In the danger of getting corrected by George twice in the same time
(burning stakes excluded...)
I am not doubting at all if its doable, but if the final result will
be more accurate / useful.
Thinking about it, with 1.5 A data it is very likely to be more
accurate than manual handling,
but not as certain as if 1.2 A data are available. Its very likely
that I am not up to date with resolution
limits for getting accurate results for correlated parameters as B
and Occ and what it will really tell
you at that resolution for a bound ligand.
A.
On Dec 17, 2007, at 15:43, George M. Sheldrick wrote:
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
