Reply To: Native gives higher (positive) than lowest energy and clustered decoys

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June 2, 2011 at 10:43 pm #5698
Anonymous

    The idealize application is more to change bond distances and angles to their “ideal” settings.

    The relax application (http://www.rosettacommons.org/manuals/archive/rosetta3.2.1_user_guide/app_relax_command.html) would likely be your best bet. To keep the backbone from moving too much, you can add the flag “-constrain_relax_to_start_coords” to the command line.

    By the way, you might also be interested in http://www.rosettacommons.org/manuals/archive/rosetta3.2.1_user_guide/preparing_structures.html