diff options
| -rw-r--r-- | doc/indexamajig.txt | 36 | ||||
| -rw-r--r-- | src/indexamajig.c | 11 |
2 files changed, 32 insertions, 15 deletions
diff --git a/doc/indexamajig.txt b/doc/indexamajig.txt index f725bee5..efd065bd 100644 --- a/doc/indexamajig.txt +++ b/doc/indexamajig.txt @@ -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 -------------- diff --git a/src/indexamajig.c b/src/indexamajig.c index a2b5e80d..de50383c 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -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" |