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| -rw-r--r-- | doc/indexamajig.txt | 75 |
1 files changed, 42 insertions, 33 deletions
diff --git a/doc/indexamajig.txt b/doc/indexamajig.txt index 7e73b896..a7cac95f 100644 --- a/doc/indexamajig.txt +++ b/doc/indexamajig.txt @@ -11,48 +11,56 @@ For minimal basic use, you need to provide the list of diffraction patterns, 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 ---indexing=dirax ---geometry mygeometry.geom --p mystructure.pdb ---near-bragg --o myoutputfile.txt +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 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 noise causes problems for the peak detection. The HDF5 files might be in some folder a long way from the current directory, so you might want to specify a full pathname to be added in front of each filename. You'll probably want to -run more than one indexing job at a time (-j <n>), and you might want to correct -the intensities of saturated peaks according to a list stored elsewhere in the -HDF5 file: - -indexamajig --i mypatternlist.lst ---indexing=dirax ---geometry mygeometry.geom --p mystructure.pdb ---near-bragg ---filter-noise ---prefix=/some/horribly/long/pathname/ending/in/a/slash/ --j 16 ---sat-corr --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 -dimensional array, where the first two columns contain x and y coordinates and -the third contains the value which should belong in a peak at location x,y. The -value will be divided by 5 and spread in a small cross centred on that location. +run more than one indexing job at a time (-j <n>). + +You can include a table of saturation values for in the HDF5 file, if you have +a method for estimating the intensities of saturated peaks. It goes in +/processing/hitfinder/peakinfo_saturated, and should be an n*3 two dimensional +array, where the first two columns contain fast scan and slow scan coordinates +(in that order) and the third contains the value which should belong in a peak +at the given location. The value will be divided by 5 and spread in a small +cross centred on that location. See doc/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. + + peaks Include peak locations and intensities from the peak + search. + + peaksifindexed As 'peaks', but only if the pattern could be indexed. + + peaksifnotindexed As 'peaks', but only if the pattern could NOT be indexed. + +So, if you just want the integrated intensities of indexed peaks, use +"--record=integrated". If you just want to check that the peak detection is +working, used "--record=peaks". + Peak Detection -------------- @@ -174,5 +182,6 @@ can be "/dev/null" if you're only interested in the other. --------- Don't run more than one indexamajig jobs simultaneously in the same working -directory - they'll overwrite each other's DirAx files, causing subtle problems +directory - they'll overwrite each other's DirAx or MOSFLM files, causing subtle +problems which can't easily be detected. |