[phenixbb] Deposition of riding H

[Dr. Mark Mayer]

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.

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.
-- 

Mark