Dale > The reward of the > full calculation is that all the complications you describe disappear. > An atom that sits 0.001 A from a special position is not unstable > in the least.
That's indeed a very interesting observation, I have to admit that I didn't think that would be achievable. But there must still be some threshold of distance at which even that fails? Presumably within rounding error? Or are you saying (I assume you aren't!) that you can even refine all co-ordinates of an atom exactly on a special position? Say the x and z co-ordinates of an atom at (0,y,0) in monoclinic? Presumably the atom would have to be given a random push one way or the other (random number generators are generally not a feature of crystallographic refinement programs, with the obvious exception of simulated annealing!)? ? I always avoid programing tests of a == b for real numbers > because the round-off errors will always bite you at some point. > This means that a test of an atom exactly on a special position > can't be done reliably in floating point math. Obviously common sense has to be applied here and tests for strict floating-point equality studiously avoided. But this is very easily remedied, my optimisation programs are full of tests like IF(ABS(X-Y).LT.1E-6) THEN ... and I'm certain so are yours (assuming of course you still program in Fortran!). This implies that in the case that an atom is off-axis and disordered you have to take care not to place it within say a few multiples of rounding error of the axis, since then it might be indeed be confused with one 'on' the special position. However if someone claims that an atom sits within say 10*rounding error of an axis as distinct from being on the axis, then a) there's no way that can be proved, and b) it would be indistinguishable from being on the s.p. and the difference in terms of structure factors and maps would be insignificant anyway, so it may as well be on-axis. I think this is how the Oxford CRYSTALS software ( http://www.xtl.ox.ac.uk/crystals.html ), which has been around for at least 30 years, deals with this issue, so I can't accept that it can't be made to work, even if I haven't got all the precise details straight of how it's done in practice. > Your preferred assumption is that any atom "near enough" to > a special position is really on the special position and should > have an occupancy of one. My assumption is that no atom is every > EXACTLY on the special position and if they are close enough to > their symmetry image to forbid coexistence the occupancy should > be 1/n. I think either assumption is reasonable but, of course, > prefer mine for what I consider practical reasons. It helps that > I have to code to make mine work. Whichever way it's done is only a matter of convention (clearly both ways work just as well), however I would reiterate that my main concern here is that convention and practice appear to have parted company in this particular instance! Cheers -- IAn
