I am not a crystallographer but I though you guys might be a good place to ask this question.

I have 2 super secondary structures, A and B and they consist of Helix-turn-Strand

Due to the turn the two structures have a poor RMSD because the two flanking fragments of Helix and Strand are far from each other but when I superimpose the two fragments individually(helixA with helix B and standA with strandB in Pymol they align very well).

Now, is there a way to express this instead of using the RMSD?

When the two structures align well the RMSD is very good but a slight movement and the RMSD is awful.

But looking at the two structures I can see they follow the same path through space.

Thank you,

Patrick

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