Kevin Cowtan, University of York, December 2002
. Last update September 2007.
||Buccaneers were pirates who attacked Spanish shipping in the Caribbean Islands during the 17th century.
The 'buccaneer' software, described here, builds protein models from electron density. It may be considered an acronym of sorts:
BUild Connected C-Alphas, Nautical Excuse for Eponym Required
'buccaneer' performs statistical chain tracing by identifying
connected alpha-carbon positions using a likelihood-based density
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 all normal cases a single carefully chosen reference
structure is used, with modifications automatically applied to the
reference structure to match its features to the work structure.
Buccaneer is quite quick, and can work at reasonably low
resolutions given good phases.
The latest version of the software is available through the CCP4 update system.
The software includes Clipper and kiss-fft, see the accompanying
COPYING* files for license details.
How to run Buccaneer
Most of the time you want to run the autobuild/refine using the CCP4i graphical user interface. However you can also run it from the command line. Something like this should do:
python $CBIN/buccaneer_pipeline.py -seqin buccaneer.seq -mtzin buccaneer.mtz -colin-fo FP,SIGFP -colin-hl HLADM,HLBDM,HLCDM,HLDDM -colin-free FreeR_flag -cycles 5
python $CBIN/buccaneer_pipeline.py -stdin << eof
Common options to add include buccaneer-fast and buccaneer-anisotropy-correction.
Release version history
- Buccaneer 1.5: Model tidying. Terminal Oxygen building.
- ccp4 6.1.13:
- Buccaneer 1.4: Cleaner MR support. Preserve known structure. Multi-model building. User-specified keywords.
- Buccaneer 1.3: New command-line interface, initial support for MR calculations, increase default number of cycles, some performance improvements.
- Buccaneer 1.2: numerous performance improvements.
- Buccaneer 1.1: improved output model, improved sequencing, improved side chain building, use multiple CPUs.
- Buccaneer/refmac recycling. NCS completion. Minor fixes.
- Sequencing upgraded to handle multiple insertions/deletions.
- Another hard-to-trigger bug fixed in -join, this time some looped chains being lost.
- PDB read now works for files with missing CRYST1. Hard-to-trigger crashes fixed in -join and -correct. Long sequenced fragments in the input model are now 'immutable'.
- 'Correlation mode' for growing after MR. Slight improvements to sequencing.
- Residues renumbered to match sequence.
- Internal recycling, support for external recycling.
- Chain linking, density filtering, improved installer.
- Auto installer, improved growing, improved sequencing, register correction, new reference data.
- Include reference data, update GUI to synchronize with Daresbury.
- When building sidechains, buccaneer now resolves clashes where multiple sidechains try to occupy the same density, when possible.
- Map coefficients may now be used, e.g. for recycling with refmac, or when using free set after pirate.
- Improved connectivity, refinement, sub-sequence docking, free-R flag.
- Includes sequece docking! It is also possible to use a command line swithces to favour particular types of secondary structure.
- Faster in most spacegroups, more consistent in amount of model built, existing models can be grown, residue types preserved through growing, side chains and Carbonyl Oxygens can be rebuilt.
- One minor bugfix, improved compatibility with old Linux distributions.
- Improved connectivity in joining and pruning stages.
- Initial release.