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MonomerLibrary / monomers

dictionary of monomers and links
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Big issue with atom nomenclature #39

Closed drlemmus closed 10 months ago

drlemmus commented 11 months ago

Because of the recent reannotation of amino-acid-like compounds, a lot of residues have changed atom names (ABU and PYR were the first ones I encountered). The whole monomer library needs to be checked against the current atom names in the Chemical Component Dictionary.

keitaroyam commented 11 months ago

Yes, we are aware of this. The plan is to change atom names in them, and keep old names as _chem_comp_atom.alt_atom_id. In this way we can also support model files with old atom names (gemmi already support this). An example could be found: https://github.com/MonomerLibrary/monomers/pull/37 @wojdyr

drlemmus commented 11 months ago

The sooner the better, literally thousands of pdb-redo databank updates fail because of this

wojdyr commented 11 months ago

yes, 635 monomers are going to be updated