It is nice to see that another old SHELX feature has now found its way into Phenix-refine:
'PART -N' = 'custom-nonbonded-symmetry-exclusion selection' ?! PART -N is indeed rather useful for the refinement of (solvent) molecules disordered about special positions, for example it allows hydrogens to be generated correctly and suppresses unwanted anti-bumping restraints. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Sat, 16 Oct 2010, Nicholas K. Sauter wrote: > 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 <t...@shelx.uni-ac.gwdg.de> 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 > > > >
