Program announcement: fffear

[Kevin Cowtan <cowtan@ysbl.york.ac.uk>]

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fffear 0.9 beta: ---- Fast Fourier FEAture Recognition ---

fffear is a program which implements Fast Fourier FEAture Recognition,
as a means to locate small molecular fragments in noisy electron
density maps. The method was inspired by Essens (Kleywegt G. J., Jones
T. A., Acta Cryst. D53, 179-185), and re-implemented in reciprocal
space (Cowtan K. D., Acta Cryst. D54, 750-756) to achieve improved
speed and discrimination.

The method implemented in fffear is based on that described in the
paper above, however the rotation of the fragment and mask have been
re-implemented in reciprocal space, giving a further 3-fold speed
improvement over the previous results.

fffear will generally find alpha helices and of 10 residues or more in
experimentally phased maps at 5.0A, and beta strands at 4.0A
resolution. At higher resolutions, the direction of the chain is
reliably predicted as well. The results at low resolution are improved
by the use of resolution-dependent atomic shape functions.

fffear is potentially useful for difficult molecular replacement
problems when some phase information is available, however this is
currently limited by the use of a conventional Fourier for the initial
calculation of the fragment and mask transforms.

Subsequent versions will include reciprocal space filtering to improve
the results when data is missing, weighted masks, and a fast Fourier
calculation for the fragment transform which will render the speed of
the calculation fully independent of fragment size, as well as other
speed optimizations. A likelihood based target is also under
investigation.

This is a beta release, and is supplied with no warrenty. Bug reports
and results will be most welcome. CCP4 libraries are required, and the
code is provided under the CCP4 license. The program may be obtained
as follows:

> ftp ftp.yorvic.york.ac.uk
login: anonymous
password: type_your_full_email_address_here
ftp > cd pub/ccp4
ftp > get fffear.tar.gz
ftp > quit
> gunzip fffear.tar.gz
> tar xvf fffear.tar
> cd fffear/src
> makefffear

Kevin Cowtan