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[Imgcif-l] ImgCIF Densiry Maps

• To: imgcif-l@iucr.org
• Subject: [Imgcif-l] ImgCIF Densiry Maps
• From: Joe Krahn <krahn@niehs.nih.gov>
• Date: Thu, 22 Mar 2007 13:45:35 -0400

How many people are working on the new electron-density dictionary?

It is useful to include a space-group name, which should be sufficient
to define the symmetry for standard settings, as defined by the
International Tables. Individual symmetry operator definitions are also
valuable. Most current software defines symmetry operators with the
simple equation form:

 -Y,Z+1/2,-X

It turns out that these equations are very easy to parse, as long as
they are written the 'normal' way, which means that any numeric value is
a simple fraction of single-digit numbers. So, the trouble of parsing
these equations can be worth avoiding the extra work of defining
matrix+vector based symmetry. Since this is an established method in
crystallography, it seems to me to be the best approach.

However, there are certainly many non-crystallographic symmetry forms
which really require a matrix+vector form. The disadvantage of a matrix
form is that many digits are needed for fractions like 1/6, and even
then there is a bit of round-off error. So, if the equation form is not
used, I propose that there should be a way to define the translation
vector in fractional units. It is possible to write all needed symmetry
translations as integers in 1/24th units.

So, matrix/vector symmetry should be supported. Are there opinions as to
whether the equation method should or should not also be supported for
things like electron-density maps?

Joe Krahn
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