[cctbxbb] any plans for PDB files with long CCD codes?

[Oleg Sobolev]

Hello Marcin,

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.

I think that mmCIF format is mature enough so we don't have to be able to
produce PDB for every mmCIF. wwPDB already deprecated models saved in
multiple files (http://www.wwpdb.org/news/news?year=2014#10-December-2014).
Another challenge is long chain ids:
https://www.wwpdb.org/news/news?year=2022#62559153c8eabd0c4864f208

We'll have to draw a line somewhere.

Best regards,
Oleg Sobolev.


_______________________________________________
> cctbxbb mailing list
> cctbxbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/cctbxbb
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/cctbxbb/attachments/20230515/b00efd0a/attachment.htm>