I am just trying some tools out for some protein-protein docking analysis. I don't have too many structures since I am just testing, only 500 structs. I choose 148 higest ranking structures to input to energy_based_clustering. It is my assumption from description of simple algorithm described, that all structures would be grouped to a cluster since it indicates "until there are no structures remaining" however I only have 127 pdb files at the end of this. I think this question is robust against any flags in the input file but I can provide if needed.
Also I would expect the lowest total_energy structure from the local_refine score file to be in the first cluster since the algorithm first "Select the lowest-energy structure remaining in the unclustered list as the centre of the current cluster" and this should be the lowest energy structure. However the structure in the c.1.1.pdb file, which I assumed would be the lowest "total_score" of all the structures, only had the 28th lowest total_score. Does this maybe have something to do with difference in energy and total_score. Is this actually choosing the lowest energy? I tested a few energies with Amoeba and saw some resemblance to score and energy. Going to create a graph to check it out.