[phenixbb] Riding H

Jianghai Zhu jzhu at idi.harvard.edu
Fri Oct 29 14:56:58 PDT 2010

That is what I thought.  But wouldn't the nuclear distance be more accurate? and we should use the molprobity bond length, the longer one?

On the other hand, phenix knows how to rotate a methyl group to avoid the H-H collision.  

-- Jianghai

On Oct 29, 2010, at 5:42 PM, Nathaniel Echols wrote:

> 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).
> -Nat
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