[phenixbb] alternatives to RMSD

Pavel Afonine pafonine at lbl.gov
Fri Jul 4 20:34:33 PDT 2014

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,

> 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

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