@@ -131,6 +131,30 @@ If the unit cell is centered (i.e. if the space group begins with I, F, H, A, B,
.PP
The default is \fB--cell-reduction=none\fR.
.SH PEAK INTEGRATION
If the pattern could be successfully indexed and the cell reduction gave a
positive match, peaks will be predicted in the pattern and their intensities
measured. The peak integration relies on knowing an accurate radius to
integrate the peak within, and that the annulus used to estimate the background
level is not so big that that it covers neighbouring peaks. However,
indexamajig cannot (yet) determine these values for you. You need to specify
them using the \fB--int-radius\fR option (see below).
.PP
To determine appropriate values, index some patterns with the default values and
view the results using \fBcheck-near-bragg\fR (in the scripts folder). Set the
binning in \fBhdfsee\fR to 1, and adjust the ring radius until none of the rings
overlap for any of the patterns. This ring radius is the outer radius to use.
Then reduce the radius until the circles match the sizes of the peaks as
closely as possible. This value is the inner radius. The middle radius should
be between the two, ideally between two and three pixels smaller than the outer
radius.
.PP
If it's difficult to do this without setting the middle radius to the
same value as the inner radius, then the peaks are too close together to be
accurately integrated. Perhaps you got greedy with the resolution and put the
detector too close to the interaction region? Improved integration algorithms,
designed to handle such difficult cases, are under development.
.SH OPTIONS
.PD 0
.IP "\fB-i\fR \fIfilename\fR"
...
...
@@ -342,8 +366,6 @@ Don't run more than one indexamajig jobs simultaneously in the same working
directory - they'll overwrite each other's DirAx or MOSFLM files, causing subtle
problems which can't easily be detected.
.PP
The way indexamajig calculates the intensities and errors of peaks sucks, for want of a better word. In particular, I/sigma(I) is not accurately estimated and many of the options don't make sense. Development of improved integration algorithms is in progress, so this issue will be addressed in a future version of CrystFEL.
.PP
ReAx indexing is experimental. It works very nicely for some people, and crashes for others. In a future version, it will be improved and fully supported.