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  • Gemmi 0. 7. 6-dev documentation
    Gemmi is a library, accompanied by a set of programs, developed primarily for use in structural biology, and in particular in macromolecular crystallography (MX)
  • Reciprocal space - Gemmi 0. 7. 6-dev documentation
    Reciprocal space ¶ This section is primarily for people working with crystallographic data Gemmi supports four reflection file formats: MTZ files – the most popular format in macromolecular crystallography, structure factor mmCIF files – used for data archiving in the Protein Data Bank, XDS ASCII format – data from processing images with XDS, and small molecule structure factor CIF
  • Installation - Gemmi 0. 7. 6-dev documentation
    Installation ¶ C++ library ¶ Gemmi was a header-only library until ver 0 6 0 Some parts, such as CIF syntax parsing, remain header-only If you happen to use only these parts, just ensure that Gemmi’s include directory is in your project’s include path For example:
  • Structure analysis - Gemmi 0. 7. 6-dev documentation
    Structure analysis ¶ Neighbor search ¶ Fixed-radius near neighbor search is usually implemented using the cell lists method, also known as binning, bucketing, or the cell technique (or cubing – as it was called in an article from 1966) The method is simple The unit cell (or the area where the molecules are located) is divided into small cells The size of these cells depends on the
  • Chemistry - Gemmi 0. 7. 6-dev documentation
    Chemistry ¶ This section covers: working with small molecule models in structural chemistry and working with chemical components in structural biology (chemical components describe parts of macromolecular models) Elements ¶ When working with molecular structures, it is good to have basic data from the periodic table at hand
  • Grids and maps - Gemmi 0. 7. 5 documentation
    Grids and maps ¶ Volumetric grid ¶ Introduction ¶ Macromolecular models are often accompanied by 3D data on an evenly spaced, rectangular grid (but note that the spacing in different directions may differ) The data may represent electron density, a mask of the protein area, or any other scalar data In Gemmi such a data is stored in a class called Grid Actually, it is a set of classes for
  • Math and unit cell - Gemmi 0. 7. 6-dev documentation
    Math and unit cell ¶ Vectors and coordinates ¶ Coordinates are represented by two classes: Position for coordinates in Angstroms (orthogonal coordinates), Fractional for coordinates relative to the unit cell (fractional coordinates) Both Position and Fractional are derived from Vec3, which has three numeric properties: x, y and z





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