Commit fb3b1df9 authored by Thomas White's avatar Thomas White Committed by Thomas White
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Update docs

parent cdaa57c6
......@@ -8,14 +8,12 @@ at Bragg locations and produce a list in the form "h k l I", with some extra
information about the locations of the peaks.
For minimal basic use, you need to provide the list of diffraction patterns,
the method which will be used to index (currently there is only one available
method), a file describing the geometry of the detector, a PDB file which
contains the unit cell which will be used for the indexing, and that you'd like
the program to output a list of intensities for each successfully indexed
pattern. You should redirect the output (stdout, but not stderr) of the program
to a file for later analysis. Here is what the minimal use looks like on the
command line, with each argument shown on a separate line. In practice, you'd
put this all on one line:
the method which will be used to index, a file describing the geometry of the
detector, a PDB file which contains the unit cell which will be used for the
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 looks like on
the command line, with each argument shown on a separate line. In practice,
you'd put this all on one line:
indexamajig
-i mypatternlist.lst
......@@ -23,7 +21,7 @@ indexamajig
--geometry mygeometry.geom
-p mystructure.pdb
--near-bragg
> myoutputfile.txt
-o myoutputfile.txt
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
......@@ -44,7 +42,7 @@ indexamajig
--prefix=/some/horribly/long/pathname/ending/in/a/slash/
-j 16
--sat-corr
> myoutputfile.txt
-o myoutputfile.txt
The table of saturation values for --sat-corr should be located in the HDF5 file
as follows: /processing/hitfinder/peakinfo_saturated. It should be an n*3 two
......@@ -86,6 +84,24 @@ You can suppress peak detection altogether for a panel in the geometry file by
specifying the "no_index" value for the panel as non-zero.
Indexing Methods
----------------
You can choose between a variety of indexing methods. You can choose more than
one method, in which case each method will be tried in turn until the later cell
reduction step says that the cell is a "hit". Choose from:
dirax : invoke DirAx
mosflm : invoke MOSFLM (DPS)
template : index by template matching
Depending on what you have installed. For "dirax" and "mosflm", you need to
have the dirax or ipmosflm binaries in your PATH. "template" is not ready for
use at the moment, so don't choose that option.
Example: --indexing=dirax,mosflm
Cell Reduction
--------------
......
......@@ -124,11 +124,12 @@ static void show_help(const char *s)
" '-' means stdin, which is the default.\n"
" -o, --output=<filename> Write indexed stream to this file. '-' for stdout.\n"
"\n"
" --indexing=<method> Use 'method' for indexing. Choose from:\n"
" none : no indexing (default)\n"
" dirax : invoke DirAx\n"
" mosflm : invoke MOSFLM (DPS)\n"
" template : index by template matching\n"
" --indexing=<methods> Use 'methods' for indexing. Provide one or more\n"
" methods separated by commas. Choose from:\n"
" none : no indexing (default)\n"
" dirax : invoke DirAx\n"
" mosflm : invoke MOSFLM (DPS)\n"
" template : index by template matching\n"
" -g. --geometry=<file> Get detector geometry from file.\n"
" -b, --beam=<file> Get beam parameters from file (provides nominal\n"
" wavelength value if no per-shot value is found in\n"
......
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