Helical reconstruction in RELION is increasingly being used to determine the atomic structures of amyloid filaments from electron cryo-microscopy (cryo-EM) images. However, because the energy landscape of amyloid refinements is typically fraught with local optima, amyloid structure determination is often difficult. This paper aims to help RELION users in this process. It discusses aspects of helical reconstruction that are particularly relevant to amyloids, it illustrates the problem of local optima in refinement and how to detect them, and it introduces a new method to calculate 3D initial models from reference-free 2D class averages. By providing starting models that are closer to the global optimum, this method makes amyloid structure determination easier. All methods described are open-source and distributed within RELION-3.1. Their use is illustrated using a publicly available data set on tau filaments from the brain of an individual with Alzheimer's disease.

Fragment-based molecular replacement exploits the use of very accurate yet incomplete search models. In the case of the ARCIMBOLDO programs, consistent phase sets produced from the placement and refinement of fragments with Phaser can be combined in order to increase their signal before proceeding to the step of density modification and autotracing with SHELXE. The program ALIXE compares multiple phase sets, evaluating mean phase differences to determine their common origin, and subsequently produces sets of combined phases that group consistent solutions. In this work, its use on different scenarios of very partial molecular-replacement solutions and its performance after the development of a much-optimized set of algorithms are described. The program is available both standalone and integrated within the ARCIMBOLDO programs. ALIXE has been analysed to identify its rate-limiting steps while exploring the best parameterization to improve its performance and make this software efficient enough to work on modest hardware. The algorithm has been parallelized and redesigned to meet the typical landscape of solutions. Analysis of pairwise correlation between the phase sets has also been explored to test whether this would provide additional insight. ALIXE can be used to exhaustively analyse all partial solutions produced or to complement those already selected for expansion, and also to reduce the number of redundant solutions, which is particularly relevant to the case of coiled coils, or to combine partial solutions from different programs. In each case parallelization and optimization to provide speedup makes its use amenable to typical hardware found in crystallography. ARCIMBOLDO_BORGES and ARCIMBOLDO_SHREDDER now call on ALIXE by default.

Obtaining crystals and solving the phase problem remain major hurdles encountered by bio-crystallographers in their race to obtain new high-quality structures. Both issues can be overcome by the crystallophore, Tb-Xo4, a lanthanide-based molecular complex with unique nucleating and phasing properties. This article presents examples of new crystallization conditions induced by the presence of Tb-Xo4. These new crystalline forms bypass crystal defects often encountered by crystallographers, such as low-resolution diffracting samples or crystals with twinning. Thanks to Tb-Xo4's high phasing power, the structure determination process is greatly facilitated and can be extended to serial crystallography approaches.

Single-crystal elastic constants have been derived by lattice strain measurements using neutron diffraction on polycrystalline Ti-6Al-4V, Ti-6Al-2Sn-4Zr-6Mo and Ti-3Al-8V-6Cr-4Zr-4Mo alloy samples. A variety of model approximations for the grain-to-grain interactions, namely approaches by Voigt, Reuss, Hill, Kroener, de Wit and Matthies, including texture weightings, have been applied and compared. A load-transfer approach for multiphase alloys was also implemented and the results are compared with single-phase data. For the materials under investigation, the results for multiphase alloys agree well with the results for single-phase materials in the corresponding phases. In this respect, all eight elastic constants in the dual-phase Ti-6Al-2Sn-4Zr-6Mo alloy have been derived for the first time.

Bragg intensities can be used to analyse crystal size distributions in a method called FXD-CSD, which is based on the fast measurement of many Bragg spots using two-dimensional detectors. This work presents the Python-based software and its graphical user interface FXD-CSD-GUI. The GUI enables user-friendly data handling and processing and provides both graphical and numerical crystal size distribution results.

The microstructures of six stacking-faulted industrially produced cobalt- and aluminium-bearing nickel layered double hydroxide (LDH) samples that are used as precursors for Li(Ni1−x−yCoxAly)O2 battery materials were investigated. Shifts from the brucite-type (AγB)□(AγB)□ stacking pattern to the CdCl2-type (AγB)□(CβA)□(BαC)□ and the CrOOH-type (BγA)□(AβC)□(CαB)□ stacking order, as well as random intercalation of water molecules and carbonate ions, were found to be the main features of the microstructures. A recursive routine for generating and averaging supercells of stacking-faulted layered substances implemented in the TOPAS software was used to calculate diffraction patterns of the LDH phases as a function of the degree of faulting and to refine them against the measured diffraction data. The microstructures of the precursor materials were described by a model containing three parameters: transition probabilities for generating CdCl2-type and CrOOH-type faults and a transition probability for the random intercalation of water/carbonate layers. Automated series of simulations and refinements were performed, in which the transition probabilities were modified incrementally and thus the microstructures optimized by a grid search. All samples were found to exhibit the same fraction of CdCl2-type and CrOOH-type stacking faults, which indicates that they have identical Ni, Co and Al contents. Different degrees of interstratification faulting were determined, which could be correlated to different heights of intercalation-water-related mass-loss steps in the thermal analyses.

