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:

  hydrogens
  {
    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.

Pavel.


On 3/4/2008 11:26 AM, Schubert, Carsten [PRDUS] wrote:
Question about occupancy refinement of riding hydrogens

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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