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
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