Hi Rosetta users,
I was trying to recapitulate a loop conformation in a protein by using RosettaRemodel (Rosetta3.5). The loop was taken out so in the blueprint file I specified "0 x L PIKAA [native aa]". I turned on the clustering functionality in RosettaRemodel to focus on only the unique structures that score well in the first stage. From my understanding, it should generate several cluster centers based on the specified cluster radius, which have the lowest energy within each cluster. However, I only got ONE cluster center after the clustering and therefore only one final refined structure will be generated at most, no matter how many were generated in the building stage (-num_trajectories and -save_top were both 100 in my case). The cluster radius was 0.2. So I am wondering if I am giving a wrong cluster radius, or there is anything I didn't notice. And how is it different from the "standalone" clustering application? Thanks.