Could someone please explain what each stage does in the Rosetta Mini application? For example, I have noticed that the ClassicFragmentMover moves around everything a great deal each time it is run, the SmoothFragmentMover_GunnCost moves everything around a smaller amount each time it is run compared to the ClassicFramentMover, and FastRelax moves everything around a small amount to perform a high resolution search and often allows the protein being folded release massive amounts of energy compared to the other stages each time it runs. Are my guesses correct, and what do the other stages that I did not mention do? I have seen movers related to centroids and membranes, and do not know what they are supposed to do.

Bump

HI Jeese and Mike:

The Rosetta ab initio protocol consists of two stages: in the initial stage (‘centroid’) side-chains are represented by fixed center-of-mass atoms allowing for rapid generation and evaluation of various protein-like topologies. Here you see large moves, because "fragments" (3 to 9 residues) are inserted from a library of fragments.

The second stage (‘full-atom’) builds in explicit side-chains (amino acid rotatmers) and carries out all atom energy minimization. Here you see the larges change in energy.

If you wanna read the official documentation check out the following link:
https://www.rosettacommons.org/docs/latest/abinitio-relax.html


Besides Rosetta ab initio, we also run other protocols that have "stages". If you are curious about a specific job, please post the name and I can investigate =]

Thanks