[phenixbb] XN-refinement

Johannes Schiebel johannes.schiebel2 at gmail.com
Thu Oct 13 08:06:36 PDT 2016

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,

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