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Article ID: 898 - Last Modified: December 4, 2010

I am having trouble getting a valid RMSD from the Superposition panel, because it seems that the atom numbering in my structures is different. Is there a way to have the superposition done and correctly identify the atom pairs independent of their atom numbers?

There are several ways of performing the superposition with the "correct" atom pairs. The first is to manually pick the atom pairs. This works if you are superimposing two structures. It is the most reliable method as you are defining precisely what to compare. All other methods make the software pick the "corresponding atoms" automatically, which can be challenging. The best alternative is to superimpose by SMARTS. In this case, the atoms in the SMARTS pattern are used for the RMSD, and should be the correctly corresponding atoms. The algorithms used should handle degeneracies (such as flipping a phenyl ring) correctly.

Keywords: rmsd, superposition, atom number, Maestro

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