I did ab initio modeling with rosetta and then performed clustering. Initially I generated 500 decoys and then I did 1000 with a difference sequence. When I performed clustering, I still get 4 clusters yet I have not specified the number of clusters in my flags file.My question is whether this is a correct output?
Secondly, I don't understand the numbering of the pdb files. When I read the log file I see that it uses c.i.j but I don't know which is the correct mapping. This is because of the different numbering in the log file and especially since I am sorting by energy levels.
Also, do I take the model with the lowest energy level in the largest cluster as the most correct model?
I will appreciate some answers. Thanks.