[phenixbb] submission of neutron structure containing "H" atoms on the pdb database problematic
tim.gruene at psi.ch
Tue Sep 11 09:23:16 PDT 2018
did you already contact the PDB directly about this?
In my experience the PDB staff are very helpful and open minded about
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
> 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
> phenixbb mailing list
> phenixbb at phenix-online.org
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