[phenixbb] H related bond deviaion

Jeff Headd jjheadd at lbl.gov
Tue Dec 6 07:49:11 PST 2011

Hi Dialing,

As I stated yesterday, different programs have different definitions
of bond lengths for H atoms. If you are adding the hydrogens in
MolProbity, the bond lengths will be slightly longer than is used in
the monomer library that Coot uses. While the z scores are quite high,
the sigmas on bond lengths are so small that even a slight length
deviation will result in a very large z score. This is not a major
concern, and is not indicative of a specific problem with your

If the hydrogens indicate any clashes > 0.4A, then those are still
areas of concern that you should look at.


On Tue, Dec 6, 2011 at 3:49 AM, Dialing Pretty <hdc123hdc123 at yahoo.com> wrote:
> Dear All,
> I did a Phenix refine, and before the refine all the H were added.
> MolProbity analysis demonstrated that almost everything are acceptable after
> the refinement.
> However when I did the geometry analysis by the COOT validation, I find all
> the residues having a significant deviation bond involving H. with z score
> higher than 7.
> I am looking forward to  getting an explanation from you on it,including how
> to avoid it.
> Cheers,
> Dialing
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