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Reflections & Invariants
- Reflections
- Number of Reflections to use: Enter the number of reflections
to be used in the dual-space (Shake-and-Bake) phasing procedure.
Note that this number may not exceed the number of reflections in
the input reflection file (next parameter). Occasionally (especially
for substructure data) an error message will appear indicating that
the requested number of reflections could not be found. In such
cases, one easy fix is to reduce the allowable |E|/sig(|E|)
ratio (see below), but this does have the drawback of reducing the
reliability of the permissable reflections.
The reflections used will be those with the largest normalized structure-factor magnitudes (|E|s). Depending on the resolution, the minimum |E| value for these reflections should be in the range 1.2-1.5 for Basic applications. Depending on data quality and the difference |E| cut-offs used, this minimum will probably be lower for SIR and SAS substructure applications. Although it is desirable for the minimum |E| to be as large as possible, minimums as low as 0.8 have been used successfully in substructure cases.
- Input Reflection File: Typically, the input reflection
file for SnB is the final reflection file output by DREAR
following normalization. This
file contains H, K, L, |F|, Sig(F), |E|, Sig(E) in FORMAT(3I5, 2F9.2,
2F9.3). Reflection files, in this format, which contain |E| values
computed by other programs may also be used here. Any reflection
file in this format is New to SnB. If SnB has already
been applied to the same data, the previous job will have created
a file "prefix.SnB_ref"
after application of the final selection criteria (see next parameter).
If the same criteria are to be used in a second job, this reflection
file, which has a format different from the DREAR output file, may
be reused as an input file by specifying Previous SnB
File. This avoids writing another duplicate reflection file.
- Final Reflection Selection Criteria: Reflections passing
these criteria will be used for phasing and will be written into
the SnB reflection output file "prefix.SnB_ref".
Resolution Range: Specify the minimum and maximum resolution (in Angstroms) for reflections to be used for phasing.
Minimum |E|/sig(|E|): Minimum signal-to-noise ratio for reflections to be used for phasing. Applied to all data types. Equivalent to the difference |E| cut-off, Zmin. It is sometimes necessary to reduce this parameter (i.e. reduce the significance level) in order to retain a sufficient number of reflections for phasing. Reducing the value of this parameter to less than 2.0 should be avoided if possible.
Maximum |E|: Largest allowed |E| value for reflections used for phasing. This parameter provides the last opportunity to eliminate reflections that have unrealistically large normalized structure-factor magnitudes. Magnitudes larger than 5.0 are unlikely unless the structure is quite small. This is especially true for acentric structures.
- Number of Reflections to use: Enter the number of reflections
to be used in the dual-space (Shake-and-Bake) phasing procedure.
Note that this number may not exceed the number of reflections in
the input reflection file (next parameter). Occasionally (especially
for substructure data) an error message will appear indicating that
the requested number of reflections could not be found. In such
cases, one easy fix is to reduce the allowable |E|/sig(|E|)
ratio (see below), but this does have the drawback of reducing the
reliability of the permissable reflections.
- Invariants
- Input Invariant File: Click New to create and use
a new triplet invariant file ("prefix.SnB_inv"). The invariants
are sorted in decreasing order according to the triple product of
the three associated magnitudes (|E|s). To reuse an existing
invariant file that was created with the same set of reflections,
select Existing.
- Number of Triplet Invariants to Use: Enter the number of triplet invariants to be used during the phasing process and written into the output file. Those invariants for which the triple product of the three associated magnitudes (|E|s) are largest will be used because these invariants are statistically the most reliable. Notice that there is a possibility (especially for substructure data) that the requested number of triples cannot be generated using the specified number of reflections (see above). In this case, an error message will appear. To fix this, the number of invariants requested can be reduced. However, it is not advisable to reduce the reflection:invariant ratio to less than 1:5 in order to allow for sufficient overdetermination of the phases. Alternatively, the number of reflections can be raised because the number of invariants that can be generated increases exponentially as the number of reflections increases.
- Input Invariant File: Click New to create and use
a new triplet invariant file ("prefix.SnB_inv"). The invariants
are sorted in decreasing order according to the triple product of
the three associated magnitudes (|E|s). To reuse an existing
invariant file that was created with the same set of reflections,
select Existing.
