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

[Marcin Wojdyr]

Hi Oleg,

yes, having files in the PDB format is not as important as it was 15 years ago.
FTR, I ended up replacing long monomer names with 3-"letter" codes
that end with a tilde (for example: BB~).

Marcin

On Tue, May 16, 2023 at 1:19 AM Oleg Sobolev <osobolev at lbl.gov> wrote:
>
> 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.
>
>
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