On 9/15/10 3:54 PM, Ed Pozharski wrote:
Don't you agree that using the riding model does not add
additional refinable parameters?
(snip)
instance, when hydrogens are added, the average N-H distance is
1.00001(5), but upon refinement the value is down to 0.85998(4). I
So the riding hydrogen model is imperfect. At least with phenix.refine
you can measure it, unlike the default behavior of REFMAC. (But you can
tell it to write hydrogens out, I believe).
Obviously this question is not one amenable to a simple answer. In some
sense (as per George) riding hydrogens are merely a restraint. In some
other sense they are fundamentally a part of the model - they have very
directional properties via bumping restraints that most certainly alter
the atomic model for the heavy atoms in a very direct way via collision.
Since the nature of these atoms - locationally specific - differs from
the more amorphous "extended atom" restraints (CH3E for methyl in CNS
etc) it could make sense to include them in the model at deposition.
As far as I know we do not delete atoms from the final model that
contribute to scattering and geometric restraints under any other
circumstances, except perhaps in the nearly-as-contentious "how do I
model my disordered side-chain" case. Also not amenable to a simple answer.
Both approaches (REFMAC-esque and PHENIX-esque) have their merits.
I doubt I'm the only person here conflicted over what to do about it.
However this thread appears to have reached the point where not much new
ground is being broken.
Phil Jeffrey
Princeton
