diff options
Diffstat (limited to 'doc/man/indexamajig.1')
| -rw-r--r-- | doc/man/indexamajig.1 | 26 |
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 |