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authorThomas White <taw@physics.org>2011-06-16 18:24:40 +0200
committerThomas White <taw@physics.org>2012-02-22 15:27:28 +0100
commited3696ce29ddc5372a467cf7e96966f3407b6f04 (patch)
tree33d6daa76506c7056e41f22bc35b6e349b583166 /doc/man/indexamajig.1
parent34b21127ea75e6a714a6c04a09f226180b2eb541 (diff)
Add to the documentation
Diffstat (limited to 'doc/man/indexamajig.1')
-rw-r--r--doc/man/indexamajig.117
1 files changed, 8 insertions, 9 deletions
diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1
index fcb1afc4..501ed896 100644
--- a/doc/man/indexamajig.1
+++ b/doc/man/indexamajig.1
@@ -29,7 +29,11 @@ indexing, and that you'd like the program to output a list of intensities for
each successfully indexed pattern. Here is what the minimal use might look like
on the command line:
-indexamajig -i mypatterns.lst -j 10 -g mygeometry.geom --indexing=mosflm,dirax --peaks=hdf5 --cell-reduction=reduce -b myxfel..beam -o test.stream -p mycell.pdb --record=integrated
+indexamajig -i mypatterns.lst -j 10 -g mygeometry.geom \
+.br
+ --indexing=mosflm,dirax --peaks=hdf5 --cell-reduction=reduce
+.br
+ -b myxfel.beam -o test.stream -p mycell.pdb --record=integrated
More typical use includes all the above, but might also include a noise or
common mode filter (--filter-noise or --filter-cm respectively) if detector
@@ -46,21 +50,16 @@ array, where the first two columns contain fast scan and slow scan coordinates
at the given location. The value will be spread in a small cross centred on
that location.
-See doc/geometry for information about how to create a geometry description
-file.
+See `man crystfel_geometry' for information about how to create a geometry description file.
You can control what information is included in the output stream using
' --record=<flags>'. Possible flags are:
- pixels Include a list of sums of pixel values within the
- integration domain, correcting for individual pixel
- solid angles.
-
integrated Include a list of reflection intensities, produced by
- integrating around predicted peak locations.
+ integrating around predicted peak locations.
peaks Include peak locations and intensities from the peak
- search.
+ search.
peaksifindexed As 'peaks', but only if the pattern could be indexed.