[phenixbb] ramachanran plot refinement or restraint?
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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