diff options
| -rw-r--r-- | doc/indexamajig.txt | 39 | ||||
| -rw-r--r-- | src/indexamajig.c | 8 |
2 files changed, 44 insertions, 3 deletions
diff --git a/doc/indexamajig.txt b/doc/indexamajig.txt index 71bd9991..eca053e4 100644 --- a/doc/indexamajig.txt +++ b/doc/indexamajig.txt @@ -56,6 +56,45 @@ See doc/geometry for information about how to create a geometry description file. +Cell Reduction +-------------- + +You can choose from various options for cell reduction with the +"--cell-reduction=" option. The choices are "none", "reduce" and "compare". +This choice is important because all autoindexing methods produce an "ab +initio" estimate of the unit cell (nine parameters), rather than just finding +the orientation of the target cell (three parameters). It's clear that this is +not optimal, and will hopefully be fixed in future versions. + +With "none", the raw cell from the autoindexer will be used. The cell probably +won't match the target cell, but it'll still get used. Use this option to test +whether the patterns are basically "indexable" or not, or if you don't know the +cell parameters. In the latter case, you'll need to plot some kind of histogram +of the resulting parameters from the output stream to see which are the most +popular. If you're lucky, this will reveal the true unit cell. + +With "reduce", linear combinations of the raw cell will be checked against the +target cell. If at least one candidate is found for each axis of the target +cell, the angles will be checked to correspondence. If a match is found, this +cell will be used for further processing. This option should generate the most +matches, but might produce spurious results in many cases. The "--check-sanity" +option can help with this. + +The "compare" method is like "reduce", but linear combinations are not taken. +That means that the cell must either match or match after a simple permutation +of the axes. This is useful when the target cell is subject to reticular +twinning, such as if one cell axis length is close to twice another. With +"reduce", there is a possibility that the axes might be confused in this +situation. This happens for lysozyme (1VDS), so watch out. + +The tolerance for matching with "reduce" and "compare" is hardcoded as 5% in +the reciprocal axis lengths and 1.5 degrees in the (reciprocal) angles. Cells +from these reduction routines are further constrained to be right-handed. The +unmatched raw cell might be left-handed: CrystFEL doesn't check this for you. +Always using a right-handed cell means that the Bijvoet pairs can be told +apart. + + Unconventional Use ------------------ diff --git a/src/indexamajig.c b/src/indexamajig.c index 2b733f04..05a91683 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -163,9 +163,11 @@ static void show_help(const char *s) " centroid/integration procedure.\n" "\n" "\nFor more control over the process, you might need:\n\n" -" --no-match Don't attempt to match the indexed cell to the\n" -" model, just proceed with the one generated by the\n" -" auto-indexing procedure.\n" +" --cell-reduction=<m> Use <m> as the cell reduction method. Choose from:\n" +" none : no matching, just use the raw cell.\n" +" reduce : full cell reduction.\n" +" compare : match by at most changing the order of\n" +" the indices.\n" " --check-sanity Check that indexed locations approximately correspond\n" " with detected peaks.\n" " --filter-cm Perform common-mode noise subtraction on images\n" |