submission of neutron structure containing "H" atoms on the pdb database problematic
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
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
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Hi Maxime, I agree with Tim: getting in touch with PDB and having a constructive dialogue to solve the issues likely is the best way forward! Also, don't forget to run Comprehensive Validation in Phenix GUI that now takes special care of neutron derived models, as described here: https://journals.iucr.org/d/issues/2018/08/00/mn5114/ Good luck! Pavel On 9/11/18 09:23, Tim Gruene wrote:
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]
participants (3)
-
Maxime Cuypers -
Pavel Afonine -
Tim Gruene