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Crystallographic Analysis Tools

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  • Display crystallographic cell . The crystal structure of a protein is often discussed in terms of its unit cell. The unit cell is a box containing one or more motifs, a spatial arrangement of atoms. The units cells are tiled in three-dimensional space to describe the crystal. The unit cell is given by its lattice parameters, the length of the cell edges and the angles between them, while the positions of the atoms inside the unit cell are described by the set of atomic positions measured from a lattice point.
  • Apply crystallographic symmetry. Molecular objects and 3D density maps may contain information about crystallographic symmetry. It consists of the following parameters: 1. Crystallographic group eg. P2121 that determine N (depends on a group) transformations for the atoms in the asymetric unit. 2. Crystallographic cell parameters A, B, C, Alpha, Beta and Gamma To generate the coordinates within one cell one needs to apply N transformations and then to generate neigboring cells the content of one cell needs to be translated in space according to the cell position.
  • Apply biological symmetry to build a bio-molecule (e.g. the whole virus particle). It is very useful to know how a protein from the PDB may look in a biological environment. The PDB entries solved by X-ray crystallography and deposited in the PDB contain the information about the crystal structure rather than the biologically relevant structure. For example, for a viral capsid only one instance of capsid protein complex will be deposited and only one or two molecules of haemoglobin that is a tetramer in solution maybe deposited. In some other cases the asymetric unit may contain more than one copy of a biologically monomeric protein. ICM reads the biological unit information and has a tool to generate a biological unit. Not every PDB entry has the biological unit information.
  • Load electron density maps directly from the electron density map server in Uppsala Sweden.
  • Contour the whole protein electron density map.
  • Display the original crystallographic cell of an electron density map.
  • Convert Xray density to a grid.

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