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,
Tim

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





_______________________________________________
phenixbb mailing list
[email protected]
http://phenix-online.org/mailman/listinfo/phenixbb
Unsubscribe: [email protected]

_______________________________________________
phenixbb mailing list
[email protected]
http://phenix-online.org/mailman/listinfo/phenixbb
Unsubscribe: [email protected]