Pirate: Phase Improvement Requires Another Tenuous Eponym
Pirate is a new statistical phase improvement program.
'pirate' performs statistical phase improvement by classifying the electron density map by sparseness/denseness and order/disorder, with the aim of obtaining superior results to conventional solvent mask based methods without requiring knowledge of the solvent content.
A release is available for Linux(x86) and MacOSX(G5) (the latter is unsupported). These are recommended for use with CCP4 version 6.0.0 or later.
You may install this software for your use within your site for testing and structure solution. You may not modify or redistribute it. This software includes Clipper and kiss-fft, see the accompanying COPYING* files for license details.
'pirate' performs statistical phase improvement by classifying the electron density map by sparseness/denseness and order/disorder, with the aim of obtaining superior results to conventional solvent mask based methods without requiring knowledge of the solvent content.
The target distributions are generated by a simulation calculation using a known 'reference' structure for which calculated phases are available. The success of the method is dependent on the features of the reference structure matching those of the unsolved, 'work' structure. For the common case of a protein of mostly equal atoms (i.e. not a metalloprotein), a single reference structures can be used, with modifications automatically applied to the reference structure to match its features to the work structure.
To get the best results from 'pirate', you should allow it to modify the cell contents of the reference structure to match the contents of the work structure. To do this, simply leave the 'auto-content' option selected, and use a generic reference structure of medium solvent content, such as 1AJR.
A standard reference structure is now provided as part of the distribution. This is suitable for common light-atom protein structures with varying solvent content and resolution up to 1.85A. For exotic cases and high resolution cases you will have to provide your own reference structures.