[phenixbb] XN-refinement

Leif Hanson leif.hanson at gmail.com
Fri Oct 14 06:11:16 PDT 2016

Dear Johannes,
What is your completeness in your neutron data? I think at some point we
need to stop hiding behind a joint refinement and use only the neutron
data, especially with this level of resolution. I like your idea of fixing
the ADP ratio. The more scientifically interesting question in this case is
the exchange and not the B-factors. If you are really bothered by your X+N
H/D coordinate and occupancy results, and your completeness is near 90% or
higher, the more conservative result is to refine with SHELX.
Best wishes,
Leif Hanson

On Fri, Oct 14, 2016 at 5:45 AM, Johannes Schiebel <
johannes.schiebel2 at gmail.com> wrote:

> Dear Tim,
> thank you very much for your reply! I agree that it will be very difficult
> to get reasonable values for both, occupancy and ADPs, at usual neutron
> diffraction resolutions of around 2 A. However, we are talking about
> neutron diffraction data to 1.4 A and X-ray diffraction data to 0.9 A. So,
> we have a lot of data. I should have mentioned this right away, sorry. Do
> you think that in such a rare case it might be possible to get reasonable
> values?
> Also, I like your idea to group H/D sites by expected exchange values.
> However, from the high-quality data we have, it is obvious that in a lot of
> cases the exchange rate is not really easy to predict by chemical intuition
> alone. There are sites where you clearly would expect at least a partial
> exchange but yet you observe a strong negative peak in the neutron
> scattering length density indicating the presence of an almost
> non-exchanged hydrogen . Wouldn't it also be possible to fix the ADP ratio
> between the H/D atoms and the atom to which they are attached to a
> chemically likely value between 1.0 and 1.5 and then refine only the
> occupancy? To me auch an approach seems less prone to errors introduced
> into the model by the crystallographer's expectations.
> Best wishes,
> Johannes
> Am 13.10.2016 um 17:25 schrieb Tim Gruene:
> Dear Johannes,
> I would recommend not to refine the occupancy of individual H/D pairs, unless
> you have high resolution and other evidence for the resulting values.
> Occupancy and ADP-values are very strongly correlated, and the correlation
> becomes higher the worse your resolution. And neutron data often have
> resolution of 2A or worse.
> You could group atoms together where you expect similar exchange ratios (based
> on chemical intuition) and refine one ratio per group. You can find a more
> detailed explanation in https://doi.org/10.1107/S1600576713027659
> That article also recommends to treat X-ray data as additional information by
> means of geometry restraints to avoid the complications you get with joint
> refinement. The main effect of joint refinement are prettier maps <flame> and
> you may need to decide whether you want to focus on science or on art
> </flame>. This way we refined the structure also has the side effect to
> constrain H and D to the same location, although, admittedly, the coordinate
> difference in the structure you quote is probably negligible.
> Best,
> Tim
> On Thursday, October 13, 2016 05:06:36 PM Johannes Schiebel wrote:
> Hi everyone,
> I am currently working on an X-ray/neutron (XN) joint refinement using
> phenix.refine. As it should be, H/D coordinates and ADPs at exchangable
> sites are refined to equal values when using Phenix version 1.10.1-2155
> and neutron data only. This is also stated in the paper describing the
> development of the method (Afonine et al. (2010) Joint X-ray and neutron
> refinement with phenix.refine. Acta Crystallogr D Biol Crystallogr 66,
> 1153-1163) as the default behavior: "Currently, phenix.refine maintains
> the H and D atoms at coinciding positions and constrains their ADPs to
> be equal to each other". However, when switching to XN-refinement using
> the same Phenix version, H and D atoms refine to different coordinates
> and ADPs, which should not be the case as it leads to unrealistic
> artifacts as can be seen from the deposited PDB 3X2P:
> ATOM    186  H  AALA A  13       3.486 -18.200 -14.123  0.38
> 14.54           H
> ATOM    187  D  BALA A  13       3.488 -18.195 -14.111  0.62
> 38.07           D
> In this example, the D-occupancy is likely overestimated, while the
> H-occupancy is underestimated because the ADPs refine to very different
> values, which is chemically not reasonable.
> Hence my question: How can I treat my data in a way that ADPs and
> coordinates refine to the same values at exchangeable H/D sites also for
> XN-refinement? Is there a specific keyword I am currently overlooking or
> do I have to use another Phenix version?
> I would be really glad to receive your feedback. Thanks in advance!
> Kind regards,
> Johannes
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