Extend NMR-STAR internal dictionary to accomodate the original NEF nomenclature in distance restraints

[dmaziuk]

(apologies if another copy of this already exists and my search-fu failed)

Request by Masashi copy-pasted from DAOTHER-5569 @ https://rcsbpdb.atlassian.net/browse/DAOTHER-5569

Current validation report module for NMR assumes that _Atom_chem_shift.Auth_atom_ID in mmCIF has IUPAC atom name for CS data, but on the other hand NEFTranslator uses the tag for author provided atom name in NMR-STAR. The nomenclature inconsistency for the same tag in two different formats should be handled by STAR to CIF converter.

To work with the validation report, the STAR to CIF converter relocates _Atom_chem_shift.Auth_atom_ID in NMR-STAR to _Atom_chem_shift.Original_PDB_atom_name in mmCIF. Subsequently, it copies _Atom_chem_shift.Atom_ID in NMR-STAR to _Atom_chem_shift.Auth_atom_ID in mmCIF. The procedure satisfies compatibility of validation report and preservation of the author provided data.

As for NEF deposition, which combines CS and MR data, the same problem occurs in atom name tags of distance restraints;
_Gen_dist_constraint.Auth_atom_ID_1 and _Gen_dist_constraint.Auth_atom_ID_2.

However, there is no official items to temporary preserve the author provided atom name in NMR-STAR. I think it is big concern about losing the author provided atom name in BMRB Core Archive.

To resolve my concerns, we need to define the following items in NMR-STAR internal dictionary using the same analogy for CS data:

_Gen_dist_constraint.Original_PDB_strand_ID_1
_Gen_dist_constraint.Original_PDB_residue_no_1
_Gen_dist_constraint.Original_PDB_residue_name_1
_Gen_dist_constraint.Original_PDB_atom_name_1
_Gen_dist_constraint.Original_PDB_strand_ID_2
_Gen_dist_constraint.Original_PDB_residue_no_2
_Gen_dist_constraint.Original_PDB_residue_name_2
_Gen_dist_constraint.Original_PDB_atom_name_2

The attached NMR data in mmCIF, generated by NEF deposition, should be handled by tools for PDB bioculation and BMRB annotation, in which Dimitri's mmCIF to NMR-STAR converter is to be involved.

It may effect on NMR restraint validation.

[dmaziuk]

@yokochi47 -- this should subscribe Masashi I believe?