.\" .\" process_hkl man page .\" .\" (c) 2009-2011 Thomas White .\" .\" Part of CrystFEL - crystallography with a FEL .\" .TH PROCESS\_HKL 1 .SH NAME process\_hkl \- Monte Carlo merging program .SH SYNOPSIS .PP .B process\_hkl -i mypatterns.stream -o mydata.hkl -y mypointgroup [options] .SH DESCRIPTION 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 .SH CHOICE OF POINT GROUP FOR MERGING 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). Some Laue classes are merohedral. This means that the orientation will have an 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 point group corresponding holohedral Laue class. You can also tell process_hkl the "apparent" symmetry, which is the symmetry as far as whatever produced the stream was concerned. In the case of most indexing algorithms, this will be the corresponding holohedral point group (not the Laue class nor the holohedral Laue class). If you use the "-a" option to give this information, process_hkl will try to resolve the remaining orientational ambiguities to get from the apparent symmetry to the true symmetry (given with "-y"). Currently, it won't do a very good job of it. The document twin-calculator.pdf contains more detailed information about this issue, as well as tables which contain all the required information.