From 34b21127ea75e6a714a6c04a09f226180b2eb541 Mon Sep 17 00:00:00 2001 From: Thomas White Date: Thu, 16 Jun 2011 17:53:28 +0200 Subject: Move documentation to manpages --- doc/man/process_hkl.1 | 51 +++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 doc/man/process_hkl.1 (limited to 'doc/man/process_hkl.1') diff --git a/doc/man/process_hkl.1 b/doc/man/process_hkl.1 new file mode 100644 index 00000000..6c626e31 --- /dev/null +++ b/doc/man/process_hkl.1 @@ -0,0 +1,51 @@ +.\" +.\" 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. -- cgit v1.2.3