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
