Deleting Hydrogens

Axel T. Brunger brunger at LAPLACE.CSB.YALE.EDU
Fri Sep 20 10:17:11 EST 1996

> Axel,
> >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

I agree.  I'll have an option in the molecular structure generation
files to include or exclude hydrogens.  Really, that's the only
change required.  All other files work without or with hydrogens (polar
or all hydrogens).  

Axel Brunger

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