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[ccp4bb]: Clipper C++ libraries for crystallography...

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Just in case anyone here does not read the CCP4 newsletter, I'll give Clipper 
its annual plug:

Clipper is an independent project to provide a set of object-oriented 
libraries in C++ for the organisation of crystallographic data and the 
performance of crystallographic computation. The libraries are designed as a 
framework for new crystallographic software, which will allow the full power 
of modern programming techniques to be exploited by the developer. This will 
lead to greater functionality from simpler code which will be easier to 
develop and debug. 

Clipper works in conjunction with MMDB to provide all the tools necessary for  
manipulation of reflection data, maps and models, and a wide range of other  
facilities for crystallographic computation. Its dependencies are MMDB and  

Additional facilities may be added through optional interfaces to CCP4 (for  
CCP4 file i/o), CCTBX (for additional symmetry requirements and other stuff),  
and SHELX (PHS file i/o).

The API has now remain almost unchanged for 3 months, so it is fairly stable,  
although some backend will be required in the CCP4 interface. Documentation 
is extensive (500+ pages), and fairly comprehensive.

Initial applications demonstrate a 10-fold reduction in the code required for 
a particular task. Examples include sigma-a calculation (<100 lines of code), 
and automated chain tracing at low resolution (<800 lines of code). Common 
tasks such as ffts, skeletonisation, structure factor and electron density 
calculation (including anisotropic U values) are a single instruction, 
however all the components are modular and can be replaced if desired.

Clipper is currently being used in a number of projects, including the 
following projects at York
 - 'CCP4mg', the CCP4 molecular graphics project (and Mapview, its testbed).
 - 'Buccaneer', a new auto-tracing application.
 - 'Pirate', a new phase improvement application.

The last two both rely on a new approach involving statistical analysis of 
sample maps. 'Pirate' is particularly unusual in that it discards the 
traditional distinction between solvent and protein.

The Clipper homepage is at:

Announcements are made most months to the ccp4-dev mailing list.

Kevin Cowtan

York Structural Biology Laboratory, University of York, York YO10 5YW