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 <[log in to unmask]> 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
> >
>
>
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