[phenixbb] Deposition of riding H

Jeff Headd jjheadd at lbl.gov
Tue Sep 14 11:23:46 PDT 2010

Hi Mark,

If hydrogens are used to arrive at a final refined model (whether
riding or not) it is essential for the reproducibility of results that
the H atom records be included in the deposited model.  How B-factors
are specified and some final atomic positions (such as rotatable
methyl groups) are difficult or impossible to predict once removed, so
without their deposition this information would be lost and any
published statistics would not be reproducible as published.  This
point is illustrated in one of our recent papers:

Afonine PV, Grosse-Kunstleve RW, Chen VB, Headd JJ, Moriarty NW,
Richardson JS, Richardson DC, Urzhumtsev A, Zwart PH, Adams PD:
phenix.model_vs_data: a high-level tool for the calculation of
crystallographic model and data statistics. J. Appl. Cryst. 2010, 43,

Further, there is no universal standard currently in use that
specifies H bond-lengths (some use electron cloud distances, others
neutron distances, some a mixture of both), meaning that without
inclusion of H atom records (or at least a reference to which library
was used) it is very difficult to know where the H atoms were placed.


On Tue, Sep 14, 2010 at 10:32 AM, Dr. Mark Mayer <mayerm at mail.nih.gov> 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?
> 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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