[phenixbb] Question about occupancy refinement of riding hydrogens

Pavel Afonine PAfonine at lbl.gov
Tue Mar 4 12:07:34 PST 2008

Hi Carsten,

in phenix.refine H atoms are treated as a very special case (if you are 
not refining a structure at 0.37A resolution or so).

Here is what refined for hydrogens by default:

    refine_sites = individual *riding
    refine_adp = one_b_per_residue *one_b_per_molecule individual
    refine_occupancies = one_q_per_residue *one_q_per_molecule individual
    contribute_to_f_calc = True

You can stop refining occupancies for H by using 
"hydrogens.refine_occupancies=none", same for their B-factors, but I 
would never do it.


On 3/4/2008 11:26 AM, Schubert, Carsten [PRDUS] wrote:
> I just noticed that occupancies of riding hydrogens are being refined 
> by default, in fact I am unable to turn this feature off (CCI-APPs 
> from Jan-8).  I was just (very naively) wondering what is the 
> rationale behind this? The B-factor refinement for riding hydrogens is 
> already enabled and should take care of this or not?  It looks a bit 
> odd to have hydrogens with occupancy 0.9 sitting on a carbon with 
> occupancy 1.0 at 2.0 A resolution.
> Cheers
>         Carsten
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