I have a question regarding the results of FoldMason.

[tzjsdss]

I have a question regarding the results of FoldMason.

For clustering a series of proteins, such as 40 proteins (A, B, C, D, E, ...), using FoldMason --precluster for pairwise comparison and clustering, how can I obtain the scores of protein A compared to protein B, protein C, protein E, etc.?

In other words, I want to generate a table with 40×40 rows, where each row records the structural similarity scores between every pair of proteins. However, I did not find such a table in the existing --precluster results. Am I operating incorrectly, or is there currently no way to generate such an Excel file?

I would like to obtain this kind of Excel file. Is there any way to achieve this?

[gamcil]

You are right, currently there is no way to produce a file like this in FoldMason. For clustering, I think using Foldseek cluster would be more appropriate. For just generating an all-vs-all comparison table, you could follow the procedure described here, replacing mmseqs with foldseek.