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-rw-r--r--doc/man/indexamajig.126
1 files changed, 24 insertions, 2 deletions
diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1
index 4160d25c..4360bd1d 100644
--- a/doc/man/indexamajig.1
+++ b/doc/man/indexamajig.1
@@ -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.
.SH AUTHOR