Structure.from_pdbid broken: MMTF download deprecated

[dominiquesydow]

The MMTF format is no longer supported by the RCSB and replaced by the BCIF format.
https://www.rcsb.org/news/feature/65a1af31c76ca3abcc925d0c

Hence, also the mmtf package, which is a Python implementation of the MMTF API, is not in use any more:

opencadd/opencadd/structure/core.py

Line 22 in c76e87c

return cls(mmtf.fetch(pdbid))

As the corresponding function in opencadd‘s Structure object mimics mdanalysis‘ Universe object, I think we also have to check in there.
https://github.com/MDAnalysis/mdanalysis/blob/develop/package/MDAnalysis/coordinates/MMTF.py#L56

[dominiquesydow]

We could try this:

https://github.com/biotite-dev/biotite/blob/0404084283765baef765cc869d86ee07a898d82f/src/biotite/database/rcsb/download.py#L119-L122

[dominiquesydow]

Asked for help here: rcsb/mmtf-python#63

[fernan]

Hi, chiming in here. Since you're already using MDAnalysis Universe, they seem to have something going which needs finishing. Check MDAnalysis/mdanalysis#4907.

I suppose once it's in MDAnalysis, then the code will start working again?