Member Site Forums Rosetta++ Rosetta++ – General Increase compactness of decoys Reply To: Increase compactness of decoys

Sally Ride

    I mean rather decreasing the radius of gyration.

    I am folding a structure containing six helices. It folds into two three-helix-bundle units which, however, in most decoys do not interact closely with each other. In other words in most decoys the two helical units do not form common hydrophobic core.

    I would like to try to force rosetta to generate higher fraction of “compact” structures.

    Regarding the scores: for some random set I have averages:

    sasapack 1.57

    rg 17.13

    After changing -rg_reweight to 2.0:

    sasapack 1.63

    rg 16.7

    And -vdw_reweight 2.0:

    sasapack 1.82

    rg 17.16

    so virtually there is no difference. What else I could do?

    > Do you mean you want to increase the packing of the protein?Is there a sasapack score in the outputs?
    > What is the average number?