#7564 closed enhancement (not a bug)
Handle 5-character residue names from Protein Databank
Reported by: | Tom Goddard | Owned by: | Greg Couch |
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Priority: | moderate | Milestone: | |
Component: | Input/Output | Version: | |
Keywords: | Cc: | Eric Pettersen | |
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The PDB announced the will switch from 3 character to 5 character residue names by 2024, possibly sooner because they will run out of 3 character names.
https://www.wwpdb.org/news/news?year=2022#630fee4cebdf34532a949c34
I'm not sure if any of our code will need fixing for this. I think we handle residue names of any length. But I am not sure whether our Chemical Components Dictionary (CCD) fetching code makes any assumptions about 3 character names. Also might be worth checking of the Chimera mmCIF reader handles the 5 character residues names.
Change History (3)
comment:1 by , 3 years ago
Cc: | added; removed |
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Owner: | changed from | to
comment:2 by , 3 years ago
Resolution: | → not a bug |
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Status: | assigned → closed |
The mmCIF reading code uses fixed width columns for speed, but the column widths are determined dynamically from how the data is presented. Residue names are the atomstruct::ResName, so no limits on size.
follow-up: 3 comment:3 by , 3 years ago
I'm not sure if the PDB offers test files with 5 character residue names. It would seem highly desirable to actually test such a file if available.
Residue names are unlimited in length. Reassigning to Greg to check that CCD fetching and mmCIF reading (doesn't it use "fixed format" for speed?) are unaffected by this change.