The unique nucleating and phasing capabilities of the crystallophore, Tb-Xo4, are illustrated through challenging cases.

It was an exciting and busy 24 hours at the National Zoo’s Conservation and Research Center in Front Royal, Va., last week as three births took place just hours apart. On the evening of July 9, a clouded leopard cub was born, followed by a Przewalski’s horse foal and a red panda cub.

The post Baby Boom of Endangered Species at Smithsonian’s National Zoo’s Conservation and Research Center appeared first on Smithsonian Insider.

The Smithsonian’s National Air and Space Museum has opened a new Public Observatory that contains a 16-inch, 3,000-pound Boller and Chivens telescope, on loan from the Smithsonian Astrophysical Observatory. Through this powerful telescope, museum visitors can now observe the sun (with a special filter), the moon and the brighter stars and planets, such as Venus, Jupiter and Saturn, during daylight hours. Funding for the project was provided by the National Science Foundation.

The post The Smithsonian’s National Air and Space Museum opens new Public Observatory on the Mall in Washington, D.C. appeared first on Smithsonian Insider.

The National Zoo has been awarded a grant from the U.S. Fish and Wildlife Service to establish a captive population of the Virginia big-eared bat at the National Zoo’s Conservation & Research Center near Front Royal, Va. Only 15,000 Virginia big-eared bats remain living in caves in West Virginia, Virginia, Kentucky and North Carolina, and these are threatened by the white-nose syndrome.

The post In face of crisis, National Zoo to start captive population of Virginia big-eared bats appeared first on Smithsonian Insider.

Dennis W. Kelly has been named director of the Smithsonian’s National Zoo in Washington, D.C., effective Feb. 15, 2010.

The post Dennis Kelly Named Director of the Smithsonian’s National Zoo appeared first on Smithsonian Insider.

For the first time in its history, the National Zoo has bred strawberry dart frogs (Oophaga pumilio), which are known primarily for their vibrant colors and poisonous skin. These frogs also stand out among others because of their dedication to their young as they undergo metamorphosis from egg to tadpole to frog.

The post Strawberry dart frogs bred at National Zoo for first time in Zoo’s history appeared first on Smithsonian Insider.

Staff had been on a pregnancy watch focused on the 3 1/2-year-old clouded leopard Jao Chu (JOW-chew) for four days. Jao Chu gave birth to the first cub at 6:04 p.m. and the second cub at 6:20 p.m.

The post Clouded leopard cubs born at National Zoo’s Front Royal campus on Valentine’s Day appeared first on Smithsonian Insider.

The Stephen L. Wood collection brings the collection of bark beetles held in the Natural History Museum’s Department of Entomology to an impressive 180,000 specimens, making it one of the most extensive collections in world.

The post Eighty-thousand bark beetles enter National Museum of Natural History collections appeared first on Smithsonian Insider.

The research and patience has paid off. The sisters, Nababiep and Shera, have spent short periods of time with the male, Luke, individually and simultaneously. This happened only after they each had spent more than a year sniffing Luke through a mesh door (called a “howdy door”).

The post Patience and research may bring lion cubs to the National Zoo appeared first on Smithsonian Insider.

Based on current hormone analyses, and not having seen a fetus during the ultrasound exams, Zoo researchers have determined that Mei Xiang experienced a pseudopregnancy.

The post National Zoo’s giant panda Mei Xiang is not pregnant appeared first on Smithsonian Insider.

The Smithsonian’s National Zoo recently acquired Japanese giant salamanders given to the Zoo by the City of Hiroshima Asa Zoological Park. This donation will be the foundation of a new long-term breeding program in the United States and may play an important role in saving amphibians around the globe.

The post Japanese giant salamanders given to the National Zoo by Asa Zoological Park in Hiroshima appeared first on Smithsonian Insider.

Kiwis come to National Zoo. The Smithsonian’s National Zoo will be using a new kiwi pair donated by the New Zealand Embassy to establish a breeding science center. […]

The post New Zealand Embassy donates kiwi pair to National Zoo Breeding Science Center appeared first on Smithsonian Insider.

The anemones—both of which are commonly called Tealia red anemones under the species of Urticina—spawned in late April and early May, just days apart. Henley collected the eggs and sperm from the more than 2,000-gallon tank and put them together in smaller tanks to increase the chances of fertilization. After fertilization, the larvae settled and metamorphosed into a polyp.

