Member Site Forums Rosetta++ Rosetta++ – General clustering_decoy Reply To: clustering_decoy

Sally Ride

    Ad 1) I usually do as following:

    ^find /full/path/to/decoys/folder/ -maxdepth 1 -name ‘*.pdb’ -size +1 > list^
    ^/home/kosa/bin/ 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