Is there not some significant prior art in iterative phase refinement by
an "FFT then flip" algorithm?
See for example:
Acta Cryst. (1996). D52, 30-42 [ doi:10.1107/S0907444995008754 ]
"Methods used in the structure determination of bovine mitochondrial F1
ATPase" J. P. Abrahams and A. G. W. Leslie
Abstract: With a size of 372 kDa, the F1 ATPase particle is the largest
asymmetric structure solved to date. lsomorphous differences arising
from reacting the crystals with methyl-mercury nitrate at two
concentrations allowed the structure determination. Careful data
collection and data processing were essential in this process as well as
a new form of electron-density modification, `solvent flipping'. The
most important feature of this new procedure is that the electron
density in the solvent region is inverted rather than set to a constant
value, as in conventional solvent flattening. All non-standard
techniques and variations on new techniques which were employed in the
structure determination are described.
Acta Cryst. (2000). D56, 1137-1147 [ doi:10.1107/S090744490000932X ]
"A flexible and efficient procedure for the solution and phase
refinement of protein structures"
J. Foadi, M. M. Woolfson, E. J. Dodson, K. S. Wilson, Y. Jia-xing and Z.
Chao-de
Abstract: An ab initio method is described for solving protein
structures for which atomic resolution (better than 1.2 Å) data are
available. The problem is divided into two stages. Firstly, a
substructure composed of a small percentage (~5%) of the scattering
matter of the unit cell is positioned. This is used to generate a
starting set of phases that are slightly better than random. Secondly,
the full structure is developed from this phase set. The substructure
can be a constellation of atoms that scatter anomalously, such as metal
or S atoms. Alternatively, a structural fragment such as an idealized
[alpha]-helix or a motif from some distantly related protein can be
orientated and sometimes positioned by an extensive
molecular-replacement search, checking the correlation coefficient
between observed and calculated structure factors for the highest
normalized structure-factor amplitudes |E|. The top solutions are
further ranked on the correlation coefficient for all E values. The
phases generated from such fragments are improved using Patterson
superposition maps and Sayre-equation refinement carried out with fast
Fourier transforms. Phase refinement is completed using a novel
density-modification process referred to as dynamic density modification
(DDM). The method is illustrated by the solution of a number of known
proteins. It has proved fast and very effective, able in these tests to
solve proteins of up to 5000 atoms. The resulting electron-density maps
show the major part of the structures at atomic resolution and can
readily be interpreted by automated procedures.
