Traditional Rosetta Scripts does not have a built-in interface that allows the user to filter trajectories based on their global ranking. It instead relies on predetermined filtration cutoffs. Predicting the correct cutoff to use without first running the script can be difficult, so these filter cutoffs tend to be conservative in practice. Multistage Rosetta Scripts (M.R.S.) allows you to filter after each "stage" based on a trajectory's global rank using the metric of your choice.
Instead of running each rosetta script trajectory in isolation, M.R.S. breaks the trajectory up into stages as shown below. Each stage is run to completion for all trajectories before the next stage is started. This gives Rosetta the ability to sort the results by a user-defined score and filter based on global position.
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