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diff --git a/doc/symmetry b/doc/symmetry new file mode 100644 index 00000000..4e6298fb --- /dev/null +++ b/doc/symmetry @@ -0,0 +1,56 @@ +How CrystFEL handles symmetry +----------------------------- + +Currently, only process_hkl and render_hkl understand symmetry (and render_hkl +only understands it when plotting a zone axis pattern). get_hkl does NOT +currently understand symmetry, which means you'll have to expand any molecular +model (the PDB) out to P1 to get the correct results. You can achieve that, for +example, by loading it into Mercury, turning on "Packing", and re-saving. + +Symmetry definitions are included in src/symmetry.c. Point group definitions +are required for merging and the display of merged results (since merging does +not care about systematic absences (i.e. the space group) - as far as merging is +concerned, systematic absences are just measurements which happen to have values +of zero. Each space group belongs to exactly one point group, which you can +look up in the International Tables for X-Ray Crystallography. + +Space groups would be needed to make get_hkl handle symmetry properly, but that +hasn't been done yet, so symmetry.c just handles point groups for now. The +method used in symmetry.c is general to both point groups and space groups, even +though the code currently is not. + +Point groups are being added here as they are required, so it's likely that the +exact one you want hasn't been added yet. Here's how to add a new one: + +First, expand the check_cond() function to include a description of the +asymmetric reciprocal unit cell for the point group. Every reflection in the +whole of reciprocal space must map onto exactly one reflection in the asymmetric +unit cell so defined. The asymmetric cell is usually defined with positive h, k +and l, but it doesn't really matter. Working out the required condition means +visualising the cell and taking care to properly handle situations such as the +(000) reflection. + +Now, expand the num_equivs() function. Given a point group and a set of Miller +indices, this function must return the number of equivalent reflections, +including the given reflection, taking into account the multiplicity of the +reflection. For example, high-symmetry reflections (usually ones with zeroes +in their indices) have fewer equivalents. Label the different classes of +reflection according to their Wyckoff letters. This information can be found in +the International Tables. + +Finally, add the new point group to the get_equiv() function. This function +takes a set of Miller indices, a point group and an index, "n", and returns (by +reference) the indices of the "n"th equivalent reflection. Again, you have to +distinguish between the different Wyckoff positions. Lists of equivalent +reflection, grouped according to Wyckoff symbol, can also be found in the +International Tables. + +It's not normally necessary to write an individual table of equivalents for each +Wyckoff position, because many positions are just "truncated" sub-classes of +other positions. For example, in 6/mmm, the equivalent reflections for "b" and +"c" can be generated simply by working through the list for "g" (the general +position) with indices set to zero or equal as appropriate, and by stopping +after the first six equivalents. Therefore, the num_equivs() function combined +with a single table for positions b-g in get_equivs() is sufficient to deal with +all cases. Check carefully whether this really works for your chosen point +group first. |