April 2011 issue
From crystal to structure with CCP4
Proceedings of the CCP4 study weekend
An overview of the CCP4 software suite for macromolecular crystallography is given.
Protein surface engineering is increasingly used as a routine tool to enhance the crystallization propensity of proteins. Future possibilities include the use of multi-site protein variants, rational modulation of solubility and the development of strategies to tackle membrane proteins.
The Protein Information Management System (PiMS) is described together with a discussion of how its features make it well suited to laboratories of all sizes.
Thoughts about the decisions made in designing macromolecular X-ray crystallography experiments at synchrotron beamlines are presented.
A new graphical user interface to the MOSFLM program has been developed to simplify the processing of macromolecular diffraction data. The interface, iMOSFLM, allows data processing via a series of clearly defined tasks and provides visual feedback on the progress of each stage.
A summary of how to run the data-reduction programs in the CCP4 suite.
Typical topics and problems encountered during data processing of diffraction experiments are discussed and the tools provided in the autoPROC software are described.
The molecular-replacement model-improvement program Sculptor is described, with an analysis of the algorithms used.
Some future challenges for the PDB and its guardians are discussed and current and future activities in structural bioinformatics at the Protein Data Bank in Europe (PDBe) are described.
Recent developments in the CRANK software suite for experimental phasing have led to many more structures being built automatically.
A cross-validation-based method for bias reduction in `classical' iterative density modification of experimental X-ray crystallography maps provides significantly more accurate phase-quality estimates and leads to improved automated model building.
The general principles behind the macromolecular crystal structure refinement program REFMAC5 are described.
The software suite Xsolve semi-exhaustively explores key parameters of the X-ray structure-determination process to compute multiple three-dimensional protein structures independently and in parallel from a set of diffraction images. An optimal consensus model for subsequent manual refinement is computed from these structures.
Methods for the analysis of the relationship between macromolecular complexes and interactions and their manifestation in crystal packing are described and discussed.
The CCP4 molecular-graphics program now uses the Qt framework to provide a modern look and feel. There are many new features including rendering for publication-quality images and sequence alignment.