Hello,
Currently, in the foldseek server https://search.foldseek.com/, foldseek and foldmason are independent tools. Since foldseek calculates structures on the fly, I think it makes sense that a user would like to then compute a structural MSA with those structures. If foldseek could communicate with foldmason, or if a file could be downloaded from foldseek in a format compatible with foldmason input, that would be great.