On Mon, 2021-06-14 at 17:51 +0200, Cryo EM wrote:
>
> Can someone please guide what could be the best method to compare two PDB models of the same protein?
>
> The first model was generated from cryo EM map of about 6A resolution. Second model is created from cryo EM map of
> about 3 A.
> Which software should be used? How to calculate RMSD?
>
If you merely want to superpose your molecules and calculate the rmsd, then you can do that with LSQ in Coot.
But your question is about comparison, and for that I would use ProSMART, which is for conformation-independent
structural comparison.
(And also for restraint-generation but that's a different mode.)
Paul.
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