The post National Zoo scientists successfully grow two species of anemones in aquarium tanks appeared first on Smithsonian Insider.

The Smithsonian’s National Zoo celebrated the completion of Phase I of Elephant Trails, an innovative and expanded home for Asian elephants, on Sept. 2. Phase […]

The post Elephant Trails exhibition opens at National Zoological Park appeared first on Smithsonian Insider.

On Aug, 31, the Smithsonian’s National Zoo welcomed this year’s second litter of African lion (Panthera leo) cubs. Five-year-old Shera (shown at right) gave birth […]

The post Shera, a 5-year-old lioness at the National Zoological Park appeared first on Smithsonian Insider.

The Smithsonian’s National Zoo recently welcomed two litters of lion cubs over a three-week period – bringing the total number of cubs to seven during the summer of 2010.

The post Seven lion cubs born recently at the National Zoo appeared first on Smithsonian Insider.

This circa 1910 Yup'ik mask from Good News Bay, Alaska--made of driftwood, baleen, feathers, paint and cotton twine--is part of "Infinity of Nations: Art and History in the Collections of the National Museum of the American Indian," an exhibition at the National Museum of the American Indian, opening Saturday, Oct. 23.

The post Yup’ik mask in “Infinity of Nations” exhibition at the American Indian Museum appeared first on Smithsonian Insider.

Although the La Loma tree frog, Hyloscirtus colymba, is notoriously difficult to care for in captivity, the Panama Amphibian Rescue and Conservation Project is the first to successfully breed this species.

The post National Zoo and partners first to breed critically endangered tree frog appeared first on Smithsonian Insider.

The Scarlet Knight, as the glider is called, made nautical history as the first submersible glider to successfully cross the Atlantic Ocean.

The post Rutgers glider added to the collections of the National Museum of Natural History appeared first on Smithsonian Insider.

This 'hot Jupiter', now named Qatar-1b, adds to the growing list of alien planets orbiting distant stars, or exoplanets. Its discovery demonstrates the power of science to cross political boundaries and increase ties between nations.

The post International team discovers alien planet that’s Jupiter-sized appeared first on Smithsonian Insider.

At the Smithsonian Conservation Biology Institute in Front Royal, Va., the seven-month-old white-naped cranes Cal and Bill are thriving.

The post White-naped crane chicks thriving at National Zoo appeared first on Smithsonian Insider.

A. sediba was discovered in 2008 in the Malapa Cave at the Cradle of Humankind World Heritage Site located outside Johannesburg.

The post Skeletal casts of early hominin ancestor from Africa donated to National Museum of Natural History appeared first on Smithsonian Insider.

For more than three decades JoGayle Howard dedicated her life and work to reproducing endangered species.

The post JoGayle Howard, National Zoological Park pioneer in reproductive biology, dies appeared first on Smithsonian Insider.

On the heels of spring’s arrival, a wattled crane (Bugeranus carunculatus) chick hatched at the Smithsonian’s National Zoo March 20, the third of its kind […]

The post Wattled crane chick hatches at the National Zoo appeared first on Smithsonian Insider.

Discovery, the longest-serving orbiter in the space shuttle fleet, will be accepted into the Smithsonian’s National Air and Space Museum collection. The space shuttle has been the icon for American spaceflight for a generation, and Discovery has flown every type of mission during its 27-year career.

The post Space shuttle Discovery to be added to National Air and Space Museum collection appeared first on Smithsonian Insider.

The predictability and scale of seasonal changes in a habitat help determine the distance migratory species move and whether the animals always travel together to the same place or independently to different locations.

The post Changes in vegetation determine how animals migrate, scientists find in new National Zoo study appeared first on Smithsonian Insider.

A study published in the journal Global Change Biology finds that while fertilizer has been the dominant source of nitrogen pollution in Caribbean coastal ecosystems for the past 50 years, such pollution is on the decline, thanks in part to the introduction of more advanced, environmentally responsible agricultural practices during the last decade.

The post National Museum of Natural History’s coral collection used in Caribbean agricultural and sewage pollution study appeared first on Smithsonian Insider.

Scientists at the Smithsonian’s National Zoo detected a secondary rise in urinary progesterone levels in the Zoo’s female giant panda Mei Xiang (may-SHONG). This hormone rise indicates that it should be 40 to 50 days before Mei Xiang either gives birth to a cub or comes to the end of a pseudopregnancy, or false pregnancy, which is common in giant pandas.

The post Hormone tests show Mei Xiang, the National Zoo’s female giant panda, may be pregnant appeared first on Smithsonian Insider.

