any plans for PDB files with long CCD codes?
Hello Cctbx and Phenix developers, 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? 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
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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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
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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participants (2)
-
Marcin Wojdyr -
Oleg Sobolev