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authorThomas White <taw@bitwiz.org.uk>2010-09-25 22:51:29 +0200
committerThomas White <taw@physics.org>2012-02-22 15:26:59 +0100
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tree0048e4460c9471989b1677dcbcb33806f3561a8c /doc/symmetry.txt
parent73f10c77950e8f398e3a1e4540f1a46f398c108f (diff)
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Let's not make life difficult just for the sake of it.
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+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).
+
+Symmetry definitions are included in src/symmetry.c. Point group definitions
+are required for merging and the display of merged results, but space groups are
+not taken into account since merging does not care about systematic absences -
+as far as process_hkl 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.
+
+Please read doc/process_hkl for important information on how symmetry is used
+during the indexing and merging procedures.
+
+
+Adding a new point group
+------------------------
+
+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 by
+editing src/symmetry.c.
+
+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. Get this right, otherwise you'll go crazy when it breaks in
+weird ways.
+
+Next, expand the num_general_equivs() function. Given a point group, this
+function must return the number of equivalent reflections for a general
+reflection, including the input reflection. High-symmetry reflections (usually
+ones with zeroes in their indices) have fewer equivalents, but the num_equivs()
+function will work this out for you.
+
+Finally, add the new point group to the get_general_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. You just
+have to worry about the general position, because get_equiv() will work out the
+special positions for you. get_general_equiv() must return the original indices
+when idx=0.
+
+
+The symmetry of the molecular model (the space group)
+-----------------------------------------------------
+
+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. Alternatively, you can do this using CCP4 with a command like:
+
+$ echo symgen P63 | pdbset xyzin model.pdb xyzout model-P1.pdb
+
+While on this subject, you might also want to include hydrogens in the model
+using something like:
+$ echo HYDROGENS APPEND | hgen xyzin model.pdb xyzout model-with-H.pdb