I use pymol. Here is my procedure.

1. Load structures

2. Split states of NMR structure bundle

3. Align #1 NMR model and X-ray model. Usually #1 model is the lowest energy model but to be sure read header section of the file. 

Hi L. Glez,

you can use Pymol as suggested by W. Lee. Also, Chimera tool can be very useful.

1. open structures simultaneously in the same window. Then by choosing 'match alignment' module in 'structure comparison' in 'tools module', you can perform structure alignment. Select the lowest energy pose of NMR structure as suggested by W. Lee.

2. RMSD of the two structures will be indicated in the lower panel.

regards

Tanuj

Thank you for both for your help. Now that I have the overall rmsd I am looking for the rmsd for each residue to see on a graph where in the chain are the bigest differences. Could you help me?

Please use:

https://pymolwiki.org/index.php/Rms_cur