sto to json

[wenhuihuang19791109]

I have some precomputed receptors in sto formats, how could I convert it into json file?

[Augustin-Zidek]

You will need to do the following steps (which could be automated using e.g. Python):

1. Convert all 4 files from Stockholm to a3m. You could use e.g. esl-reformat from the HMMER Suite to do that, or you could use our Stockholm to a3m function from https://github.com/google-deepmind/alphafold3/blob/main/src/alphafold3/data/parsers.py#L104.
2. Crop, merge and deduplicate all 4 a3m files into a single a3m, in the following order and crop size: UniRef90 (10,000), Small BFD (5,000), MGnify (5,000). The cropping, and deduplication is optional. We don't use PDB hits as MSA, so feel free to not include that one. You can use the tooling from https://github.com/google-deepmind/alphafold3/blob/main/src/alphafold3/data/pipeline.py#L85 to achieve all of this. Or simply just concatenate the 4 a3m files if you don't care about cropping and duplicate sequences in the MSA.
3. Get the resulting a3m and put it in the unpairedMsa field in the input JSON. Set unpairedMsa to an empty string, templates to an empty list.

Hope this helps!

[wenhuihuang19791109]

thanks a lot, that's very helpful!