[phenixbb] XN-refinement

Johannes Schiebel johannes.schiebel2 at gmail.com
Fri Oct 14 02:45:01 PDT 2016

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,

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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