I did several HADDOCK runs using different parameters and I’d like to see how similar are the models obtained in these different runs. For this I’m clustering all obtained models (basically, cluster*_1.pdb files) using the FCC clustering (GitHub - haddocking/fcc: Fraction of Common Contacts Clustering Algorithm for Protein Structures). The reported coverage is between 34% (for 0.75 cutoff) and 57% (for 0.33 cutoff).
My question is: Why are not all models clustered? Are some models so distant from the others so they can’t form a cluster of even 2 members?
Many thanks in advance.