[phenixbb] [ccp4bb] Adding H in refinement

Pavel Afonine PAfonine at lbl.gov
Wed Jan 13 11:04:57 PST 2010

Hi Carsten,

> A question about the riding Hydrogens and their B-factors. I noticed that at least with earlier versions of PHENIX the B-factor of the Hydrogens was not fixed to the B-factor of the bonded atoms. 

I was not accurate when writing yesterday that the B-factor of a 
hydrogen in X-H bond is exactly equal to the B-factor of the atom it is 
bonded to, X. In fact, B(H) = B(X) * scale, where the scale in general 
may be from 1.0 to 1.5 (as described in SHELXL manual and in small 
molecule structural papers). phenix.refine uses scale=1.2. This scale is 
not a refinable parameter, but just a fixed value.

> but during the course of the refinement and rebuilding they would start to diverge, sometimes drastically. 

This was a possibility in very old versions of phenix.refine. I fixed 
this more than a year ago. So please make sure you are using a recent 


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