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Global Docking with output analysis RMS

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Global Docking with output analysis RMS

Hello, Rosetta team

I performed global docking for two proteins and got the file, there are different "RMS"s reported, Irms, Irms_leg, cen_rms, rms, and st_rmsd, what values are more useful for analysis?  I wonder if term "rms" is calcualted based on what? since I started with two far away proteins for global docking, I wonder if this rms is calcualted based on the intinial structure?

I did not provide native structure for global docking. 

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Fri, 2024-02-23 09:17

Irms is the interface rmsd - that is, the rmsd calculated over the interface residues (from the "native" pose).

Irms_leg is the legacy interface rmsd -- from what I can tell, it uses a slightly different way of calcuating the interface. (Primarily, using a distance of 8 Ang instead of 10 Ang for counting what's in the interface.)

cen_rms is the full-pose rmsd after the low resolution (centroid) stage and before the high resolution refinement stage.

st_rmsd is the starting rmsd, the rmsd before either the low resolution or high resoultion stages.

rms is the full-pose rmsd at the end of the protocol

Which one is best for analysis depends on what you're looking to see.

I was under the impression that these terms would only show up if you give a "native" reference pose (e.g. with -in:file:native). If you haven't given an explicit native and they're showing up anyway, then I would believe that they're in reference to the starting structure, though I wouldn't necessarily trust/pay attention to rmsd metrics unless you've deliberately set the reference structure.

Mon, 2024-02-26 08:24