[phenixbb] Histidine as a hydrogen bond acceptor in Phenix refine

Nathaniel Echols nechols at lbl.gov
Fri Sep 26 02:59:32 PDT 2014

On Fri, Sep 26, 2014 at 1:16 AM, Tim Gruene <tg at shelx.uni-ac.gwdg.de> wrote:

> out of curiosity: By 'explicit hydrogen atoms' do you mean that you
> refine the hydrogen parameters rather than using the riding hydrogen
> model? This is very bold for even at and beyond Acta C resolution limits
> (0.8A) one usually only uses the riding atom model for hydrogens.


Jason, I think you may be misunderstanding how hydrogens are handled
internally.  The geometry restraints used in Phenix (and Refmac, etc.) are
based on the assumption that the data guide the atoms reasonably well, and
do not include any attractive forces or explicit hydrogen-bonding.  Reduce
will take hydrogen bonding into account when it adds hydrogens to the
model, but that's it - and I'm not sure how well this will handle hydroxyl

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