[phenixbb] alternatives to RMSD
pafonine at lbl.gov
Fri Jul 4 20:34:33 PDT 2014
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,
> 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
> 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,
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