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debbiemarkslab / EVcouplings

Evolutionary couplings from protein and RNA sequence alignments
http://evcouplings.org
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PDB no longer provides MMTF files #307

Open pedrobfer opened 3 weeks ago

pedrobfer commented 3 weeks ago

In trying to run the EVcouplings pipeline, I couldn't download the MMTF files needed. Then I found the following message from RCSB:

"As of July 2, 2024, RCSB PDB will no longer serve PDB data in the MMTF compression format. Users are strongly encouraged to switch to accessing the data files offered in the compressed BinaryCIF (BCIF) format."

I don't have the expertise to suggest changes, but wanted to keep this record in case anyone finds the same issue.

thomashopf commented 3 weeks ago

Well that is rather unfortunate 😬

The fix will be to swap out the MMTF loading+transformation in the PDB class to load binary CIF files and turn that into our internal dataframe-based structure https://github.com/debbiemarkslab/EVcouplings/blob/af27842c5fc72c291831261c9a19849a3e313efd/evcouplings/compare/pdb.py#L403

Hope to work on this in the next weeks as top priority on this repository - any PRs highly welcome (starting from v0.2 branch)!

Thanks a lot for the notice @pedrobfer!

thomashopf commented 3 weeks ago

I started to work on a fix, tapping into BioPythons bCIF parser

thomashopf commented 3 weeks ago

Basic bCIF integration is done (c2a766d), remaining integration with pipeline still to be tested (e.g. model number defaults need to be changed from 0 to 1)

thomashopf commented 2 weeks ago

I released a fix on the develop branch - please have a look and let me know if this works in your hands.

Please note this depends on biopython >= 1.84, so please upgrade that accordingly.

Keeping the issue open for now to track any other questions around the MMTF->bCIF change.

pedrobfer commented 2 weeks ago

I released a fix on the develop branch - please have a look and let me know if this works in your hands.

Please note this depends on biopython >= 1.84, so please upgrade that accordingly.

Keeping the issue open for now to track any other questions around the MMTF->bCIF change.

It worked perfectly! Thank you very much for the quick work on this!