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
structure.
If the hydrogens indicate any clashes > 0.4A, then those are still
areas of concern that you should look at.
Jeff
On Tue, Dec 6, 2011 at 3:49 AM, Dialing Pretty
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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