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process_hkl - data scaling and merging program
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This program takes as input the data stream from "indexamajig". It merges the
many individual intensities together to form a single list of reflection
intensities which are useful for crystallography.
Typical usage is of the form:
$ process_hkl -i mypatterns.stream -o mydata.hkl -y mypointgroup
How to choose the point group
-----------------------------
One of the main features of serial crystallography is that the orientations of
individual crystals are random. That means that the orientation of each
crystal must be determined independently, with no information about its
relationship to the orientation of crystals in other patterns (as would be the
case for a rotation series of patterns).
The orientation of a crystal can be determined from the diffraction pattern only
within certain limits. For example, it is never possible, by geometry alone, to
distinguish between a diffraction pattern and its inverse, e.g. to tell the
[001] zone axis from [00-1]. That means that it is impossible to tell the
difference between a reflection and its Friedel opposite. If Friedel's Law is
not strictly observed, as is the case for data showing anomalous effects, and if
we wish to measure the anomalous differences, then another way to distinguish
the orientations apart must be determined.
So far, there is no such method which works reliably. You will need to take
this into account when deciding how to merge the data.
Because of the above, the use of symmetry in serial crystallography is
"backwards" with respect to the method in conventional crystallography. If you
are not interested in distinguishing between any of the possible ambiguities,
then you would just treat ambiguous reflections as equivalent and merge them
together in a high-symmetry point group. If you needed to distinguish between
them, then you would merge into a lower symmetry.
Having first determined the point group for the structure under examination,
decide whether or not you need to tell Friedel opposites (Bijvoet pairs) apart.
If not, merge according to the Laue class corresponding to the point group. The
Laue class is just the point group after introducing a centre of symmetry. The
point group is equivalent to the Laue class if the structure is centrosymmetric.
Some Laue classes are merohedral. This means that the orientation will have an
additional ambiguity, but this time more serious. The two (or more) possible
orientations could be called "twins", but the mechanism of their formation is
somewhat different to the conventional use of the term. In these cases, you
will need to merge according to the corresponding holohedral Laue class.
The document twin-calculator.pdf contains more detailed information about this
issue, as well as tables which contain all the required information.
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