[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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