How to calculate RMSD between two transitional states of a 3D structure of protein?

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Krishnendu Bera

You can calculate using vmd/pymol etc. Take both conformations and superimpose them and calculate the RMSD.

Nelson David Arias Olivares

As Hera said, you could use the RMSD Tool plugin in VMD. Check this page

https://www.ks.uiuc.edu/Research/vmd/plugins/rmsd/

or this one

https://www.ks.uiuc.edu/Research/vmd/plugins/rmsdvt/

Tushar Chakraborty

Open both the structures in pymol and align them. You will get the rmsd value.