Deleting Hydrogens

Chris Haydock haydock.christopher at
Fri Sep 20 09:17:22 EST 1996

On Sep 19,  8:52pm, Axel T. Brunger wrote:
> Subject: Re: charges on Asp, Glu, Arg, Lys residues
> Thanks for the suggestion about deleting all hydrogens for
> crystallographic structure refinement (at > 1.2 A resolution).
> I just ran a number of tests which appear to be satisfactory.
> Computational efficiency is improved and communication with O
> is simplified.
> Does anybody have any negative experiences with deleting all
> hydrogens?
> If I don't hear about any serious concerns, I'll change the tutorial
> example files accordingly.
> Axel Brunger
>-- End of excerpt from Axel T. Brunger


>From the point of view of a crystallographer
solving a protein structure and submitting coordinates
to the PDB, deleting hydrogens may be a great idea.
However, other experimentalists (NMR, fluorescence,
hydrogen exchange, etc.) frequently must go back
and reconstruct the hydrogen positions.
Admittedly, this is now done by building hydrogens
on PDB heavy atom coordinates.
It is widely (?) recognized that there is more information
in crystallographic data than can be extracted
by fitting this data to current molecular mechanics
models.  (Thus the renewed emphasis on depositing
structure factors.)  It may well be that in the
future hydrogen positions will increasingly be
built by going back to the original X-ray data.
In this case, as well as that of higher resolution data,
it would be best not to have only tutorial examples
with hydrogens deleted.

Chris Haydock

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