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Hello, I would like to use or be able to visualize in the score file some terms or information related to docking and similar protocols, for example, interface_score and rms in other scoring functions executing other movers. Can this be done with flags? I hope you can help me, thanks.

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Sat, 2022-02-12 00:16

It depends a bit on what you mean by "visualize". If you mean you want to map the scores to the 3D structure of the protein so you can do things like coloring the protein by the score, the common way to do that is to change the PDB such that the B-factor column of the PDB contains the score of interest. Then you can use the features of your standard protein viewer (PyMol, Chimera, etc.) to color the structure by B-factor. There is a script `tools/protein_tools/scripts/`  that's distributed with Rosetta which should help you do that. It's mainly based on the score table Rosetta puts at the end of the PDB. It does have a --score_list option, which will allow you to specify a file with two columns, the first being the residue number and the second being the score to map.

Generating that file is left as an exercise for the person doing it. That's going to be the problem you run into with interface_score & rms -- those are typically calculated at the whole-protein level, not at the residue level, though there are related metrics which may give you per-residue output.

If you are talking about the whole-protein level metrics, you're going to have to clarify what sort of visualization you have in mind.

Fri, 2022-02-18 11:14