[phenixbb] XN-refinement

Pavel Afonine pafonine at lbl.gov
Fri Oct 14 07:09:55 PDT 2016

Hi Johannes,

historically, in joint Xray+Neutron refinement first tried by Coppens et 
al (1981) in small molecule world and later (1982) by Wlodawer & 
Hen­drickson in bio-macromolecules, and way later implemented in 
refinement tools such as nCNS (2009) and Phenix (2010), one single model 
is refined against two data sets, Xray and neutron.

The rationale to use two data sets, Xray and neutron, is to alleviate 
the seemingly poor data-to-parameters ratio because H and D are used 
explicitly in refinement using neutron data. This is all discussed in 
great details in that 6 years old paper:


Turns out with a proper data / restraints weight the problem of 
data-to-parameters amount is not as bad as it may appear, since by 
varying the weight one can dose the amount of a priori knowledge 
(restraints) as desired. This makes it possible to refine one model 
against X-ray or neutron data individually without problems.

Also, we know that X-H distances for X-ray and neutron are different 
(X-ray are shorter a tiny bit). We also know that both data sets may be 
collected at different temperatures (neutron at room, and X-ray at 
cryo), which means B factors are going to be different, some rotamers 
may be different, water structure may be slightly different, and so on. 
All in all we really do need to have two structures to maximize the use 
of available information. This is the new refinement paradigm that's 
being implemented in phenix.refine and will become available at some point.

The best you can do right now is:

1) Get the best possible refined X-ray structure (refined against x-ray 
data set alone);
2) Use refined x-ray structure as a starting point for neutron 
refinement (add H,D as appropriate - trivially done using 
phenix.ready_set or using Phenix GUI);
3) Refine structure from #2 against neutron data set alone. This will 
make sure H and D have identical coordinates and B. If really needed you 
can supply X-ray structure as a reference model - also trivially done 
from the phenix.refine GUI.

Let us know should you have questions or need help.


On 10/13/16 23:06, 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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