On Thu, 2010-10-21 at 18:59 +0100, Clemens Vonrhein wrote:
> I think I understand what you're getting at: you have a lower symmetry
> with a NCS axis that is basically perfectly aligned with the
> corresponding crystallographic axis in the higher symmetry
> spacegroup. And the only part of the model not obeying this NCS is the
> ligand.
>
precisely
> But then what about a water on a special position (2-fold with
> occ=0.5)? If I remove that 2-fold from my spacegroup symmetry and
> refine I get ... a single water with occupancy 1.0 ... or 2 waters
> with occupancy 0.5? Hmmm, diffcult to decide on the true spacegroup
> here ;-)
>
water is symmetrical (no hydrogens, please), shall use the higher
symmetry
> So it all depends
>
> * how clear the difference between high-symmetry/double conformation
> and low-symmetry/single-conformation is
>
Hard to put a specific number on it. I'd inspect the density and play
Potter Stewart.
> * how symmetrical the ligand is
>
same deal as with water
> * how the refinement in the lower-symmetry spacegroup is done - since
> there is a real danger (in case it is the high-symmetry spacegroup
> after all) that because of model bias and poorer (independent
> observations)/parameter ratio what seems like a clear single
> conformation is difficult to confirm.
Absolutely true. As we discussed before, restraining protein copies is
a must as well as maybe some bias removal.
Cheers,
Ed.
--
"I'd jump in myself, if I weren't so good at whistling."
Julian, King of Lemurs
