[phenixbb] H related bond deviaion

Pavel Afonine pafonine at lbl.gov
Tue Dec 6 07:46:55 PST 2011

Hi Dialing,

H geometry should be ideal after phenix.refine. If it is not the case 
then please send me the PDB and I will have a look.


On 12/6/11 3:49 AM, Dialing Pretty 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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