Hi Patrick,

RMSD is a poor measure in this case as it does not account for B-factors, occupancies, alternative conformations and so on information a crystal structure model may make available. Macromolecules are not a bunch of points in space.

While I'm sure more thorough methods exist, I would vote for the simplest, most direct and obvious one. You can calculate electron density map using a Gaussian approximation from model A and B (yes, electron density map - not a Fourier image of it!). That will naturally account for all: B-factors, occupancies, other disorder. Then you can calculate a map similarity measure, such as map correlation, for instance. After all, why use a cannon to kill a fly?!

If you are interested to follow this route I can explain the details.

All the best,
Pavel

Hi Phenix users,

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