[phenixbb] XN-refinement

Pavel Afonine pafonine at lbl.gov
Fri Oct 14 18:19:11 PDT 2016

Hi Johannes,

> Thank you very much for your answer and explanations. Actually, in the 
> first place I already refined against neutron data (without X-ray) 
> until convergence and the results are quite good. However, water 
> orientations (in which we are particularly interested) are not easily 
> discernible in the maps since the knowledge about water oxygen 
> positions from the X-ray data are not explicitly implemented during 
> refinement. Hence, we collected room-temperature X-ray data from a 
> deuterated crystal grown in the same drop as the crystal used for 
> neutron diffraction experiments. With the combined XN-data, it is 
> astonishing how the R-free of both X-ray and neutron data drop 
> significantly (by 2% for the neutron part) and how well the data 
> agree. To account for the longer X-D/H bond lengths in nuclear density 
> maps, we used the respective restraints for neutron data (Settings --> 
> Advanced --> Model interpretation --> Use the nuclear distances for 
> X-H/D).

this is good to hear, and this demonstrates the power of using more 
data. The only issue here, as I mentioned before, is that in joint XN 
refinement we refine one single model against two data sets, while 
ideally it should be two models in order to account for genuine unique 
information that is contained in X-ray and neutron data. This will be 
addressed at some point.

> Overall, I would really like to use the XN-refinement approach to 
> improve the model in particular with respect to its water structure. 
> Ultimately, we will anyhow deposit the neutron, X-ray and joint XN 
> structures. 

Sounds like a very good plan!

> Is it not possible at all to achieve coinciding coordinates and 
> identical ADPs when using X and N at the same time?

I afraid no, sorry. This is purely technical limitation of current 

> The only alternative that I have not already used and would further 
> improve the water structure in the model would be what you describe 
> under 3. From what I read about it, however, it will be difficult to 
> generate restraints also for water oxygens for which it would be 
> particularly important in our case. Or is this possible in addition to 
> the dihedral restraints for the protein? Thanks a lot!

The reference model restraints are applied to macro-molecule only (not 


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