[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:
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:
>
> 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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