[phenixbb] Deposition of riding H

Dr. Mark Mayer mayerm at mail.nih.gov
Tue Sep 14 10:32:38 PDT 2010

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 
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.


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