[phenixbb] ramachanran plot refinement or restraint?

Pavel Afonine pafonine at lbl.gov
Thu Jul 26 07:01:21 PDT 2007

Frank von Delft wrote:
> Jianghai Zhu wrote:
>> Adding riding hydrogens into the structure was a powerful validation 
>> tool.  But now we all add riding hydrogens into the refinement since it 
>> makes the refinement better.  At the same time, we lose some power in 
>> the validation.  We still think it is worth doing so, don't we?
> No:  they are RIDING hydrogens, they do not influence the refinement 
> (i.e. bumps), only the Rfactors/maps.  Which is not the same as you ask 
> for with the phi/psi angles.

Not at all. Adding the hydrogen atoms from high to low resolution can be 
viewed as adding additional anti-bumping restraints. The improvement in 
the R/Rfree factors in this case is mostly attributed to overall model 
geometry improvement and less attributed to adding additional scattering 
power to the structure (depending on resolution).
Saying differently, the X-ray gradients for H atoms are zero, H atoms 
come to Fcalc and hence to X-ray target. However, the geometry 
restraints target "sees" hydrogens as good as other atoms.

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