Using the CCP4 software

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CCP4 provides software for every stage of the crystallographic structure solution process, from processing X-ray diffraction images through to producing images and movies for presentations and publications. Documentation has been provided for each of these, and is organised in the same order as the structure solution process.

Contents

[edit] General CCP4 documentation

  • CCP4 installation: The CCP4 software may be installed using pre-compiled binary packages for a variety of platforms, or by compiling directly from source.
  • How to use the CCP4 graphical user interface: The CCP4 graphical user interface (CCP4i) is the normal method of running CCP4 software.
  • How to run CCP4 programs from the command line: This is only usually necessary for very specialist problems, although it may also help to understand what is happening behind the graphical user interface.
  • CCP4 file formats: CCP4 has special formats for reflection data and for electron density maps. If you have data in another format, this can be converted to the equivalent CCP4 format. For atomic models, the standard PDB format is used.

[edit] Documentation on the steps of the structure solution process

The structure solution process may be divided into the following steps, starting from the diffraction images obtained from the experiment.

  • Data processing with CCP4:
    The first step is to process the diffraction images to obtain a list of X-ray diffraction intensities, indexed by [h,k,l]. This initial list of diffraction intensities is analysed to determine the possible spacegroup symmetries, and any other features such as twinning. The list of reflections is reduced to a unique list of merged reflections for the appropriate spacegroup. The spacegroup may need to be reconsidered later. A final step is to calculate the structure amplitude |F| from the intensity (|F| ≈ √I) and examine the intensity distributions for pathologies such as twinning.
  • Phasing in CCP4:
    Having obtained the spacegroup and merged the reflections accordingly, the next step is to determine phases, from which an electron density map may be calculated. These are usually obtained in one of two ways:
    • Molecular replacement with CCP4:
      Molecular replacement allows phases to be determined by fitting a model from a known, homologous structure to the observed structure factors of the unknown structure.
    • Experimental phasing with CCP4:
      Experimental phasing is the determination of phased from multiple structure factor observations, for example, the anomalous differences between Bijvoet pairs, or structure factor magnitudes from crystals with slightly differing contents.
  • Phase improvement with CCP4:
    Phase improvement exploits our chemical knowledge about what a good electron density map should look like to improve initial phase estimates, in order to obtain a better electron density map.
  • Model building with CCP4:
    Model building involves the fitting of an atomic model into the electron density map. This may be done automatically, or using graphical tools.
  • Refinement with CCP4:
    Model refinement involves the adjustment of the parameters of the atomic model (i.e. the positions and other properties of the atoms) in order to better explain the observed structure factors. This leads to a more accurate model.

[edit] Supporting tools

[edit] Automated pipelines for structure solution

[edit] Related packages

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