Re: [ccp4bb]: Riding Hydrogens

[Ethan Merritt <merritt@u.washington.edu>]

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On Friday 06 September 2002 11:30, you wrote:
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> Surprisingly, I found that adding the hydrogens in lowered both R and
> R free by about 1%. 
> So I am unclear on on the requirements for adding the hydrogens on in
> refinement. At what resolutions do they become justified? Why are
> they lowering my R and R-free?

This question is a bit more subtle than you may think.
Since hydrogen is a weak scatterer, it only contributes significantly at
low resolution (yes - low not high).  So if you can place all those H 
electrons at their correct position in the cell then your R and Rfree 
should improve even at quite low resolution.  The difficulty is in that
"correct position" bit.  Usually it is only when your structure is well
refined to high resolution (better than 2A let's say) that the heavy atom
positions are accurate enough that you have a good shot at placing
the hydrogens correctly.

So if you take a model refined at atomic resolution and calculate
R factors against 3A data with and without hydrogens, it is likely
you will see an improvement from including the hydrogen scattering.
But if you only had 3A data to begin with for that same structure,
it is unlikely that you would have been able to generate a model 
accurate enough to benefit from adding hydrogens.  Not because
the hydrogen scattering is insignificant, but because you cannot
place the hydrogens correctly.

The bottom line IMHO is that the lower R-free you observe is in itself the
justification you are asking for.  You have added what - 12 parameters?
(I'm not sure exactly how many parameters are in the refmac riding-H
model but it must be on that order).  If adding 12 parameters lowers 
R-free by 1% that is good justification for including them in your model.
The fact that these particular 12 parameters describe hydrogen atoms
is almost beside the point.  Suppose you had added 3 water molecules -
that also is 12 parameters - and saw Rfree go down by 1%.  Would you
have posted to the bulletin board asking whether you were justified in
keeping your three new waters?

-- 
Ethan A Merritt       merritt@u.washington.edu
Biomolecular Structure Center Box 357742
University of Washington, Seattle, WA 98195
phone: (206)543-1421
FAX:   (206)685-7002