SHELXL also expects that the occupancy of a fully occupied atom on a threefold axis should be set at 1/3, and will generate this automatically if necessary. It will also generate automatically the necessary constraints for the x, y and z parameters (and for the Uij if the atom is anisotropic). It is essential that this is done correctly if a full-matrix refinement is being performed (e.g. to get esd estimates), otherwise the refinement can explode. The user may change or switch off the tolerance for detecting whether an atom is on a special position (with the SPEC instruction). Setting the occupancy to a fraction avoided a complicated IF construction inside a loop and 35 years ago computers were so slow! I can't change it now because I have to preserve upwards compatibility. Unfortunately the CIF committee decided to use the other definition (i.e. the Zn on the threefold axis has an occupancy of 1.0) and this has caused considerable confusion in the small molecule world ever since; atoms are frequently encountered on special positions in inorganic and mineral structures.
George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Fri, 10 Dec 2010, Ed Pozharski wrote: > On Fri, 2010-12-10 at 21:53 +0000, Ian Tickle wrote: > > Hmmm - but shouldn't the occupancy of the Zn be 1.00 if it's on the > > special position > > Shouldn't 1/3 be better for programming purposes? If you set occupancy > to 1.0, then you should specify that symmetry operators do not apply for > these atoms, making Fc calculation a bit more cumbersome. > > If definition of the "asu content" is "you get full content of the unit > cell after applying symmetry operators", then occupancy *must* be 1/3, > right? > > The first zinc and the water are on special position, but because they > are not excluded from positional refinement (perhaps they should be), > they will drift a bit. CNS has distance cutoff for treating atoms as > special positions, if it jumps over the limit during, say, simulated > annealing, it will cause problems. Perhaps PROLSQ did something > similar. It is a good question if it's better to fix these in place or > let them wobble a bit to account for some potential disorder. While I > see the formal argument that it should be nailed to three-fold axes, it > is also true that this is a mathematical compromise to simplify modeling > that does not reflect physical reality (i.e. you don't have three > partially occupied zinc ions, it's just one). In any event, given that > this is a 1.5A structure, (-0.002 0.004) is statistically speaking the > same as (0 0). > > Cheers, > > Ed. > > -- > "I'd jump in myself, if I weren't so good at whistling." > Julian, King of Lemurs > >
