I thought that I would never have to disagree with both Eleanor and
Tassos in the same email, let alone risk being burnt at a stake as a
heretic for doubting the Gospel according to Kleywegt, but in my
experience, given the very fortunate position that you have data to
1.5A, the refinement of one occupancy parameter for the whole ligand
(e.g. one SHELX free variable) will be rather well defined provided
that sensible restraints are applied to the B-values. A common variant
of this for ligands or side-chains is to refine one component with
occupancy p and an alternative component or conformation with an
occupancy 1-p, still only requiring the addition of ONE refinable
parameter. If you are using SHELX and your ligand (or part of it)
happens to be rigid, the rigid group refinement offers a further
way of keeping the number of refinable parameters down. The Dundee
PRODRG server is an excellent source of ligand geometries and
restraints for such refinements.
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. +49-551-39-2582
On Mon, 17 Dec 2007, Anastassis Perrakis wrote:
> > I have already changed occupancies as Eleanor mentioned, and got
> > approximate values. But my hope is to try to get much precise ones if
> > possible.
> >
> I never expected to preach the 'Kleywegt Gospel' in the ccp4bb,
> but in this case what you need is more accurate answers, not more precise ones
> (or better both, but precision alone can be a problem, and you can easily get
> 'precise' but inaccurate data easily by making the wrong assumptions
> in your experiment)
>
> http://en.wikipedia.org/wiki/Accuracy
>
> > I have heard from my colleague SHELX can refine occupancies, and
> > got its license. I'll next try SHELX.
>
> I think that phenix.refine can also do occupancies ?
> The problem is not if the program can do it, but if at your specific case
> you have enough information to do that in a meaningful way.
>
> For a soaking experiment and 1.5 A data, I would say that Eleanor's suggestion
> of tuning Occ based on B, is as close as you would get, accurate enough given
> the data,
> although not necessarily too precise.
>
> Tassos
>
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