[phenixbb] occupancy refinement
Pavel Afonine
PAfonine at lbl.gov
Tue Nov 24 20:37:16 PST 2009
Hi Maia,
the atom parameters, such as occupancy, B-factor and even position are
interdependent in some sense. That is, if you have somewhat incorrect
occupancy, that B-factor refinement may compensate for it; if you
misplaced an atom the refinement of its occupancy or/and B-factor will
compensate for this. Note in all the above cases the 2mFo-DFc and
mFo-DFc maps will appear almost identical, as well as R-factors.
So, I think your goal of finding a "true" occupancy is hardly achievable.
Although, I think you can approach it by doing very many refinements
(say, several hundreds) (where you refine occupancies, B-factors and
coordinates) each refinement starting with different occupancy and
B-factor values, and make sure that each refinement converges. Then
select a subset of refined structures with similar and low R-factors
(discard those cases where refinement got stuck for whatever reason and
R-factors are higher) (and probably similar looking 2mFo-DFc and mFo-DFc
maps in the region of interest). Then see where the refined occupancies
and B-factors are clustering, and the averaged values will probably give
you an approximate values for occupancy and B. I did not try this myself
but always wanted to.
If you have a structure consisting of 9 carbons and one gold atom, then
I would expect that the "second digit" in gold's occupancy would
matter. However, if we speak about dozen of ligand atoms (which are
probably a combination of C,N,O) out of a few thousands of atoms of the
whole structure, then I would not expect the "second digit" to be
visibly important.
Pavel.
On 11/24/09 8:08 PM, chern wrote:
> Thank you Kendall and Pavel for your responces.
>
> I really want to determine the occupancy of my ligand. I saw one
> suggestion to try different refinements with different occupancies and
> compare the B-factors.
> The occupancy with a B-factor that is at the level with the average
> protein B-factors, is a "true" occupancy.
> I also noticed the dependence of the ligand occupancy on the
> initial occupancy. I saw the difference of 10 to 15%, that is why I am
> wondering if the second digit after the decimal point makes any sence.
>
> Maia
>
>
> ----- Original Message -----
> *From:* Kendall Nettles <mailto:knettles at scripps.edu>
> *To:* PHENIX user mailing list <mailto:phenixbb at phenix-online.org>
> *Sent:* Tuesday, November 24, 2009 8:22 PM
> *Subject:* Re: [phenixbb] occupancy refinement
>
> Hi Maia,
> I think the criteria for occupancy refinement of ligands is
> similar to a decision to add an alt conformation for an amino
> acid. I don't refine occupancy of a ligand unless the difference
> map indicates that we have to. Sometimes part of the igand may be
> conformationally mobile and show poor density, but I personally
> don't think this justifies occupancy refinement without evidence
> from the difference map. I agree with Pavel that you shouldn't
> expect much change in overall statistics, unless the ligand has
> very low occupancy., or you have a very small protein. We
> typically see 0.5-1% difference in R factors from refining with
> ligand versus without for nuclear receptor igand binding domains
> of about 250 amino acids, and we see very small differences from
> occupancy refinement of the ligands.
>
> Regarding the error, I have noticed differences of 10% percent
> occupancy depending on what you set the starting occupancy before
> refinement. That is, if the starting occupancy starts at 1, you
> might end up with 50%, but if you start it at 0.01, you might get
> 40%. I don't have the expertise to explain why this is, but I also
> don't think it is necessarily important. I think it is more
> important to convince yourself that the ligand binds how you think
> it does. With steroid receptors, the ligand is usually planer, and
> tethered by hydrogen bonds on two ends. That leaves us with with
> four possible poses, so if in doubt, we will dock in the ligand in
> all of the four orientations and refine. So far, we have had only
> one of several dozen structures where the ligand orientation was
> not obvious after this procedure. I worry about a letter to the
> editor suggesting that the electron density for the ligand
> doesn't support the conclusions of the paper, not whether the
> occupancy is 40% versus 50%.
>
> You might also want to consider looking at several maps, such as
> the simple or simulated annealing composite omit maps. These can
> be noisy, so also try the kicked maps (
> http://www.phenix-online.org/pipermail/phenixbb/2009-September/002573.html),
> <http://www.phenix-online.org/pipermail/phenixbb/2009-September/002573.html%29,>
> which I have become a big fan of.
>
> Regards,
> Kendall Nettles
>
> On 11/24/09 3:07 PM, "chern at ualberta.ca" <chern at ualberta.ca> wrote:
>
> Hi,
> I am wondering what is the criteria for occupancy refinement of
> ligands. I noticed that R factors change very little, but the
> ligand
> B-factors change significantly . On the other hand, the
> occupancy is
> refined to the second digit after the decimal point. How can I
> find
> out the error for the refined occupancy of ligands?
>
> Maia
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