Ad 1) I usually do as following:
^find /full/path/to/decoys/folder/ -maxdepth 1 -name ‘*.pdb’ -size +1 > list^
^/home/kosa/bin/compose_score_silent.py t228.out list^
^/home/kosa/bin/cluster_info_silent.out ../t228.out – t228 5,25,50,100 2,5^
and eventually re-running the last step with different options.
Ad 2) I think nobody knows the answer for this question 
You might try to cluster decoys after generating lets say 10 000 decoys, analyze the results and then if you do not see big clusters generate more decoys … The results depend also on the particular protein, some of them “fold more easily” with rosetta (ex. those with simple topologies).
> hi..
>
> how to identify the best decoy according to clustering tree.
> if my protein is 176 aa, how many decoy should i generate