[phenixbb] XN-refinement

Pavel Afonine pafonine at lbl.gov
Fri Oct 14 20:40:49 PDT 2016

>> 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.
> Out of curiosity, could you elaborate on why it would be preferred to refine two separate models?  It seems to me, admittedly not having any experience with neutron diffraction, that the ultimate goal is to model the system of the crystal, and given 2 data sets, we would want to create the single model describing the structure in the crystal that best agrees with all the available data.  Are the neutron and X-ray data so different that using them for joint refinement is disadvantageous?

I think I wrote that already in previous email.. Structures 
corresponding to two data sets are of course overall similar may be 
different in local details:
- Different X-H(D) distances (see figure 4 here: 
- Different data collection temperatures:
   -- Different B factors;
   -- Different visible water structure;
   -- Different local disorder (that may be captured as distinct 
conformations at low temperature, but may be blurred at higher temperature);
- Different completeness and resolution of one data set may allow 
features in one model corresponding to this data set that may not be 
supported by the other data set. For example, you may see a well 
resolved water with one or two D in neutron map but you may not even see 
any water at all in X-ray map, or the other way around.
- etc etc etc.

So it is advantageous to use both X-ray and neutron data sets together 
but these nuances need to be carefully taken care of which isn't the 
case in current implementations of joint XN refinement protocols. This 
makes a good room for future improvements.


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