question about

[Mia1349]

Hi there!

I recently read your paper on phylogenetic tree building using 3Di characters and found it both inspiring and informative. Your demonstration of the practical applications of this method was particularly enlightening.

I am currently working on building phylogenetic trees using a few clusters generated by Foldseek, and I am interested in adapting the pipeline you developed for my analysis. I noticed that in the initial step, you clip the PDB files to single chains. As someone new to structural biology, I am a bit confused about this step. Could you please elaborate on why it is necessary to clip the protein structures to single chains? Is this step essential for my goal of constructing "genetrees" using structural clusters?

Cheers,
Mia