Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provid...

The recent rapid development of single-particle electron cryo-microscopy (cryo-EM) now allows structures to be solved by this method at resolutions close to 3 Å. Here, a number of tools to facilitate the interpretation of EM reconstructions with stereochemically reasonable all-atom models are described. The BALBES database has been repurposed as a tool for identifying protein folds from density...

Background: Present study was carried out in north of Iran to investigate the concentration of mercury (Hg) as one of the most toxic metals in tissues of two species of birds. Methods: In this study, 15 birds from coot (Fulica atra) and 18 birds from cormorant (Phalacrocorax carbo) were hunted in Anzali and Gomishan wetlands. Data-analyses carried out using SPSS software version 17 licenced...

Optimal transport (OT) compares probability distributions by computing a meaningful alignment between their samples. CO-optimal (COOT) takes this comparison further inferring an features as well. While approach leads to better alignments and generalizes both OT Gromov-Wasserstein distances, we provide theoretical result showing that it is sensitive outliers are omnipresent in real-world data. T...

G. S. Pegg*, F. R. Giblin, A. R. McTaggart, G. P. Guymer, H. Taylor, K. B. Ireland, R. G. Shivas and S. Perry Department of Agriculture, Fisheries and Forestry, Horticulture and Forestry Science, Agri-Science Queensland, GPO Box 267, Brisbane, Qld 4001; Forest Industries Research Centre, University of the Sunshine Coast, Locked Bag 4, Maroochydore DC, Qld 4558; Queensland Alliance for Agricultu...

Siblings compete for parental care and feeding, while parents must allocate scarce resources to those offspring most likely to survive and reproduce. This could cause offspring to evolve traits that advertise health, and thereby attract parental resources. For example, experimental evidence suggests that bright orange filaments covering the heads of North American coot chicks may have evolved f...

CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics. The map-fitting tools are available as a stand-alone package, distributed as 'Coot'.