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Fourier Refinement
- Contraints
- Number of Peaks to Select: The default value is
a function of the number of non-H atoms in the asymmetric
unit, the presence of heavier atoms, the type of data, and
the resolution of the data. Typically, the number of peaks
requested for large structures is less than the number of
atoms in these structures because of the likelihood that high
thermal motion or disorder at some sites will decrease the
number of atoms observable during early stages of the solution
process. More details are given on the Parameters page.
- Minimum Interpeak Distance:
This parameter specifies the minimum distance that will be
permitted between any two atoms in the trial structure (or
substructure). For "Basic" high-resolution data,
this parameter has a default value of 1.0Å. For SIR
and SAS substructure data, which are used at lower resolution,
this value has a default of 3.0Å.
- Minimum Distance between symmetry-related peaks:
In space groups where special positions occur, this parameter
is used to eliminate peaks located near such positions. This
feature is especially useful when it is known that atoms cannot
occur at these sites (e.g. Se atoms in selenomethionine
derivatives). For example, the default value of 3A, when applied
to a structure in space group P222, will create a cylinder
(with a diameter of 3A) of excluded volume about each of the
rotation axes. Experience has shown that, without this constraint,
there is a tendency for false minima to develop by building
up density at the special positions.
- Number of special position peaks to keep: Enter
an appropriate non-zero value here if it is known, a priori,
that a certain number of atoms will be located on the special
positions. The requested number of the largest peaks that
volunteer at the special positions will then be retained.
- Number of Peaks to Select: The default value is
a function of the number of non-H atoms in the asymmetric
unit, the presence of heavier atoms, the type of data, and
the resolution of the data. Typically, the number of peaks
requested for large structures is less than the number of
atoms in these structures because of the likelihood that high
thermal motion or disorder at some sites will decrease the
number of atoms observable during early stages of the solution
process. More details are given on the Parameters page.
- Fourier Grid
- Fourier Grid Size: By default,
this value is set to 1/3 of the maximum resolution of the
data set. Coarser grids (as coarse as 2/3 of the maximum resolution)
can often be used successfully for substructures. Significantly
coarser grids greatly reduce the number of points at which
the Fourier series must by calculated and, consequently, the
running time of the SnB procedure can also be greatly
reduced. However, the number and quality of correct sites
obtained may not be as large in such cases. Therefore, if
a coarse grid is used, it is advisable to perform a second,
single-trial, run of SnB in which the peak output of
the first job is used as a Model
Structure.
- Fourier Grid Size: By default,
this value is set to 1/3 of the maximum resolution of the
data set. Coarser grids (as coarse as 2/3 of the maximum resolution)
can often be used successfully for substructures. Significantly
coarser grids greatly reduce the number of points at which
the Fourier series must by calculated and, consequently, the
running time of the SnB procedure can also be greatly
reduced. However, the number and quality of correct sites
obtained may not be as large in such cases. Therefore, if
a coarse grid is used, it is advisable to perform a second,
single-trial, run of SnB in which the peak output of
the first job is used as a Model
Structure.
- Extra Cycles
- Perform extra cycles with more peaks?: In cases
where a greatly reduced number of peaks are selected during
most of the Shake-and-Bake cycles in order to increase
the efficiency of the solution process, it is desirable to
perform some additional cycles requesting that the number
of peaks used be closer to the number of atoms expected. If
a solution has already been obtained, the quality of this
solution will improve considerably during the extra refinement
cycles. In some cases, it has been essential to increase the
number of correct peaks during the dual-space refinement before
proceeding to Fourier refinement or the solution would otherwise
be lost. The extra-cycle feature is automatically activated
when the number of peaks selected during the preliminary cycles
is less than 80% of the expected number of atoms.
- Number of Extra Cycles: By default, the number of
extra cycles performed is equal to 10% of the normal (preliminary)
cycles.
- Number of Peaks: By default, the number of peaks
selected during the extra cycles is equal to the number of
atoms expected.
- Perform extra cycles with more peaks?: In cases
where a greatly reduced number of peaks are selected during
most of the Shake-and-Bake cycles in order to increase
the efficiency of the solution process, it is desirable to
perform some additional cycles requesting that the number
of peaks used be closer to the number of atoms expected. If
a solution has already been obtained, the quality of this
solution will improve considerably during the extra refinement
cycles. In some cases, it has been essential to increase the
number of correct peaks during the dual-space refinement before
proceeding to Fourier refinement or the solution would otherwise
be lost. The extra-cycle feature is automatically activated
when the number of peaks selected during the preliminary cycles
is less than 80% of the expected number of atoms.
- Twice Baking (Fourier Refinement)
- Trials for E-Fourier Filtering: The number
of reflections phased during the dual-space Shake-and-Bake
cycles is a relatively small fraction of the total available
(typically 1/6-1/8 for basic data). The number of reflections
used in direct-method procedures is restricted because the
invariant relationships are more reliable when they involve
only those reflections with large |E| values. However,
the severity of the resultant series termination reduces the
quality of the electron-density maps. The quality of solutions
can be increased by adding additional reflections and performing
Fourier refinement since this type of refinement does not
involve the invariants. This procedure has been termed "E-Fourier
filtering" in the context of the program SHELXS. In the
interest of computational efficiency, Fourier refinement is
recommended only if the current trial structure is better
(lower Rmin value) than the previous best trial structure.
By default, Fourier refinement is not used for substructures
since the reliability of the smaller magnitude differences
is often suspect.
- Number of Cycles: By default, the number of Fourier
refinement cycles performed (if any) is equal to 10% of the
number of dual-space (Shake-and-Bake) cycles. The number
of reflections phased in successive cycles is increased in
equal increments until all the reflections that pass the minimum
|E| cutoff (see below) are phased in the last cycle.
- Number of Peaks: It is reasonable to request more
peaks here. As map quality improves, a larger number of peaks
are reliable.
- Minimum |E|: Enter the minimum |E| value for reflections to be included for Fourier refinement. The minimum selected should give more reflections than the number used during the dual-space direct-method cycles, but it should not include weak reflections if they are unreliable.
- Trials for E-Fourier Filtering: The number
of reflections phased during the dual-space Shake-and-Bake
cycles is a relatively small fraction of the total available
(typically 1/6-1/8 for basic data). The number of reflections
used in direct-method procedures is restricted because the
invariant relationships are more reliable when they involve
only those reflections with large |E| values. However,
the severity of the resultant series termination reduces the
quality of the electron-density maps. The quality of solutions
can be increased by adding additional reflections and performing
Fourier refinement since this type of refinement does not
involve the invariants. This procedure has been termed "E-Fourier
filtering" in the context of the program SHELXS. In the
interest of computational efficiency, Fourier refinement is
recommended only if the current trial structure is better
(lower Rmin value) than the previous best trial structure.
By default, Fourier refinement is not used for substructures
since the reliability of the smaller magnitude differences
is often suspect.
