A collection of programs, associated data and software libraries which can be used for macromolecular structure determination by X-ray crystallography. CCP4 is designed to be flexible, allowing users a number of methods of achieving their aims. The programs are from a wide variety of sources but are connected by a common infrastructure provided by standard file formats, data objects and graphical interfaces. Structure solution by macromolecular crystallography is becoming increasingly automated and the CCP4 suite includes several automation pipelines. A method for experimental X-ray data analysis called AUSPEX was integrated in CCP4.
Includes different conformational search components into a unified process. MR-REX aims to improve the efficiency of molecular replacement (MR). It can take into account a clash score during the MR search to increase the success rate. This tool can estimate possible inaccurate segments of the structural model and optimizing the occupancies of these segments during MR. It employs iterative replica-exchange Monte Carlo simulations to work.
Serves to resolve problem of distant-homology proteins in X-ray crystallography. I-TASSER-MR produces full-length models working with I-TASSER by iterative structural fragment reassembly. Then, it uses a progressive sequence truncation procedure for editing the models based on local variations of the structural assembly simulations. This tool permits users to decide between different methods for setting B-factors and the number of models used for phasing.
Automates the replacement of molecules. Molrep employs cross rotation function (RF), full-symmetry translation function (TF) and packing function (PF) to work. It permits users to check several peaks of the rotation function (NP) by calculating a correlation coefficient for each peak and sorting the result. This tool enables the discovery of pseudo-translations and the definition of pseudo-translation vectors.
Provides a graphical user interface for the SHELX programs. HKL2MAP connects several crystallographic programs and assists users from the investigation of the diffraction data to the inspection of an electron density map. It returns plots of the correlation coefficient between signed anomalous differences measured at different wavelengths and the signal to noise ratio for the anomalous signal.
Reduces the need for expensive and time-consuming phasing experiments. CaspR executes an optimized molecular replacement procedure using a combination of well-established stand-alone software tools. It provides a progress report in the form of hierarchically organized summary sheets that describe the different stages of the computation with an increasing level of detail. The tool is useful in simple molecular replacement cases by automatically replacing the amino acid sequence of the template by those of the molecule of interest, thus accelerating the tedious refinement process.