[phenixbb] Riding H

Nathaniel Echols nechols at lbl.gov
Fri Oct 29 14:42:56 PDT 2010

On Fri, Oct 29, 2010 at 2:01 PM, Jianghai Zhu <jzhu at idi.harvard.edu> wrote:
> If I use the riding H atoms come out of phenix.refine in molprobity, it gives me a decent clash score.  But if I strip the H atoms and let molprobity to add H atoms, I get a much worse clash score.  I saw the manual of phenix recommends the first method.  So what is the cause of the difference here?  I know long time ago that phenix and molprobity used different bond length to add the riding H atoms. I don't know what the situation is now.  Does phenix.refine refine the riding H atom positions?

It won't refine them against X-ray data, but it will perform geometry
regularization to idealize their positions - which also includes
shortening the bond lengths to match what we observe by X-ray
diffraction.  The program Reduce (used by Molprobity and Phenix), on
the other hand, uses the nuclear distances, which I think are on
average 0.1A longer.  The Richardson lab is working on standardizing
and reconciling the different bond lengths, but it's a messy problem
(especially when neutron diffraction is involved).


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