I have clustered 1,000 decoys by using cluster application in Rosetta with flags below.
I appreciate with its quick result, however, I wonder with the -cluster:sort_groups_by_energy option. I'd like to sort the clusters by score, but the result seems that the clusters are not sorted by the score, It just only sorted the decoys in each cluster by score. Why?, How does it sort clusters?
I have attached the summary file of clustering.
The -cluster:sort_groups_by_energy flag should sort the clusters by energy, but it doesn't use straight energy. It uses a weighted combination of the energy of the lowest energy structure in the cluster as well as the size of the cluster. (The exact formula is (1-p)*score - p*size, where p is the population weight, with a default value of 0.09). This weighting can be controlled by the -cluster:population_weight option. If you set it to 0, the sorting of the clusters should be strictly by the energy of the lowest energy structure in the cluster, regardless of size.
I see. Thank you very much!!