On Tuesday 14 September 2010 10:34:00 am Dr. Mark Mayer wrote:
> Here's one for the community, which I'll post to both Phenix and CCP4 BBs.
>
> Where does the crystallographic community stand
> on deposition of coordinates with riding
> hydrogens?
I do not favor depositing riding hydrogen coordinates for
the same reason that I do not like the recent PDB preference
for depositing ANISOU records for structures that have been
refined with TLS.
In both cases the enumeration of these many thousands of
parameter values gives the strong, but false, impression that
they have been individually modeled. They have not.
There are really only a dozen or so parameters in the riding
hydrogen model. All those coordinates follow directly from
application of this same small set of values.
Similarly, there are really only 20 parameters per TLS group in
your model, no matter how many atoms you applied it to.
There is IMHO no justification for presenting the resulting model
in a form that makes it appear that 6 additional parameters per
atom have been modeled, when in fact that number is either 0 or 1.
Ethan
> Explicit H are required for calculating all atom
> clash scores with Molprobity, and their use
> frequently gives better geometry (especially at
> low resolution). Phenix uses explicit riding H
> for refinement, and outputs these in the refined
> PDB. Refmac also uses riding H but does not
> output H coordinates.
>
> While depositing a series of structures refined
> at 1.4 - 2.75 A with Phenix got the following
> email from the RCSB, who asked I resupply
> coordinates without H for two of the structures.
> Since we can't see H even at 1.4 Å I don't
> understand why an arbitrary cut off of 1.5 Å was
> chosen, and also why explicit H atoms used in
> refinement and geometry validation should be
> stripped from the file.
>
> FROM RCSB
>
> We encourage depositors not to use hydrogens in the final PDB file for
> the low resolution structures (> 1.5 A). Please provide an updated PDB
> file. We request you to use processed PDB file as a starting point for
> making any corrections to the coordinates and/or re-refinement.
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742
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