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There is a new development release of buccaneer out today for Linux/x86, Mac/x86 and Mac/ppc. This is the first development which will run on Intel Macs, and features a few other improvements:
- A new 'link' stage allows nearby chains to be linked by an automatic short loop building step. This is a pre-sequence loop build, which therefore enhances connectivity for sequencing, however unlike post sequence loop building there is no information about how many residues to insert, so it tries 0, 1 and 2.
- A new 'filter' stage removes residues which are in poor density, and also removes residues in sequence breaks so that in the output model there is only one sequence range allocated per chain fragment. The filtering stage significantly increases the accuracy of the resulting model, for a small cost in completeness.
- A minor improvement in the sequencing algorithm makes it more likely to fit serveral sequence fragments to one chain.
These improvements are aimed towards the long term goal of implementing buccaneer inside an automatic procedure with refinement and recycling to enable model building to completion. Only one more major feature - a specialised search for unmodelled density - is required before tackling this, although I may also implement a feature to encourage extended secondary structure features as well.
The development version of Buccaneer is available here: http://www.ysbl.york.ac.uk/~cowtan/buccaneer/buccaneer.html Kevin
