this information to accelerate the search. Firstly, it can quickly score all alternative models of a component once a correct solution has been found. Secondly, it can perform extensive analysis of identified solutions to find protein assemblies and can employ assembled models for subsequent searches. Thirdly, it is able to use a priori assembly information (derived from, for example, homologues) to speculatively place and score molecules, thereby customizing the search procedure to a certain class of protein molecule (for example, antibodies) and incorporating additional biological information into molecular replacement

Cultivating equality: delivering just and sustainable food systems in a changing climate

T oday, the world faces a greater challenge perhaps than ever before: tackling hunger and malnutrition in the face of climate change and increasing natural resource scarcity. Civil society, governments, researchers, donors, and the private sector are simultaneously debating and collaborating to find solutions. But the dialogue is over-emphasizing food production. Improving yields is important, particularly in places where there is not enough food or where food producers live in poverty. But simply producing more is not enough to tackle hunger. Furthermore, acknowledging that lack of food is not the sole cause of hunger is important. Inequality shapes who has access to food and the resources to grow it and buy it. It governs who eats first and who eats worst. Inequality determines who can adapt more readily to a changing climate. Hunger and poverty are not an accident – they are the result of social and economic injustice and inequality at all levels, from household to global. The reality of inequality is no truer for anyone than it is for women – half the world’s population, with far less than their fair share of the world’s resources. If we are to achieve the new Sustainable Development Goal of ending hunger by 2030, we must address the underlying inequalities in food systems. In a changing climate, agriculture and food systems must be sustainable and productive – but our efforts cannot end there. They must be profitable for those for whom it is a livelihood; they must be equitable, to facilitate a level playing field in the market, to secure rights to resources for food producers, and to ensure access to nutritious food for all; they must be resilient to build the capacity of populations vulnerable to economic shocks, political instability, and increasing, climate-induced natural hazards to recover and still lift themselves out of poverty

Automated identification of elemental ions in macromolecular crystal structures.

Many macromolecular model-building and refinement programs can automatically place solvent atoms in electron density at moderate-to-high resolution. This process frequently builds water molecules in place of elemental ions, the identification of which must be performed manually. The solvent-picking algorithms in phenix.refine have been extended to build common ions based on an analysis of the chemical environment as well as physical properties such as occupancy, B factor and anomalous scattering. The method is most effective for heavier elements such as calcium and zinc, for which a majority of sites can be placed with few false positives in a diverse test set of structures. At atomic resolution, it is observed that it can also be possible to identify tightly bound sodium and magnesium ions. A number of challenges that contribute to the difficulty of completely automating the process of structure completion are discussed

Revisiting the transatlantic divergence over GMOs: Toward a cultural-political analysis

'Revisiting the transatlantic divergence over GMOs: towards a cultural-political analysis' applies a constructivist perspective to the persistent transatlantic divergence over the regulation of GM foods and crops. Political economy and institutionalism have so far dominated the literature. Notwithstanding their crucial insights, this article argues that to achieve a better understanding of the nature and depth of transatlantic regulatory divergence, one should also study prevalent cultural values and identity-related public concerns regarding food and agriculture. These factors can be identified in public opinion trends and have fuelled Europeans' resistance, while contributing to relative regulatory stability in the US. By conceptualizing cultural contexts as catalytic structures, the article also differs from more explicitly discursive accounts of political mobilization. The cultural politics of agricultural biotechnology (agbiotech) relies both on pre-existing values and identities, on the one hand, and on the strategies (and material or other power resources) of political agents

Macromolecular X-ray structure determination using weak, single-wavelength anomalous data.

We describe a likelihood-based method for determining the substructure of anomalously scattering atoms in macromolecular crystals that allows successful structure determination by single-wavelength anomalous diffraction (SAD) X-ray analysis with weak anomalous signal. With the use of partial models and electron density maps in searches for anomalously scattering atoms, testing of alternative values of parameters and parallelized automated model-building, this method has the potential to extend the applicability of the SAD method in challenging cases

Concert recording 2015-11-30

[Track 01]. Danza brasiliera / Jorge Morel -- [Track 02]. Sunburst / Andrew York -- [Track 03]. Ladron broma / Chase Chamberlin -- [Track 04]. Etudes 1, 2, & 3 / Matteo Carcassi -- [Track 05]. Invitation / Bronislaw Kaper -- [Track 06]. Ami etude / Ferdinando Carulli -- Variation (slur study) / Mauro Giuliani -- [Track 07]. Tango / Isaac Albeniz -- [Track 08]. Invention no. 8 / J.S. Bach -- [Track 09]. Don\u27t get around much anymore / Duke Ellington -- [Track 10]. Turnaround / Omette Coleman -- [Track 11]. Julia Florida / Augustin Barrios -- [Track 12]. Estudio 9 / Fernando Sor -- [Track 13]. Billie\u27s bounce / C. Parker -- [Track 14]. Emily / J. Mandel -- [Track 15]. Lagrima, Adelita / F. Tarrega

Automating crystallographic structure solution and refinement of protein-ligand complexes.

High-throughput drug-discovery and mechanistic studies often require the determination of multiple related crystal structures that only differ in the bound ligands, point mutations in the protein sequence and minor conformational changes. If performed manually, solution and refinement requires extensive repetition of the same tasks for each structure. To accelerate this process and minimize manual effort, a pipeline encompassing all stages of ligand building and refinement, starting from integrated and scaled diffraction intensities, has been implemented in Phenix. The resulting system is able to successfully solve and refine large collections of structures in parallel without extensive user intervention prior to the final stages of model completion and validation

Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution

Recent developments in PHENIX are reported that allow the use of reference-model torsion restraints, secondary-structure hydrogen-bond restraints and Ramachandran restraints for improved macromolecular refinement in phenix.refine at low resolution

Mothers of Soldiers in Wartime: A National News Narrative

National news media represent mothers of US combat soldiers in the Iraq War as archetypal good mothers, that is, mothers who continue their maternal work even after their children are deployed. However, not all mothers are depicted as the archetypal patriotic mother, i.e., a good mother who is also stoic and silent about the war and her child\u27s role in it. Mothers of soldiers are portrayed as good mothers who sometimes also voice their attitudes about the war effort. The maternal attitudes ranged from complete support for the war to opposition to the war but support for the soldiers. The findings suggest a picture of wartime motherhood that is more nuanced than the historical image of the patriotic mother suggests