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Diffstat (limited to 'doc/man/indexamajig.1')
| -rw-r--r-- | doc/man/indexamajig.1 | 17 |
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. |