From d6fbf62c239cb4f9bd94c2cf4fdb47bf808df985 Mon Sep 17 00:00:00 2001 From: Thomas White Date: Sun, 26 Sep 2010 19:07:01 +0200 Subject: Move documentation around --- doc/process_hkl.txt | 48 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) (limited to 'doc/process_hkl.txt') diff --git a/doc/process_hkl.txt b/doc/process_hkl.txt index b6411285..51742b3f 100644 --- a/doc/process_hkl.txt +++ b/doc/process_hkl.txt @@ -4,3 +4,51 @@ process_hkl - data scaling and merging program 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. -- cgit v1.2.3