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+.\"
+.\" process_hkl man page
+.\"
+.\" (c) 2009-2011 Thomas White <taw@physics.org>
+.\"
+.\" 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.