CODEWITHSUNDEEP
biopython
El Dude
El Dude

Reputation: 5618

Bio.PDB.Superimposer - what is RMS?

I am comparing two structures and a bit confused about meaning of the result parameters: What is the value returned saved in super_imposer.rms ? I guess it's RMSD, but why is it not written as such?

Upvotes: 1

Views: 1141

Answers (1)

David Cain
David Cain

Reputation: 17323

super_imposer.rms is indeed the root-mean-square deviation.

If you consult the source of Bio.PDB.Superimposer, you'll see that the rms attribute is the result of a call to get_rms(). The docstring for get_rms() reads:

Root mean square deviation of superimposed coordinates.

The Tutorial does say that "The RMSD is stored in the rmsd attribute," however. No idea why this discrepancy exists.

Upvotes: 4

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