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Another buccaneer development release today - this one is quite major,
since it introduces the capability for recycling. It will also probably
be the last for a while, since I have some teaching and admin to do. The
changes are as follows:
1. The 'C-alpha finding' code has been re-written to make use of an
existing model. This is turned into a prior which encourages the finding
of C-alphas at likely distances from existing chain. So for example it
is more likely to find a new beta strand next to an existing one. This
turns out to be very useful for recycling - sufficiently so that it is
possible to recycle buccaneer without even refining the existing model.
This leads to a fast 'internal recycling' option. Alternatively, it can
also be used for 'external recycling' in which buccaneer is run
alternately with refmac to refine the model and improve the phases -
this gives better results but is slower.
2. A new program, cbuccaneer-refmac-prune, which takes the model from
refmac and a map (either 2mFoDFC or mFoDFc) and filters unsequenced
residues of the model on the basis of B-factor and difference density.
This is designed for use in a recycling script, so doesn't have a GUI.
3. A demonstration script is provided illustrating the use of buccaneer,
refmac, and cbuccaneer-refmac-prune. This more intended to show how you
can use the various components together than as an actual working
scheme. I just threw the bits together in the most obvious way. The
refmac options are certainly wrong - the geometry is too loose, and the
B-factors need restraint. Even so, it works better than not using refmac.
4. Minor improvements and bugfixes in the sequencing, linking and
filtering stages.
5. One feature has been removed: the ability to search for multiple
specialised secondary structure targets in a single run. The code was
messy and it didn't really help. If you want to use more than one
secondary structure target, you need to run the program more than once.
..
If you want to use refmac on a buccaneer model, you need a cif
dictionary for the UNK unsequenced residue type. This is included in the
etc directory, along with the demonstration script.
The installer should work for any of the platforms (Linux/x86, Mac/x86,
Mac/PPC), and should not cause any problems if you run it more than
once, e.g. to update your existing buccaneer development version.
There is still a great deal to do, including:
- annotating the built chains with their sequence numbers and chain
ids for more convenient completion in coot
- post-sequence loop building to complete the structure
- improved growing using correlated Ramachandran
- improved sequencing
but it should certainly be useful as it stands.
More here:
http://www.ysbl.york.ac.uk/~cowtan/buccaneer/buccaneer.html
--
I like to select my rotamer and gloat a little.. eleanor
