[phenixbb] submission of neutron structure containing "H" atoms on the pdb database problematic

Maxime Cuypers maximecuypers at gmail.com
Tue Sep 11 08:43:41 PDT 2018

Dear all,

i was wondering if others have encountered the same problems with the PDB
database curation rules or if this is a first.

I am trying to submit a neutron structure with 'free' H atoms (protons)
clearly identified. (not D atoms here), this is a situation similar to how
D atoms can be reported in a pdb neutron structure close to a carboxylic
residue or other situation like in the D‐xylose isomerase (XI).

I have first tried to submit the neutron structure with the H atoms part of
the complex molecules nearby but i faced refusal and was asked to make it
as simple 'H' atoms.

once i had done the 'free' H atoms version of the pdb, the structure was
again refused by curators because there is no library available to the pdb
curators to accept such H atoms. I was explained that it had been decided
to ban the 'H' atom only coordinate from depositions some years ago.

What would you recommand me to do to get the structure deposited and
curated keeping the valid coordinates of the H atoms in the pdb file?

PS: this is not fantasy.

Dr. Maxime Cuypers
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