Phenix can refine a tartaric acid on the twofold if you set the occupancy to 0.5 AND set the custom-nonbonded-symmetry-exclusion selection to the tartaric acid. It's a new feature.
Nick Sent from my iPhone Nicholas K. Sauter (510)847-1592 cell (510)486-5713 desk On Oct 16, 2010, at 1:25 AM, Tim Gruene <[email protected]> wrote: > Hello Jackie Vitali, > > What happens if you model the tartaric acid as if it were not on a symmetry > axis > and then let phenix deal with the symmetry? I once had a water of which refmac > stubbornly lowered the occupancy to 0.5 even though i kept on bringing it back > to 1.0 until I realised that it was on a 2-fold axis. And this was seven years > ago, so by now programs might be able to deal with more complicated molecules > than just an oxygen. > > As for the SO4, you should set the occupancy of S and O to 0.33 because you > only > have one third per asymmetric unit. Now since the other oxygens belong to the > same molecule, their occupancies should also be 0.33. But again, of you leave > it > at 1 and feed it into phenix, that should be corrected for. If it's not, try > refmac! > > Cheers, Tim > > On Fri, Oct 15, 2010 at 06:28:52PM -0400, Jacqueline Vitali wrote: >> Dear colleagues, >> >> I have a tartaric acid on a two fold axis with its two halves related >> by the two fold. How do I refine this in Phenix? >> >> Also I have a SO4 on a 3 fold with S and one O on tthe 3 fold. The >> other 3 oxygens are related by the 3-fold. How do I refine this in >> phenix? I can put S and one O occupancy 1, what occupancy do I put >> for the 3 oxygens that overlap their symmetry mates? >> >> And how do I maintain stereochemistry around the symmetry axis? These >> are not just one atom. For the tartaric acid the 2 fold goes through >> the middle of the bond. I could split it in two halves but I do not >> see how to keep stereochemistry. >> >> I would appreciate all suggestions. >> >> I apologize because the question should go to another newsgroup but I am >> still working with my subscription in phenixbb. >> >> Jackie Vitali > > -- > -- > Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > phone: +49 (0)551 39 22149 > > GPG Key ID = A46BEE1A >
