[phenixbb] Deposition of riding H

sbiswas2 at ncsu.edu sbiswas2 at ncsu.edu
Tue Sep 14 11:36:13 PDT 2010

Hi Mark,
I think it depends who is handling your deposited pdb file recently I
submitted a file with hydrogen added and had no problems. My resolution
was 1.8A.

> 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?
> 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.
> 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.
> --
> Mark
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