as you know, extended CCD codes arrive this year. I'm looking into examples
https://github.com/wwPDB/extended-wwPDB-identifier-examples
and thinking what's the best way to convert such files to PDB.
Do you plan anything in this matter, like it was done with
https://cci.lbl.gov/hybrid_36/ in the past?
Presently we don't plan to be able to convert files with extended CCD to PDB format.
I wonder why this may be necessary or useful?
Tentatively, I'm thinking about mapping residue names in the HETNAM record.
For example, BB87Q would be mapped to a "3 letter code" that code
would have a special character to make it different from normal
3-letter codes (let's say '%', or maybe '+' or '_' - I don't have a
strong preference), and the original CCD code would be given in
columns 72-79 of HETNAM that are currently unused:
HETNAM BB% PHOSPHOSERINE [...] BB87Q
This idea looks fine to me if one actually needs to have new models in PDB format.
Another challenge is long chain ids:
We'll have to draw a line somewhere.
Best regards,
Oleg Sobolev.
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