The National Zoo’s great cat program recently expanded with the arrival of two-and-a-half-year-old female Sumatran tiger, Damai, who is now out of quarantine and spending time outside in her exhibit where visitors can see her.

The post Damai, a two-and-a-half-year-old female Sumatran tiger, makes her debut at the National Zoo appeared first on Smithsonian Insider.

Kandula, an 8-year-old male Asian elephant at the Smithsonian’s National Zoo, recently demonstrated to researchers for the first time that elephants are capable of insightful problem solving.

The post A first: National Zoo elephant shows insightful problem solving appeared first on Smithsonian Insider.

The fossil represents the youngest nodosaur ever discovered, and the only known specimen of a new genus and species of dinosaur that lived approximately 110 million years ago during the Early Cretaceous Era.

The post New dinosaur species named from hatchling fossil donated to National Museum of Natural History appeared first on Smithsonian Insider.

Thunder, lightning and strong winds greeted the National Zoo’s two female red panda cubs when they were born June 17, and that stormy night has […]

The post National Zoo’s red pandas named “Pili” and “Damini” for stormy night appeared first on Smithsonian Insider.

Suzan Murray, chief veterinary medical officer at the Smithsonian’s National Zoological Park, recently returned from Hanoi, where she led a team of scientists training pathologists from Laos, Cambodia and Vietnam to better sample, recognize and detect wildlife diseases in hopes of preventing emerging pandemic disease.

The post Q&A: National Zoo veterinarian Suzan Murray is working to halt pandemic disease in hotspots around the world appeared first on Smithsonian Insider.

A member of one of the world’s most endangered species—the brown kiwi (Apteryx mantelli)—successfully hatched at the Smithsonian’s National Zoo’s Bird House Dec. 11 at 10:25 a.m. The egg was laid Oct. 1 and keepers began looking for signs of the chick hatching starting in early December. The chick is the sixth kiwi successfully hatched at the National Zoo.

The post Kiwi chick hatching a success at the National Zoo appeared first on Smithsonian Insider.

A baby boom is underway at the Smithsonian’s National Zoo. Two Guam rail (Gallirallus owstoni) chicks hatched March 3 and 4; they join six others in the Zoo’s collection—three of which live at the Smithsonian Conservation Biology Institute in Front Royal, Va.

The post Extremely rare Guam rails hatch at the Smithsonian’s National Zoo appeared first on Smithsonian Insider.

The same device used to detect early warning signs of heart disease in humans will now benefit two male sub-adult gorillas at the Smithsonian’s National Zoo.

The post Heart disease study to benefit lowland gorillas at the National Zoo appeared first on Smithsonian Insider.

The young primate seems bright, alert, and increases its activity and independence day by day.

The post Howler monkey born at National Zoo appeared first on Smithsonian Insider.

The National Museum of Natural History will construct a new dinosaur exhibition hall made possible by a $35 million donation from David H. Koch, executive vice president of Koch Industries and philanthropist.

The post $35-million donation will build new dinosaur hall at National Museum of Natural History appeared first on Smithsonian Insider.

Scientists have discovered several specimens of tiny insects covered with pollen grains in two pieces of amber, revealing the first record of pollen transport and social behavior in this group of animals.

The post First ever record of insect pollination captured in 100 million-year-old amber appeared first on Smithsonian Insider.

By attaching tiny radio transmitters to more than 400 seeds, Patrick Jansen, scientist at the Smithsonian Tropical Research Institute and Wageningen University, and his colleagues found that 85 percent of the seeds were buried in caches by agoutis, common, house cat-sized rodents in tropical lowlands.

The post Thieving rodents hiding seeds drives continual rejuvination of tropical forests appeared first on Smithsonian Insider.

Two Cuban crocodiles were born at the Smithsonian’s National Zoo on July 6 and 14 and they are among the most genetically valuable in the […]

The post Two rare Cuban crocodiles born at the National Zoo appeared first on Smithsonian Insider.

Mei Xiang (may-SHONG), the National Zoo’s female giant panda, gave birth to a cub Sunday, Sept. 16, at 10:46 p.m.

The post Panda cub born at National Zoo to Mei Xiang appeared first on Smithsonian Insider.

The Smithsonian’s National Zoo community mourns the loss of the giant panda cub born Sunday, Sept. 16.

The post New panda cub dies at National Zoo appeared first on Smithsonian Insider.

The goal of the project—the Smithsonian’s Tennenbaum Marine Observatories—is to monitor the ocean’s coastal ecosystems over a long period of time.

The post Smithsonian launches Global Marine Biodiversity Project with $10 million donation appeared first on Smithsonian Insider.