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Buccaneer 0.4 is available today, for Linux (x86) and OSX (not x86).
Changes include:
- Improved connectivity in the chain tracing.
(This fixes a problem with occasional breaks due to long bonds in
the chain trace).
- Internal refinement of C-alpha groups during finding and growing.
(This significantly improves the amount of model built, the
accuracy of the model, the precision of the model, and the fraction
sequenced, for a small cost in time).
- Sub-sequence matching.
(This allows some sequencing to take place even when the trace jumps
chain or skips a residue).
- You can now enter a free-R flag.
(But the results are worse if you do - eventually I'll make a hook
to allow use of density modified F's to help here).
- You can now employ several secondary structure filters at once,
to build helix, strand and general features separately. This takes
much longer, but when the data is good leads to a more complete
model straight away.
- You can now enter a job title.
Buccaneer has been applied to a few more real datasets, including one at
3.6A. (The phases were admittedly very good. The new version builds a
lot of the structure and sequences some of it.)
You can run the new version with the old GUI, but to use the free-R flag
or secondary structure filters you need to reinstall the GUI package.
Get it from the usual place:
http://www.ysbl.york.ac.uk/~cowtan/buccaneer/buccaneer.html
..
In other news, I've got a nucleotide finding program, but it isn't very
good, so I haven't tackled growing. This is on hold till I get some more
ideas. I also need to spend a few months catching up on non-buccaneer work.
