[phenixbb] XN-refinement

Tim Gruene tim.gruene at psi.ch
Thu Oct 13 08:25:14 PDT 2016

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.


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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Paul Scherrer Institut
Dr. Tim Gruene
- persoenlich -
Principal Investigator
Biology and Chemistry
CH-5232 Villigen PSI

Phone: +41 (0)56 310 5297


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