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
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