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

Tim Gruene tim.gruene at psi.ch
Tue Sep 11 09:23:16 PDT 2018

Dear Maxime,

did you already contact the PDB directly about this?
In my experience the PDB staff are very helpful and open minded about
exceptional situations.

Best regards,

On 09/11/2018 05:43 PM, Maxime Cuypers wrote:
> 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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Paul Scherrer Institut
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